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<center><b>
[ <a href="module-tree.html">Module Hierarchy</a>
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<h1 class="epydoc">Class Hierarchy</h1>
<ul class="nomargin-top">
<li> <strong class="uidlink"><a href="obitools.alignment.AlignedSequence-class.html">obitools.alignment.AlignedSequence</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.svg.Circle-class.html">obitools.svg.Circle</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.gzip.GzipFile-class.html">obitools.gzip.GzipFile</a></strong>:
<em class="summary">The GzipFile class simulates most of the methods of a file object
with the exception of the readinto() and truncate() methods.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.svg.Line-class.html">obitools.svg.Line</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.svg.Rectangle-class.html">obitools.svg.Rectangle</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.SVGelement-class.html">obitools.SVGdraw.SVGelement</a></strong>:
<em class="summary">SVGelement(type,attributes,elements,text,namespace,**args) Creates
a arbitrary svg element and is intended to be subclassed not used
on its own.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.animate-class.html">obitools.SVGdraw.animate</a></strong>:
<em class="summary">an=animate(attribute,from,to,during,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.animateColor-class.html">obitools.SVGdraw.animateColor</a></strong>:
<em class="summary">ac=animateColor(attribute,type,from,to,dur,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.animateMotion-class.html">obitools.SVGdraw.animateMotion</a></strong>:
<em class="summary">an=animateMotion(pathdata,dur,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.animateTransform-class.html">obitools.SVGdraw.animateTransform</a></strong>:
<em class="summary">antr=animateTransform(type,from,to,dur,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.circle-class.html">obitools.SVGdraw.circle</a></strong>:
<em class="summary">c=circle(x,y,radius,fill,stroke,stroke_width,**args)</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.point-class.html">obitools.SVGdraw.point</a></strong>:
<em class="summary">p=point(x,y,color)</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.cursor-class.html">obitools.SVGdraw.cursor</a></strong>:
<em class="summary">c=cursor(url,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.defs-class.html">obitools.SVGdraw.defs</a></strong>:
<em class="summary">d=defs(**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.description-class.html">obitools.SVGdraw.description</a></strong>:
<em class="summary">d=description(text,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.ellipse-class.html">obitools.SVGdraw.ellipse</a></strong>:
<em class="summary">e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.group-class.html">obitools.SVGdraw.group</a></strong>:
<em class="summary">g=group(id,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.image-class.html">obitools.SVGdraw.image</a></strong>:
<em class="summary">im=image(url,width,height,x,y,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.line-class.html">obitools.SVGdraw.line</a></strong>:
<em class="summary">l=line(x1,y1,x2,y2,stroke,stroke_width,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.lineargradient-class.html">obitools.SVGdraw.lineargradient</a></strong>:
<em class="summary">lg=lineargradient(x1,y1,x2,y2,id,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.link-class.html">obitools.SVGdraw.link</a></strong>:
<em class="summary">a=link(url,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.marker-class.html">obitools.SVGdraw.marker</a></strong>:
<em class="summary">m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.path-class.html">obitools.SVGdraw.path</a></strong>:
<em class="summary">p=path(path,fill,stroke,stroke_width,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.pattern-class.html">obitools.SVGdraw.pattern</a></strong>:
<em class="summary">p=pattern(x,y,width,height,patternUnits,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.polygon-class.html">obitools.SVGdraw.polygon</a></strong>:
<em class="summary">pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.polyline-class.html">obitools.SVGdraw.polyline</a></strong>:
<em class="summary">pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.radialgradient-class.html">obitools.SVGdraw.radialgradient</a></strong>:
<em class="summary">rg=radialgradient(cx,cy,r,fx,fy,id,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.rect-class.html">obitools.SVGdraw.rect</a></strong>:
<em class="summary">r=rect(width,height,x,y,fill,stroke,stroke_width,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.script-class.html">obitools.SVGdraw.script</a></strong>:
<em class="summary">sc=script(type,type,cdata,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.set-class.html">obitools.SVGdraw.set</a></strong>:
<em class="summary">st=set(attribute,to,during,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.stop-class.html">obitools.SVGdraw.stop</a></strong>:
<em class="summary">st=stop(offset,stop_color,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.style-class.html">obitools.SVGdraw.style</a></strong>:
<em class="summary">st=style(type,cdata=None,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.svg-class.html">obitools.SVGdraw.svg</a></strong>:
<em class="summary">s=svg(viewbox,width,height,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.switch-class.html">obitools.SVGdraw.switch</a></strong>:
<em class="summary">sw=switch(**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.symbol-class.html">obitools.SVGdraw.symbol</a></strong>:
<em class="summary">sy=symbol(id,viewbox,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.text-class.html">obitools.SVGdraw.text</a></strong>:
<em class="summary">t=text(x,y,text,font_size,font_family,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.textpath-class.html">obitools.SVGdraw.textpath</a></strong>:
<em class="summary">tp=textpath(text,link,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.title-class.html">obitools.SVGdraw.title</a></strong>:
<em class="summary">t=title(text,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.tref-class.html">obitools.SVGdraw.tref</a></strong>:
<em class="summary">tr=tref(link='',**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.tspan-class.html">obitools.SVGdraw.tspan</a></strong>:
<em class="summary">ts=tspan(text='',**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.use-class.html">obitools.SVGdraw.use</a></strong>:
<em class="summary">u=use(link,x,y,width,height,**args)</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.view-class.html">obitools.SVGdraw.view</a></strong>:
<em class="summary">v=view(id,**args)</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.svg.Scene-class.html">obitools.svg.Scene</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.svg.Text-class.html">obitools.svg.Text</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.zipfile.ZipExtFile-class.html" onclick="show_private();">obitools.zipfile.ZipExtFile</a></strong>:
<em class="summary">File-like object for reading an archive member.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.zipfile.ZipFile-class.html">obitools.zipfile.ZipFile</a></strong>:
<em class="summary">Class with methods to open, read, write, close, list zip files.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.zipfile.PyZipFile-class.html">obitools.zipfile.PyZipFile</a></strong>:
<em class="summary">Class to create ZIP archives with Python library files and
packages.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.zipfile._ZipDecrypter-class.html" onclick="show_private();">obitools.zipfile._ZipDecrypter</a></strong>:
<em class="summary">Class to handle decryption of files stored within a ZIP archive.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.drawing-class.html">obitools.SVGdraw.drawing</a></strong>:
<em class="summary">d=drawing()</em>
</li>
<li> <strong class="uidlink">object</strong>:
<em class="summary">The most base type</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedSequence-class.html">obitools.seqdb.AnnotatedSequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedAASequence-class.html">obitools.seqdb.AnnotatedAASequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GpepSequence-class.html">obitools.seqdb.genbank.GpepSequence</a></strong>:
<em class="summary">Class used to represent a peptidic sequence issued from Genpep.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedNucSequence-class.html">obitools.seqdb.AnnotatedNucSequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.embl.EmblSequence-class.html">obitools.seqdb.embl.EmblSequence</a></strong>:
<em class="summary">Class used to represent a nucleic sequence issued from EMBL.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GbSequence-class.html">obitools.seqdb.genbank.GbSequence</a></strong>:
<em class="summary">Class used to represent a nucleic sequence issued from Genbank.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink">exceptions.BaseException</strong>:
<em class="summary">Common base class for all exceptions</em>
<ul>
<li> <strong class="uidlink">exceptions.Exception</strong>:
<em class="summary">Common base class for all non-exit exceptions.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.zipfile.BadZipfile-class.html">obitools.zipfile.BadZipfile</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.FileFormatError-class.html">obitools.obo.parser.FileFormatError</a></strong>:
<em class="summary">An error derived from the class Exception.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.zipfile.LargeZipFile-class.html">obitools.zipfile.LargeZipFile</a></strong>:
<em class="summary">Raised when writing a zipfile, the zipfile requires ZIP64
extensions and those extensions are disabled.</em>
</li>
<li> <strong class="uidlink">exceptions.StandardError</strong>:
<em class="summary">Base class for all standard Python exceptions that do not represent
interpreter exiting.</em>
<ul>
<li> <strong class="uidlink"><a href="exceptions.AssertionError-class.html">exceptions.AssertionError</a></strong>:
<em class="summary">Assertion failed.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.dnaparser.UnknownFormatError-class.html">obitools.seqdb.dnaparser.UnknownFormatError</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.BioSequence-class.html">obitools.BioSequence</a></strong>:
<em class="summary">BioSequence class is the base class for biological sequence
representation.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.AASequence-class.html">obitools.AASequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedAASequence-class.html">obitools.seqdb.AnnotatedAASequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GpepSequence-class.html">obitools.seqdb.genbank.GpepSequence</a></strong>:
<em class="summary">Class used to represent a peptidic sequence issued from Genpep.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.NucSequence-class.html">obitools.NucSequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedNucSequence-class.html">obitools.seqdb.AnnotatedNucSequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.embl.EmblSequence-class.html">obitools.seqdb.embl.EmblSequence</a></strong>:
<em class="summary">Class used to represent a nucleic sequence issued from EMBL.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GbSequence-class.html">obitools.seqdb.genbank.GbSequence</a></strong>:
<em class="summary">Class used to represent a nucleic sequence issued from Genbank.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.solexa.SolexaSequence-class.html">obitools.solexa.SolexaSequence</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.tagmatcher.TagMatcherSequence-class.html">obitools.tagmatcher.TagMatcherSequence</a></strong>:
<em class="summary">Class used to represent a nucleic sequence issued mapped on a
genome by the tagMatcher software.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.WrappedBioSequence-class.html">obitools.WrappedBioSequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.DNAComplementSequence-class.html">obitools.DNAComplementSequence</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html">obitools.align.homopolymere.HomoNucBioSeq</a></strong>:
<em class="summary">classdocs</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SubSequence-class.html">obitools.SubSequence</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.blast.Blast-class.html">obitools.blast.Blast</a></strong>:
<em class="summary">Run blast</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.blast.NetBlast-class.html">obitools.blast.NetBlast</a></strong>:
<em class="summary">Run blast on ncbi servers</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.utils.CachedDB-class.html">obitools.utils.CachedDB</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.utils.ColumnFile-class.html">obitools.utils.ColumnFile</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecopcr.EcoPCRFile-class.html">obitools.ecopcr.EcoPCRFile</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.ecotag.parser.EcoTagAbstractIterator-class.html">obitools.ecotag.parser.EcoTagAbstractIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.ecotag.parser.EcoTagFileIterator-class.html">obitools.ecotag.parser.EcoTagFileIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.goa.parser.GoAFileIterator-class.html">obitools.goa.parser.GoAFileIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.solexa.SolexaFile-class.html">obitools.solexa.SolexaFile</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obischemas.kb.Connection-class.html">obitools.obischemas.kb.Connection</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obischemas.kb.Cursor-class.html">obitools.obischemas.kb.Cursor</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.distances.DistanceMatrix-class.html">obitools.distances.DistanceMatrix</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.distances.observed.Pairewise-class.html">obitools.distances.observed.Pairewise</a></strong>:
<em class="summary">Observed divergeance matrix from an alignment.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.distances.observed.PairewiseGapRemoval-class.html">obitools.distances.observed.PairewiseGapRemoval</a></strong>:
<em class="summary">Observed divergeance matrix from an alignment.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.eutils.EUtils-class.html">obitools.eutils.EUtils</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.eutils.EFetch-class.html">obitools.eutils.EFetch</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi.NCBIAccession-class.html">obitools.seqdb.genbank.ncbi.NCBIAccession</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi.NCBIGenbank-class.html">obitools.seqdb.genbank.ncbi.NCBIGenbank</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi.NCBIGenpep-class.html">obitools.seqdb.genbank.ncbi.NCBIGenpep</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter-class.html">obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter</a></strong>:
<em class="summary">Class used to write Annotation description in EcoPCRDB format.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.EcoPCRDBFile-class.html">obitools.ecopcr.EcoPCRDBFile</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence.EcoPCRDBSequenceIterator-class.html">obitools.ecopcr.sequence.EcoPCRDBSequenceIterator</a></strong>:
<em class="summary">Build an iterator over the sequences include in a sequence database
formated for ecoPCR</em>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy.EcoTaxonomyDB-class.html">obitools.ecopcr.taxonomy.EcoTaxonomyDB</a></strong>:
<em class="summary">A taxonomy database class</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence.EcoPCRDBSequenceWriter-class.html">obitools.ecopcr.sequence.EcoPCRDBSequenceWriter</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.Edge-class.html">obitools.graph.Edge</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.phylogeny.PhylogenicEdge-class.html">obitools.phylogeny.PhylogenicEdge</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.Edge-class.html">obitools.seqdb.genbank.graph.Edge</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo.Entry-class.html">obitools.format.ontology.go_obo.Entry</a></strong>:
<em class="summary">a Stanza entry, like [Typedef] for example</em>
</li>
<li> <strong class="uidlink"><a href="obitools.fast.Fast-class.html">obitools.fast.Fast</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.carto.Feature-class.html">obitools.carto.Feature</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.carto.MultiPartFeature-class.html">obitools.carto.MultiPartFeature</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.carto.SimpleFeature-class.html">obitools.carto.SimpleFeature</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.carto.BoxFeature-class.html">obitools.carto.BoxFeature</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.carto.TagFeature-class.html">obitools.carto.TagFeature</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.genbank.ncbi.Genbank-class.html">obitools.genbank.ncbi.Genbank</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.format.genericparser.GenericParser-class.html">obitools.format.genericparser.GenericParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.Graph-class.html">obitools.graph.Graph</a></strong>:
<em class="summary">Class used to represent directed or undirected graph.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.DiGraph-class.html">obitools.graph.DiGraph</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.dag.DAG-class.html">obitools.graph.dag.DAG</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.rootedtree.RootedTree-class.html">obitools.graph.rootedtree.RootedTree</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.rootedtree.RootedTree-class.html">obitools.seqdb.genbank.graph.rootedtree.RootedTree</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag.DAG-class.html">obitools.seqdb.genbank.graph.dag.DAG</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.UndirectedGraph-class.html">obitools.graph.UndirectedGraph</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.tree.Forest-class.html">obitools.graph.tree.Forest</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.phylogeny.PhylogenicTree-class.html">obitools.phylogeny.PhylogenicTree</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.tree.Forest-class.html">obitools.seqdb.genbank.graph.tree.Forest</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.Graph-class.html">obitools.seqdb.genbank.graph.Graph</a></strong>:
<em class="summary">Class used to represent directed or undirected graph.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.DiGraph-class.html">obitools.seqdb.genbank.graph.DiGraph</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.UndirectedGraph-class.html">obitools.seqdb.genbank.graph.UndirectedGraph</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo.Header-class.html">obitools.format.ontology.go_obo.Header</a></strong>:
<em class="summary">class representing a GO header.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.statistics.noncentralhypergeo.Interval-class.html">obitools.statistics.noncentralhypergeo.Interval</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue.Job-class.html">obitools.parallel.jobqueue.Job</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue.JobIterator-class.html">obitools.parallel.jobqueue.JobIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.carto.Level-class.html">obitools.carto.Level</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.location.Location-class.html">obitools.location.Location</a></strong>:
<em class="summary">Define a location on a sequence.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.location.ComplementLocation-class.html">obitools.location.ComplementLocation</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.location.CompositeLocation-class.html">obitools.location.CompositeLocation</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.location.feature.Feature-class.html">obitools.location.feature.Feature</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.location.PointLocation-class.html">obitools.location.PointLocation</a></strong>:
<em class="summary">A point location describes a location on a sequence limited to a
single position</em>
</li>
<li> <strong class="uidlink"><a href="obitools.location.SimpleLocation-class.html">obitools.location.SimpleLocation</a></strong>:
<em class="summary">A simple location is describe a continuous region of a sequence
define by a <code>begin</code> and a <code>end</code> position.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.carto.Map-class.html">obitools.carto.Map</a></strong>:
<em class="summary">Map represente une instance d'une carte genetique physique.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.Node-class.html">obitools.seqdb.genbank.graph.Node</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.Node-class.html">obitools.graph.Node</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.dag.DAGNode-class.html">obitools.graph.dag.DAGNode</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.rootedtree.RootedTreeNode-class.html">obitools.graph.rootedtree.RootedTreeNode</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.rootedtree.RootedTreeNode-class.html">obitools.seqdb.genbank.graph.rootedtree.RootedTreeNode</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag.DAGNode-class.html">obitools.seqdb.genbank.graph.dag.DAGNode</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.tree.TreeNode-class.html">obitools.graph.tree.TreeNode</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.phylogeny.PhylogenicNode-class.html">obitools.phylogeny.PhylogenicNode</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.tree.TreeNode-class.html">obitools.seqdb.genbank.graph.tree.TreeNode</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo.OBOFile-class.html">obitools.format.ontology.go_obo.OBOFile</a></strong>:
<em class="summary">Iterator over all entries of an OBO file</em>
</li>
<li> <strong class="uidlink"><a href="obitools.statistics.noncentralhypergeo.Product-class.html">obitools.statistics.noncentralhypergeo.Product</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo.RelatedTerm-class.html">obitools.format.ontology.go_obo.RelatedTerm</a></strong>:
<em class="summary">RelatedTerm.relation RelatedTerm relation
RelatedTerm.related_term RelatedTerm GO identifier
RelatedTerm.comment all terms have 0 or 1 comment</em>
</li>
<li> <strong class="uidlink"><a href="obitools.sequenceencoder.SequenceEncoder-class.html">obitools.sequenceencoder.SequenceEncoder</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.sequenceencoder.DNAComplementEncoder-class.html">obitools.sequenceencoder.DNAComplementEncoder</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.sequenceencoder.SeqFragmentEncoder-class.html">obitools.sequenceencoder.SeqFragmentEncoder</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.align.ssearch.SsearchParser-class.html">obitools.align.ssearch.SsearchParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.carto.SubLevel-class.html">obitools.carto.SubLevel</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.table.TableIteratorAsDict-class.html">obitools.table.TableIteratorAsDict</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.table.TableRow-class.html">obitools.table.TableRow</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.blast.BlastMatch-class.html">obitools.blast.BlastMatch</a></strong>:
<em class="summary">Blast high scoring pair between two sequences</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tagmatcher.parser.TagMatcherIterator-class.html">obitools.tagmatcher.parser.TagMatcherIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.TaggedValue-class.html">obitools.obo.parser.TaggedValue</a></strong>:
<em class="summary">A couple 'tag:value' of an OBOEntry.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.parser.DefValue-class.html">obitools.obo.parser.DefValue</a></strong>:
<em class="summary">A couple 'def:value' inherited from the class TaggedValue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.NameValue-class.html">obitools.obo.parser.NameValue</a></strong>:
<em class="summary">A couple 'name:value' inherited from the class TaggedValue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.NamespaceValue-class.html">obitools.obo.parser.NamespaceValue</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.RelationshipValue-class.html">obitools.obo.parser.RelationshipValue</a></strong>:
<em class="summary">A couple 'xref:value' inherited from the class TaggedValue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.RemarkValue-class.html">obitools.obo.parser.RemarkValue</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.SynonymValue-class.html">obitools.obo.parser.SynonymValue</a></strong>:
<em class="summary">A couple 'synonym:value' inherited from the class TaggedValue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.XrefValue-class.html">obitools.obo.parser.XrefValue</a></strong>:
<em class="summary">A couple 'xref:value' inherited from the class TaggedValue.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.Task-class.html">obitools.parallel.Task</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.TaskPool-class.html">obitools.parallel.TaskPool</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy.Taxonomy-class.html">obitools.ecopcr.taxonomy.Taxonomy</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy.EcoTaxonomyDB-class.html">obitools.ecopcr.taxonomy.EcoTaxonomyDB</a></strong>:
<em class="summary">A taxonomy database class</em>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy.TaxonomyDump-class.html">obitools.ecopcr.taxonomy.TaxonomyDump</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo.Term-class.html">obitools.format.ontology.go_obo.Term</a></strong>:
<em class="summary">representing a GO term.</em>
</li>
<li> <strong class="uidlink">unittest.TestCase</strong>:
<em class="summary">A class whose instances are single test cases.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.unit.obitools.BioseqTest-class.html">obitools.unit.obitools.BioseqTest</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.unit.obitools.AABioseqTest-class.html">obitools.unit.obitools.AABioseqTest</a></strong>:
<em class="summary">Test obitools.AASequence class</em>
</li>
<li> <strong class="uidlink"><a href="obitools.unit.obitools.NucBioseqTest-class.html">obitools.unit.obitools.NucBioseqTest</a></strong>:
<em class="summary">Test obitools.NucSequence class</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tree.TreeNode-class.html">obitools.tree.TreeNode</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.WrapperSetIterator-class.html">obitools.WrapperSetIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo.Xref-class.html">obitools.format.ontology.go_obo.Xref</a></strong>:
<em class="summary">Xref.db Xref database
Xref.id Xref identifier</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.Xref-class.html">obitools.obo.parser.Xref</a></strong>:
<em class="summary">A xref object of an OBOentry.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.zipfile.ZipInfo-class.html">obitools.zipfile.ZipInfo</a></strong>:
<em class="summary">Class with attributes describing each file in the ZIP archive.</em>
</li>
<li> <strong class="uidlink">dict</strong>:
<em class="summary">dict() -&gt; new empty dictionary.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecotag.EcoTagResult-class.html">obitools.ecotag.EcoTagResult</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.location.feature.Feature-class.html">obitools.location.feature.Feature</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.Indexer-class.html">obitools.graph.Indexer</a></strong>:
<em class="summary">Allow to manage convertion between an arbitrarly hashable python
value and an unique integer key</em>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.Indexer-class.html">obitools.seqdb.genbank.graph.Indexer</a></strong>:
<em class="summary">Allow to manage convertion between an arbitrarly hashable python
value and an unique integer key</em>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue.JobPool-class.html">obitools.parallel.jobqueue.JobPool</a></strong>:
<em class="summary">JobPool is dedicated to manage a job queue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.tree.layout.NodeLayout-class.html">obitools.tree.layout.NodeLayout</a></strong>:
<em class="summary">Layout data associated to a tree node.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.OBOEntry-class.html">obitools.obo.parser.OBOEntry</a></strong>:
<em class="summary">An entry of an OBOFile.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.go.parser.GOEntry-class.html">obitools.obo.go.parser.GOEntry</a></strong>:
<em class="summary">An entry of a GeneOntology .obo file.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.OBOTerm-class.html">obitools.obo.parser.OBOTerm</a></strong>:
<em class="summary">A stanza named 'Term'.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.go.parser.GOTerm-class.html">obitools.obo.go.parser.GOTerm</a></strong>:
<em class="summary">A stanza named 'Term'.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.TrailingModifier-class.html">obitools.obo.parser.TrailingModifier</a></strong>:
<em class="summary">A class object which inherits from the class dict.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.tree.layout.TreeLayout-class.html">obitools.tree.layout.TreeLayout</a></strong>:
<em class="summary">Description of a phylogenetic tree layout</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.table.iTableIterator-class.html">obitools.table.iTableIterator</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.blast.BlastResultIterator-class.html">obitools.blast.BlastResultIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.table.ProjectionIterator-class.html">obitools.table.ProjectionIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.table.SelectionIterator-class.html">obitools.table.SelectionIterator</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.blast.BlastCovMinFilter-class.html">obitools.blast.BlastCovMinFilter</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.table.TableIterator-class.html">obitools.table.TableIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.table.UnionIterator-class.html">obitools.table.UnionIterator</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink">list</strong>:
<em class="summary">list() -&gt; new list list(sequence) -&gt; new list initialized
from sequence's items</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.align.Alignement-class.html">obitools.align.Alignement</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.alignment.Alignement-class.html">obitools.alignment.Alignement</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.cns.quality.QualitySequence-class.html">obitools.cns.quality.QualitySequence</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.table.Table-class.html">obitools.table.Table</a></strong>:
<em class="summary">Tables are list of rows of the same model</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.blast.BlastResult-class.html">obitools.blast.BlastResult</a></strong>:
<em class="summary">Results of a blast run</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.table._Row-class.html">obitools.table._Row</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink">set</strong>:
<em class="summary">set(iterable) --&gt; set object</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.tree.Tree-class.html">obitools.tree.Tree</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.WrapperSet-class.html">obitools.WrapperSet</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.pathdata-class.html">obitools.SVGdraw.pathdata</a></strong>:
<em class="summary">class used to create a pathdata object which can be used for a
path.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.SVGdraw.spannedtext-class.html">obitools.SVGdraw.spannedtext</a></strong>:
<em class="summary">st=spannedtext(textlist=[])</em>
</li>
</ul>
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exceptions ::
AssertionError ::
Class&nbsp;AssertionError
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class AssertionError</h1><p class="nomargin-top"></p>
<pre class="base-tree">
object --+
|
BaseException --+
|
Exception --+
|
StandardError --+
|
<strong class="uidshort">AssertionError</strong>
</pre>
<hr />
<p>Assertion failed.</p>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="exceptions.AssertionError-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">...</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
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<span class="summary-type">a new object with type S, a subtype of T</span>
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<td><span class="summary-sig"><a href="exceptions.AssertionError-class.html#__new__" class="summary-sig-name">__new__</a>(<span class="summary-sig-arg">T</span>,
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<p class="indent-wrapped-lines"><b>Inherited from <code>BaseException</code></b>:
<code>__delattr__</code>,
<code>__getattribute__</code>,
<code>__getitem__</code>,
<code>__getslice__</code>,
<code>__reduce__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__setstate__</code>,
<code>__str__</code>,
<code>__unicode__</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__format__</code>,
<code>__hash__</code>,
<code>__reduce_ex__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>BaseException</code></b>:
<code>args</code>,
<code>message</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">...</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
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</td>
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<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
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<dt>Overrides:
object.__init__
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<span class="sig-arg">S</span>,
<span class="sig-arg">...</span>)</span>
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</td><td align="right" valign="top"
>&nbsp;
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</tr></table>
<dl class="fields">
<dt>Returns: a new object with type S, a subtype of T</dt>
<dt>Overrides:
object.__new__
</dt>
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<h1 class="epydoc"> API Documentation </h1>
<p> This document contains the API (Application Programming Interface)
documentation for this project. Documentation for the Python
objects defined by the project is divided into separate pages for each
package, module, and class. The API documentation also includes two
pages containing information about the project as a whole: a trees
page, and an index page. </p>
<h2> Object Documentation </h2>
<p>Each <strong>Package Documentation</strong> page contains: </p>
<ul>
<li> A description of the package. </li>
<li> A list of the modules and sub-packages contained by the
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<li> A detailed description of each variable defined by the
package. </li>
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<p>Each <strong>Module Documentation</strong> page contains:</p>
<ul>
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<li> A summary of the functions defined by the module. </li>
<li> A summary of the variables defined by the module. </li>
<li> A detailed description of each function defined by the
module. </li>
<li> A detailed description of each variable defined by the
module. </li>
</ul>
<p>Each <strong>Class Documentation</strong> page contains: </p>
<ul>
<li> A class inheritance diagram. </li>
<li> A list of known subclasses. </li>
<li> A description of the class. </li>
<li> A summary of the methods defined by the class. </li>
<li> A summary of the instance variables defined by the class. </li>
<li> A summary of the class (static) variables defined by the
class. </li>
<li> A detailed description of each method defined by the
class. </li>
<li> A detailed description of each instance variable defined by the
class. </li>
<li> A detailed description of each class (static) variable defined
by the class. </li>
</ul>
<h2> Project Documentation </h2>
<p> The <strong>Trees</strong> page contains the module and class hierarchies: </p>
<ul>
<li> The <em>module hierarchy</em> lists every package and module, with
modules grouped into packages. At the top level, and within each
package, modules and sub-packages are listed alphabetically. </li>
<li> The <em>class hierarchy</em> lists every class, grouped by base
class. If a class has more than one base class, then it will be
listed under each base class. At the top level, and under each base
class, classes are listed alphabetically. </li>
</ul>
<p> The <strong>Index</strong> page contains indices of terms and
identifiers: </p>
<ul>
<li> The <em>term index</em> lists every term indexed by any object's
documentation. For each term, the index provides links to each
place where the term is indexed. </li>
<li> The <em>identifier index</em> lists the (short) name of every package,
module, class, method, function, variable, and parameter. For each
identifier, the index provides a short description, and a link to
its documentation. </li>
</ul>
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<p> The table of contents occupies the two frames on the left side of
the window. The upper-left frame displays the <em>project
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<table class="help summary" border="1" cellspacing="0" cellpadding="3">
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<p> The <strong>project contents frame</strong> contains a list of all packages
and modules that are defined by the project. Clicking on an entry
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special entry, labeled "Everything," will display the contents of
the entire project. </p>
<p> The <strong>module contents frame</strong> contains a list of every
submodule, class, type, exception, function, and variable defined by a
module or package. Clicking on an entry will display its
documentation in the API documentation frame. Clicking on the name of
the module, at the top of the frame, will display the documentation
for the module itself. </p>
<p> The "<strong>frames</strong>" and "<strong>no frames</strong>" buttons below the top
navigation bar can be used to control whether the table of contents is
displayed or not. </p>
<h2> The Navigation Bar </h2>
<p> A navigation bar is located at the top and bottom of every page.
It indicates what type of page you are currently viewing, and allows
you to go to related pages. The following table describes the labels
on the navigation bar. Note that not some labels (such as
[Parent]) are not displayed on all pages. </p>
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<p> A timestamp below the bottom navigation bar indicates when each
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<h1 class="epydoc">Module Hierarchy</h1>
<ul class="nomargin-top">
<li> <strong class="uidlink"><a href="obitools-module.html">obitools</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.SVGdraw-module.html">obitools.SVGdraw</a></strong>: <em class="summary">Use SVGdraw to generate your SVGdrawings.</em> </li>
<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.align.homopolymere-module.html">obitools.align.homopolymere</a></strong>: <em class="summary">Created on 14 mai 2009</em> </li>
<li> <strong class="uidlink"><a href="obitools.align.ssearch-module.html">obitools.align.ssearch</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.alignment-module.html">obitools.alignment</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.alignment.ace-module.html">obitools.alignment.ace</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.blast-module.html">obitools.blast</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.carto-module.html">obitools.carto</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.cns-module.html">obitools.cns</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.cns.fasta-module.html">obitools.cns.fasta</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.cns.quality-module.html">obitools.cns.quality</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.decorator-module.html">obitools.decorator</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.distances-module.html">obitools.distances</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.distances.observed-module.html">obitools.distances.observed</a></strong>: <em class="summary">Module dedicated to compute observed divergeances from an
alignment.</em> </li>
<li> <strong class="uidlink"><a href="obitools.distances.phylip-module.html">obitools.distances.phylip</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.distances.r-module.html">obitools.distances.r</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.dnahash-module.html">obitools.dnahash</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.ecopcr-module.html">obitools.ecopcr</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecopcr.annotation-module.html">obitools.ecopcr.annotation</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence-module.html">obitools.ecopcr.sequence</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy-module.html">obitools.ecopcr.taxonomy</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.ecotag-module.html">obitools.ecotag</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecotag.parser-module.html">obitools.ecotag.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.eutils-module.html">obitools.eutils</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.fast-module.html">obitools.fast</a></strong>: <em class="summary">implement fastn/fastp sililarity search algorithm for BioSequence.</em> </li>
<li> <strong class="uidlink"><a href="obitools.fasta-module.html">obitools.fasta</a></strong>: <em class="summary">fasta module provides functions to read and write sequences in
fasta format.</em> </li>
<li> <strong class="uidlink"><a href="obitools.format-module.html">obitools.format</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.format.genericparser-module.html">obitools.format.genericparser</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.ontology-module.html">obitools.format.ontology</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo-module.html">obitools.format.ontology.go_obo</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.obo-module.html">obitools.format.ontology.obo</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.format.sequence-module.html">obitools.format.sequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.format.sequence.embl-module.html">obitools.format.sequence.embl</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.sequence.fasta-module.html">obitools.format.sequence.fasta</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.sequence.genbank-module.html">obitools.format.sequence.genbank</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.sequence.tagmatcher-module.html">obitools.format.sequence.tagmatcher</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.genbank-module.html">obitools.genbank</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.genbank.ncbi-module.html">obitools.genbank.ncbi</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.goa-module.html">obitools.goa</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.goa.parser-module.html">obitools.goa.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph-module.html">obitools.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms-module.html">obitools.graph.algorithms</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.clique-module.html">obitools.graph.algorithms.clique</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.compact-module.html">obitools.graph.algorithms.compact</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.component-module.html">obitools.graph.algorithms.component</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.dag-module.html">obitools.graph.dag</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.layout-module.html">obitools.graph.layout</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.layout.radialtree-module.html">obitools.graph.layout.radialtree</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.rootedtree-module.html">obitools.graph.rootedtree</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.tree-module.html">obitools.graph.tree</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.gzip-module.html">obitools.gzip</a></strong>: <em class="summary">Functions that read and write gzipped files.</em> </li>
<li> <strong class="uidlink"><a href="obitools.location-module.html">obitools.location</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.location.feature-module.html">obitools.location.feature</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.nucdb-module.html">obitools.nucdb</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.nucdb.genbank-module.html">obitools.nucdb.genbank</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.nucdb.genbank.ncbi-module.html">obitools.nucdb.genbank.ncbi</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.nucdb.genbank.parser-module.html">obitools.nucdb.genbank.parser</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obischemas-module.html">obitools.obischemas</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.obischemas.kb-module.html">obitools.obischemas.kb</a></strong>: <em class="summary">kb package is devoted to manage access to postgresql database from
python script</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.obischemas.kb.extern-module.html">obitools.obischemas.kb.extern</a></strong>: <em class="summary">Module : KB.extern Author : Eric Coissac Date : 03/05/2004</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obischemas.options-module.html">obitools.obischemas.options</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obo-module.html">obitools.obo</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.go-module.html">obitools.obo.go</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.go.parser-module.html">obitools.obo.go.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser-module.html">obitools.obo.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.oligo-module.html">obitools.oligo</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.oligo.options-module.html">obitools.oligo.options</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.oligo.predicat-module.html">obitools.oligo.predicat</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.options-module.html">obitools.options</a></strong>: <em class="summary">Module providing high level functions to manage command line
options.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.options.bioseqcutter-module.html">obitools.options.bioseqcutter</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.options.bioseqedittag-module.html">obitools.options.bioseqedittag</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.options.bioseqfilter-module.html">obitools.options.bioseqfilter</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.options.taxonomyfilter-module.html">obitools.options.taxonomyfilter</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel-module.html">obitools.parallel</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue-module.html">obitools.parallel.jobqueue</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.phylogeny-module.html">obitools.phylogeny</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.phylogeny.newick-module.html">obitools.phylogeny.newick</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb-module.html">obitools.seqdb</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.blastdb-module.html">obitools.seqdb.blastdb</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.dnaparser-module.html">obitools.seqdb.dnaparser</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.embl-module.html">obitools.seqdb.embl</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.embl.parser-module.html">obitools.seqdb.embl.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank-module.html">obitools.seqdb.genbank</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph-module.html">obitools.seqdb.genbank.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms-module.html">obitools.seqdb.genbank.graph.algorithms</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.clique-module.html">obitools.seqdb.genbank.graph.algorithms.clique</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.component-module.html">obitools.seqdb.genbank.graph.algorithms.component</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag-module.html">obitools.seqdb.genbank.graph.dag</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.rootedtree-module.html">obitools.seqdb.genbank.graph.rootedtree</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.tree-module.html">obitools.seqdb.genbank.graph.tree</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi-module.html">obitools.seqdb.genbank.ncbi</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.parser-module.html">obitools.seqdb.genbank.parser</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.sequenceencoder-module.html">obitools.sequenceencoder</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.solexa-module.html">obitools.solexa</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.statistics-module.html">obitools.statistics</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.statistics.hypergeometric-module.html">obitools.statistics.hypergeometric</a></strong>: <em class="summary">Module de calcules statistiques.</em> </li>
<li> <strong class="uidlink"><a href="obitools.statistics.noncentralhypergeo-module.html">obitools.statistics.noncentralhypergeo</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.svg-module.html">obitools.svg</a></strong>: <em class="summary">SVG.py - Construct/display SVG scenes.</em> </li>
<li> <strong class="uidlink"><a href="obitools.table-module.html">obitools.table</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.table.csv-module.html">obitools.table.csv</a></strong>: <em class="summary">obitools.table.csv module provides an iterator adapter allowing to
parse csv (comma separatted value) file</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tagmatcher-module.html">obitools.tagmatcher</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.tagmatcher.options-module.html">obitools.tagmatcher.options</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.tagmatcher.parser-module.html">obitools.tagmatcher.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tree-module.html">obitools.tree</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.tree.dot-module.html">obitools.tree.dot</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.tree.layout-module.html">obitools.tree.layout</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.tree.newick-module.html">obitools.tree.newick</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.tree.svg-module.html">obitools.tree.svg</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.tree.unrooted-module.html">obitools.tree.unrooted</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.unit-module.html">obitools.unit</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.unit.obitools-module.html">obitools.unit.obitools</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.utils-module.html">obitools.utils</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.utils.bioseq-module.html">obitools.utils.bioseq</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.utils.crc64-module.html">obitools.utils.crc64</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.utils.iterator-module.html">obitools.utils.iterator</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.word-module.html">obitools.word</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.word.options-module.html">obitools.word.options</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.word.predicat-module.html">obitools.word.predicat</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.zipfile-module.html">obitools.zipfile</a></strong>: <em class="summary">Read and write ZIP files.</em> </li>
</ul>
</li>
</ul>
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Package&nbsp;obitools
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package obitools</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html">source&nbsp;code</a></span></p>
<!-- ==================== SUBMODULES ==================== -->
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<ul class="nomargin">
<li> <strong class="uidlink"><a href="obitools.SVGdraw-module.html">obitools.SVGdraw</a></strong>: <em class="summary">Use SVGdraw to generate your SVGdrawings.</em> </li>
<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.align.homopolymere-module.html">obitools.align.homopolymere</a></strong>: <em class="summary">Created on 14 mai 2009</em> </li>
<li> <strong class="uidlink"><a href="obitools.align.ssearch-module.html">obitools.align.ssearch</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.alignment-module.html">obitools.alignment</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.alignment.ace-module.html">obitools.alignment.ace</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.blast-module.html">obitools.blast</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.carto-module.html">obitools.carto</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.cns-module.html">obitools.cns</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.cns.fasta-module.html">obitools.cns.fasta</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.cns.quality-module.html">obitools.cns.quality</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.decorator-module.html">obitools.decorator</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.distances-module.html">obitools.distances</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.distances.observed-module.html">obitools.distances.observed</a></strong>: <em class="summary">Module dedicated to compute observed divergeances from an
alignment.</em> </li>
<li> <strong class="uidlink"><a href="obitools.distances.phylip-module.html">obitools.distances.phylip</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.distances.r-module.html">obitools.distances.r</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.dnahash-module.html">obitools.dnahash</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.ecopcr-module.html">obitools.ecopcr</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecopcr.annotation-module.html">obitools.ecopcr.annotation</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence-module.html">obitools.ecopcr.sequence</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy-module.html">obitools.ecopcr.taxonomy</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.ecotag-module.html">obitools.ecotag</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecotag.parser-module.html">obitools.ecotag.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.eutils-module.html">obitools.eutils</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.fast-module.html">obitools.fast</a></strong>: <em class="summary">implement fastn/fastp sililarity search algorithm for BioSequence.</em> </li>
<li> <strong class="uidlink"><a href="obitools.fasta-module.html">obitools.fasta</a></strong>: <em class="summary">fasta module provides functions to read and write sequences in
fasta format.</em> </li>
<li> <strong class="uidlink"><a href="obitools.format-module.html">obitools.format</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.format.genericparser-module.html">obitools.format.genericparser</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.ontology-module.html">obitools.format.ontology</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.format.ontology.go_obo-module.html">obitools.format.ontology.go_obo</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.ontology.obo-module.html">obitools.format.ontology.obo</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.format.sequence-module.html">obitools.format.sequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.format.sequence.embl-module.html">obitools.format.sequence.embl</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.sequence.fasta-module.html">obitools.format.sequence.fasta</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.sequence.genbank-module.html">obitools.format.sequence.genbank</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.format.sequence.tagmatcher-module.html">obitools.format.sequence.tagmatcher</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.genbank-module.html">obitools.genbank</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.genbank.ncbi-module.html">obitools.genbank.ncbi</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.goa-module.html">obitools.goa</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.goa.parser-module.html">obitools.goa.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph-module.html">obitools.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms-module.html">obitools.graph.algorithms</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.clique-module.html">obitools.graph.algorithms.clique</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.compact-module.html">obitools.graph.algorithms.compact</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.component-module.html">obitools.graph.algorithms.component</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.dag-module.html">obitools.graph.dag</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.layout-module.html">obitools.graph.layout</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.graph.layout.radialtree-module.html">obitools.graph.layout.radialtree</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.rootedtree-module.html">obitools.graph.rootedtree</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.graph.tree-module.html">obitools.graph.tree</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.gzip-module.html">obitools.gzip</a></strong>: <em class="summary">Functions that read and write gzipped files.</em> </li>
<li> <strong class="uidlink"><a href="obitools.location-module.html">obitools.location</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.location.feature-module.html">obitools.location.feature</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.nucdb-module.html">obitools.nucdb</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.nucdb.genbank-module.html">obitools.nucdb.genbank</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.nucdb.genbank.ncbi-module.html">obitools.nucdb.genbank.ncbi</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.nucdb.genbank.parser-module.html">obitools.nucdb.genbank.parser</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obischemas-module.html">obitools.obischemas</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.obischemas.kb-module.html">obitools.obischemas.kb</a></strong>: <em class="summary">kb package is devoted to manage access to postgresql database from
python script</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.obischemas.kb.extern-module.html">obitools.obischemas.kb.extern</a></strong>: <em class="summary">Module : KB.extern Author : Eric Coissac Date : 03/05/2004</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obischemas.options-module.html">obitools.obischemas.options</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obo-module.html">obitools.obo</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.go-module.html">obitools.obo.go</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.obo.go.parser-module.html">obitools.obo.go.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser-module.html">obitools.obo.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.oligo-module.html">obitools.oligo</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.oligo.options-module.html">obitools.oligo.options</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.oligo.predicat-module.html">obitools.oligo.predicat</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.options-module.html">obitools.options</a></strong>: <em class="summary">Module providing high level functions to manage command line
options.</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.options.bioseqcutter-module.html">obitools.options.bioseqcutter</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.options.bioseqedittag-module.html">obitools.options.bioseqedittag</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.options.bioseqfilter-module.html">obitools.options.bioseqfilter</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.options.taxonomyfilter-module.html">obitools.options.taxonomyfilter</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel-module.html">obitools.parallel</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue-module.html">obitools.parallel.jobqueue</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.phylogeny-module.html">obitools.phylogeny</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.phylogeny.newick-module.html">obitools.phylogeny.newick</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb-module.html">obitools.seqdb</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.blastdb-module.html">obitools.seqdb.blastdb</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.dnaparser-module.html">obitools.seqdb.dnaparser</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.embl-module.html">obitools.seqdb.embl</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.embl.parser-module.html">obitools.seqdb.embl.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank-module.html">obitools.seqdb.genbank</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph-module.html">obitools.seqdb.genbank.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms-module.html">obitools.seqdb.genbank.graph.algorithms</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.clique-module.html">obitools.seqdb.genbank.graph.algorithms.clique</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.component-module.html">obitools.seqdb.genbank.graph.algorithms.component</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag-module.html">obitools.seqdb.genbank.graph.dag</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.rootedtree-module.html">obitools.seqdb.genbank.graph.rootedtree</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.tree-module.html">obitools.seqdb.genbank.graph.tree</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi-module.html">obitools.seqdb.genbank.ncbi</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.parser-module.html">obitools.seqdb.genbank.parser</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.sequenceencoder-module.html">obitools.sequenceencoder</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.solexa-module.html">obitools.solexa</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.statistics-module.html">obitools.statistics</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.statistics.hypergeometric-module.html">obitools.statistics.hypergeometric</a></strong>: <em class="summary">Module de calcules statistiques.</em> </li>
<li> <strong class="uidlink"><a href="obitools.statistics.noncentralhypergeo-module.html">obitools.statistics.noncentralhypergeo</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.svg-module.html">obitools.svg</a></strong>: <em class="summary">SVG.py - Construct/display SVG scenes.</em> </li>
<li> <strong class="uidlink"><a href="obitools.table-module.html">obitools.table</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.table.csv-module.html">obitools.table.csv</a></strong>: <em class="summary">obitools.table.csv module provides an iterator adapter allowing to
parse csv (comma separatted value) file</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tagmatcher-module.html">obitools.tagmatcher</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.tagmatcher.options-module.html">obitools.tagmatcher.options</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.tagmatcher.parser-module.html">obitools.tagmatcher.parser</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tree-module.html">obitools.tree</a></strong>
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<a href="obitools.BioSequence-class.html" class="summary-name">BioSequence</a><br />
BioSequence class is the base class for biological sequence
representation.
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<span class="summary-type">&nbsp;</span>
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<a href="obitools.NucSequence-class.html" class="summary-name">NucSequence</a>
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<a href="obitools.DNAComplementSequence-class.html" class="summary-name">DNAComplementSequence</a>
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<td><span class="summary-sig"><a name="_isNucSeq"></a><span class="summary-sig-name">_isNucSeq</span>(<span class="summary-sig-arg">text</span>)</span></td>
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<span class="codelink"><a href="obitools-pysrc.html#_isNucSeq">source&nbsp;code</a></span>
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<td><span class="summary-sig"><a name="bioSeqGenerator"></a><span class="summary-sig-name">bioSeqGenerator</span>(<span class="summary-sig-arg">id</span>,
<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**info</span>)</span></td>
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<span class="codelink"><a href="obitools-pysrc.html#bioSeqGenerator">source&nbsp;code</a></span>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;AASequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class AASequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#AASequence">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.BioSequence-class.html">BioSequence</a> --+
|
<strong class="uidshort">AASequence</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.seqdb.AnnotatedAASequence-class.html">seqdb.AnnotatedAASequence</a></li> </ul>
</dd></dl>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="isNucleotide"></a><span class="summary-sig-name">isNucleotide</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="obitools-pysrc.html#AASequence.isNucleotide">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#__contains__">__contains__</a></code>,
<code><a href="obitools.BioSequence-class.html#__delitem__">__delitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__getitem__">__getitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__init__">__init__</a></code>,
<code><a href="obitools.BioSequence-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.BioSequence-class.html#__len__">__len__</a></code>,
<code><a href="obitools.BioSequence-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__str__">__str__</a></code>,
<code><a href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a></code>,
<code><a href="obitools.BioSequence-class.html#getDefinition">getDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#getId">getId</a></code>,
<code><a href="obitools.BioSequence-class.html#getRoot">getRoot</a></code>,
<code><a href="obitools.BioSequence-class.html#getStr">getStr</a></code>,
<code><a href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a></code>,
<code><a href="obitools.BioSequence-class.html#getSymbolAt">getSymbolAt</a></code>,
<code><a href="obitools.BioSequence-class.html#getTags">getTags</a></code>,
<code><a href="obitools.BioSequence-class.html#getWrappers">getWrappers</a></code>,
<code><a href="obitools.BioSequence-class.html#items">items</a></code>,
<code><a href="obitools.BioSequence-class.html#iteritems">iteritems</a></code>,
<code><a href="obitools.BioSequence-class.html#iterkeys">iterkeys</a></code>,
<code><a href="obitools.BioSequence-class.html#keys">keys</a></code>,
<code><a href="obitools.BioSequence-class.html#register">register</a></code>,
<code><a href="obitools.BioSequence-class.html#setDefinition">setDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#setId">setId</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b> (private):
<code><a href="obitools.BioSequence-class.html#_unregister" onclick="show_private();">_unregister</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#definition">definition</a></code>,
<code><a href="obitools.BioSequence-class.html#id">id</a></code>,
<code><a href="obitools.BioSequence-class.html#wrappers">wrappers</a></code>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;BioSequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BioSequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#BioSequence">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">BioSequence</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.AASequence-class.html">AASequence</a></li><li>, <a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></li><li>, <a href="obitools.NucSequence-class.html">NucSequence</a></li> </ul>
</dd></dl>
<hr />
<p>BioSequence class is the base class for biological sequence
representation.</p>
<p>It provides storage of :</p>
<ul>
<li>
the sequence itself,
</li>
<li>
an identifier,
</li>
<li>
a definition an manage
</li>
<li>
a set of complementary information on a key / value principle.
</li>
</ul>
<p>BioSequence is an abstract class and must be instanciated from its
subclasses</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.BioSequence-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>,
<span class="summary-sig-arg">seq</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**info</span>)</span><br />
BioSequence constructor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__init__">source&nbsp;code</a></span>
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</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.BioSequence-class.html#getDefinition" class="summary-sig-name">getDefinition</a>(<span class="summary-sig-arg">self</span>)</span><br />
Sequence definition getter</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getDefinition">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="setDefinition"></a><span class="summary-sig-name">setDefinition</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.setDefinition">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getId"></a><span class="summary-sig-name">getId</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getId">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="setId"></a><span class="summary-sig-name">setId</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.setId">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.BioSequence-class.html#getStr" class="summary-sig-name">getStr</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the sequence as a string</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getStr">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>str</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.BioSequence-class.html#getSymbolAt" class="summary-sig-name">getSymbolAt</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span><br />
Return the symbole at position in the sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getSymbolAt">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getSubSeq"></a><span class="summary-sig-name">getSubSeq</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">location</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getSubSeq">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="extractTaxon"></a><span class="summary-sig-name">extractTaxon</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.extractTaxon">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.BioSequence-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
str(x)</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__str__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__getitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__setitem__"></a><span class="summary-sig-name">__setitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>,
<span class="summary-sig-arg">value</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__setitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__delitem__"></a><span class="summary-sig-name">__delitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__delitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__iter__"></a><span class="summary-sig-name">__iter__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate through the sequence symbols</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__iter__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__len__"></a><span class="summary-sig-name">__len__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__len__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__contains__"></a><span class="summary-sig-name">__contains__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.__contains__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="iteritems"></a><span class="summary-sig-name">iteritems</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.iteritems">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="items"></a><span class="summary-sig-name">items</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.items">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="iterkeys"></a><span class="summary-sig-name">iterkeys</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.iterkeys">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="keys"></a><span class="summary-sig-name">keys</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.keys">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getTags"></a><span class="summary-sig-name">getTags</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getTags">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getRoot"></a><span class="summary-sig-name">getRoot</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getRoot">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getWrappers"></a><span class="summary-sig-name">getWrappers</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.getWrappers">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="register"></a><span class="summary-sig-name">register</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">wrapper</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence.register">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_unregister"></a><span class="summary-sig-name">_unregister</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ref</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#BioSequence._unregister">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.BioSequence-class.html#wrappers" class="summary-name">wrappers</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.BioSequence-class.html#definition" class="summary-name">definition</a><br />
Sequence Definition
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.BioSequence-class.html#id" class="summary-name">id</a><br />
Sequence identifier
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>,
<span class="sig-arg">seq</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**info</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#BioSequence.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>BioSequence constructor.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>id</code></strong> (str) - sequence identifier</li>
<li><strong class="pname"><code>seq</code></strong> (str) - the sequence</li>
<li><strong class="pname"><code>definition</code></strong> (str) - sequence definition (optional)</li>
<li><strong class="pname"><code>info</code></strong> - extra named parameters can be add to associate complementary data
to the sequence</li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="getDefinition"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getDefinition</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#BioSequence.getDefinition">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Sequence definition getter</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the sequence definition</dd>
</dl>
</td></tr></table>
</div>
<a name="getStr"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getStr</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#BioSequence.getStr">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the sequence as a string</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the string representation of the sequence</dd>
</dl>
</td></tr></table>
</div>
<a name="getSymbolAt"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getSymbolAt</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#BioSequence.getSymbolAt">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the symbole at position in the sequence</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>position</code></strong> (<code>int</code>) - the desired position. Position start from 0 if position is &lt; 0
then they are considered to reference the end of the sequence.</li>
</ul></dd>
<dt>Returns: <code>str</code></dt>
<dd>a one letter string</dd>
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#BioSequence.__str__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>str(x)</p>
<dl class="fields">
<dt>Overrides:
object.__str__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
<a name="section-PropertyDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Property Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-PropertyDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="wrappers"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">wrappers</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.BioSequence-class.html#getWrappers" class="summary-sig-name">getWrappers</a>(<span class="summary-sig-arg">self</span>)</span>
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<a name="definition"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">definition</h3>
<p>Sequence Definition</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.BioSequence-class.html#getDefinition" class="summary-sig-name">getDefinition</a>(<span class="summary-sig-arg">self</span>)</span>
- Sequence definition getter
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.BioSequence-class.html#setDefinition" class="summary-sig-name">setDefinition</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="id"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">id</h3>
<p>Sequence identifier</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.BioSequence-class.html#getId" class="summary-sig-name">getId</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.BioSequence-class.html#setId" class="summary-sig-name">setId</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;DNAComplementSequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DNAComplementSequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.BioSequence-class.html">BioSequence</a> --+
|
<a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a> --+
|
<strong class="uidshort">DNAComplementSequence</strong>
</pre>
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<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">reference</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**info</span>)</span><br />
BioSequence constructor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.__init__">source&nbsp;code</a></span>
</td>
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</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#getId" class="summary-sig-name">getId</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.getId">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.__len__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#getStr" class="summary-sig-name">getStr</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the sequence as a string</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.getStr">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate through the sequence symbols</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.__iter__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#_posInWrapped" class="summary-sig-name" onclick="show_private();">_posInWrapped</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence._posInWrapped">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>str</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#getSymbolAt" class="summary-sig-name">getSymbolAt</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span><br />
Return the symbole at position in the sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.getSymbolAt">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="complement"></a><span class="summary-sig-name">complement</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.complement">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></code></b>:
<code><a href="obitools.WrappedBioSequence-class.html#__getitem__">__getitem__</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getDefinition">getDefinition</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getRoot">getRoot</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getWrapped">getWrapped</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#isNucleotide">isNucleotide</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#iteritems">iteritems</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#iterkeys">iterkeys</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#posInWrapped">posInWrapped</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#__contains__">__contains__</a></code>,
<code><a href="obitools.BioSequence-class.html#__delitem__">__delitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__str__">__str__</a></code>,
<code><a href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a></code>,
<code><a href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a></code>,
<code><a href="obitools.BioSequence-class.html#getTags">getTags</a></code>,
<code><a href="obitools.BioSequence-class.html#getWrappers">getWrappers</a></code>,
<code><a href="obitools.BioSequence-class.html#items">items</a></code>,
<code><a href="obitools.BioSequence-class.html#keys">keys</a></code>,
<code><a href="obitools.BioSequence-class.html#register">register</a></code>,
<code><a href="obitools.BioSequence-class.html#setDefinition">setDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#setId">setId</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b> (private):
<code><a href="obitools.BioSequence-class.html#_unregister" onclick="show_private();">_unregister</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
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<td align="left"><span class="table-header">Class Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassVariables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.DNAComplementSequence-class.html#_comp" class="summary-name" onclick="show_private();">_comp</a> = <code title="{'-': '-',
'a': 't',
'b': 'v',
'c': 'g',
'd': 'h',
'g': 'c',
'h': 'd',
'k': 'm',
..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">a</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">t</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">b</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">v</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">c</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">g</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">d</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">h</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">g</code><code class="variable-quote">'</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
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<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.DNAComplementSequence-class.html#id" class="summary-name">id</a><br />
Sequence Identifier
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></code></b>:
<code><a href="obitools.WrappedBioSequence-class.html#definition">definition</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#wrapped">wrapped</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#wrappers">wrappers</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="__init__"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">reference</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**info</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>BioSequence constructor.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>id</code></strong> - sequence identifier</li>
<li><strong class="pname"><code>seq</code></strong> - the sequence</li>
<li><strong class="pname"><code>definition</code></strong> - sequence definition (optional)</li>
<li><strong class="pname"><code>info</code></strong> - extra named parameters can be add to associate complementary data
to the sequence</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getId"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getId</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.getId">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getId">BioSequence.getId</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.__len__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__len__">BioSequence.__len__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getStr"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getStr</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.getStr">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the sequence as a string</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the string representation of the sequence</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getStr">BioSequence.getStr</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__iter__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.__iter__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Iterate through the sequence symbols</p>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__iter__">BioSequence.__iter__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_posInWrapped"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_posInWrapped</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence._posInWrapped">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.WrappedBioSequence-class.html#_posInWrapped" onclick="show_private();">WrappedBioSequence._posInWrapped</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getSymbolAt"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getSymbolAt</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#DNAComplementSequence.getSymbolAt">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the symbole at position in the sequence</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>position</code></strong> - the desired position. Position start from 0 if position is &lt; 0
then they are considered to reference the end of the sequence.</li>
</ul></dd>
<dt>Returns: <code>str</code></dt>
<dd>a one letter string</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getSymbolAt">BioSequence.getSymbolAt</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
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<h3 class="epydoc">_comp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">a</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">t</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">b</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">v</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">c</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">g</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">d</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">h</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">g</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">c</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">h</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">d</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">k</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">m</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
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<br />
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<h3 class="epydoc">id</h3>
<p>Sequence Identifier</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.DNAComplementSequence-class.html#getId" class="summary-sig-name">getId</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.setId(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;NucSequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class NucSequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#NucSequence">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.BioSequence-class.html">BioSequence</a> --+
|
<strong class="uidshort">NucSequence</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.tagmatcher.TagMatcherSequence-class.html">tagmatcher.TagMatcherSequence</a></li><li>, <a href="obitools.seqdb.AnnotatedNucSequence-class.html">seqdb.AnnotatedNucSequence</a></li><li>, <a href="obitools.solexa.SolexaSequence-class.html">solexa.SolexaSequence</a></li> </ul>
</dd></dl>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="complement"></a><span class="summary-sig-name">complement</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#NucSequence.complement">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a name="isNucleotide"></a><span class="summary-sig-name">isNucleotide</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#NucSequence.isNucleotide">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#__contains__">__contains__</a></code>,
<code><a href="obitools.BioSequence-class.html#__delitem__">__delitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__getitem__">__getitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__init__">__init__</a></code>,
<code><a href="obitools.BioSequence-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.BioSequence-class.html#__len__">__len__</a></code>,
<code><a href="obitools.BioSequence-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__str__">__str__</a></code>,
<code><a href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a></code>,
<code><a href="obitools.BioSequence-class.html#getDefinition">getDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#getId">getId</a></code>,
<code><a href="obitools.BioSequence-class.html#getRoot">getRoot</a></code>,
<code><a href="obitools.BioSequence-class.html#getStr">getStr</a></code>,
<code><a href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a></code>,
<code><a href="obitools.BioSequence-class.html#getSymbolAt">getSymbolAt</a></code>,
<code><a href="obitools.BioSequence-class.html#getTags">getTags</a></code>,
<code><a href="obitools.BioSequence-class.html#getWrappers">getWrappers</a></code>,
<code><a href="obitools.BioSequence-class.html#items">items</a></code>,
<code><a href="obitools.BioSequence-class.html#iteritems">iteritems</a></code>,
<code><a href="obitools.BioSequence-class.html#iterkeys">iterkeys</a></code>,
<code><a href="obitools.BioSequence-class.html#keys">keys</a></code>,
<code><a href="obitools.BioSequence-class.html#register">register</a></code>,
<code><a href="obitools.BioSequence-class.html#setDefinition">setDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#setId">setId</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b> (private):
<code><a href="obitools.BioSequence-class.html#_unregister" onclick="show_private();">_unregister</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#definition">definition</a></code>,
<code><a href="obitools.BioSequence-class.html#id">id</a></code>,
<code><a href="obitools.BioSequence-class.html#wrappers">wrappers</a></code>
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module SVGdraw</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html">source&nbsp;code</a></span></p>
<pre class="literalblock">
Use SVGdraw to generate your SVGdrawings.
SVGdraw uses an object model drawing and a method toXML to create SVG graphics
by using easy to use classes and methods usualy you start by creating a drawing eg
d=drawing()
#then you create a SVG root element
s=svg()
#then you add some elements eg a circle and add it to the svg root element
c=circle()
#you can supply attributes by using named arguments.
c=circle(fill='red',stroke='blue')
#or by updating the attributes attribute:
c.attributes['stroke-width']=1
s.addElement(c)
#then you add the svg root element to the drawing
d.setSVG(s)
#and finaly you xmlify the drawing
d.toXml()
this results in the svg source of the drawing, which consists of a circle
on a white background. Its as easy as that;)
This module was created using the SVG specification of www.w3c.org and the
O'Reilly (www.oreilly.com) python books as information sources. A svg viewer
is available from www.adobe.com
</pre>
<hr />
<div class="fields"> <p><strong>Version:</strong>
1.0
</p>
</div><!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Classes</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Classes"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.pathdata-class.html" class="summary-name">pathdata</a><br />
class used to create a pathdata object which can be used for a
path.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.SVGelement-class.html" class="summary-name">SVGelement</a><br />
SVGelement(type,attributes,elements,text,namespace,**args) Creates
a arbitrary svg element and is intended to be subclassed not used
on its own.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.tspan-class.html" class="summary-name">tspan</a><br />
ts=tspan(text='',**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.tref-class.html" class="summary-name">tref</a><br />
tr=tref(link='',**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.spannedtext-class.html" class="summary-name">spannedtext</a><br />
st=spannedtext(textlist=[])
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.rect-class.html" class="summary-name">rect</a><br />
r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.ellipse-class.html" class="summary-name">ellipse</a><br />
e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.circle-class.html" class="summary-name">circle</a><br />
c=circle(x,y,radius,fill,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.point-class.html" class="summary-name">point</a><br />
p=point(x,y,color)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.line-class.html" class="summary-name">line</a><br />
l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.polyline-class.html" class="summary-name">polyline</a><br />
pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.polygon-class.html" class="summary-name">polygon</a><br />
pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.path-class.html" class="summary-name">path</a><br />
p=path(path,fill,stroke,stroke_width,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.text-class.html" class="summary-name">text</a><br />
t=text(x,y,text,font_size,font_family,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.textpath-class.html" class="summary-name">textpath</a><br />
tp=textpath(text,link,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.pattern-class.html" class="summary-name">pattern</a><br />
p=pattern(x,y,width,height,patternUnits,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.title-class.html" class="summary-name">title</a><br />
t=title(text,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.description-class.html" class="summary-name">description</a><br />
d=description(text,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.lineargradient-class.html" class="summary-name">lineargradient</a><br />
lg=lineargradient(x1,y1,x2,y2,id,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.radialgradient-class.html" class="summary-name">radialgradient</a><br />
rg=radialgradient(cx,cy,r,fx,fy,id,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.stop-class.html" class="summary-name">stop</a><br />
st=stop(offset,stop_color,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.style-class.html" class="summary-name">style</a><br />
st=style(type,cdata=None,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.image-class.html" class="summary-name">image</a><br />
im=image(url,width,height,x,y,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.cursor-class.html" class="summary-name">cursor</a><br />
c=cursor(url,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.marker-class.html" class="summary-name">marker</a><br />
m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.group-class.html" class="summary-name">group</a><br />
g=group(id,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.symbol-class.html" class="summary-name">symbol</a><br />
sy=symbol(id,viewbox,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.defs-class.html" class="summary-name">defs</a><br />
d=defs(**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.switch-class.html" class="summary-name">switch</a><br />
sw=switch(**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.use-class.html" class="summary-name">use</a><br />
u=use(link,x,y,width,height,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.link-class.html" class="summary-name">link</a><br />
a=link(url,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.view-class.html" class="summary-name">view</a><br />
v=view(id,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.script-class.html" class="summary-name">script</a><br />
sc=script(type,type,cdata,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.animate-class.html" class="summary-name">animate</a><br />
an=animate(attribute,from,to,during,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.animateMotion-class.html" class="summary-name">animateMotion</a><br />
an=animateMotion(pathdata,dur,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.animateTransform-class.html" class="summary-name">animateTransform</a><br />
antr=animateTransform(type,from,to,dur,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.animateColor-class.html" class="summary-name">animateColor</a><br />
ac=animateColor(attribute,type,from,to,dur,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.set-class.html" class="summary-name">set</a><br />
st=set(attribute,to,during,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.svg-class.html" class="summary-name">svg</a><br />
s=svg(viewbox,width,height,**args)
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw.drawing-class.html" class="summary-name">drawing</a><br />
d=drawing()
</td>
</tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Functions</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Functions"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">file object</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw-module.html#file" class="summary-sig-name">file</a>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">mode</span>=<span class="summary-sig-default">...</span>,
<span class="summary-sig-arg">buffering</span>=<span class="summary-sig-default">...</span>)</span><br />
Open a file using the file() type, returns a file object.</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw-module.html#_escape" class="summary-sig-name" onclick="show_private();">_escape</a>(<span class="summary-sig-arg">data</span>,
<span class="summary-sig-arg">entities</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span><br />
Escape &amp;, &lt;, and &gt; in a string of data.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_escape">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw-module.html#_quoteattr" class="summary-sig-name" onclick="show_private();">_quoteattr</a>(<span class="summary-sig-arg">data</span>,
<span class="summary-sig-arg">entities</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span><br />
Escape and quote an attribute value.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_quoteattr">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_xypointlist"></a><span class="summary-sig-name">_xypointlist</span>(<span class="summary-sig-arg">a</span>)</span><br />
formats a list of xy pairs</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_xypointlist">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_viewboxlist"></a><span class="summary-sig-name">_viewboxlist</span>(<span class="summary-sig-arg">a</span>)</span><br />
formats a tuple</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_viewboxlist">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_pointlist"></a><span class="summary-sig-name">_pointlist</span>(<span class="summary-sig-arg">a</span>)</span><br />
formats a list of numbers</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_pointlist">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.SVGdraw-module.html#__doc__" class="summary-name">__doc__</a> = <code title="&quot;&quot;&quot;Use SVGdraw to generate your SVGdrawings.
SVGdraw uses an object model drawing and a method toXML to create SVG \
graphics
by using easy to use classes and methods usualy you start by creating \
a drawing eg
d=drawing()
...">&quot;&quot;&quot;Use SVGdraw to generate your SVGdrawin<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="use_dom_implementation"></a><span class="summary-name">use_dom_implementation</span> = <code title="0">0</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="True"></a><span class="summary-name">True</span> = <code title="1">1</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="False"></a><span class="summary-name">False</span> = <code title="0">0</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools'"><code class="variable-quote">'</code><code class="variable-string">obitools</code><code class="variable-quote">'</code></code>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Function Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-FunctionDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="file"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">file</span>(<span class="sig-arg">name</span>,
<span class="sig-arg">mode</span>=<span class="sig-default">...</span>,
<span class="sig-arg">buffering</span>=<span class="sig-default">...</span>)</span>
</h3>
</td><td align="right" valign="top"
>&nbsp;
</td>
</tr></table>
<p>Open a file using the file() type, returns a file object. This is the
preferred way to open a file.</p>
<dl class="fields">
<dt>Returns: file object</dt>
</dl>
</td></tr></table>
</div>
<a name="_escape"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_escape</span>(<span class="sig-arg">data</span>,
<span class="sig-arg">entities</span>=<span class="sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_escape">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Escape &amp;, &lt;, and &gt; in a string of data.</p>
<p>You can escape other strings of data by passing a dictionary as the
optional entities parameter. The keys and values must all be strings;
each key will be replaced with its corresponding value.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_quoteattr"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_quoteattr</span>(<span class="sig-arg">data</span>,
<span class="sig-arg">entities</span>=<span class="sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#_quoteattr">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Escape and quote an attribute value.</p>
<p>Escape &amp;, &lt;, and &gt; in a string of data, then quote it for
use as an attribute value. The &quot; character will be escaped as well,
if necessary.</p>
<p>You can escape other strings of data by passing a dictionary as the
optional entities parameter. The keys and values must all be strings;
each key will be replaced with its corresponding value.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
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><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="__doc__"></a>
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<h3 class="epydoc">__doc__</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
&quot;&quot;&quot;Use SVGdraw to generate your SVGdrawings.
SVGdraw uses an object model drawing and a method toXML to create SVG <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
graphics
by using easy to use classes and methods usualy you start by creating <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
a drawing eg
d=drawing()
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;SVGelement
</span>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SVGelement</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#SVGelement">source&nbsp;code</a></span></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.SVGdraw.animate-class.html">animate</a></li><li>, <a href="obitools.SVGdraw.animateColor-class.html">animateColor</a></li><li>, <a href="obitools.SVGdraw.animateMotion-class.html">animateMotion</a></li><li>, <a href="obitools.SVGdraw.animateTransform-class.html">animateTransform</a></li><li>, <a href="obitools.SVGdraw.circle-class.html">circle</a></li><li>, <a href="obitools.SVGdraw.cursor-class.html">cursor</a></li><li>, <a href="obitools.SVGdraw.defs-class.html">defs</a></li><li>, <a href="obitools.SVGdraw.description-class.html">description</a></li><li>, <a href="obitools.SVGdraw.ellipse-class.html">ellipse</a></li><li>, <a href="obitools.SVGdraw.group-class.html">group</a></li><li>, <a href="obitools.SVGdraw.image-class.html">image</a></li><li>, <a href="obitools.SVGdraw.line-class.html">line</a></li><li>, <a href="obitools.SVGdraw.lineargradient-class.html">lineargradient</a></li><li>, <a href="obitools.SVGdraw.link-class.html">link</a></li><li>, <a href="obitools.SVGdraw.marker-class.html">marker</a></li><li>, <a href="obitools.SVGdraw.path-class.html">path</a></li><li>, <a href="obitools.SVGdraw.pattern-class.html">pattern</a></li><li>, <a href="obitools.SVGdraw.polygon-class.html">polygon</a></li><li>, <a href="obitools.SVGdraw.polyline-class.html">polyline</a></li><li>, <a href="obitools.SVGdraw.radialgradient-class.html">radialgradient</a></li><li>, <a href="obitools.SVGdraw.rect-class.html">rect</a></li><li>, <a href="obitools.SVGdraw.script-class.html">script</a></li><li>, <a href="obitools.SVGdraw.set-class.html">set</a></li><li>, <a href="obitools.SVGdraw.stop-class.html">stop</a></li><li>, <a href="obitools.SVGdraw.style-class.html">style</a></li><li>, <a href="obitools.SVGdraw.svg-class.html">svg</a></li><li>, <a href="obitools.SVGdraw.switch-class.html">switch</a></li><li>, <a href="obitools.SVGdraw.symbol-class.html">symbol</a></li><li>, <a href="obitools.SVGdraw.text-class.html">text</a></li><li>, <a href="obitools.SVGdraw.textpath-class.html">textpath</a></li><li>, <a href="obitools.SVGdraw.title-class.html">title</a></li><li>, <a href="obitools.SVGdraw.tref-class.html">tref</a></li><li>, <a href="obitools.SVGdraw.tspan-class.html">tspan</a></li><li>, <a href="obitools.SVGdraw.use-class.html">use</a></li><li>, <a href="obitools.SVGdraw.view-class.html">view</a></li> </ul>
</dd></dl>
<hr />
<p>SVGelement(type,attributes,elements,text,namespace,**args) Creates a
arbitrary svg element and is intended to be subclassed not used on its
own. This element is the base of every svg element it defines a class
which resembles a xml-element. The main advantage of this kind of
implementation is that you don't have to create a toXML method for every
different graph object. Every element consists of a type, attribute,
optional subelements, optional text and an optional namespace. Note the
elements==None, if elements = None:self.elements=[] construction. This is
done because if you default to elements=[] every object has a reference
to the same empty list.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">type</span>,
<span class="summary-sig-arg">attributes</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">elements</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">text</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">namespace</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#SVGelement.__init__">source&nbsp;code</a></span>
</td>
</tr>
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</td>
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.SVGelement-class.html#addElement" class="summary-sig-name">addElement</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">SVGelement</span>)</span><br />
adds an element to a SVGelement</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#SVGelement.addElement">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="toXml"></a><span class="summary-sig-name">toXml</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">level</span>,
<span class="summary-sig-arg">f</span>,
<span class="summary-sig-arg">**kwargs</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#SVGelement.toXml">source&nbsp;code</a></span>
</td>
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<!-- ==================== METHOD DETAILS ==================== -->
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="addElement"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">addElement</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">SVGelement</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#SVGelement.addElement">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>adds an element to a SVGelement</p>
<p>SVGelement.addElement(SVGelement)</p>
<dl class="fields">
</dl>
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Class&nbsp;animate
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class animate</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animate">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">animate</strong>
</pre>
<hr />
<p>an=animate(attribute,from,to,during,**args)</p>
<p>animates an attribute.</p>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.animate-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">attribute</span>,
<span class="summary-sig-arg">fr</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">to</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">dur</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animate.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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class="privatelink" onclick="toggle_private();"
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">attribute</span>,
<span class="sig-arg">fr</span>=<span class="sig-default">None</span>,
<span class="sig-arg">to</span>=<span class="sig-default">None</span>,
<span class="sig-arg">dur</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animate.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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Class&nbsp;animateColor
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class animateColor</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateColor">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">animateColor</strong>
</pre>
<hr />
<p>ac=animateColor(attribute,type,from,to,dur,**args)</p>
<p>Animates the color of a element</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.animateColor-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">type</span>=<span class="summary-sig-default">None</span>,
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateColor.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">attribute</span>,
<span class="sig-arg">type</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fr</span>=<span class="sig-default">None</span>,
<span class="sig-arg">to</span>=<span class="sig-default">None</span>,
<span class="sig-arg">dur</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateColor.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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Class&nbsp;animateMotion
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class animateMotion</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateMotion">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">animateMotion</strong>
</pre>
<hr />
<p>an=animateMotion(pathdata,dur,**args)</p>
<p>animates a SVGelement over the given path in dur seconds</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.animateMotion-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pathdata</span>,
<span class="summary-sig-arg">dur</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateMotion.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">pathdata</span>,
<span class="sig-arg">dur</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateMotion.__init__">source&nbsp;code</a></span>&nbsp;
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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Class&nbsp;animateTransform
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class animateTransform</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateTransform">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">animateTransform</strong>
</pre>
<hr />
<p>antr=animateTransform(type,from,to,dur,**args)</p>
<p>transform an element from and to a value.</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.animateTransform-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">type</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">fr</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">to</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">dur</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateTransform.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">type</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fr</span>=<span class="sig-default">None</span>,
<span class="sig-arg">to</span>=<span class="sig-default">None</span>,
<span class="sig-arg">dur</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#animateTransform.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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Class&nbsp;circle
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class circle</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#circle">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">circle</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.SVGdraw.point-class.html">point</a></li> </ul>
</dd></dl>
<hr />
<p>c=circle(x,y,radius,fill,stroke,stroke_width,**args)</p>
<p>The circle creates an element using a x, y and radius values eg</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.circle-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">cx</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">cy</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">r</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke_width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#circle.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">cx</span>=<span class="sig-default">None</span>,
<span class="sig-arg">cy</span>=<span class="sig-default">None</span>,
<span class="sig-arg">r</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fill</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#circle.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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Class&nbsp;cursor
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class cursor</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#cursor">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">cursor</strong>
</pre>
<hr />
<p>c=cursor(url,**args)</p>
<p>defines a custom cursor for a element or a drawing</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.cursor-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
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<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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Class&nbsp;defs
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class defs</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#defs">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">defs</strong>
</pre>
<hr />
<p>d=defs(**args)</p>
<p>container for defining elements</p>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
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<dt>Overrides:
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Class&nbsp;description
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<h1 class="epydoc">Class description</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#description">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">description</strong>
</pre>
<hr />
<p>d=description(text,**args)</p>
<p>a description can be added to any element and is used for a tooltip
Add this element before adding other elements.</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.description-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">text</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#description.__init__">source&nbsp;code</a></span>&nbsp;
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<dl class="fields">
<dt>Overrides:
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Class&nbsp;drawing
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class drawing</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#drawing">source&nbsp;code</a></span></p>
<p>d=drawing()</p>
<p>this is the actual SVG document. It needs a svg element as a root. Use
the addSVG method to set the svg to the root. Use the toXml method to
write the SVG source to the screen or to a file d=drawing() d.addSVG(svg)
d.toXml(optionalfilename)</p>
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<td><span class="summary-sig"><a name="setSVG"></a><span class="summary-sig-name">setSVG</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">svg</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#drawing.setSVG">source&nbsp;code</a></span>
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<td><span class="summary-sig"><a name="toXml"></a><span class="summary-sig-name">toXml</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">compress</span>=<span class="summary-sig-default">False</span>)</span><br />
drawing.toXml() ----&gt;to the screen
drawing.toXml(filename)----&gt;to the file writes a svg drawing to
the screen or to a file compresses if filename ends with svgz or if
compress is true</td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#drawing.toXml">source&nbsp;code</a></span>
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<td><span class="summary-sig"><a name="validate"></a><span class="summary-sig-name">validate</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#drawing.validate">source&nbsp;code</a></span>
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Class&nbsp;ellipse
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class ellipse</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#ellipse">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">ellipse</strong>
</pre>
<hr />
<p>e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)</p>
<p>an ellipse is defined as a center and a x and y radius.</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.ellipse-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">cx</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">cy</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">rx</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">ry</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke_width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#ellipse.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">cx</span>=<span class="sig-default">None</span>,
<span class="sig-arg">cy</span>=<span class="sig-default">None</span>,
<span class="sig-arg">rx</span>=<span class="sig-default">None</span>,
<span class="sig-arg">ry</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fill</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#ellipse.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;group
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<!-- hide/show private -->
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class group</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#group">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">group</strong>
</pre>
<hr />
<p>g=group(id,**args)</p>
<p>a group is defined by an id and is used to contain elements
g.addElement(SVGelement)</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.group-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#group.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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<!-- ==================== METHOD DETAILS ==================== -->
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cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Method Details</span></td>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#group.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
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Class&nbsp;image
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<!-- hide/show private -->
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target="_top">no&nbsp;frames</a>]</span></td></tr>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class image</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#image">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">image</strong>
</pre>
<hr />
<p>im=image(url,width,height,x,y,**args)</p>
<p>adds an image to the drawing. Supported formats are .png, .jpg and
.svg.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.image-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">url</span>,
<span class="summary-sig-arg">x</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">height</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#image.__init__">source&nbsp;code</a></span>
</td>
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<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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<!-- ==================== METHOD DETAILS ==================== -->
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><span class="options">[<a href="#section-MethodDetails"
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<a name="__init__"></a>
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">url</span>,
<span class="sig-arg">x</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y</span>=<span class="sig-default">None</span>,
<span class="sig-arg">width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">height</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#image.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;line
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<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class line</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#line">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">line</strong>
</pre>
<hr />
<p>l=line(x1,y1,x2,y2,stroke,stroke_width,**args)</p>
<p>A line is defined by a begin x,y pair and an end x,y pair</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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><span class="options">[<a href="#section-InstanceMethods"
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.line-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x1</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y1</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">x2</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y2</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke_width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#line.__init__">source&nbsp;code</a></span>
</td>
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</td>
</tr>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
</td>
</tr>
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<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="__init__"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">x1</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y1</span>=<span class="sig-default">None</span>,
<span class="sig-arg">x2</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y2</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#line.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
</td></tr></table>
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Class&nbsp;lineargradient
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class lineargradient</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#lineargradient">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">lineargradient</strong>
</pre>
<hr />
<p>lg=lineargradient(x1,y1,x2,y2,id,**args)</p>
<p>defines a lineargradient using two xy pairs. stop elements van be
added to define the gradient colors.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.lineargradient-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x1</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y1</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">x2</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y2</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#lineargradient.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">x1</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y1</span>=<span class="sig-default">None</span>,
<span class="sig-arg">x2</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y2</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#lineargradient.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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Class&nbsp;link
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class link</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#link">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">link</strong>
</pre>
<hr />
<p>a=link(url,**args)</p>
<p>a link is defined by a hyperlink. add elements which have to be
linked a.addElement(SVGelement)</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.link-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">link</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#link.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">link</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#link.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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Class&nbsp;marker
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class marker</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#marker">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">marker</strong>
</pre>
<hr />
<p>m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)</p>
<p>defines a marker which can be used as an endpoint for a line or other
pathtypes add an element to it which should be used as a marker.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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><span class="options">[<a href="#section-InstanceMethods"
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</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.marker-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">viewBox</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">refx</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">refy</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">markerWidth</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">markerHeight</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#marker.__init__">source&nbsp;code</a></span>
</td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">viewBox</span>=<span class="sig-default">None</span>,
<span class="sig-arg">refx</span>=<span class="sig-default">None</span>,
<span class="sig-arg">refy</span>=<span class="sig-default">None</span>,
<span class="sig-arg">markerWidth</span>=<span class="sig-default">None</span>,
<span class="sig-arg">markerHeight</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#marker.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
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Class&nbsp;path
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class path</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#path">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">path</strong>
</pre>
<hr />
<p>p=path(path,fill,stroke,stroke_width,**args)</p>
<p>a path is defined by a path object and optional width, stroke and
fillcolor</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.path-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pathdata</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke_width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#path.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
</td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">pathdata</span>,
<span class="sig-arg">fill</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#path.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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Class&nbsp;pathdata
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class pathdata</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata">source&nbsp;code</a></span></p>
<p>class used to create a pathdata object which can be used for a path.
although most methods are pretty straightforward it might be useful to
look at the SVG specification.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.__init__">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a name="closepath"></a><span class="summary-sig-name">closepath</span>(<span class="summary-sig-arg">self</span>)</span><br />
ends the path</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.closepath">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a name="move"></a><span class="summary-sig-name">move</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
move to absolute</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.move">source&nbsp;code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relmove"></a><span class="summary-sig-name">relmove</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
move to relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relmove">source&nbsp;code</a></span>
</td>
</tr>
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</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="line"></a><span class="summary-sig-name">line</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
line to absolute</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.line">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relline"></a><span class="summary-sig-name">relline</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
line to relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relline">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="hline"></a><span class="summary-sig-name">hline</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>)</span><br />
horizontal line to absolute</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.hline">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relhline"></a><span class="summary-sig-name">relhline</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>)</span><br />
horizontal line to relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relhline">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="vline"></a><span class="summary-sig-name">vline</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">y</span>)</span><br />
verical line to absolute</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.vline">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relvline"></a><span class="summary-sig-name">relvline</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">y</span>)</span><br />
vertical line to relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relvline">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="bezier"></a><span class="summary-sig-name">bezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x1</span>,
<span class="summary-sig-arg">y1</span>,
<span class="summary-sig-arg">x2</span>,
<span class="summary-sig-arg">y2</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
bezier with xy1 and xy2 to xy absolut</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.bezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relbezier"></a><span class="summary-sig-name">relbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x1</span>,
<span class="summary-sig-arg">y1</span>,
<span class="summary-sig-arg">x2</span>,
<span class="summary-sig-arg">y2</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
bezier with xy1 and xy2 to xy relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="smbezier"></a><span class="summary-sig-name">smbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x2</span>,
<span class="summary-sig-arg">y2</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
smooth bezier with xy2 to xy absolut</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.smbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relsmbezier"></a><span class="summary-sig-name">relsmbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x2</span>,
<span class="summary-sig-arg">y2</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
smooth bezier with xy2 to xy relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relsmbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="qbezier"></a><span class="summary-sig-name">qbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x1</span>,
<span class="summary-sig-arg">y1</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
quadratic bezier with xy1 to xy absolut</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.qbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relqbezier"></a><span class="summary-sig-name">relqbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x1</span>,
<span class="summary-sig-arg">y1</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
quadratic bezier with xy1 to xy relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relqbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="smqbezier"></a><span class="summary-sig-name">smqbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
smooth quadratic bezier to xy absolut</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.smqbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relsmqbezier"></a><span class="summary-sig-name">relsmqbezier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
smooth quadratic bezier to xy relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relsmqbezier">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="ellarc"></a><span class="summary-sig-name">ellarc</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">rx</span>,
<span class="summary-sig-arg">ry</span>,
<span class="summary-sig-arg">xrot</span>,
<span class="summary-sig-arg">laf</span>,
<span class="summary-sig-arg">sf</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
elliptival arc with rx and ry rotating with xrot using large-arc-flag
and sweep-flag to xy absolut</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.ellarc">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="relellarc"></a><span class="summary-sig-name">relellarc</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">rx</span>,
<span class="summary-sig-arg">ry</span>,
<span class="summary-sig-arg">xrot</span>,
<span class="summary-sig-arg">laf</span>,
<span class="summary-sig-arg">sf</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>)</span><br />
elliptival arc with rx and ry rotating with xrot using large-arc-flag
and sweep-flag to xy relative</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.relellarc">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pathdata.__repr__">source&nbsp;code</a></span>
</td>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;pattern
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class pattern</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pattern">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">pattern</strong>
</pre>
<hr />
<p>p=pattern(x,y,width,height,patternUnits,**args)</p>
<p>A pattern is used to fill or stroke an object using a pre-defined
graphic object which can be replicated (&quot;tiled&quot;) at fixed
intervals in x and y to cover the areas to be painted.</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.pattern-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">height</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">patternUnits</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pattern.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">x</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y</span>=<span class="sig-default">None</span>,
<span class="sig-arg">width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">height</span>=<span class="sig-default">None</span>,
<span class="sig-arg">patternUnits</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#pattern.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;point
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class point</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#point">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<a href="obitools.SVGdraw.circle-class.html">circle</a> --+
|
<strong class="uidshort">point</strong>
</pre>
<hr />
<p>p=point(x,y,color)</p>
<p>A point is defined as a circle with a size 1 radius. It may be more
efficient to use a very small rectangle if you use many points because a
circle is difficult to render.</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.point-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">black</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#point.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">x</span>,
<span class="sig-arg">y</span>,
<span class="sig-arg">fill</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">black</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#point.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
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Class&nbsp;polygon
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class polygon</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#polygon">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">polygon</strong>
</pre>
<hr />
<p>pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)</p>
<p>a polygon is defined by a list of xy pairs</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.polygon-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">points</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default">None</span>,
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#polygon.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">points</span>,
<span class="sig-arg">fill</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#polygon.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;polyline
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class polyline</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#polyline">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">polyline</strong>
</pre>
<hr />
<p>pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)</p>
<p>a polyline is defined by a list of xy pairs</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.polyline-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">points</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke_width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#polyline.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">points</span>,
<span class="sig-arg">fill</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#polyline.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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Class&nbsp;radialgradient
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class radialgradient</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#radialgradient">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">radialgradient</strong>
</pre>
<hr />
<p>rg=radialgradient(cx,cy,r,fx,fy,id,**args)</p>
<p>defines a radial gradient using a outer circle which are defined by a
cx,cy and r and by using a focalpoint. stop elements van be added to
define the gradient colors.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.radialgradient-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">cx</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">cy</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">r</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">fx</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">fy</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#radialgradient.__init__">source&nbsp;code</a></span>
</td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">cx</span>=<span class="sig-default">None</span>,
<span class="sig-arg">cy</span>=<span class="sig-default">None</span>,
<span class="sig-arg">r</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fx</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fy</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#radialgradient.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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Class&nbsp;rect
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class rect</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#rect">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">rect</strong>
</pre>
<hr />
<p>r=rect(width,height,x,y,fill,stroke,stroke_width,**args)</p>
<p>a rectangle is defined by a width and height and a xy pair</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.rect-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">x</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">height</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">fill</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stroke_width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#rect.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">x</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y</span>=<span class="sig-default">None</span>,
<span class="sig-arg">width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">height</span>=<span class="sig-default">None</span>,
<span class="sig-arg">fill</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stroke_width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#rect.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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Class&nbsp;script
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class script</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#script">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">script</strong>
</pre>
<hr />
<p>sc=script(type,type,cdata,**args)</p>
<p>adds a script element which contains CDATA to the SVG drawing</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.script-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">type</span>,
<span class="sig-arg">cdata</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#script.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class set</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#set">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">set</strong>
</pre>
<hr />
<p>st=set(attribute,to,during,**args)</p>
<p>sets an attribute to a value for a</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.set-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">attribute</span>,
<span class="summary-sig-arg">to</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">dur</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#set.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">attribute</span>,
<span class="sig-arg">to</span>=<span class="sig-default">None</span>,
<span class="sig-arg">dur</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#set.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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<?xml version="1.0" encoding="ascii"?>
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
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Class&nbsp;spannedtext
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class spannedtext</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#spannedtext">source&nbsp;code</a></span></p>
<p>st=spannedtext(textlist=[])</p>
<p>a spannedtext can be used for text which consists of text, tspan's and
tref's You can use it to add to a text element or path element. Don't add
it directly to a svg or a group element. usage:</p>
<p>ts=tspan('this text is bold') ts.attributes['font-weight']='bold'
tr=tref('#linktotext') tr.attributes['fill']='red' st=spannedtext()
st.addtspan(ts) st.addtref(tr) st.addtext('This text is not bold')
t=text(3,5,st)</p>
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">textlist</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#spannedtext.__init__">source&nbsp;code</a></span>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="addtext"></a><span class="summary-sig-name">addtext</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#spannedtext.addtext">source&nbsp;code</a></span>
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a name="addtspan"></a><span class="summary-sig-name">addtspan</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tspan</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#spannedtext.addtspan">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="addtref"></a><span class="summary-sig-name">addtref</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tref</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#spannedtext.addtref">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#spannedtext.__repr__">source&nbsp;code</a></span>
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Class&nbsp;stop
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class stop</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#stop">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">stop</strong>
</pre>
<hr />
<p>st=stop(offset,stop_color,**args)</p>
<p>Puts a stop color at the specified radius</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.stop-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">offset</span>,
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">offset</span>,
<span class="sig-arg">stop_color</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#stop.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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Class&nbsp;style
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class style</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#style">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">style</strong>
</pre>
<hr />
<p>st=style(type,cdata=None,**args)</p>
<p>Add a CDATA element to this element for defing in line stylesheets
etc..</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.style-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">type</span>,
<span class="summary-sig-arg">cdata</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#style.__init__">source&nbsp;code</a></span>
</td>
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</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="__init__"></a>
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<tr><td>
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">type</span>,
<span class="sig-arg">cdata</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#style.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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Class&nbsp;svg
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<!-- hide/show private -->
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class svg</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#svg">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">svg</strong>
</pre>
<hr />
<p>s=svg(viewbox,width,height,**args)</p>
<p>a svg or element is the root of a drawing add all elements to a svg
element. You can have different svg elements in one svg file
s.addElement(SVGelement)</p>
<p>eg d=drawing() s=svg((0,0,100,100),'100%','100%') c=circle(50,50,20)
s.addElement(c) d.setSVG(s) d.toXml()</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.svg-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">viewBox</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">height</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#svg.__init__">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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class="privatelink" onclick="toggle_private();"
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">viewBox</span>=<span class="sig-default">None</span>,
<span class="sig-arg">width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">height</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#svg.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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Class&nbsp;switch
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class switch</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#switch">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">switch</strong>
</pre>
<hr />
<p>sw=switch(**args)</p>
<p>Elements added to a switch element which are &quot;switched&quot; by
the attributes requiredFeatures, requiredExtensions and systemLanguage.
Refer to the SVG specification for details.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.switch-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#switch.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#switch.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
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Class&nbsp;symbol
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<!-- hide/show private -->
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class symbol</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#symbol">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">symbol</strong>
</pre>
<hr />
<p>sy=symbol(id,viewbox,**args)</p>
<p>defines a symbol which can be used on different places in your graph
using the use element. A symbol is not rendered but you can use 'use'
elements to display it by referencing its id.
sy.addElement(SVGelement)</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.symbol-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">viewBox</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#symbol.__init__">source&nbsp;code</a></span>
</td>
</tr>
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</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">viewBox</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#symbol.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
</td></tr></table>
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Class&nbsp;text
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class text</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#text">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
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<strong class="uidshort">text</strong>
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<hr />
<p>t=text(x,y,text,font_size,font_family,**args)</p>
<p>a text element can bge used for displaying text on the screen</p>
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<td><span class="summary-sig"><a href="obitools.SVGdraw.text-class.html#toXml" class="summary-sig-name">toXml</a>(<span class="summary-sig-arg">self</span>,
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<span class="summary-sig-arg">**kwargs</span>)</span></td>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">x</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y</span>=<span class="sig-default">None</span>,
<span class="sig-arg">text</span>=<span class="sig-default">None</span>,
<span class="sig-arg">font_size</span>=<span class="sig-default">None</span>,
<span class="sig-arg">font_family</span>=<span class="sig-default">None</span>,
<span class="sig-arg">text_anchor</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#text.__init__">source&nbsp;code</a></span>&nbsp;
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">toXml</span>(<span class="sig-arg">self</span>,
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<span class="sig-arg">**kwargs</span>)</span>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#toXml">SVGelement.toXml</a>
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Class&nbsp;textpath
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class textpath</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#textpath">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">textpath</strong>
</pre>
<hr />
<p>tp=textpath(text,link,**args)</p>
<p>a textpath places a text on a path which is referenced by a link.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.textpath-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">link</span>,
<span class="summary-sig-arg">text</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">link</span>,
<span class="sig-arg">text</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#textpath.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class title</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#title">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">title</strong>
</pre>
<hr />
<p>t=title(text,**args)</p>
<p>a title is a text element. The text is displayed in the title bar add
at least one to the root svg element</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.title-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">text</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#title.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
</td></tr></table>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;tref
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
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target="_top">no&nbsp;frames</a>]</span></td></tr>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class tref</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tref">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">tref</strong>
</pre>
<hr />
<p>tr=tref(link='',**args)</p>
<p>a tref element can be used for referencing text by a link to its id.
usage: tr=tref('#linktotext') st=spannedtext() st.addtref(tr)
t=text(3,5,st)</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
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<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.tref-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">link</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tref.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tref.__repr__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
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<a name="__init__"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">link</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tref.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
</td></tr></table>
</div>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;tspan
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</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
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target="_top">no&nbsp;frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class tspan</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tspan">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">tspan</strong>
</pre>
<hr />
<p>ts=tspan(text='',**args)</p>
<p>a tspan element can be used for applying formatting to a textsection
usage: ts=tspan('this text is bold') ts.attributes['font-weight']='bold'
st=spannedtext() st.addtspan(ts) t=text(3,5,st)</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.tspan-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tspan.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tspan.__repr__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">text</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#tspan.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
</td></tr></table>
</div>
<br />
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View File

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Class&nbsp;use
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>]&nbsp;|&nbsp;<a href="obitools.SVGdraw.use-class.html"
target="_top">no&nbsp;frames</a>]</span></td></tr>
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</td>
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</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class use</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#use">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">use</strong>
</pre>
<hr />
<p>u=use(link,x,y,width,height,**args)</p>
<p>references a symbol by linking to its id and its position, height and
width</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SVGdraw.use-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">link</span>,
<span class="summary-sig-arg">x</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">y</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">height</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#use.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
</p>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">link</span>,
<span class="sig-arg">x</span>=<span class="sig-default">None</span>,
<span class="sig-arg">y</span>=<span class="sig-default">None</span>,
<span class="sig-arg">width</span>=<span class="sig-default">None</span>,
<span class="sig-arg">height</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#use.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.SVGdraw-module.html">Module&nbsp;SVGdraw</a> ::
Class&nbsp;view
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class view</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#view">source&nbsp;code</a></span></p>
<pre class="base-tree">
<a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a> --+
|
<strong class="uidshort">view</strong>
</pre>
<hr />
<p>v=view(id,**args)</p>
<p>a view can be used to create a view with different attributes</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="obitools.SVGdraw.view-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**args</span>)</span></td>
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<span class="codelink"><a href="obitools.SVGdraw-pysrc.html#view.__init__">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.SVGdraw.SVGelement-class.html">SVGelement</a></code></b>:
<code><a href="obitools.SVGdraw.SVGelement-class.html#addElement">addElement</a></code>,
<code><a href="obitools.SVGdraw.SVGelement-class.html#toXml">toXml</a></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**args</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.SVGdraw-pysrc.html#view.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.SVGdraw.SVGelement-class.html#__init__">SVGelement.__init__</a>
</dt>
</dl>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;SubSequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SubSequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#SubSequence">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.BioSequence-class.html">BioSequence</a> --+
|
<a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a> --+
|
<strong class="uidshort">SubSequence</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
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<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="obitools.SubSequence-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">reference</span>,
<span class="summary-sig-arg">location</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">stop</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**info</span>)</span><br />
BioSequence constructor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SubSequence-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence.__len__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SubSequence-class.html#getStr" class="summary-sig-name">getStr</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the sequence as a string</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence.getStr">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SubSequence-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate through the sequence symbols</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence.__iter__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.SubSequence-class.html#_posInWrapped" class="summary-sig-name" onclick="show_private();">_posInWrapped</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence._posInWrapped">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="complement"></a><span class="summary-sig-name">complement</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence.complement">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></code></b>:
<code><a href="obitools.WrappedBioSequence-class.html#__getitem__">__getitem__</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getDefinition">getDefinition</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getId">getId</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getRoot">getRoot</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getSymbolAt">getSymbolAt</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getWrapped">getWrapped</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#isNucleotide">isNucleotide</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#iteritems">iteritems</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#iterkeys">iterkeys</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#posInWrapped">posInWrapped</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#__contains__">__contains__</a></code>,
<code><a href="obitools.BioSequence-class.html#__delitem__">__delitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__str__">__str__</a></code>,
<code><a href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a></code>,
<code><a href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a></code>,
<code><a href="obitools.BioSequence-class.html#getTags">getTags</a></code>,
<code><a href="obitools.BioSequence-class.html#getWrappers">getWrappers</a></code>,
<code><a href="obitools.BioSequence-class.html#items">items</a></code>,
<code><a href="obitools.BioSequence-class.html#keys">keys</a></code>,
<code><a href="obitools.BioSequence-class.html#register">register</a></code>,
<code><a href="obitools.BioSequence-class.html#setDefinition">setDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#setId">setId</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b> (private):
<code><a href="obitools.BioSequence-class.html#_unregister" onclick="show_private();">_unregister</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== STATIC METHODS ==================== -->
<a name="section-StaticMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
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<tr valign="top">
<td align="left"><span class="table-header">Static Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-StaticMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_sign"></a><span class="summary-sig-name">_sign</span>(<span class="summary-sig-arg">x</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#SubSequence._sign">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></code></b>:
<code><a href="obitools.WrappedBioSequence-class.html#definition">definition</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#id">id</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#wrapped">wrapped</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#wrappers">wrappers</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">reference</span>,
<span class="sig-arg">location</span>=<span class="sig-default">None</span>,
<span class="sig-arg">start</span>=<span class="sig-default">None</span>,
<span class="sig-arg">stop</span>=<span class="sig-default">None</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**info</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#SubSequence.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>BioSequence constructor.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>id</code></strong> - sequence identifier</li>
<li><strong class="pname"><code>seq</code></strong> - the sequence</li>
<li><strong class="pname"><code>definition</code></strong> - sequence definition (optional)</li>
<li><strong class="pname"><code>info</code></strong> - extra named parameters can be add to associate complementary data
to the sequence</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#SubSequence.__len__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__len__">BioSequence.__len__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getStr"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">getStr</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#SubSequence.getStr">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the sequence as a string</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the string representation of the sequence</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getStr">BioSequence.getStr</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__iter__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#SubSequence.__iter__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Iterate through the sequence symbols</p>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__iter__">BioSequence.__iter__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
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<a name="_posInWrapped"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_posInWrapped</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#SubSequence._posInWrapped">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.WrappedBioSequence-class.html#_posInWrapped" onclick="show_private();">WrappedBioSequence._posInWrapped</a>
</dt>
</dl>
</td></tr></table>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;WrappedBioSequence
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class WrappedBioSequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.BioSequence-class.html">BioSequence</a> --+
|
<strong class="uidshort">WrappedBioSequence</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.DNAComplementSequence-class.html">DNAComplementSequence</a></li><li>, <a href="obitools.SubSequence-class.html">SubSequence</a></li><li>, <a href="obitools.align.homopolymere.HomoNucBioSeq-class.html">align.homopolymere.HomoNucBioSeq</a></li> </ul>
</dd></dl>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">reference</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**info</span>)</span><br />
BioSequence constructor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.__init__">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="getWrapped"></a><span class="summary-sig-name">getWrapped</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getWrapped">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getDefinition" class="summary-sig-name">getDefinition</a>(<span class="summary-sig-arg">self</span>)</span><br />
Sequence definition getter</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getDefinition">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getId" class="summary-sig-name">getId</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getId">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="isNucleotide"></a><span class="summary-sig-name">isNucleotide</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.isNucleotide">source&nbsp;code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#iterkeys" class="summary-sig-name">iterkeys</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.iterkeys">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#iteritems" class="summary-sig-name">iteritems</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.iteritems">source&nbsp;code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.__getitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>str</code></span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getSymbolAt" class="summary-sig-name">getSymbolAt</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span><br />
Return the symbole at position in the sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getSymbolAt">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="posInWrapped"></a><span class="summary-sig-name">posInWrapped</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>,
<span class="summary-sig-arg">reference</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.posInWrapped">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getStr" class="summary-sig-name">getStr</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the sequence as a string</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getStr">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getRoot" class="summary-sig-name">getRoot</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getRoot">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_posInWrapped"></a><span class="summary-sig-name">_posInWrapped</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence._posInWrapped">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#__contains__">__contains__</a></code>,
<code><a href="obitools.BioSequence-class.html#__delitem__">__delitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.BioSequence-class.html#__len__">__len__</a></code>,
<code><a href="obitools.BioSequence-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__str__">__str__</a></code>,
<code><a href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a></code>,
<code><a href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a></code>,
<code><a href="obitools.BioSequence-class.html#getTags">getTags</a></code>,
<code><a href="obitools.BioSequence-class.html#getWrappers">getWrappers</a></code>,
<code><a href="obitools.BioSequence-class.html#items">items</a></code>,
<code><a href="obitools.BioSequence-class.html#keys">keys</a></code>,
<code><a href="obitools.BioSequence-class.html#register">register</a></code>,
<code><a href="obitools.BioSequence-class.html#setDefinition">setDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#setId">setId</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b> (private):
<code><a href="obitools.BioSequence-class.html#_unregister" onclick="show_private();">_unregister</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.WrappedBioSequence-class.html#definition" class="summary-name">definition</a><br />
Sequence Definition
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.WrappedBioSequence-class.html#id" class="summary-name">id</a><br />
Sequence Identifier
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.WrappedBioSequence-class.html#wrapped" class="summary-name">wrapped</a><br />
Wrapped's Docstring
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#wrappers">wrappers</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">reference</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**info</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>BioSequence constructor.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>id</code></strong> - sequence identifier</li>
<li><strong class="pname"><code>seq</code></strong> - the sequence</li>
<li><strong class="pname"><code>definition</code></strong> - sequence definition (optional)</li>
<li><strong class="pname"><code>info</code></strong> - extra named parameters can be add to associate complementary data
to the sequence</li>
</ul></dd>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getDefinition"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getDefinition</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getDefinition">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Sequence definition getter</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the sequence definition</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getDefinition">BioSequence.getDefinition</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getId"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getId</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getId">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getId">BioSequence.getId</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="iterkeys"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">iterkeys</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.iterkeys">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#iterkeys">BioSequence.iterkeys</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="iteritems"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">iteritems</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.iteritems">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#iteritems">BioSequence.iteritems</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__getitem__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">key</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.__getitem__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__getitem__">BioSequence.__getitem__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getSymbolAt"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getSymbolAt</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getSymbolAt">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the symbole at position in the sequence</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>position</code></strong> - the desired position. Position start from 0 if position is &lt; 0
then they are considered to reference the end of the sequence.</li>
</ul></dd>
<dt>Returns: <code>str</code></dt>
<dd>a one letter string</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getSymbolAt">BioSequence.getSymbolAt</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getStr"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getStr</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getStr">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the sequence as a string</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the string representation of the sequence</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getStr">BioSequence.getStr</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getRoot"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getRoot</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools-pysrc.html#WrappedBioSequence.getRoot">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getRoot">BioSequence.getRoot</a>
</dt>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
<a name="section-PropertyDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Property Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-PropertyDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="definition"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">definition</h3>
<p>Sequence Definition</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getDefinition" class="summary-sig-name">getDefinition</a>(<span class="summary-sig-arg">self</span>)</span>
- Sequence definition getter
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.setDefinition(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="id"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">id</h3>
<p>Sequence Identifier</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getId" class="summary-sig-name">getId</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.setId(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="wrapped"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">wrapped</h3>
<p>Wrapped's Docstring</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.WrappedBioSequence-class.html#getWrapped" class="summary-sig-name">getWrapped</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
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View File

@ -1,298 +0,0 @@
<?xml version="1.0" encoding="ascii"?>
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<title>obitools.WrapperSet</title>
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<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Class&nbsp;WrapperSet
</span>
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<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class WrapperSet</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#WrapperSet">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
set --+
|
<strong class="uidshort">WrapperSet</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.WrapperSet-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
iter(x)</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools-pysrc.html#WrapperSet.__iter__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>set</code></b>:
<code>__and__</code>,
<code>__cmp__</code>,
<code>__contains__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__gt__</code>,
<code>__iand__</code>,
<code>__init__</code>,
<code>__ior__</code>,
<code>__isub__</code>,
<code>__ixor__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__or__</code>,
<code>__rand__</code>,
<code>__reduce__</code>,
<code>__repr__</code>,
<code>__ror__</code>,
<code>__rsub__</code>,
<code>__rxor__</code>,
<code>__sizeof__</code>,
<code>__sub__</code>,
<code>__xor__</code>,
<code>add</code>,
<code>clear</code>,
<code>copy</code>,
<code>difference</code>,
<code>difference_update</code>,
<code>discard</code>,
<code>intersection</code>,
<code>intersection_update</code>,
<code>isdisjoint</code>,
<code>issubset</code>,
<code>issuperset</code>,
<code>pop</code>,
<code>remove</code>,
<code>symmetric_difference</code>,
<code>symmetric_difference_update</code>,
<code>union</code>,
<code>update</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Class Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassVariables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>set</code></b>:
<code>__hash__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
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<p>iter(x)</p>
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<h1 class="epydoc">Class WrapperSetIterator</h1><p class="nomargin-top"><span class="codelink"><a href="obitools-pysrc.html#WrapperSetIterator">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">WrapperSetIterator</strong>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
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<h1 class="epydoc">Package align</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.align-pysrc.html">source&nbsp;code</a></span></p>
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<li> <strong class="uidlink"><a href="obitools.align.homopolymere-module.html">obitools.align.homopolymere</a></strong>: <em class="summary">Created on 14 mai 2009</em> </li>
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<td><span class="summary-sig"><a name="alignmentReader"></a><span class="summary-sig-name">alignmentReader</span>(<span class="summary-sig-arg">file</span>,
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<h1 class="epydoc">Source Code for <a href="obitools.align-module.html">Package obitools.align</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class obitools.BioSequence=obitools.BioSequence-class.html"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-1', 'BioSequence', 'link-1');">BioSequence</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
<a name="Alignement"></a><div id="Alignement-def"><a name="L3"></a><tt class="py-lineno"> 3</tt> <a class="py-toggle" href="#" id="Alignement-toggle" onclick="return toggle('Alignement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html">Alignement</a><tt class="py-op">(</tt><tt class="py-base-class">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Alignement-expanded"><a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
<a name="Alignement._assertData"></a><div id="Alignement._assertData-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="Alignement._assertData-toggle" onclick="return toggle('Alignement._assertData');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html#_assertData">_assertData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement._assertData-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement._assertData-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-2', 'BioSequence', 'link-1');">BioSequence</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'You must only add bioseq to an alignement'</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">'_alignlen'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alignlen</tt><tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'All aligned sequences must have the same length'</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alignlen</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">data</tt> </tt>
</div><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="Alignement.append"></a><div id="Alignement.append-def"><a name="L13"></a><tt class="py-lineno">13</tt> <a class="py-toggle" href="#" id="Alignement.append-toggle" onclick="return toggle('Alignement.append');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.append-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.append-expanded"><a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method obitools.align.Alignement._assertData()=obitools.align.Alignement-class.html#_assertData,Method obitools.alignment.Alignement._assertData()=obitools.alignment.Alignement-class.html#_assertData"><a title="obitools.align.Alignement._assertData
obitools.alignment.Alignement._assertData" class="py-name" href="#" onclick="return doclink('link-3', '_assertData', 'link-3');">_assertData</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">list</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.alignment.Alignement.append()=obitools.alignment.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
</div><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="Alignement.__setitem__"></a><div id="Alignement.__setitem__-def"><a name="L17"></a><tt class="py-lineno">17</tt> <a class="py-toggle" href="#" id="Alignement.__setitem__-toggle" onclick="return toggle('Alignement.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">index</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.__setitem__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.__setitem__-expanded"><a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="obitools.align.Alignement._assertData
obitools.alignment.Alignement._assertData" class="py-name" href="#" onclick="return doclink('link-5', '_assertData', 'link-3');">_assertData</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">list</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method obitools.BioSequence.__setitem__()=obitools.BioSequence-class.html#__setitem__,Method obitools.align.Alignement.__setitem__()=obitools.align.Alignement-class.html#__setitem__,Method obitools.alignment.Alignement.__setitem__()=obitools.alignment.Alignement-class.html#__setitem__,Method obitools.cns.quality.QualitySequence.__setitem__()=obitools.cns.quality.QualitySequence-class.html#__setitem__,Method obitools.graph.Edge.__setitem__()=obitools.graph.Edge-class.html#__setitem__,Method obitools.graph.Node.__setitem__()=obitools.graph.Node-class.html#__setitem__,Method obitools.seqdb.genbank.graph.Edge.__setitem__()=obitools.seqdb.genbank.graph.Edge-class.html#__setitem__,Method obitools.seqdb.genbank.graph.Node.__setitem__()=obitools.seqdb.genbank.graph.Node-class.html#__setitem__,Method obitools.table.Table.__setitem__()=obitools.table.Table-class.html#__setitem__,Method obitools.table.TableRow.__setitem__()=obitools.table.TableRow-class.html#__setitem__"><a title="obitools.BioSequence.__setitem__
obitools.align.Alignement.__setitem__
obitools.alignment.Alignement.__setitem__
obitools.cns.quality.QualitySequence.__setitem__
obitools.graph.Edge.__setitem__
obitools.graph.Node.__setitem__
obitools.seqdb.genbank.graph.Edge.__setitem__
obitools.seqdb.genbank.graph.Node.__setitem__
obitools.table.Table.__setitem__
obitools.table.TableRow.__setitem__" class="py-name" href="#" onclick="return doclink('link-6', '__setitem__', 'link-6');">__setitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">index</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
</div><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> </tt>
<a name="Alignement.getSite"></a><div id="Alignement.getSite-def"><a name="L22"></a><tt class="py-lineno">22</tt> <a class="py-toggle" href="#" id="Alignement.getSite-toggle" onclick="return toggle('Alignement.getSite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html#getSite">getSite</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.getSite-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.getSite-expanded"><a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">]</tt> </tt>
</div><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="Alignement.isFullGapSite"></a><div id="Alignement.isFullGapSite-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="Alignement.isFullGapSite-toggle" onclick="return toggle('Alignement.isFullGapSite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html#isFullGapSite">isFullGapSite</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.isFullGapSite-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.isFullGapSite-expanded"><a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">and</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method obitools.align.Alignement.getSite()=obitools.align.Alignement-class.html#getSite,Method obitools.alignment.Alignement.getSite()=obitools.alignment.Alignement-class.html#getSite"><a title="obitools.align.Alignement.getSite
obitools.alignment.Alignement.getSite" class="py-name" href="#" onclick="return doclink('link-7', 'getSite', 'link-7');">getSite</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-8" class="py-name" targets="Variable obitools.SVGdraw.True=obitools.SVGdraw-module.html#True"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-8', 'True', 'link-8');">True</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> </tt>
<a name="Alignement.isGappedSite"></a><div id="Alignement.isGappedSite-def"><a name="L29"></a><tt class="py-lineno">29</tt> <a class="py-toggle" href="#" id="Alignement.isGappedSite-toggle" onclick="return toggle('Alignement.isGappedSite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.Alignement-class.html#isGappedSite">isGappedSite</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.isGappedSite-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.isGappedSite-expanded"><a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">or</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="obitools.align.Alignement.getSite
obitools.alignment.Alignement.getSite" class="py-name" href="#" onclick="return doclink('link-9', 'getSite', 'link-7');">getSite</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-10" class="py-name" targets="Variable obitools.SVGdraw.False=obitools.SVGdraw-module.html#False"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-10', 'False', 'link-10');">False</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="alignmentReader"></a><div id="alignmentReader-def"><a name="L32"></a><tt class="py-lineno">32</tt> <a class="py-toggle" href="#" id="alignmentReader-toggle" onclick="return toggle('alignmentReader');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align-module.html#alignmentReader">alignmentReader</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt><tt class="py-param">sequenceIterator</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="alignmentReader-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="alignmentReader-expanded"><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">sequenceIterator</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">alignement</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Class obitools.align.Alignement=obitools.align.Alignement-class.html,Class obitools.alignment.Alignement=obitools.alignment.Alignement-class.html"><a title="obitools.align.Alignement
obitools.alignment.Alignement" class="py-name" href="#" onclick="return doclink('link-11', 'Alignement', 'link-11');">Alignement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seq</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seqs</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-name">alignement</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-12', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">alignement</tt> </tt>
</div><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt><script type="text/javascript">
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.align-module.html">Package&nbsp;align</a> ::
Class&nbsp;Alignement
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Alignement</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.align-pysrc.html#Alignement">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
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list --+
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<strong class="uidshort">Alignement</strong>
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<td><span class="summary-sig"><a name="_assertData"></a><span class="summary-sig-name">_assertData</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align-pysrc.html#Alignement._assertData">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.align.Alignement-class.html#append" class="summary-sig-name">append</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>)</span><br />
append object to end</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align-pysrc.html#Alignement.append">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.align.Alignement-class.html#__setitem__" class="summary-sig-name">__setitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index</span>,
<span class="summary-sig-arg">data</span>)</span><br />
x[i]=y</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align-pysrc.html#Alignement.__setitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getSite"></a><span class="summary-sig-name">getSite</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align-pysrc.html#Alignement.getSite">source&nbsp;code</a></span>
</td>
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</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="isFullGapSite"></a><span class="summary-sig-name">isFullGapSite</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align-pysrc.html#Alignement.isFullGapSite">source&nbsp;code</a></span>
</td>
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</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="isGappedSite"></a><span class="summary-sig-name">isGappedSite</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align-pysrc.html#Alignement.isGappedSite">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>list</code></b>:
<code>__add__</code>,
<code>__contains__</code>,
<code>__delitem__</code>,
<code>__delslice__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__getitem__</code>,
<code>__getslice__</code>,
<code>__gt__</code>,
<code>__iadd__</code>,
<code>__imul__</code>,
<code>__init__</code>,
<code>__iter__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__mul__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__repr__</code>,
<code>__reversed__</code>,
<code>__rmul__</code>,
<code>__setslice__</code>,
<code>__sizeof__</code>,
<code>count</code>,
<code>extend</code>,
<code>index</code>,
<code>insert</code>,
<code>pop</code>,
<code>remove</code>,
<code>reverse</code>,
<code>sort</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
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<p class="indent-wrapped-lines"><b>Inherited from <code>list</code></b>:
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<!-- ==================== METHOD DETAILS ==================== -->
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class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="append"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">append</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">data</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align-pysrc.html#Alignement.append">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>append object to end</p>
<dl class="fields">
<dt>Overrides:
list.append
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__setitem__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__setitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">index</span>,
<span class="sig-arg">data</span>)</span>
<br /><em class="fname">(Index assignment operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align-pysrc.html#Alignement.__setitem__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x[i]=y</p>
<dl class="fields">
<dt>Overrides:
list.__setitem__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.align-module.html">Package&nbsp;align</a> ::
Module&nbsp;homopolymere
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<!-- hide/show private -->
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module homopolymere</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html">source&nbsp;code</a></span></p>
<p>Created on 14 mai 2009</p>
<hr />
<div class="fields"> <p><strong>Author:</strong>
coissac
</p>
</div><!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.align.homopolymere.HomoNucBioSeq-class.html" class="summary-name">HomoNucBioSeq</a><br />
classdocs
</td>
</tr>
</table>
<!-- ==================== VARIABLES ==================== -->
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools.align'"><code class="variable-quote">'</code><code class="variable-string">obitools.align</code><code class="variable-quote">'</code></code>
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Class&nbsp;HomoNucBioSeq
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class HomoNucBioSeq</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.BioSequence-class.html">BioSequence</a> --+
|
<a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a> --+
|
<strong class="uidshort">HomoNucBioSeq</strong>
</pre>
<hr />
<p>classdocs</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
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<td><span class="summary-sig"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">reference</span>,
<span class="summary-sig-arg">id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">definition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**info</span>)</span><br />
Constructor</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__init__">source&nbsp;code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__cleanHomopolymer"></a><span class="summary-sig-name">__cleanHomopolymer</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__cleanHomopolymer">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__len__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">str</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html#getStr" class="summary-sig-name">getStr</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the sequence as a string</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.getStr">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate through the sequence symbols</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__iter__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html#_posInWrapped" class="summary-sig-name" onclick="show_private();">_posInWrapped</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq._posInWrapped">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></code></b>:
<code><a href="obitools.WrappedBioSequence-class.html#__getitem__">__getitem__</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getDefinition">getDefinition</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getId">getId</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getRoot">getRoot</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getSymbolAt">getSymbolAt</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#getWrapped">getWrapped</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#isNucleotide">isNucleotide</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#iteritems">iteritems</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#iterkeys">iterkeys</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#posInWrapped">posInWrapped</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#__contains__">__contains__</a></code>,
<code><a href="obitools.BioSequence-class.html#__delitem__">__delitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.BioSequence-class.html#__str__">__str__</a></code>,
<code><a href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a></code>,
<code><a href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a></code>,
<code><a href="obitools.BioSequence-class.html#getTags">getTags</a></code>,
<code><a href="obitools.BioSequence-class.html#getWrappers">getWrappers</a></code>,
<code><a href="obitools.BioSequence-class.html#items">items</a></code>,
<code><a href="obitools.BioSequence-class.html#keys">keys</a></code>,
<code><a href="obitools.BioSequence-class.html#register">register</a></code>,
<code><a href="obitools.BioSequence-class.html#setDefinition">setDefinition</a></code>,
<code><a href="obitools.BioSequence-class.html#setId">setId</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b> (private):
<code><a href="obitools.BioSequence-class.html#_unregister" onclick="show_private();">_unregister</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
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<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a></code></b>:
<code><a href="obitools.WrappedBioSequence-class.html#definition">definition</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#id">id</a></code>,
<code><a href="obitools.WrappedBioSequence-class.html#wrapped">wrapped</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.BioSequence-class.html">BioSequence</a></code></b>:
<code><a href="obitools.BioSequence-class.html#wrappers">wrappers</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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</td>
</tr>
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>hide private</a>]</span></td>
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<a name="__init__"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">reference</span>,
<span class="sig-arg">id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">definition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**info</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Constructor</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>id</code></strong> - sequence identifier</li>
<li><strong class="pname"><code>seq</code></strong> - the sequence</li>
<li><strong class="pname"><code>definition</code></strong> - sequence definition (optional)</li>
<li><strong class="pname"><code>info</code></strong> - extra named parameters can be add to associate complementary data
to the sequence</li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__len__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__len__">BioSequence.__len__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="getStr"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">getStr</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.getStr">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Return the sequence as a string</p>
<dl class="fields">
<dt>Returns: str</dt>
<dd>the string representation of the sequence</dd>
<dt>Overrides:
<a href="obitools.BioSequence-class.html#getStr">BioSequence.getStr</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__iter__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq.__iter__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Iterate through the sequence symbols</p>
<dl class="fields">
<dt>Overrides:
<a href="obitools.BioSequence-class.html#__iter__">BioSequence.__iter__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_posInWrapped"></a>
<div class="private">
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_posInWrapped</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.align.homopolymere-pysrc.html#HomoNucBioSeq._posInWrapped">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.WrappedBioSequence-class.html#_posInWrapped" onclick="show_private();">WrappedBioSequence._posInWrapped</a>
</dt>
</dl>
</td></tr></table>
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ssearch</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.align.ssearch-pysrc.html">source&nbsp;code</a></span></p>
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<h1 class="epydoc">Source Code for <a href="obitools.align.ssearch-module.html">Module obitools.align.ssearch</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module obitools.cns.fasta=obitools.cns.fasta-module.html,Module obitools.fasta=obitools.fasta-module.html,Module obitools.format.sequence.fasta=obitools.format.sequence.fasta-module.html"><a title="obitools.cns.fasta
obitools.fasta
obitools.format.sequence.fasta" class="py-name" href="#" onclick="return doclink('link-1', 'fasta', 'link-1');">fasta</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Function obitools.fasta.formatFasta()=obitools.fasta-module.html#formatFasta"><a title="obitools.fasta.formatFasta" class="py-name" href="#" onclick="return doclink('link-2', 'formatFasta', 'link-2');">formatFasta</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="SsearchParser"></a><div id="SsearchParser-def"><a name="L6"></a><tt class="py-lineno"> 6</tt> <a class="py-toggle" href="#" id="SsearchParser-toggle" onclick="return toggle('SsearchParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.align.ssearch.SsearchParser-class.html">SsearchParser</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SsearchParser-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="SsearchParser-expanded"><a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Variable obitools.align.ssearch.SsearchParser._matchQuery=obitools.align.ssearch.SsearchParser-class.html#_matchQuery"><a title="obitools.align.ssearch.SsearchParser._matchQuery" class="py-name" href="#" onclick="return doclink('link-3', '_matchQuery', 'link-3');">_matchQuery</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"^Query:.+\n.+?&gt;+([^ ]+)"</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">MULTILINE</tt><tt class="py-op">)</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable obitools.align.ssearch.SsearchParser._matchLQuery=obitools.align.ssearch.SsearchParser-class.html#_matchLQuery"><a title="obitools.align.ssearch.SsearchParser._matchLQuery" class="py-name" href="#" onclick="return doclink('link-4', '_matchLQuery', 'link-4');">_matchLQuery</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"^Query:.+\n.+?(\d+)(?= nt\n)"</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">MULTILINE</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt id="link-5" class="py-name" targets="Variable obitools.align.ssearch.SsearchParser._matchProp=obitools.align.ssearch.SsearchParser-class.html#_matchProp"><a title="obitools.align.ssearch.SsearchParser._matchProp" class="py-name" href="#" onclick="return doclink('link-5', '_matchProp', 'link-5');">_matchProp</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"^The best scores are:.*\n(.+?)&gt;&gt;&gt;"</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">DOTALL</tt><tt class="py-op">+</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">MULTILINE</tt><tt class="py-op">)</tt> </tt>
<a name="SsearchParser.__init__"></a><div id="SsearchParser.__init__-def"><a name="L11"></a><tt class="py-lineno">11</tt> <a class="py-toggle" href="#" id="SsearchParser.__init__-toggle" onclick="return toggle('SsearchParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.ssearch.SsearchParser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SsearchParser.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SsearchParser.__init__-expanded"><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name" targets="Function obitools.gzip.open()=obitools.gzip-module.html#open,Method obitools.zipfile.ZipFile.open()=obitools.zipfile.ZipFile-class.html#open"><a title="obitools.gzip.open
obitools.zipfile.ZipFile.open" class="py-name" href="#" onclick="return doclink('link-6', 'open', 'link-6');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt><tt class="py-string">'rU'</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method obitools.gzip.GzipFile.read()=obitools.gzip.GzipFile-class.html#read,Method obitools.zipfile.ZipExtFile.read()=obitools.zipfile.ZipExtFile-class.html#read,Method obitools.zipfile.ZipFile.read()=obitools.zipfile.ZipFile-class.html#read"><a title="obitools.gzip.GzipFile.read
obitools.zipfile.ZipExtFile.read
obitools.zipfile.ZipFile.read" class="py-name" href="#" onclick="return doclink('link-7', 'read', 'link-7');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Variable obitools.blast.BlastResultIterator.query=obitools.blast.BlastResultIterator-class.html#query"><a title="obitools.blast.BlastResultIterator.query" class="py-name" href="#" onclick="return doclink('link-8', 'query', 'link-8');">query</a></tt><tt class="py-op">=</tt> <tt id="link-9" class="py-name" targets="Class obitools.align.ssearch.SsearchParser=obitools.align.ssearch.SsearchParser-class.html"><a title="obitools.align.ssearch.SsearchParser" class="py-name" href="#" onclick="return doclink('link-9', 'SsearchParser', 'link-9');">SsearchParser</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="obitools.align.ssearch.SsearchParser._matchQuery" class="py-name" href="#" onclick="return doclink('link-10', '_matchQuery', 'link-3');">_matchQuery</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Class obitools.SVGdraw.group=obitools.SVGdraw.group-class.html"><a title="obitools.SVGdraw.group" class="py-name" href="#" onclick="return doclink('link-11', 'group', 'link-11');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">queryLength</tt><tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="obitools.align.ssearch.SsearchParser" class="py-name" href="#" onclick="return doclink('link-12', 'SsearchParser', 'link-9');">SsearchParser</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="obitools.align.ssearch.SsearchParser._matchLQuery" class="py-name" href="#" onclick="return doclink('link-13', '_matchLQuery', 'link-4');">_matchLQuery</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="obitools.SVGdraw.group" class="py-name" href="#" onclick="return doclink('link-14', 'group', 'link-11');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">props</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="obitools.align.ssearch.SsearchParser" class="py-name" href="#" onclick="return doclink('link-15', 'SsearchParser', 'link-9');">SsearchParser</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="obitools.align.ssearch.SsearchParser._matchProp" class="py-name" href="#" onclick="return doclink('link-16', '_matchProp', 'link-5');">_matchProp</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">props</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-name">props</tt><tt class="py-op">=</tt><tt class="py-name">props</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="obitools.SVGdraw.group" class="py-name" href="#" onclick="return doclink('link-17', 'group', 'link-11');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">props</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-18" class="py-name" targets="Class obitools.SVGdraw.line=obitools.SVGdraw.line-class.html,Method obitools.SVGdraw.pathdata.line()=obitools.SVGdraw.pathdata-class.html#line"><a title="obitools.SVGdraw.line
obitools.SVGdraw.pathdata.line" class="py-name" href="#" onclick="return doclink('link-18', 'line', 'link-18');">line</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">props</tt><tt class="py-op">:</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-name">subject</tt><tt class="py-op">,</tt><tt class="py-name">tab</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="obitools.SVGdraw.line
obitools.SVGdraw.pathdata.line" class="py-name" href="#" onclick="return doclink('link-19', 'line', 'link-18');">line</a></tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'\t'</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">tab</tt><tt class="py-op">=</tt><tt class="py-name">tab</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">ssp</tt> <tt class="py-op">=</tt> <tt class="py-name">subject</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">ac</tt> <tt class="py-op">=</tt> <tt class="py-name">ssp</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">dbl</tt><tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">ssp</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-name">ident</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">tab</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">matchlen</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">tab</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">tab</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">props</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.alignment.Alignement.append()=obitools.alignment.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-20', 'append', 'link-20');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">{</tt><tt class="py-string">"ac"</tt> <tt class="py-op">:</tt><tt class="py-name">ac</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-string">"identity"</tt> <tt class="py-op">:</tt><tt class="py-name">ident</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-string">"subjectlength"</tt><tt class="py-op">:</tt><tt class="py-name">dbl</tt><tt class="py-op">,</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-string">'matchlength'</tt> <tt class="py-op">:</tt> <tt class="py-name">matchlen</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> </tt>
<a name="run"></a><div id="run-def"><a name="L34"></a><tt class="py-lineno">34</tt> <a class="py-toggle" href="#" id="run-toggle" onclick="return toggle('run');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.ssearch-module.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt><tt class="py-param">database</tt><tt class="py-op">,</tt><tt class="py-param">program</tt><tt class="py-op">=</tt><tt class="py-string">'fasta35'</tt><tt class="py-op">,</tt><tt class="py-param">opts</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="run-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="run-expanded"><a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">ssearchin</tt><tt class="py-op">,</tt><tt class="py-name">ssearchout</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen2</tt><tt class="py-op">(</tt><tt class="py-string">"%s %s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-21" class="py-name" targets="Variable obitools.blast.Blast.program=obitools.blast.Blast-class.html#program"><a title="obitools.blast.Blast.program" class="py-name" href="#" onclick="return doclink('link-21', 'program', 'link-21');">program</a></tt><tt class="py-op">,</tt><tt class="py-name">opts</tt><tt class="py-op">,</tt><tt class="py-name">database</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">ssearchin</tt><tt class="py-op">,</tt><tt id="link-22" class="py-name"><a title="obitools.fasta.formatFasta" class="py-name" href="#" onclick="return doclink('link-22', 'formatFasta', 'link-2');">formatFasta</a></tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">ssearchin</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method obitools.gzip.GzipFile.close()=obitools.gzip.GzipFile-class.html#close,Method obitools.zipfile.ZipExtFile.close()=obitools.zipfile.ZipExtFile-class.html#close,Method obitools.zipfile.ZipFile.close()=obitools.zipfile.ZipFile-class.html#close"><a title="obitools.gzip.GzipFile.close
obitools.zipfile.ZipExtFile.close
obitools.zipfile.ZipFile.close" class="py-name" href="#" onclick="return doclink('link-23', 'close', 'link-23');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="obitools.align.ssearch.SsearchParser" class="py-name" href="#" onclick="return doclink('link-24', 'SsearchParser', 'link-9');">SsearchParser</a></tt><tt class="py-op">(</tt><tt class="py-name">ssearchout</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">seq</tt><tt class="py-op">,</tt><tt class="py-name">result</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt>
<a name="ssearchIterator"></a><div id="ssearchIterator-def"><a name="L41"></a><tt class="py-lineno">41</tt> <a class="py-toggle" href="#" id="ssearchIterator-toggle" onclick="return toggle('ssearchIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.align.ssearch-module.html#ssearchIterator">ssearchIterator</a><tt class="py-op">(</tt><tt class="py-param">sequenceIterator</tt><tt class="py-op">,</tt><tt class="py-param">database</tt><tt class="py-op">,</tt><tt class="py-param">program</tt><tt class="py-op">=</tt><tt class="py-string">'ssearch35'</tt><tt class="py-op">,</tt><tt class="py-param">opts</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ssearchIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="ssearchIterator-expanded"><a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seq</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sequenceIterator</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-25" class="py-name" targets="Function obitools.align.ssearch.run()=obitools.align.ssearch-module.html#run"><a title="obitools.align.ssearch.run" class="py-name" href="#" onclick="return doclink('link-25', 'run', 'link-25');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">,</tt><tt class="py-name">database</tt><tt class="py-op">,</tt><tt id="link-26" class="py-name"><a title="obitools.blast.Blast.program" class="py-name" href="#" onclick="return doclink('link-26', 'program', 'link-21');">program</a></tt><tt class="py-op">,</tt><tt class="py-name">opts</tt><tt class="py-op">)</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt><script type="text/javascript">
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<h1 class="epydoc">Class SsearchParser</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.align.ssearch-pysrc.html#SsearchParser">source&nbsp;code</a></span></p>
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object --+
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<strong class="uidshort">SsearchParser</strong>
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<td><span class="summary-sig"><a href="obitools.align.ssearch.SsearchParser-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
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x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
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<span class="summary-type">&nbsp;</span>
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<a name="_matchQuery"></a><span class="summary-name">_matchQuery</span> = <code title="re.compile(r'(?m)^Query:.+\n.+?&gt;+([^ ]+)')">re.compile(r'<code class="re-flags">(?m)</code>^Query:.<code class="re-op">+</code>\n.<code class="re-op">+?</code>&gt;<code class="re-op">+</code><code class="re-group">(</code><code class="re-group">[^</code> <code class="re-group">]</code><code class="re-op">+</code><code class="re-group">)</code>')</code>
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<a name="_matchLQuery"></a><span class="summary-name">_matchLQuery</span> = <code title="re.compile(r'(?m)^Query:.+\n.+?(\d+)(?= nt\n)')">re.compile(r'<code class="re-flags">(?m)</code>^Query:.<code class="re-op">+</code>\n.<code class="re-op">+?</code><code class="re-group">(</code>\d<code class="re-op">+</code><code class="re-group">)</code><code class="re-group">(?=</code> nt\n<code class="re-group">)</code>')</code>
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<a href="obitools.align.ssearch.SsearchParser-class.html#_matchProp" class="summary-name" onclick="show_private();">_matchProp</a> = <code title="re.compile(r'(?ms)^The best scores are:.*\n(.+?)&gt;&gt;&gt;')">re.compile(r'<code class="re-flags">(?ms)</code>^The best scores are:.<code class="re-op">*</code>\n<code class="re-group">(</code>.<code class="re-op">+?</code><code class="re-group">)</code>&gt;<code class="variable-ellipsis">...</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">file</span>)</span>
<br /><em class="fname">(Constructor)</em>
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</td><td align="right" valign="top"
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object.__init__
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<h3 class="epydoc">_matchProp</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
re.compile(r'<code class="re-flags">(?ms)</code>^The best scores are:.<code class="re-op">*</code>\n<code class="re-group">(</code>.<code class="re-op">+?</code><code class="re-group">)</code>&gt;&gt;&gt;')
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<h1 class="epydoc">Package alignment</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.alignment-pysrc.html">source&nbsp;code</a></span></p>
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<a href="obitools.alignment.AlignedSequence-class.html" class="summary-name">AlignedSequence</a>
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<td><span class="summary-sig"><a name="alignmentReader"></a><span class="summary-sig-name">alignmentReader</span>(<span class="summary-sig-arg">file</span>,
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<td><span class="summary-sig"><a name="columnIterator"></a><span class="summary-sig-name">columnIterator</span>(<span class="summary-sig-arg">alignment</span>)</span></td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools.alignment'"><code class="variable-quote">'</code><code class="variable-string">obitools.alignment</code><code class="variable-quote">'</code></code>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Package&nbsp;alignment
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<h1 class="epydoc">Source Code for <a href="obitools.alignment-module.html">Package obitools.alignment</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class obitools.BioSequence=obitools.BioSequence-class.html"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-1', 'BioSequence', 'link-1');">BioSequence</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="AlignedSequence"></a><div id="AlignedSequence-def"><a name="L4"></a><tt class="py-lineno"> 4</tt> <a class="py-toggle" href="#" id="AlignedSequence-toggle" onclick="return toggle('AlignedSequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.alignment.AlignedSequence-class.html">AlignedSequence</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignedSequence-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="AlignedSequence-expanded"><a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="Alignement"></a><div id="Alignement-def"><a name="L8"></a><tt class="py-lineno"> 8</tt> <a class="py-toggle" href="#" id="Alignement-toggle" onclick="return toggle('Alignement');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html">Alignement</a><tt class="py-op">(</tt><tt class="py-base-class">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Alignement-expanded"><a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="Alignement._assertData"></a><div id="Alignement._assertData-def"><a name="L10"></a><tt class="py-lineno">10</tt> <a class="py-toggle" href="#" id="Alignement._assertData-toggle" onclick="return toggle('Alignement._assertData');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html#_assertData">_assertData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement._assertData-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement._assertData-expanded"><a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-2', 'BioSequence', 'link-1');">BioSequence</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'You must only add bioseq to an alignement'</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">'_alignlen'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alignlen</tt><tt class="py-op">==</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'All aligned sequences must have the same length'</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alignlen</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">data</tt> </tt>
</div><a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt>
<a name="Alignement.append"></a><div id="Alignement.append-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="Alignement.append-toggle" onclick="return toggle('Alignement.append');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.append-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.append-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method obitools.align.Alignement._assertData()=obitools.align.Alignement-class.html#_assertData,Method obitools.alignment.Alignement._assertData()=obitools.alignment.Alignement-class.html#_assertData"><a title="obitools.align.Alignement._assertData
obitools.alignment.Alignement._assertData" class="py-name" href="#" onclick="return doclink('link-3', '_assertData', 'link-3');">_assertData</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">list</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.alignment.Alignement.append()=obitools.alignment.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-4', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
</div><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> </tt>
<a name="Alignement.__setitem__"></a><div id="Alignement.__setitem__-def"><a name="L22"></a><tt class="py-lineno">22</tt> <a class="py-toggle" href="#" id="Alignement.__setitem__-toggle" onclick="return toggle('Alignement.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">index</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.__setitem__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.__setitem__-expanded"><a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="obitools.align.Alignement._assertData
obitools.alignment.Alignement._assertData" class="py-name" href="#" onclick="return doclink('link-5', '_assertData', 'link-3');">_assertData</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">list</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method obitools.BioSequence.__setitem__()=obitools.BioSequence-class.html#__setitem__,Method obitools.align.Alignement.__setitem__()=obitools.align.Alignement-class.html#__setitem__,Method obitools.alignment.Alignement.__setitem__()=obitools.alignment.Alignement-class.html#__setitem__,Method obitools.cns.quality.QualitySequence.__setitem__()=obitools.cns.quality.QualitySequence-class.html#__setitem__,Method obitools.graph.Edge.__setitem__()=obitools.graph.Edge-class.html#__setitem__,Method obitools.graph.Node.__setitem__()=obitools.graph.Node-class.html#__setitem__,Method obitools.seqdb.genbank.graph.Edge.__setitem__()=obitools.seqdb.genbank.graph.Edge-class.html#__setitem__,Method obitools.seqdb.genbank.graph.Node.__setitem__()=obitools.seqdb.genbank.graph.Node-class.html#__setitem__,Method obitools.table.Table.__setitem__()=obitools.table.Table-class.html#__setitem__,Method obitools.table.TableRow.__setitem__()=obitools.table.TableRow-class.html#__setitem__"><a title="obitools.BioSequence.__setitem__
obitools.align.Alignement.__setitem__
obitools.alignment.Alignement.__setitem__
obitools.cns.quality.QualitySequence.__setitem__
obitools.graph.Edge.__setitem__
obitools.graph.Node.__setitem__
obitools.seqdb.genbank.graph.Edge.__setitem__
obitools.seqdb.genbank.graph.Node.__setitem__
obitools.table.Table.__setitem__
obitools.table.TableRow.__setitem__" class="py-name" href="#" onclick="return doclink('link-6', '__setitem__', 'link-6');">__setitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">index</tt><tt class="py-op">,</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
</div><a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> </tt>
<a name="Alignement.getSite"></a><div id="Alignement.getSite-def"><a name="L27"></a><tt class="py-lineno">27</tt> <a class="py-toggle" href="#" id="Alignement.getSite-toggle" onclick="return toggle('Alignement.getSite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html#getSite">getSite</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.getSite-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.getSite-expanded"><a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">]</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> </tt>
<a name="Alignement.isFullGapSite"></a><div id="Alignement.isFullGapSite-def"><a name="L31"></a><tt class="py-lineno">31</tt> <a class="py-toggle" href="#" id="Alignement.isFullGapSite-toggle" onclick="return toggle('Alignement.isFullGapSite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html#isFullGapSite">isFullGapSite</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.isFullGapSite-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.isFullGapSite-expanded"><a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">and</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method obitools.align.Alignement.getSite()=obitools.align.Alignement-class.html#getSite,Method obitools.alignment.Alignement.getSite()=obitools.alignment.Alignement-class.html#getSite"><a title="obitools.align.Alignement.getSite
obitools.alignment.Alignement.getSite" class="py-name" href="#" onclick="return doclink('link-7', 'getSite', 'link-7');">getSite</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-8" class="py-name" targets="Variable obitools.SVGdraw.True=obitools.SVGdraw-module.html#True"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-8', 'True', 'link-8');">True</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> </tt>
<a name="Alignement.isGappedSite"></a><div id="Alignement.isGappedSite-def"><a name="L34"></a><tt class="py-lineno">34</tt> <a class="py-toggle" href="#" id="Alignement.isGappedSite-toggle" onclick="return toggle('Alignement.isGappedSite');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.Alignement-class.html#isGappedSite">isGappedSite</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignement.isGappedSite-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="Alignement.isGappedSite-expanded"><a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">or</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">==</tt><tt class="py-string">'-'</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="obitools.align.Alignement.getSite
obitools.alignment.Alignement.getSite" class="py-name" href="#" onclick="return doclink('link-9', 'getSite', 'link-7');">getSite</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-10" class="py-name" targets="Variable obitools.SVGdraw.False=obitools.SVGdraw-module.html#False"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-10', 'False', 'link-10');">False</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="alignmentReader"></a><div id="alignmentReader-def"><a name="L37"></a><tt class="py-lineno">37</tt> <a class="py-toggle" href="#" id="alignmentReader-toggle" onclick="return toggle('alignmentReader');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment-module.html#alignmentReader">alignmentReader</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt><tt class="py-param">sequenceIterator</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="alignmentReader-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="alignmentReader-expanded"><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">sequenceIterator</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">alignement</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Class obitools.align.Alignement=obitools.align.Alignement-class.html,Class obitools.alignment.Alignement=obitools.alignment.Alignement-class.html"><a title="obitools.align.Alignement
obitools.alignment.Alignement" class="py-name" href="#" onclick="return doclink('link-11', 'Alignement', 'link-11');">Alignement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seq</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seqs</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">alignement</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-12', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">alignement</tt> </tt>
</div><a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> </tt>
<a name="columnIterator"></a><div id="columnIterator-def"><a name="L48"></a><tt class="py-lineno">48</tt> <a class="py-toggle" href="#" id="columnIterator-toggle" onclick="return toggle('columnIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment-module.html#columnIterator">columnIterator</a><tt class="py-op">(</tt><tt class="py-param">alignment</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="columnIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="columnIterator-expanded"><a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">lali</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name" targets="Package obitools.alignment=obitools.alignment-module.html"><a title="obitools.alignment" class="py-name" href="#" onclick="return doclink('link-13', 'alignment', 'link-13');">alignment</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">lali</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt id="link-14" class="py-name"><a title="obitools.alignment" class="py-name" href="#" onclick="return doclink('link-14', 'alignment', 'link-13');">alignment</a></tt><tt class="py-op">]</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">c</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> </tt><script type="text/javascript">
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class AlignedSequence</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.alignment-pysrc.html#AlignedSequence">source&nbsp;code</a></span></p>
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<h1 class="epydoc">Class Alignement</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
list --+
|
<strong class="uidshort">Alignement</strong>
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<td><span class="summary-sig"><a name="_assertData"></a><span class="summary-sig-name">_assertData</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>)</span></td>
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<td><span class="summary-sig"><a href="obitools.alignment.Alignement-class.html#append" class="summary-sig-name">append</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>)</span><br />
append object to end</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.append">source&nbsp;code</a></span>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="obitools.alignment.Alignement-class.html#__setitem__" class="summary-sig-name">__setitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index</span>,
<span class="summary-sig-arg">data</span>)</span><br />
x[i]=y</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.__setitem__">source&nbsp;code</a></span>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="getSite"></a><span class="summary-sig-name">getSite</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.getSite">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="isFullGapSite"></a><span class="summary-sig-name">isFullGapSite</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.isFullGapSite">source&nbsp;code</a></span>
</td>
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</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="isGappedSite"></a><span class="summary-sig-name">isGappedSite</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.isGappedSite">source&nbsp;code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>list</code></b>:
<code>__add__</code>,
<code>__contains__</code>,
<code>__delitem__</code>,
<code>__delslice__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__getitem__</code>,
<code>__getslice__</code>,
<code>__gt__</code>,
<code>__iadd__</code>,
<code>__imul__</code>,
<code>__init__</code>,
<code>__iter__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__mul__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__repr__</code>,
<code>__reversed__</code>,
<code>__rmul__</code>,
<code>__setslice__</code>,
<code>__sizeof__</code>,
<code>count</code>,
<code>extend</code>,
<code>index</code>,
<code>insert</code>,
<code>pop</code>,
<code>remove</code>,
<code>reverse</code>,
<code>sort</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
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<a name="append"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">append</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">data</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.append">source&nbsp;code</a></span>&nbsp;
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<p>append object to end</p>
<dl class="fields">
<dt>Overrides:
list.append
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<a name="__setitem__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__setitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">index</span>,
<span class="sig-arg">data</span>)</span>
<br /><em class="fname">(Index assignment operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.alignment-pysrc.html#Alignement.__setitem__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x[i]=y</p>
<dl class="fields">
<dt>Overrides:
list.__setitem__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ace</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.alignment.ace-pysrc.html">source&nbsp;code</a></span></p>
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<td><span class="summary-sig"><a name="contigIterator"></a><span class="summary-sig-name">contigIterator</span>(<span class="summary-sig-arg">file</span>)</span></td>
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<span class="codelink"><a href="obitools.alignment.ace-pysrc.html#contigIterator">source&nbsp;code</a></span>
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<a name="_contigIterator"></a><span class="summary-name">_contigIterator</span> = <code title="GenericParser('^CO ')">GenericParser('^CO ')</code>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools.alignment'"><code class="variable-quote">'</code><code class="variable-string">obitools.alignment</code><code class="variable-quote">'</code></code>
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<h1 class="epydoc">Source Code for <a href="obitools.alignment.ace-module.html">Module obitools.alignment.ace</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.format=obitools.format-module.html"><a title="obitools.format" class="py-name" href="#" onclick="return doclink('link-1', 'format', 'link-1');">format</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package obitools.format.genericparser=obitools.format.genericparser-module.html"><a title="obitools.format.genericparser" class="py-name" href="#" onclick="return doclink('link-2', 'genericparser', 'link-2');">genericparser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class obitools.format.genericparser.GenericParser=obitools.format.genericparser.GenericParser-class.html"><a title="obitools.format.genericparser.GenericParser" class="py-name" href="#" onclick="return doclink('link-3', 'GenericParser', 'link-3');">GenericParser</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-4', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package obitools.utils=obitools.utils-module.html"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-5', 'utils', 'link-5');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Function obitools.utils.universalOpen()=obitools.utils-module.html#universalOpen"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-6', 'universalOpen', 'link-6');">universalOpen</a></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-7', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Module obitools.cns.fasta=obitools.cns.fasta-module.html,Module obitools.fasta=obitools.fasta-module.html,Module obitools.format.sequence.fasta=obitools.format.sequence.fasta-module.html"><a title="obitools.cns.fasta
obitools.fasta
obitools.format.sequence.fasta" class="py-name" href="#" onclick="return doclink('link-8', 'fasta', 'link-8');">fasta</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Function obitools.fasta.parseFastaDescription()=obitools.fasta-module.html#parseFastaDescription"><a title="obitools.fasta.parseFastaDescription" class="py-name" href="#" onclick="return doclink('link-9', 'parseFastaDescription', 'link-9');">parseFastaDescription</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-10', 'obitools', 'link-0');">obitools</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Class obitools.NucSequence=obitools.NucSequence-class.html"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-11', 'NucSequence', 'link-11');">NucSequence</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">itertools</tt> <tt class="py-keyword">import</tt> <tt class="py-name">imap</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt id="link-12" class="py-name" targets="Variable obitools.alignment.ace._contigIterator=obitools.alignment.ace-module.html#_contigIterator"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-12', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="obitools.format.genericparser.GenericParser" class="py-name" href="#" onclick="return doclink('link-13', 'GenericParser', 'link-3');">GenericParser</a></tt><tt class="py-op">(</tt><tt class="py-string">'^CO '</tt><tt class="py-op">)</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt id="link-14" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-14', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method obitools.format.genericparser.GenericParser.addParseAction()=obitools.format.genericparser.GenericParser-class.html#addParseAction"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-15', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'AF'</tt><tt class="py-op">,</tt> <tt class="py-string">'\nAF +(\S+) +([UC]) +(-?[0-9]+)'</tt><tt class="py-op">)</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt id="link-16" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-16', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-17', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'RD'</tt><tt class="py-op">,</tt> <tt class="py-string">'\nRD +(\S+) +([0-9]+) +([0-9]+) +([0-9]+) *\n([A-Za-z\n*]+?)\n\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt id="link-18" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-18', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-19', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'DS'</tt><tt class="py-op">,</tt> <tt class="py-string">'\nDS +(.+)'</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt id="link-20" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-20', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-21', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'CO'</tt><tt class="py-op">,</tt> <tt class="py-string">'^CO (\S+)'</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="contigIterator"></a><div id="contigIterator-def"><a name="L17"></a><tt class="py-lineno">17</tt> <a class="py-toggle" href="#" id="contigIterator-toggle" onclick="return toggle('contigIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.ace-module.html#contigIterator">contigIterator</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="contigIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="contigIterator-expanded"><a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-22', 'universalOpen', 'link-6');">universalOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt id="link-23" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-23', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">contig</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rd</tt><tt class="py-op">,</tt><tt class="py-name">ds</tt><tt class="py-op">,</tt><tt class="py-name">af</tt> <tt class="py-keyword">in</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'RD'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'DS'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'AF'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt id="link-24" class="py-name" targets="Variable obitools.BioSequence.id=obitools.BioSequence-class.html#id,Variable obitools.DNAComplementSequence.id=obitools.DNAComplementSequence-class.html#id,Variable obitools.WrappedBioSequence.id=obitools.WrappedBioSequence-class.html#id,Variable obitools.cns.quality.QualitySequence.id=obitools.cns.quality.QualitySequence-class.html#id,Variable obitools.obo.parser.OBOTerm.id=obitools.obo.parser.OBOTerm-class.html#id"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-24', 'id', 'link-24');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">rd</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt id="link-25" class="py-name" targets="Method obitools.location.ComplementLocation.shift()=obitools.location.ComplementLocation-class.html#shift,Method obitools.location.CompositeLocation.shift()=obitools.location.CompositeLocation-class.html#shift,Method obitools.location.Location.shift()=obitools.location.Location-class.html#shift,Method obitools.location.PointLocation.shift()=obitools.location.PointLocation-class.html#shift,Method obitools.location.SimpleLocation.shift()=obitools.location.SimpleLocation-class.html#shift,Method obitools.location.feature.Feature.shift()=obitools.location.feature.Feature-class.html#shift"><a title="obitools.location.ComplementLocation.shift
obitools.location.CompositeLocation.shift
obitools.location.Location.shift
obitools.location.PointLocation.shift
obitools.location.SimpleLocation.shift
obitools.location.feature.Feature.shift" class="py-name" href="#" onclick="return doclink('link-25', 'shift', 'link-25');">shift</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">af</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-26" class="py-name"><a title="obitools.location.ComplementLocation.shift
obitools.location.CompositeLocation.shift
obitools.location.Location.shift
obitools.location.PointLocation.shift
obitools.location.SimpleLocation.shift
obitools.location.feature.Feature.shift" class="py-name" href="#" onclick="return doclink('link-26', 'shift', 'link-25');">shift</a></tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt><tt class="py-string">"Sequence %s in contig %s has a negative paddng value %d : skipped"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-27', 'id', 'link-24');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'CO'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt id="link-28" class="py-name"><a title="obitools.location.ComplementLocation.shift
obitools.location.CompositeLocation.shift
obitools.location.Location.shift
obitools.location.PointLocation.shift
obitools.location.SimpleLocation.shift
obitools.location.feature.Feature.shift" class="py-name" href="#" onclick="return doclink('link-28', 'shift', 'link-25');">shift</a></tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-comment">#continue</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt id="link-29" class="py-name" targets="Variable obitools.BioSequence.definition=obitools.BioSequence-class.html#definition,Variable obitools.WrappedBioSequence.definition=obitools.WrappedBioSequence-class.html#definition,Variable obitools.cns.quality.QualitySequence.definition=obitools.cns.quality.QualitySequence-class.html#definition,Variable obitools.obo.parser.OBOTerm.definition=obitools.obo.parser.OBOTerm-class.html#definition"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-29', 'definition', 'link-29');">definition</a></tt><tt class="py-op">,</tt><tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="obitools.fasta.parseFastaDescription" class="py-name" href="#" onclick="return doclink('link-30', 'parseFastaDescription', 'link-9');">parseFastaDescription</a></tt><tt class="py-op">(</tt><tt class="py-name">ds</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-31" class="py-name"><a title="obitools.location.ComplementLocation.shift
obitools.location.CompositeLocation.shift
obitools.location.Location.shift
obitools.location.PointLocation.shift
obitools.location.SimpleLocation.shift
obitools.location.feature.Feature.shift" class="py-name" href="#" onclick="return doclink('link-31', 'shift', 'link-25');">shift</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">seq</tt> <tt class="py-op">=</tt> <tt class="py-name">rd</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'*'</tt><tt class="py-op">,</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">contig</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.alignment.Alignement.append()=obitools.alignment.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-32');">append</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-33', 'NucSequence', 'link-11');">NucSequence</a></tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-34', 'id', 'link-24');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">seq</tt><tt class="py-op">,</tt><tt id="link-35" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-35', 'definition', 'link-29');">definition</a></tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">maxlen</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">contig</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">minshift</tt><tt class="py-op">=</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">contig</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">contig</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method obitools.BioSequence.getTags()=obitools.BioSequence-class.html#getTags,Method obitools.cns.quality.QualitySequence.getTags()=obitools.cns.quality.QualitySequence-class.html#getTags"><a title="obitools.BioSequence.getTags
obitools.cns.quality.QualitySequence.getTags" class="py-name" href="#" onclick="return doclink('link-36', 'getTags', 'link-36');">getTags</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt><tt class="py-op">-=</tt><tt class="py-name">minshift</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">head</tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">tail</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">maxlen</tt> <tt class="py-op">+</tt> <tt class="py-name">minshift</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'tail'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">tail</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">newseq</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-37', 'NucSequence', 'link-11');">NucSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-38', 'id', 'link-24');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">head</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">+</tt> <tt class="py-string">'-'</tt> <tt class="py-op">*</tt> <tt class="py-name">tail</tt><tt class="py-op">,</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-39', 'definition', 'link-29');">definition</a></tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="obitools.align.Alignement.append
obitools.alignment.Alignement.append
obitools.table.Table.append
obitools.table.TableRow.append
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-40', 'append', 'link-32');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">newseq</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'CO'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">rep</tt> </tt>
</div><a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt><script type="text/javascript">
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Package&nbsp;blast
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<h1 class="epydoc">Package blast</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html">source&nbsp;code</a></span></p>
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Run blast
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Run blast on ncbi servers
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Results of a blast run
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Blast high scoring pair between two sequences
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools.blast'"><code class="variable-quote">'</code><code class="variable-string">obitools.blast</code><code class="variable-quote">'</code></code>
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<h1 class="epydoc">Class Blast</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html#Blast">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Blast</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
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<li><a href="obitools.blast.NetBlast-class.html">NetBlast</a></li> </ul>
</dd></dl>
<hr />
<p>Run blast</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.Blast-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">mode</span>,
<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">program</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">blastall</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**options</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#Blast.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getMode"></a><span class="summary-sig-name">getMode</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#Blast.getMode">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getDb"></a><span class="summary-sig-name">getDb</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#Blast.getDb">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getProgram"></a><span class="summary-sig-name">getProgram</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#Blast.getProgram">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_blastcmd"></a><span class="summary-sig-name">_blastcmd</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#Blast._blastcmd">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.Blast-class.html#__call__" class="summary-sig-name">__call__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sequence</span>)</span><br />
Run blast with one sequence object</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#Blast.__call__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.Blast-class.html#mode" class="summary-name">mode</a><br />
Mode's Docstring
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.Blast-class.html#db" class="summary-name">db</a><br />
Db's Docstring
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.Blast-class.html#program" class="summary-name">program</a><br />
Program's Docstring
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">mode</span>,
<span class="sig-arg">db</span>,
<span class="sig-arg">program</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">blastall</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**options</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#Blast.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__call__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__call__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sequence</span>)</span>
<br /><em class="fname">(Call operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#Blast.__call__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Run blast with one sequence object</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>sequence</code></strong> ()</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
<a name="section-PropertyDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Property Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-PropertyDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="mode"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">mode</h3>
<p>Mode's Docstring</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.Blast-class.html#getMode" class="summary-sig-name">getMode</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="db"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">db</h3>
<p>Db's Docstring</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.Blast-class.html#getDb" class="summary-sig-name">getDb</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="program"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">program</h3>
<p>Program's Docstring</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.Blast-class.html#getProgram" class="summary-sig-name">getProgram</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
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View File

@ -1,328 +0,0 @@
<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>obitools.blast.BlastCovMinFilter</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
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alink="#204080">
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<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.blast-module.html">Package&nbsp;blast</a> ::
Class&nbsp;BlastCovMinFilter
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>]&nbsp;|&nbsp;<a href="obitools.blast.BlastCovMinFilter-class.html"
target="_top">no&nbsp;frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BlastCovMinFilter</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html#BlastCovMinFilter">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a> --+
|
<a href="obitools.table.SelectionIterator-class.html">table.SelectionIterator</a> --+
|
<strong class="uidshort">BlastCovMinFilter</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastCovMinFilter-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">blastiterator</span>,
<span class="summary-sig-arg">covmin</span>,
<span class="summary-sig-arg">query</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">**conditions</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastCovMinFilter.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_covMinPredicat"></a><span class="summary-sig-name">_covMinPredicat</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">row</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastCovMinFilter._covMinPredicat">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastCovMinFilter-class.html#_checkCondition" class="summary-sig-name" onclick="show_private();">_checkCondition</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">row</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastCovMinFilter._checkCondition">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.SelectionIterator-class.html">table.SelectionIterator</a></code></b>:
<code><a href="obitools.table.SelectionIterator-class.html#next">next</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.SelectionIterator-class.html">table.SelectionIterator</a></code></b> (private):
<code><a href="obitools.table.SelectionIterator-class.html#_getHeaders" onclick="show_private();">_getHeaders</a></code>,
<code><a href="obitools.table.SelectionIterator-class.html#_getRowFactory" onclick="show_private();">_getRowFactory</a></code>,
<code><a href="obitools.table.SelectionIterator-class.html#_getSubrowFactory" onclick="show_private();">_getSubrowFactory</a></code>,
<code><a href="obitools.table.SelectionIterator-class.html#_getTypes" onclick="show_private();">_getTypes</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a></code></b>:
<code><a href="obitools.table.iTableIterator-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.table.iTableIterator-class.html#columnIndex">columnIndex</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a></code></b> (private):
<code><a href="obitools.table.iTableIterator-class.html#_getColcount" onclick="show_private();">_getColcount</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.SelectionIterator-class.html">table.SelectionIterator</a></code></b>:
<code><a href="obitools.table.SelectionIterator-class.html#headers">headers</a></code>,
<code><a href="obitools.table.SelectionIterator-class.html#rowFactory">rowFactory</a></code>,
<code><a href="obitools.table.SelectionIterator-class.html#subrowFactory">subrowFactory</a></code>,
<code><a href="obitools.table.SelectionIterator-class.html#types">types</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a></code></b>:
<code><a href="obitools.table.iTableIterator-class.html#colcount">colcount</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">blastiterator</span>,
<span class="sig-arg">covmin</span>,
<span class="sig-arg">query</span>=<span class="sig-default">None</span>,
<span class="sig-arg">**conditions</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastCovMinFilter.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_checkCondition"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_checkCondition</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">row</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastCovMinFilter._checkCondition">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.table.SelectionIterator-class.html#_checkCondition" onclick="show_private();">table.SelectionIterator._checkCondition</a>
</dt>
</dl>
</td></tr></table>
</div>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.blast-module.html">Package&nbsp;blast</a> ::
Class&nbsp;BlastMatch
</span>
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<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
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onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BlastMatch</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.table.TableRow-class.html">table.TableRow</a> --+
|
<strong class="uidshort">BlastMatch</strong>
</pre>
<hr />
<p>Blast high scoring pair between two sequences</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left"><span class="table-header">Instance Methods</span></td>
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><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getQueryLocation"></a><span class="summary-sig-name">getQueryLocation</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.getQueryLocation">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getSubjectLocation"></a><span class="summary-sig-name">getSubjectLocation</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.getSubjectLocation">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getSubjectSequence"></a><span class="summary-sig-name">getSubjectSequence</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">database</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.getSubjectSequence">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">float</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastMatch-class.html#queryCov" class="summary-sig-name">queryCov</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">query</span>=<span class="summary-sig-default">None</span>)</span><br />
Compute coverage of match on query sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.queryCov">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastMatch-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.__getitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.TableRow-class.html">table.TableRow</a></code></b>:
<code><a href="obitools.table.TableRow-class.html#__init__">__init__</a></code>,
<code><a href="obitools.table.TableRow-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.table.TableRow-class.html#__len__">__len__</a></code>,
<code><a href="obitools.table.TableRow-class.html#__repr__">__repr__</a></code>,
<code><a href="obitools.table.TableRow-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.table.TableRow-class.html#__str__">__str__</a></code>,
<code><a href="obitools.table.TableRow-class.html#append">append</a></code>,
<code><a href="obitools.table.TableRow-class.html#castRow">castRow</a></code>,
<code><a href="obitools.table.TableRow-class.html#extend">extend</a></code>,
<code><a href="obitools.table.TableRow-class.html#getColCount">getColCount</a></code>,
<code><a href="obitools.table.TableRow-class.html#getHIndex">getHIndex</a></code>,
<code><a href="obitools.table.TableRow-class.html#getHeaders">getHeaders</a></code>,
<code><a href="obitools.table.TableRow-class.html#getType">getType</a></code>,
<code><a href="obitools.table.TableRow-class.html#pop">pop</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.TableRow-class.html">table.TableRow</a></code></b> (private):
<code><a href="obitools.table.TableRow-class.html#_castRow" onclick="show_private();">_castRow</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== STATIC METHODS ==================== -->
<a name="section-StaticMethods"></a>
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><span class="options">[<a href="#section-StaticMethods"
class="privatelink" onclick="toggle_private();"
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<td colspan="2" class="summary">
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.TableRow-class.html">table.TableRow</a></code></b> (private):
<code><a href="obitools.table.TableRow-class.html#_castValue" onclick="show_private();">_castValue</a></code>
</p></div>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
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<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.TableRow-class.html">table.TableRow</a></code></b>:
<code><a href="obitools.table.TableRow-class.html#headers">headers</a></code>,
<code><a href="obitools.table.TableRow-class.html#types">types</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.TableRow-class.html">table.TableRow</a></code></b> (private):
<code><a href="obitools.table.TableRow-class.html#_colcount" onclick="show_private();">_colcount</a></code>,
<code><a href="obitools.table.TableRow-class.html#_hindex" onclick="show_private();">_hindex</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="queryCov"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">queryCov</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">query</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.queryCov">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>Compute coverage of match on query sequence.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>query</code></strong> (<a href="obitools.BioSequence-class.html"
class="link">obitools.BioSequence</a>) - the query sequence. Default is None. In this case the query
sequence associated to this blast result is used.</li>
</ul></dd>
<dt>Returns: float</dt>
<dd>coverage fraction</dd>
</dl>
</td></tr></table>
</div>
<a name="__getitem__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">key</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastMatch.__getitem__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>key</code></strong></li>
</ul></dd>
<dt>Overrides:
<a href="obitools.table.TableRow-class.html#__getitem__">table.TableRow.__getitem__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
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Class&nbsp;BlastResult
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>[<a href="frames.html" target="_top">frames</a
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BlastResult</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResult">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
list --+
|
<a href="obitools.table.Table-class.html">table.Table</a> --+
|
<strong class="uidshort">BlastResult</strong>
</pre>
<hr />
<p>Results of a blast run</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
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<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.Table-class.html">table.Table</a></code></b>:
<code><a href="obitools.table.Table-class.html#__add__">__add__</a></code>,
<code><a href="obitools.table.Table-class.html#__getitem__">__getitem__</a></code>,
<code><a href="obitools.table.Table-class.html#__getslice__">__getslice__</a></code>,
<code><a href="obitools.table.Table-class.html#__hash__">__hash__</a></code>,
<code><a href="obitools.table.Table-class.html#__init__">__init__</a></code>,
<code><a href="obitools.table.Table-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.table.Table-class.html#__setitem__">__setitem__</a></code>,
<code><a href="obitools.table.Table-class.html#append">append</a></code>,
<code><a href="obitools.table.Table-class.html#isCompatible">isCompatible</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.Table-class.html">table.Table</a></code></b> (private):
<code><a href="obitools.table.Table-class.html#_getHeaders" onclick="show_private();">_getHeaders</a></code>,
<code><a href="obitools.table.Table-class.html#_getTypes" onclick="show_private();">_getTypes</a></code>,
<code><a href="obitools.table.Table-class.html#_setHeaders" onclick="show_private();">_setHeaders</a></code>,
<code><a href="obitools.table.Table-class.html#_setTypes" onclick="show_private();">_setTypes</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>list</code></b>:
<code>__contains__</code>,
<code>__delitem__</code>,
<code>__delslice__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__gt__</code>,
<code>__iadd__</code>,
<code>__imul__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__mul__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__repr__</code>,
<code>__reversed__</code>,
<code>__rmul__</code>,
<code>__setslice__</code>,
<code>__sizeof__</code>,
<code>count</code>,
<code>extend</code>,
<code>index</code>,
<code>insert</code>,
<code>pop</code>,
<code>remove</code>,
<code>reverse</code>,
<code>sort</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
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<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.Table-class.html">table.Table</a></code></b>:
<code><a href="obitools.table.Table-class.html#headers">headers</a></code>,
<code><a href="obitools.table.Table-class.html#types">types</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
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View File

@ -1,583 +0,0 @@
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<title>obitools.blast.BlastResultIterator</title>
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<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.blast-module.html">Package&nbsp;blast</a> ::
Class&nbsp;BlastResultIterator
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
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target="_top">no&nbsp;frames</a>]</span></td></tr>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BlastResultIterator</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a> --+
|
<strong class="uidshort">BlastResultIterator</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
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<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">blastoutput</span>,
<span class="summary-sig-arg">query</span>=<span class="summary-sig-default">None</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getHeaders" class="summary-sig-name" onclick="show_private();">_getHeaders</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getHeaders">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getTypes" class="summary-sig-name" onclick="show_private();">_getTypes</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getTypes">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getRowFactory" class="summary-sig-name" onclick="show_private();">_getRowFactory</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getRowFactory">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getSubrowFactory" class="summary-sig-name" onclick="show_private();">_getSubrowFactory</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getSubrowFactory">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_getQuery"></a><span class="summary-sig-name">_getQuery</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getQuery">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#next" class="summary-sig-name">next</a>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator.next">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a></code></b>:
<code><a href="obitools.table.iTableIterator-class.html#__iter__">__iter__</a></code>,
<code><a href="obitools.table.iTableIterator-class.html#columnIndex">columnIndex</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a></code></b> (private):
<code><a href="obitools.table.iTableIterator-class.html#_getColcount" onclick="show_private();">_getColcount</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.BlastResultIterator-class.html#headers" class="summary-name">headers</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.BlastResultIterator-class.html#types" class="summary-name">types</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.BlastResultIterator-class.html#rowFactory" class="summary-name">rowFactory</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.BlastResultIterator-class.html#subrowFactory" class="summary-name">subrowFactory</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.blast.BlastResultIterator-class.html#query" class="summary-name">query</a>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.table.iTableIterator-class.html">table.iTableIterator</a></code></b>:
<code><a href="obitools.table.iTableIterator-class.html#colcount">colcount</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">blastoutput</span>,
<span class="sig-arg">query</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>blastoutput</code></strong> ()</li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="_getHeaders"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_getHeaders</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getHeaders">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.table.iTableIterator-class.html#_getHeaders" onclick="show_private();">table.iTableIterator._getHeaders</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_getTypes"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_getTypes</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getTypes">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.table.iTableIterator-class.html#_getTypes" onclick="show_private();">table.iTableIterator._getTypes</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_getRowFactory"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_getRowFactory</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getRowFactory">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.table.iTableIterator-class.html#_getRowFactory" onclick="show_private();">table.iTableIterator._getRowFactory</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_getSubrowFactory"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_getSubrowFactory</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator._getSubrowFactory">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.table.iTableIterator-class.html#_getSubrowFactory" onclick="show_private();">table.iTableIterator._getSubrowFactory</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="next"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">next</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#BlastResultIterator.next">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="obitools.table.iTableIterator-class.html#next">table.iTableIterator.next</a>
</dt>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
<a name="section-PropertyDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Property Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-PropertyDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="headers"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">headers</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getHeaders" class="summary-sig-name" onclick="show_private();">_getHeaders</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="types"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">types</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getTypes" class="summary-sig-name" onclick="show_private();">_getTypes</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="rowFactory"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">rowFactory</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getRowFactory" class="summary-sig-name" onclick="show_private();">_getRowFactory</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="subrowFactory"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">subrowFactory</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getSubrowFactory" class="summary-sig-name" onclick="show_private();">_getSubrowFactory</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="query"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">query</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="obitools.blast.BlastResultIterator-class.html#_getQuery" class="summary-sig-name" onclick="show_private();">_getQuery</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
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</td></tr></table>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.blast-module.html">Package&nbsp;blast</a> ::
Class&nbsp;NetBlast
</span>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class NetBlast</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.blast-pysrc.html#NetBlast">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.blast.Blast-class.html">Blast</a> --+
|
<strong class="uidshort">NetBlast</strong>
</pre>
<hr />
<p>Run blast on ncbi servers</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a href="obitools.blast.NetBlast-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">mode</span>,
<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">**options</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.blast-pysrc.html#NetBlast.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.blast.Blast-class.html">Blast</a></code></b>:
<code><a href="obitools.blast.Blast-class.html#__call__">__call__</a></code>,
<code><a href="obitools.blast.Blast-class.html#getDb">getDb</a></code>,
<code><a href="obitools.blast.Blast-class.html#getMode">getMode</a></code>,
<code><a href="obitools.blast.Blast-class.html#getProgram">getProgram</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.blast.Blast-class.html">Blast</a></code></b> (private):
<code><a href="obitools.blast.Blast-class.html#_blastcmd" onclick="show_private();">_blastcmd</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
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</table>
<!-- ==================== PROPERTIES ==================== -->
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.blast.Blast-class.html">Blast</a></code></b>:
<code><a href="obitools.blast.Blast-class.html#db">db</a></code>,
<code><a href="obitools.blast.Blast-class.html#mode">mode</a></code>,
<code><a href="obitools.blast.Blast-class.html#program">program</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">mode</span>,
<span class="sig-arg">db</span>,
<span class="sig-arg">**options</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.blast-pysrc.html#NetBlast.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>mode</code></strong></li>
<li><strong class="pname"><code>db</code></strong></li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
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Package&nbsp;carto
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package carto</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html">source&nbsp;code</a></span></p>
<!-- ==================== CLASSES ==================== -->
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.carto.Map-class.html" class="summary-name">Map</a><br />
Map represente une instance d'une carte genetique physique.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.carto.Feature-class.html" class="summary-name">Feature</a>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
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<a href="obitools.carto.Level-class.html" class="summary-name">Level</a>
</td>
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<span class="summary-type">&nbsp;</span>
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<a href="obitools.carto.SubLevel-class.html" class="summary-name">SubLevel</a>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.carto.SimpleFeature-class.html" class="summary-name">SimpleFeature</a>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.carto.BoxFeature-class.html" class="summary-name">BoxFeature</a>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.carto.MultiPartFeature-class.html" class="summary-name">MultiPartFeature</a>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.carto.TagFeature-class.html" class="summary-name">TagFeature</a>
</td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools.carto'"><code class="variable-quote">'</code><code class="variable-string">obitools.carto</code><code class="variable-quote">'</code></code>
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<h1 class="epydoc">Source Code for <a href="obitools.carto-module.html">Package obitools.carto</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># -*- coding: latin1 -*-</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module obitools.SVGdraw=obitools.SVGdraw-module.html"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-1', 'SVGdraw', 'link-1');">SVGdraw</a></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">math</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="Map"></a><div id="Map-def"><a name="L8"></a><tt class="py-lineno"> 8</tt> <a class="py-toggle" href="#" id="Map-toggle" onclick="return toggle('Map');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.Map-class.html">Map</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Map-expanded"><a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"> Map represente une instance d'une carte genetique physique.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"> Une telle carte est definie par la longueur de la sequence</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"> qui lui est associe.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> A une carte est associe un certain nombre de niveaux (Level)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> eux meme decoupe en sous-niveau (SubLevel)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> Les sous niveaux contiennent eux des features </tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Map.__init__"></a><div id="Map.__init__-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="Map.__init__-toggle" onclick="return toggle('Map.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">,</tt><tt class="py-param">seqlength</tt><tt class="py-op">,</tt><tt class="py-param">scale</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.__init__-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> Constructeur d'une nouvelle carte </tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> *Param*:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> name</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> nom de la carte</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> seqlength</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> longueur de la sequence associee a la carte</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> scale</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> echelle de la carte indicant combien de pixel</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> correspondent a une unite de la carte</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Variable obitools.obo.parser.OBOTerm.name=obitools.obo.parser.OBOTerm-class.html#name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-2', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-3', 'name', 'link-2');">name</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlength</tt> <tt class="py-op">=</tt> <tt class="py-name">seqlength</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">scale</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">basicHSize</tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="Map.__str__"></a><div id="Map.__str__-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="Map.__str__-toggle" onclick="return toggle('Map.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.__str__-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'&lt;%s&gt;'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-2');">name</a></tt> </tt>
</div><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="Map.__getitem__"></a><div id="Map.__getitem__-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="Map.__getitem__-toggle" onclick="return toggle('Map.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.__getitem__-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> retourne le niveau *level* de la carte et</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> le cree s'il n'existe pas</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">'level must be an non Zero integer value'</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">level</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-5" class="py-name" targets="Class exceptions.AssertionError=exceptions.AssertionError-class.html"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-5', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Level cannot be set to 0'</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">level</tt><tt class="py-op">]</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">level</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name" targets="Class obitools.carto.Level=obitools.carto.Level-class.html"><a title="obitools.carto.Level" class="py-name" href="#" onclick="return doclink('link-6', 'Level', 'link-6');">Level</a></tt><tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">level</tt><tt class="py-op">]</tt> </tt>
</div><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="Map.getBasicHSize"></a><div id="Map.getBasicHSize-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="Map.getBasicHSize-toggle" onclick="return toggle('Map.getBasicHSize');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#getBasicHSize">getBasicHSize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.getBasicHSize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.getBasicHSize-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> retourne la hauteur de base d'un element de cartographie</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> exprimee en pixel</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">basicHSize</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="Map.getScale"></a><div id="Map.getScale-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="Map.getScale-toggle" onclick="return toggle('Map.getScale');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#getScale">getScale</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.getScale-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.getScale-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> Retourne l'echelle de la carte en nombre de pixels par</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> unite physique de la carte</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt> </tt>
</div><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="Map.getNegativeBase"></a><div id="Map.getNegativeBase-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="Map.getNegativeBase-toggle" onclick="return toggle('Map.getNegativeBase');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#getNegativeBase">getNegativeBase</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.getNegativeBase-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.getNegativeBase-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">-</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method obitools.carto.BoxFeature.getHeight()=obitools.carto.BoxFeature-class.html#getHeight,Method obitools.carto.Level.getHeight()=obitools.carto.Level-class.html#getHeight,Method obitools.carto.Map.getHeight()=obitools.carto.Map-class.html#getHeight,Method obitools.carto.MultiPartFeature.getHeight()=obitools.carto.MultiPartFeature-class.html#getHeight,Method obitools.carto.SimpleFeature.getHeight()=obitools.carto.SimpleFeature-class.html#getHeight,Method obitools.carto.SubLevel.getHeight()=obitools.carto.SubLevel-class.html#getHeight,Method obitools.carto.TagFeature.getHeight()=obitools.carto.TagFeature-class.html#getHeight"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-7', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">z</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-8', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="Map.getPositiveBase"></a><div id="Map.getPositiveBase-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="Map.getPositiveBase-toggle" onclick="return toggle('Map.getPositiveBase');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#getPositiveBase">getPositiveBase</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.getPositiveBase-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.getPositiveBase-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method obitools.carto.Map.getNegativeBase()=obitools.carto.Map-class.html#getNegativeBase"><a title="obitools.carto.Map.getNegativeBase" class="py-name" href="#" onclick="return doclink('link-9', 'getNegativeBase', 'link-9');">getNegativeBase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">3</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method obitools.carto.Map.getBasicHSize()=obitools.carto.Map-class.html#getBasicHSize"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-10', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="Map.getHeight"></a><div id="Map.getHeight-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="Map.getHeight-toggle" onclick="return toggle('Map.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.getHeight-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-11', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> \ </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-number">4</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-12', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="Map.toXML"></a><div id="Map.toXML-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="Map.toXML-toggle" onclick="return toggle('Map.toXML');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Map-class.html#toXML">toXML</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">file</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">begin</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-param">end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Map.toXML-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Map.toXML-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">dessin</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-13', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Class obitools.SVGdraw.drawing=obitools.SVGdraw.drawing-class.html"><a title="obitools.SVGdraw.drawing" class="py-name" href="#" onclick="return doclink('link-14', 'drawing', 'link-14');">drawing</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-15" class="py-name" targets="Variable obitools.location.ComplementLocation.end=obitools.location.ComplementLocation-class.html#end,Variable obitools.location.CompositeLocation.end=obitools.location.CompositeLocation-class.html#end,Variable obitools.location.Location.end=obitools.location.Location-class.html#end,Variable obitools.location.PointLocation.end=obitools.location.PointLocation-class.html#end,Variable obitools.location.SimpleLocation.end=obitools.location.SimpleLocation-class.html#end,Variable obitools.location.feature.Feature.end=obitools.location.feature.Feature-class.html#end,Method obitools.statistics.noncentralhypergeo.Interval.end()=obitools.statistics.noncentralhypergeo.Interval-class.html#end"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-15', 'end', 'link-15');">end</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt id="link-16" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-16', 'end', 'link-15');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlength</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">hauteur</tt><tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-17', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">largeur</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-18', 'end', 'link-15');">end</a></tt><tt class="py-op">-</tt><tt id="link-19" class="py-name" targets="Variable obitools.location.ComplementLocation.begin=obitools.location.ComplementLocation-class.html#begin,Variable obitools.location.CompositeLocation.begin=obitools.location.CompositeLocation-class.html#begin,Variable obitools.location.Location.begin=obitools.location.Location-class.html#begin,Variable obitools.location.PointLocation.begin=obitools.location.PointLocation-class.html#begin,Variable obitools.location.SimpleLocation.begin=obitools.location.SimpleLocation-class.html#begin,Variable obitools.location.feature.Feature.begin=obitools.location.feature.Feature-class.html#begin,Method obitools.statistics.noncentralhypergeo.Interval.begin()=obitools.statistics.noncentralhypergeo.Interval-class.html#begin"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-19', 'begin', 'link-19');">begin</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt id="link-20" class="py-name" targets="Class obitools.SVGdraw.svg=obitools.SVGdraw.svg-class.html,Module obitools.svg=obitools.svg-module.html,Module obitools.tree.svg=obitools.tree.svg-module.html"><a title="obitools.SVGdraw.svg
obitools.svg
obitools.tree.svg" class="py-name" href="#" onclick="return doclink('link-20', 'svg', 'link-20');">svg</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-21', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="obitools.SVGdraw.svg
obitools.svg
obitools.tree.svg" class="py-name" href="#" onclick="return doclink('link-22', 'svg', 'link-20');">svg</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-23', 'begin', 'link-19');">begin</a></tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">largeur</tt><tt class="py-op">,</tt><tt class="py-name">hauteur</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-string">'%fpx'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlength</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-string">'%dpx'</tt> <tt class="py-op">%</tt> <tt class="py-name">hauteur</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">centre</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method obitools.carto.Map.getPositiveBase()=obitools.carto.Map-class.html#getPositiveBase"><a title="obitools.carto.Map.getPositiveBase" class="py-name" href="#" onclick="return doclink('link-24', 'getPositiveBase', 'link-24');">getPositiveBase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">/</tt><tt class="py-number">4</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-25', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="obitools.SVGdraw.svg
obitools.svg
obitools.tree.svg" class="py-name" href="#" onclick="return doclink('link-26', 'svg', 'link-20');">svg</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method obitools.SVGdraw.SVGelement.addElement()=obitools.SVGdraw.SVGelement-class.html#addElement"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-27', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-28', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Class obitools.SVGdraw.rect=obitools.SVGdraw.rect-class.html"><a title="obitools.SVGdraw.rect" class="py-name" href="#" onclick="return doclink('link-29', 'rect', 'link-29');">rect</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">centre</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlength</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-30', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">e</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="obitools.SVGdraw.svg
obitools.svg
obitools.tree.svg" class="py-name" href="#" onclick="return doclink('link-31', 'svg', 'link-20');">svg</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-32', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt class="py-name">e</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method obitools.carto.BoxFeature.getElement()=obitools.carto.BoxFeature-class.html#getElement,Method obitools.carto.Level.getElement()=obitools.carto.Level-class.html#getElement,Method obitools.carto.MultiPartFeature.getElement()=obitools.carto.MultiPartFeature-class.html#getElement,Method obitools.carto.SimpleFeature.getElement()=obitools.carto.SimpleFeature-class.html#getElement,Method obitools.carto.SubLevel.getElement()=obitools.carto.SubLevel-class.html#getElement,Method obitools.carto.TagFeature.getElement()=obitools.carto.TagFeature-class.html#getElement"><a title="obitools.carto.BoxFeature.getElement
obitools.carto.Level.getElement
obitools.carto.MultiPartFeature.getElement
obitools.carto.SimpleFeature.getElement
obitools.carto.SubLevel.getElement
obitools.carto.TagFeature.getElement" class="py-name" href="#" onclick="return doclink('link-33', 'getElement', 'link-33');">getElement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">dessin</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method obitools.SVGdraw.drawing.setSVG()=obitools.SVGdraw.drawing-class.html#setSVG"><a title="obitools.SVGdraw.drawing.setSVG" class="py-name" href="#" onclick="return doclink('link-34', 'setSVG', 'link-34');">setSVG</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="obitools.SVGdraw.svg
obitools.svg
obitools.tree.svg" class="py-name" href="#" onclick="return doclink('link-35', 'svg', 'link-20');">svg</a></tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dessin</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method obitools.SVGdraw.SVGelement.toXml()=obitools.SVGdraw.SVGelement-class.html#toXml,Method obitools.SVGdraw.drawing.toXml()=obitools.SVGdraw.drawing-class.html#toXml,Method obitools.SVGdraw.text.toXml()=obitools.SVGdraw.text-class.html#toXml"><a title="obitools.SVGdraw.SVGelement.toXml
obitools.SVGdraw.drawing.toXml
obitools.SVGdraw.text.toXml" class="py-name" href="#" onclick="return doclink('link-36', 'toXml', 'link-36');">toXml</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="Feature"></a><div id="Feature-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="Feature-toggle" onclick="return toggle('Feature');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.Feature-class.html">Feature</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Feature-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Feature-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="Level"></a><div id="Level-def"><a name="L106"></a><tt class="py-lineno">106</tt> <a class="py-toggle" href="#" id="Level-toggle" onclick="return toggle('Level');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.Level-class.html">Level</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Level-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Level-expanded"><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="Level.__init__"></a><div id="Level.__init__-def"><a name="L108"></a><tt class="py-lineno">108</tt> <a class="py-toggle" href="#" id="Level.__init__-toggle" onclick="return toggle('Level.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Level-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">level</tt><tt class="py-op">,</tt><tt class="py-param">map</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Level.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Level.__init__-expanded"><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">,</tt><tt id="link-37" class="py-name" targets="Class obitools.carto.Map=obitools.carto.Map-class.html"><a title="obitools.carto.Map" class="py-name" href="#" onclick="return doclink('link-37', 'Map', 'link-37');">Map</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-38" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-38', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'map is not an instance of class Map'</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">level</tt> <tt class="py-keyword">in</tt> <tt class="py-name">map</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-39" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-39', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Level %d already define for map %s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">,</tt><tt class="py-name">map</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">map</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">level</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt> <tt class="py-op">=</tt> <tt class="py-name">level</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="Level.__getitem__"></a><div id="Level.__getitem__-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="Level.__getitem__-toggle" onclick="return toggle('Level.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Level-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sublevel</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Level.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Level.__getitem__-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> retourne le niveau *sublevel* du niveau en</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> le creant s'il n'existe pas</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">sublevel</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">'sublevel must be a positive integer value'</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">sublevel</tt><tt class="py-op">&lt;</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-40" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-40', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Level cannot be negative'</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">[</tt><tt class="py-name">sublevel</tt><tt class="py-op">]</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">[</tt><tt class="py-name">sublevel</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name" targets="Class obitools.carto.SubLevel=obitools.carto.SubLevel-class.html"><a title="obitools.carto.SubLevel" class="py-name" href="#" onclick="return doclink('link-41', 'SubLevel', 'link-41');">SubLevel</a></tt><tt class="py-op">(</tt><tt class="py-name">sublevel</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">[</tt><tt class="py-name">sublevel</tt><tt class="py-op">]</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="Level.getBase"></a><div id="Level.getBase-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="Level.getBase-toggle" onclick="return toggle('Level.getBase');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Level-class.html#getBase">getBase</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Level.getBase-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Level.getBase-expanded"><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="obitools.carto.Map.getNegativeBase" class="py-name" href="#" onclick="return doclink('link-42', 'getNegativeBase', 'link-9');">getNegativeBase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">+=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-43', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">z</tt> <tt class="py-op">&lt;</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">z</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">base</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="obitools.carto.Map.getPositiveBase" class="py-name" href="#" onclick="return doclink('link-44', 'getPositiveBase', 'link-24');">getPositiveBase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">-=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-45', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt class="py-name">levels</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">z</tt> <tt class="py-op">&gt;</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">z</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">base</tt> </tt>
</div><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="Level.getElement"></a><div id="Level.getElement-def"><a name="L148"></a><tt class="py-lineno">148</tt> <a class="py-toggle" href="#" id="Level.getElement-toggle" onclick="return toggle('Level.getElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Level-class.html#getElement">getElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Level.getElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Level.getElement-expanded"><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">objet</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-46', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Class obitools.SVGdraw.group=obitools.SVGdraw.group-class.html"><a title="obitools.SVGdraw.group" class="py-name" href="#" onclick="return doclink('link-47', 'group', 'link-47');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">'level%d'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">e</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-48', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt class="py-name">e</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="obitools.carto.BoxFeature.getElement
obitools.carto.Level.getElement
obitools.carto.MultiPartFeature.getElement
obitools.carto.SimpleFeature.getElement
obitools.carto.SubLevel.getElement
obitools.carto.TagFeature.getElement" class="py-name" href="#" onclick="return doclink('link-49', 'getElement', 'link-33');">getElement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">objet</tt> </tt>
</div><a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="Level.getHeight"></a><div id="Level.getHeight-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="Level.getHeight-toggle" onclick="return toggle('Level.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.Level-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Level.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Level.getHeight-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-50', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> \ </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-number">2</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-51', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> </tt>
<a name="SubLevel"></a><div id="SubLevel-def"><a name="L160"></a><tt class="py-lineno">160</tt> <a class="py-toggle" href="#" id="SubLevel-toggle" onclick="return toggle('SubLevel');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.SubLevel-class.html">SubLevel</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubLevel-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SubLevel-expanded"><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="SubLevel.__init__"></a><div id="SubLevel.__init__-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="SubLevel.__init__-toggle" onclick="return toggle('SubLevel.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SubLevel-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sublevel</tt><tt class="py-op">,</tt><tt class="py-param">level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubLevel.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubLevel.__init__-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">,</tt><tt id="link-52" class="py-name"><a title="obitools.carto.Level" class="py-name" href="#" onclick="return doclink('link-52', 'Level', 'link-6');">Level</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-53" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-53', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'level is not an instance of class Level'</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">level</tt> <tt class="py-keyword">in</tt> <tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-54" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-54', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Sublevel %d already define for level %s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">sublevel</tt><tt class="py-op">,</tt><tt class="py-name">level</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">[</tt><tt class="py-name">sublevel</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt> <tt class="py-op">=</tt> <tt class="py-name">level</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt> <tt class="py-op">=</tt> <tt class="py-name">sublevel</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="SubLevel.getHeight"></a><div id="SubLevel.getHeight-def"><a name="L173"></a><tt class="py-lineno">173</tt> <a class="py-toggle" href="#" id="SubLevel.getHeight-toggle" onclick="return toggle('SubLevel.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SubLevel-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubLevel.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubLevel.getHeight-expanded"><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-55', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-number">4</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-56', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt>
<a name="SubLevel.getBase"></a><div id="SubLevel.getBase-def"><a name="L176"></a><tt class="py-lineno">176</tt> <a class="py-toggle" href="#" id="SubLevel.getBase-toggle" onclick="return toggle('SubLevel.getBase');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SubLevel-class.html#getBase">getBase</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubLevel.getBase-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubLevel.getBase-expanded"><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Method obitools.carto.Level.getBase()=obitools.carto.Level-class.html#getBase,Method obitools.carto.SubLevel.getBase()=obitools.carto.SubLevel-class.html#getBase"><a title="obitools.carto.Level.getBase
obitools.carto.SubLevel.getBase" class="py-name" href="#" onclick="return doclink('link-57', 'getBase', 'link-57');">getBase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">level</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">-=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-58', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">2</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-59', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">+=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-60', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">z</tt> <tt class="py-op">&lt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">-=</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-61', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">-=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt><tt class="py-op">[</tt><tt class="py-name">z</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="obitools.carto.BoxFeature.getHeight
obitools.carto.Level.getHeight
obitools.carto.Map.getHeight
obitools.carto.MultiPartFeature.getHeight
obitools.carto.SimpleFeature.getHeight
obitools.carto.SubLevel.getHeight
obitools.carto.TagFeature.getHeight" class="py-name" href="#" onclick="return doclink('link-62', 'getHeight', 'link-7');">getHeight</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">sublevels</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">z</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">-=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-63', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">base</tt> </tt>
</div><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="SubLevel.getElement"></a><div id="SubLevel.getElement-def"><a name="L191"></a><tt class="py-lineno">191</tt> <a class="py-toggle" href="#" id="SubLevel.getElement-toggle" onclick="return toggle('SubLevel.getElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SubLevel-class.html#getElement">getElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubLevel.getElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubLevel.getElement-expanded"><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="obitools.carto.Level.getBase
obitools.carto.SubLevel.getBase" class="py-name" href="#" onclick="return doclink('link-64', 'getBase', 'link-57');">getBase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">objet</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-65', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="obitools.SVGdraw.group" class="py-name" href="#" onclick="return doclink('link-66', 'group', 'link-47');">group</a></tt><tt class="py-op">(</tt><tt class="py-string">'sublevel%d'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">e</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">values</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-67', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt class="py-name">e</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="obitools.carto.BoxFeature.getElement
obitools.carto.Level.getElement
obitools.carto.MultiPartFeature.getElement
obitools.carto.SimpleFeature.getElement
obitools.carto.SubLevel.getElement
obitools.carto.TagFeature.getElement" class="py-name" href="#" onclick="return doclink('link-68', 'getElement', 'link-33');">getElement</a></tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">objet</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="SubLevel.add"></a><div id="SubLevel.add-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="SubLevel.add-toggle" onclick="return toggle('SubLevel.add');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SubLevel-class.html#add">add</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">feature</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubLevel.add-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubLevel.add-expanded"><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-69" class="py-name" targets="Module obitools.location.feature=obitools.location.feature-module.html"><a title="obitools.location.feature" class="py-name" href="#" onclick="return doclink('link-69', 'feature', 'link-69');">feature</a></tt><tt class="py-op">,</tt><tt id="link-70" class="py-name" targets="Class obitools.carto.Feature=obitools.carto.Feature-class.html,Class obitools.location.feature.Feature=obitools.location.feature.Feature-class.html"><a title="obitools.carto.Feature
obitools.location.feature.Feature" class="py-name" href="#" onclick="return doclink('link-70', 'Feature', 'link-70');">Feature</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">'feature must be an instance oof Feature'</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-71" class="py-name"><a title="obitools.location.feature" class="py-name" href="#" onclick="return doclink('link-71', 'feature', 'link-69');">feature</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-72', 'name', 'link-2');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">features</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-73" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-73', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'A feature with the same name (%s) have already be insert in this sublevel'</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt id="link-74" class="py-name"><a title="obitools.location.feature" class="py-name" href="#" onclick="return doclink('link-74', 'feature', 'link-69');">feature</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-75', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">features</tt><tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="obitools.location.feature" class="py-name" href="#" onclick="return doclink('link-76', 'feature', 'link-69');">feature</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-77', 'name', 'link-2');">name</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-78" class="py-name"><a title="obitools.location.feature" class="py-name" href="#" onclick="return doclink('link-78', 'feature', 'link-69');">feature</a></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="obitools.location.feature" class="py-name" href="#" onclick="return doclink('link-79', 'feature', 'link-69');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">=</tt><tt class="py-name">self</tt> </tt>
</div></div><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="SimpleFeature"></a><div id="SimpleFeature-def"><a name="L207"></a><tt class="py-lineno">207</tt> <a class="py-toggle" href="#" id="SimpleFeature-toggle" onclick="return toggle('SimpleFeature');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.SimpleFeature-class.html">SimpleFeature</a><tt class="py-op">(</tt><tt class="py-base-class">Feature</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimpleFeature-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SimpleFeature-expanded"><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="SimpleFeature.__init__"></a><div id="SimpleFeature.__init__-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="SimpleFeature.__init__-toggle" onclick="return toggle('SimpleFeature.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SimpleFeature-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">,</tt><tt class="py-param">begin</tt><tt class="py-op">,</tt><tt class="py-param">end</tt><tt class="py-op">,</tt><tt class="py-param">visiblename</tt><tt class="py-op">=</tt><tt id="link-80" class="py-name" targets="Variable obitools.SVGdraw.False=obitools.SVGdraw-module.html#False"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-80', 'False', 'link-80');">False</a></tt><tt class="py-op">,</tt><tt class="py-param">color</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimpleFeature.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleFeature.__init__-expanded"><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-81', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-82', 'begin', 'link-19');">begin</a></tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-83', 'end', 'link-15');">end</a></tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-84', 'end', 'link-15');">end</a></tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-85', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-86', 'name', 'link-2');">name</a></tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-name">color</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">=</tt><tt class="py-name">visiblename</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="SimpleFeature.getHeight"></a><div id="SimpleFeature.getHeight-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="SimpleFeature.getHeight-toggle" onclick="return toggle('SimpleFeature.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SimpleFeature-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimpleFeature.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleFeature.getHeight-expanded"><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-87" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-87', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Not affected Simple feature'</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">:</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-88', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-89', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="SimpleFeature.getElement"></a><div id="SimpleFeature.getElement-def"><a name="L225"></a><tt class="py-lineno">225</tt> <a class="py-toggle" href="#" id="SimpleFeature.getElement-toggle" onclick="return toggle('SimpleFeature.getElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.SimpleFeature-class.html#getElement">getElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">base</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimpleFeature.getElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleFeature.getElement-expanded"><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name" targets="Method obitools.carto.Map.getScale()=obitools.carto.Map-class.html#getScale"><a title="obitools.carto.Map.getScale" class="py-name" href="#" onclick="return doclink('link-90', 'getScale', 'link-90');">getScale</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-91', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-92', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-93', 'end', 'link-15');">end</a></tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-94', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">heigh</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-95', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">objet</tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-96', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="obitools.SVGdraw.rect" class="py-name" href="#" onclick="return doclink('link-97', 'rect', 'link-29');">rect</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">,</tt><tt class="py-name">heigh</tt><tt class="py-op">,</tt><tt class="py-name">stroke</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-98', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-99', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-100" class="py-name" targets="Class obitools.SVGdraw.description=obitools.SVGdraw.description-class.html"><a title="obitools.SVGdraw.description" class="py-name" href="#" onclick="return doclink('link-100', 'description', 'link-100');">description</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-101', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">objet</tt> </tt>
</div></div><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="BoxFeature"></a><div id="BoxFeature-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="BoxFeature-toggle" onclick="return toggle('BoxFeature');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.BoxFeature-class.html">BoxFeature</a><tt class="py-op">(</tt><tt class="py-base-class">SimpleFeature</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BoxFeature-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BoxFeature-expanded"><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="BoxFeature.getHeight"></a><div id="BoxFeature.getHeight-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="BoxFeature.getHeight-toggle" onclick="return toggle('BoxFeature.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.BoxFeature-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BoxFeature.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BoxFeature.getHeight-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-102" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-102', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Not affected Box feature'</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">:</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-103', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">4</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-104', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">3</tt> </tt>
</div><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="BoxFeature.getElement"></a><div id="BoxFeature.getElement-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="BoxFeature.getElement-toggle" onclick="return toggle('BoxFeature.getElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.BoxFeature-class.html#getElement">getElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">base</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BoxFeature.getElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BoxFeature.getElement-expanded"><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="obitools.carto.Map.getScale" class="py-name" href="#" onclick="return doclink('link-105', 'getScale', 'link-90');">getScale</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-106', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-107', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-108', 'end', 'link-15');">end</a></tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-109', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">height</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-110', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">3</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">objet</tt> <tt class="py-op">=</tt> <tt id="link-111" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-111', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="obitools.SVGdraw.rect" class="py-name" href="#" onclick="return doclink('link-112', 'rect', 'link-29');">rect</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">,</tt><tt class="py-name">height</tt><tt class="py-op">,</tt><tt class="py-name">stroke</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt><tt class="py-op">,</tt><tt class="py-name">fill</tt><tt class="py-op">=</tt><tt class="py-string">"none"</tt><tt class="py-op">)</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-113', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt id="link-114" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-114', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="obitools.SVGdraw.description" class="py-name" href="#" onclick="return doclink('link-115', 'description', 'link-100');">description</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-116', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">objet</tt> </tt>
</div></div><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt>
<a name="MultiPartFeature"></a><div id="MultiPartFeature-def"><a name="L259"></a><tt class="py-lineno">259</tt> <a class="py-toggle" href="#" id="MultiPartFeature-toggle" onclick="return toggle('MultiPartFeature');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.MultiPartFeature-class.html">MultiPartFeature</a><tt class="py-op">(</tt><tt class="py-base-class">Feature</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiPartFeature-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MultiPartFeature-expanded"><a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="MultiPartFeature.__init__"></a><div id="MultiPartFeature.__init__-def"><a name="L261"></a><tt class="py-lineno">261</tt> <a class="py-toggle" href="#" id="MultiPartFeature.__init__-toggle" onclick="return toggle('MultiPartFeature.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.MultiPartFeature-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">,</tt><tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">kargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiPartFeature.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiPartFeature.__init__-expanded"><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">limits</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-117', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-118', 'name', 'link-2');">name</a></tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-name">kargs</tt><tt class="py-op">[</tt><tt class="py-string">'color'</tt><tt class="py-op">]</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-string">"black"</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">=</tt><tt class="py-name">kargs</tt><tt class="py-op">[</tt><tt class="py-string">'visiblename'</tt><tt class="py-op">]</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flatlink</tt><tt class="py-op">=</tt><tt class="py-name">kargs</tt><tt class="py-op">[</tt><tt class="py-string">'flatlink'</tt><tt class="py-op">]</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flatlink</tt><tt class="py-op">=</tt><tt id="link-119" class="py-name"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-119', 'False', 'link-80');">False</a></tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">roundlink</tt><tt class="py-op">=</tt><tt class="py-name">kargs</tt><tt class="py-op">[</tt><tt class="py-string">'roundlink'</tt><tt class="py-op">]</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">roundlink</tt><tt class="py-op">=</tt><tt id="link-120" class="py-name"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-120', 'False', 'link-80');">False</a></tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
<a name="MultiPartFeature.getHeight"></a><div id="MultiPartFeature.getHeight-def"><a name="L287"></a><tt class="py-lineno">287</tt> <a class="py-toggle" href="#" id="MultiPartFeature.getHeight-toggle" onclick="return toggle('MultiPartFeature.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.MultiPartFeature-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiPartFeature.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiPartFeature.getHeight-expanded"><a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-121" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-121', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Not affected Simple feature'</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-122', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">3</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-123', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt> </tt>
</div><a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> </tt>
<a name="MultiPartFeature.getElement"></a><div id="MultiPartFeature.getElement-def"><a name="L295"></a><tt class="py-lineno">295</tt> <a class="py-toggle" href="#" id="MultiPartFeature.getElement-toggle" onclick="return toggle('MultiPartFeature.getElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.MultiPartFeature-class.html#getElement">getElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">base</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MultiPartFeature.getElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MultiPartFeature.getElement-expanded"><a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="obitools.carto.Map.getScale" class="py-name" href="#" onclick="return doclink('link-124', 'getScale', 'link-90');">getScale</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-125', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">height</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-126', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-name">objet</tt> <tt class="py-op">=</tt> <tt id="link-127" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-127', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="obitools.SVGdraw.group" class="py-name" href="#" onclick="return doclink('link-128', 'group', 'link-47');">group</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-129', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">debut</tt><tt class="py-op">,</tt><tt class="py-name">fin</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">limits</tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">debut</tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">fin</tt> <tt class="py-op">-</tt> <tt class="py-name">debut</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">part</tt> <tt class="py-op">=</tt> <tt id="link-130" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-130', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="obitools.SVGdraw.rect" class="py-name" href="#" onclick="return doclink('link-131', 'rect', 'link-29');">rect</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">,</tt><tt class="py-name">height</tt><tt class="py-op">,</tt><tt class="py-name">fill</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-132', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt class="py-name">part</tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">debut</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">limits</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">fin</tt><tt class="py-op">,</tt><tt id="link-133" class="py-name" targets="Method obitools.WrapperSetIterator.next()=obitools.WrapperSetIterator-class.html#next,Method obitools.blast.BlastResultIterator.next()=obitools.blast.BlastResultIterator-class.html#next,Method obitools.ecopcr.EcoPCRFile.next()=obitools.ecopcr.EcoPCRFile-class.html#next,Method obitools.ecotag.parser.EcoTagAbstractIterator.next()=obitools.ecotag.parser.EcoTagAbstractIterator-class.html#next,Method obitools.ecotag.parser.EcoTagFileIterator.next()=obitools.ecotag.parser.EcoTagFileIterator-class.html#next,Method obitools.format.ontology.go_obo.OBOFile.next()=obitools.format.ontology.go_obo.OBOFile-class.html#next,Method obitools.goa.parser.GoAFileIterator.next()=obitools.goa.parser.GoAFileIterator-class.html#next,Method obitools.gzip.GzipFile.next()=obitools.gzip.GzipFile-class.html#next,Method obitools.parallel.jobqueue.JobIterator.next()=obitools.parallel.jobqueue.JobIterator-class.html#next,Method obitools.solexa.SolexaFile.next()=obitools.solexa.SolexaFile-class.html#next,Method obitools.table.ProjectionIterator.next()=obitools.table.ProjectionIterator-class.html#next,Method obitools.table.SelectionIterator.next()=obitools.table.SelectionIterator-class.html#next,Method obitools.table.TableIterator.next()=obitools.table.TableIterator-class.html#next,Method obitools.table.TableIteratorAsDict.next()=obitools.table.TableIteratorAsDict-class.html#next,Method obitools.table.UnionIterator.next()=obitools.table.UnionIterator-class.html#next,Method obitools.table.iTableIterator.next()=obitools.table.iTableIterator-class.html#next,Method obitools.tagmatcher.parser.TagMatcherIterator.next()=obitools.tagmatcher.parser.TagMatcherIterator-class.html#next,Method obitools.utils.ColumnFile.next()=obitools.utils.ColumnFile-class.html#next,Method obitools.zipfile.ZipExtFile.next()=obitools.zipfile.ZipExtFile-class.html#next"><a title="obitools.WrapperSetIterator.next
obitools.blast.BlastResultIterator.next
obitools.ecopcr.EcoPCRFile.next
obitools.ecotag.parser.EcoTagAbstractIterator.next
obitools.ecotag.parser.EcoTagFileIterator.next
obitools.format.ontology.go_obo.OBOFile.next
obitools.goa.parser.GoAFileIterator.next
obitools.gzip.GzipFile.next
obitools.parallel.jobqueue.JobIterator.next
obitools.solexa.SolexaFile.next
obitools.table.ProjectionIterator.next
obitools.table.SelectionIterator.next
obitools.table.TableIterator.next
obitools.table.TableIteratorAsDict.next
obitools.table.UnionIterator.next
obitools.table.iTableIterator.next
obitools.tagmatcher.parser.TagMatcherIterator.next
obitools.utils.ColumnFile.next
obitools.zipfile.ZipExtFile.next" class="py-name" href="#" onclick="return doclink('link-133', 'next', 'link-133');">next</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">limits</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">debut</tt><tt class="py-op">*=</tt><tt class="py-name">scale</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">fin</tt><tt class="py-op">*=</tt><tt class="py-name">scale</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt id="link-134" class="py-name" targets="Class obitools.SVGdraw.path=obitools.SVGdraw.path-class.html"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-134', 'path', 'link-134');">path</a></tt> <tt class="py-op">=</tt> <tt id="link-135" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-135', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-136" class="py-name" targets="Class obitools.SVGdraw.pathdata=obitools.SVGdraw.pathdata-class.html"><a title="obitools.SVGdraw.pathdata" class="py-name" href="#" onclick="return doclink('link-136', 'pathdata', 'link-136');">pathdata</a></tt><tt class="py-op">(</tt><tt class="py-name">debut</tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">+</tt> <tt class="py-name">height</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">delta</tt> <tt class="py-op">=</tt> <tt class="py-name">height</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">roundlink</tt><tt class="py-op">:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt id="link-137" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-137', 'path', 'link-134');">path</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Method obitools.SVGdraw.pathdata.qbezier()=obitools.SVGdraw.pathdata-class.html#qbezier"><a title="obitools.SVGdraw.pathdata.qbezier" class="py-name" href="#" onclick="return doclink('link-138', 'qbezier', 'link-138');">qbezier</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">debut</tt><tt class="py-op">+</tt><tt class="py-name">fin</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-op">-</tt> <tt class="py-name">delta</tt><tt class="py-op">,</tt><tt class="py-name">fin</tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">+</tt> <tt class="py-name">height</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flatlink</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">delta</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt> <tt class="py-name">height</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt id="link-139" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-139', 'path', 'link-134');">path</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Class obitools.SVGdraw.line=obitools.SVGdraw.line-class.html,Method obitools.SVGdraw.pathdata.line()=obitools.SVGdraw.pathdata-class.html#line"><a title="obitools.SVGdraw.line
obitools.SVGdraw.pathdata.line" class="py-name" href="#" onclick="return doclink('link-140', 'line', 'link-140');">line</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">debut</tt><tt class="py-op">+</tt><tt class="py-name">fin</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-op">-</tt> <tt class="py-name">delta</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-141', 'path', 'link-134');">path</a></tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="obitools.SVGdraw.line
obitools.SVGdraw.pathdata.line" class="py-name" href="#" onclick="return doclink('link-142', 'line', 'link-140');">line</a></tt><tt class="py-op">(</tt><tt class="py-name">fin</tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">+</tt> <tt class="py-name">height</tt> <tt class="py-op">/</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt id="link-143" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-143', 'path', 'link-134');">path</a></tt> <tt class="py-op">=</tt> <tt id="link-144" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-144', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-145', 'path', 'link-134');">path</a></tt><tt class="py-op">(</tt><tt id="link-146" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-146', 'path', 'link-134');">path</a></tt><tt class="py-op">,</tt><tt class="py-name">fill</tt><tt class="py-op">=</tt><tt class="py-string">"none"</tt><tt class="py-op">,</tt><tt class="py-name">stroke</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-147', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt id="link-148" class="py-name"><a title="obitools.SVGdraw.path" class="py-name" href="#" onclick="return doclink('link-148', 'path', 'link-134');">path</a></tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">debut</tt> <tt class="py-op">=</tt> <tt id="link-149" class="py-name"><a title="obitools.WrapperSetIterator.next
obitools.blast.BlastResultIterator.next
obitools.ecopcr.EcoPCRFile.next
obitools.ecotag.parser.EcoTagAbstractIterator.next
obitools.ecotag.parser.EcoTagFileIterator.next
obitools.format.ontology.go_obo.OBOFile.next
obitools.goa.parser.GoAFileIterator.next
obitools.gzip.GzipFile.next
obitools.parallel.jobqueue.JobIterator.next
obitools.solexa.SolexaFile.next
obitools.table.ProjectionIterator.next
obitools.table.SelectionIterator.next
obitools.table.TableIterator.next
obitools.table.TableIteratorAsDict.next
obitools.table.UnionIterator.next
obitools.table.iTableIterator.next
obitools.tagmatcher.parser.TagMatcherIterator.next
obitools.utils.ColumnFile.next
obitools.zipfile.ZipExtFile.next" class="py-name" href="#" onclick="return doclink('link-149', 'next', 'link-133');">next</a></tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-150', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-151', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="obitools.SVGdraw.description" class="py-name" href="#" onclick="return doclink('link-152', 'description', 'link-100');">description</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-153', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">objet</tt> </tt>
</div></div><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="TagFeature"></a><div id="TagFeature-def"><a name="L328"></a><tt class="py-lineno">328</tt> <a class="py-toggle" href="#" id="TagFeature-toggle" onclick="return toggle('TagFeature');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.carto.TagFeature-class.html">TagFeature</a><tt class="py-op">(</tt><tt class="py-base-class">Feature</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TagFeature-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TagFeature-expanded"><a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="TagFeature.__init__"></a><div id="TagFeature.__init__-def"><a name="L330"></a><tt class="py-lineno">330</tt> <a class="py-toggle" href="#" id="TagFeature.__init__-toggle" onclick="return toggle('TagFeature.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.TagFeature-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">name</tt><tt class="py-op">,</tt><tt class="py-param">begin</tt><tt class="py-op">,</tt><tt class="py-param">length</tt><tt class="py-op">,</tt><tt class="py-param">ratio</tt><tt class="py-op">,</tt><tt class="py-param">visiblename</tt><tt class="py-op">=</tt><tt id="link-154" class="py-name"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-154', 'False', 'link-80');">False</a></tt><tt class="py-op">,</tt><tt class="py-param">color</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TagFeature.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TagFeature.__init__-expanded"><a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-155', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">=</tt> <tt id="link-156" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-156', 'begin', 'link-19');">begin</a></tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">length</tt> <tt class="py-op">=</tt> <tt class="py-name">length</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ratio</tt> <tt class="py-op">=</tt> <tt class="py-name">ratio</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-157', 'name', 'link-2');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-158" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-158', 'name', 'link-2');">name</a></tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-name">color</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">visiblename</tt><tt class="py-op">=</tt><tt class="py-name">visiblename</tt> </tt>
</div><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="TagFeature.getHeight"></a><div id="TagFeature.getHeight-def"><a name="L339"></a><tt class="py-lineno">339</tt> <a class="py-toggle" href="#" id="TagFeature.getHeight-toggle" onclick="return toggle('TagFeature.getHeight');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.TagFeature-class.html#getHeight">getHeight</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TagFeature.getHeight-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TagFeature.getHeight-expanded"><a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-159" class="py-name"><a title="exceptions.AssertionError" class="py-name" href="#" onclick="return doclink('link-159', 'AssertionError', 'link-5');">AssertionError</a></tt><tt class="py-op">(</tt><tt class="py-string">'Not affected Tag feature'</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-160', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">11</tt> </tt>
</div><a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
<a name="TagFeature.getElement"></a><div id="TagFeature.getElement-def"><a name="L345"></a><tt class="py-lineno">345</tt> <a class="py-toggle" href="#" id="TagFeature.getElement-toggle" onclick="return toggle('TagFeature.getElement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.carto.TagFeature-class.html#getElement">getElement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">base</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="TagFeature.getElement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TagFeature.getElement-expanded"><a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="obitools.carto.Map.getScale" class="py-name" href="#" onclick="return doclink('link-161', 'getScale', 'link-90');">getScale</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">height</tt> <tt class="py-op">=</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt class="py-name">floor</tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-162', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt> <tt class="py-number">10</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ratio</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">base</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sublevel</tt><tt class="py-op">.</tt><tt class="py-name">level</tt><tt class="py-op">.</tt><tt class="py-name">map</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="obitools.carto.Map.getBasicHSize" class="py-name" href="#" onclick="return doclink('link-163', 'getBasicHSize', 'link-10');">getBasicHSize</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">height</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-164', 'begin', 'link-19');">begin</a></tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">length</tt> <tt class="py-op">*</tt> <tt class="py-name">scale</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-name">objet</tt> <tt class="py-op">=</tt> <tt id="link-165" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-165', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="obitools.SVGdraw.rect" class="py-name" href="#" onclick="return doclink('link-166', 'rect', 'link-29');">rect</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">,</tt><tt class="py-name">width</tt><tt class="py-op">,</tt><tt class="py-name">height</tt><tt class="py-op">,</tt><tt class="py-name">stroke</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">color</tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-name">objet</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="obitools.SVGdraw.SVGelement.addElement" class="py-name" href="#" onclick="return doclink('link-167', 'addElement', 'link-27');">addElement</a></tt><tt class="py-op">(</tt><tt id="link-168" class="py-name"><a title="obitools.SVGdraw" class="py-name" href="#" onclick="return doclink('link-168', 'SVGdraw', 'link-1');">SVGdraw</a></tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="obitools.SVGdraw.description" class="py-name" href="#" onclick="return doclink('link-169', 'description', 'link-100');">description</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="obitools.obo.parser.OBOTerm.name" class="py-name" href="#" onclick="return doclink('link-170', 'name', 'link-2');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">objet</tt> </tt>
</div></div><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">carte</tt> <tt class="py-op">=</tt> <tt id="link-171" class="py-name"><a title="obitools.carto.Map" class="py-name" href="#" onclick="return doclink('link-171', 'Map', 'link-37');">Map</a></tt><tt class="py-op">(</tt><tt class="py-string">'essai'</tt><tt class="py-op">,</tt><tt class="py-number">20000</tt><tt class="py-op">,</tt><tt class="py-name">scale</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name" targets="Method obitools.carto.SubLevel.add()=obitools.carto.SubLevel-class.html#add,Method obitools.svg.Scene.add()=obitools.svg.Scene-class.html#add"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-172', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-173" class="py-name" targets="Class obitools.carto.SimpleFeature=obitools.carto.SimpleFeature-class.html"><a title="obitools.carto.SimpleFeature" class="py-name" href="#" onclick="return doclink('link-173', 'SimpleFeature', 'link-173');">SimpleFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'toto'</tt><tt class="py-op">,</tt><tt class="py-number">100</tt><tt class="py-op">,</tt><tt class="py-number">300</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-174', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-175" class="py-name"><a title="obitools.carto.SimpleFeature" class="py-name" href="#" onclick="return doclink('link-175', 'SimpleFeature', 'link-173');">SimpleFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'toto'</tt><tt class="py-op">,</tt><tt class="py-number">100</tt><tt class="py-op">,</tt><tt class="py-number">300</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-176', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-177" class="py-name"><a title="obitools.carto.SimpleFeature" class="py-name" href="#" onclick="return doclink('link-177', 'SimpleFeature', 'link-173');">SimpleFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'toto'</tt><tt class="py-op">,</tt><tt class="py-number">200</tt><tt class="py-op">,</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-178', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-179" class="py-name" targets="Class obitools.carto.MultiPartFeature=obitools.carto.MultiPartFeature-class.html"><a title="obitools.carto.MultiPartFeature" class="py-name" href="#" onclick="return doclink('link-179', 'MultiPartFeature', 'link-179');">MultiPartFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'bout'</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">1400</tt><tt class="py-op">,</tt><tt class="py-number">1450</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">1470</tt><tt class="py-op">,</tt><tt class="py-number">1550</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">1650</tt><tt class="py-op">,</tt><tt class="py-number">1800</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'red'</tt><tt class="py-op">,</tt><tt class="py-name">flatlink</tt><tt class="py-op">=</tt><tt id="link-180" class="py-name" targets="Variable obitools.SVGdraw.True=obitools.SVGdraw-module.html#True"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-180', 'True', 'link-180');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-181', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="obitools.carto.MultiPartFeature" class="py-name" href="#" onclick="return doclink('link-182', 'MultiPartFeature', 'link-179');">MultiPartFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'titi'</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">400</tt><tt class="py-op">,</tt><tt class="py-number">450</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">470</tt><tt class="py-op">,</tt><tt class="py-number">550</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">650</tt><tt class="py-op">,</tt><tt class="py-number">800</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'red'</tt><tt class="py-op">,</tt><tt class="py-name">flatlink</tt><tt class="py-op">=</tt><tt id="link-183" class="py-name"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-183', 'True', 'link-180');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-184', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-185" class="py-name"><a title="obitools.carto.MultiPartFeature" class="py-name" href="#" onclick="return doclink('link-185', 'MultiPartFeature', 'link-179');">MultiPartFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'titi'</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">400</tt><tt class="py-op">,</tt><tt class="py-number">450</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">470</tt><tt class="py-op">,</tt><tt class="py-number">550</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">650</tt><tt class="py-op">,</tt><tt class="py-number">800</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'green'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-186', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-187" class="py-name"><a title="obitools.carto.MultiPartFeature" class="py-name" href="#" onclick="return doclink('link-187', 'MultiPartFeature', 'link-179');">MultiPartFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'titi'</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">400</tt><tt class="py-op">,</tt><tt class="py-number">450</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">470</tt><tt class="py-op">,</tt><tt class="py-number">550</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt class="py-number">650</tt><tt class="py-op">,</tt><tt class="py-number">800</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'purple'</tt><tt class="py-op">,</tt><tt class="py-name">roundlink</tt><tt class="py-op">=</tt><tt id="link-188" class="py-name"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-188', 'True', 'link-180');">True</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-189', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-190" class="py-name" targets="Class obitools.carto.BoxFeature=obitools.carto.BoxFeature-class.html"><a title="obitools.carto.BoxFeature" class="py-name" href="#" onclick="return doclink('link-190', 'BoxFeature', 'link-190');">BoxFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'tutu'</tt><tt class="py-op">,</tt><tt class="py-number">390</tt><tt class="py-op">,</tt><tt class="py-number">810</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'purple'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-191', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="obitools.carto.BoxFeature" class="py-name" href="#" onclick="return doclink('link-192', 'BoxFeature', 'link-190');">BoxFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'tutu'</tt><tt class="py-op">,</tt><tt class="py-number">390</tt><tt class="py-op">,</tt><tt class="py-number">810</tt><tt class="py-op">,</tt><tt class="py-name">color</tt><tt class="py-op">=</tt><tt class="py-string">'red'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-193', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-194" class="py-name" targets="Class obitools.carto.TagFeature=obitools.carto.TagFeature-class.html"><a title="obitools.carto.TagFeature" class="py-name" href="#" onclick="return doclink('link-194', 'TagFeature', 'link-194');">TagFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'t1'</tt><tt class="py-op">,</tt><tt class="py-number">1400</tt><tt class="py-op">,</tt><tt class="py-number">20</tt><tt class="py-op">,</tt><tt class="py-number">0.8</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-195', 'add', 'link-172');">add</a></tt><tt class="py-op">(</tt><tt id="link-196" class="py-name"><a title="obitools.carto.TagFeature" class="py-name" href="#" onclick="return doclink('link-196', 'TagFeature', 'link-194');">TagFeature</a></tt><tt class="py-op">(</tt><tt class="py-string">'t2'</tt><tt class="py-op">,</tt><tt class="py-number">1600</tt><tt class="py-op">,</tt><tt class="py-number">20</tt><tt class="py-op">,</tt><tt class="py-number">0.2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">carte</tt><tt class="py-op">.</tt><tt class="py-name">basicHSize</tt><tt class="py-op">=</tt><tt class="py-number">6</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">carte</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name" targets="Method obitools.carto.Map.toXML()=obitools.carto.Map-class.html#toXML"><a title="obitools.carto.Map.toXML" class="py-name" href="#" onclick="return doclink('link-197', 'toXML', 'link-197');">toXML</a></tt><tt class="py-op">(</tt><tt class="py-string">'truc.svg'</tt><tt class="py-op">,</tt><tt id="link-198" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-198', 'begin', 'link-19');">begin</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt id="link-199" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-199', 'end', 'link-15');">end</a></tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">carte</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name"><a title="obitools.carto.Map.toXML" class="py-name" href="#" onclick="return doclink('link-200', 'toXML', 'link-197');">toXML</a></tt><tt class="py-op">(</tt><tt class="py-string">'truc2.svg'</tt><tt class="py-op">,</tt><tt id="link-201" class="py-name"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-201', 'begin', 'link-19');">begin</a></tt><tt class="py-op">=</tt><tt class="py-number">460</tt><tt class="py-op">,</tt><tt id="link-202" class="py-name"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-202', 'end', 'link-15');">end</a></tt><tt class="py-op">=</tt><tt class="py-number">2000</tt><tt class="py-op">)</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> </tt><script type="text/javascript">
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;BoxFeature
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class BoxFeature</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#BoxFeature">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.carto.Feature-class.html">Feature</a> --+
|
<a href="obitools.carto.SimpleFeature-class.html">SimpleFeature</a> --+
|
<strong class="uidshort">BoxFeature</strong>
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<td><span class="summary-sig"><a href="obitools.carto.BoxFeature-class.html#getHeight" class="summary-sig-name">getHeight</a>(<span class="summary-sig-arg">self</span>)</span></td>
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<tr>
<td><span class="summary-sig"><a href="obitools.carto.BoxFeature-class.html#getElement" class="summary-sig-name">getElement</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">base</span>)</span></td>
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<span class="codelink"><a href="obitools.carto-pysrc.html#BoxFeature.getElement">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="obitools.carto.SimpleFeature-class.html">SimpleFeature</a></code></b>:
<code><a href="obitools.carto.SimpleFeature-class.html#__init__">__init__</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">getHeight</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#BoxFeature.getHeight">source&nbsp;code</a></span>&nbsp;
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<dl class="fields">
<dt>Overrides:
<a href="obitools.carto.SimpleFeature-class.html#getHeight">SimpleFeature.getHeight</a>
</dt>
</dl>
</td></tr></table>
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<a name="getElement"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">getElement</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">base</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#BoxFeature.getElement">source&nbsp;code</a></span>&nbsp;
</td>
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<dl class="fields">
<dt>Overrides:
<a href="obitools.carto.SimpleFeature-class.html#getElement">SimpleFeature.getElement</a>
</dt>
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Class&nbsp;Feature
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Feature</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#Feature">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Feature</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.carto.SimpleFeature-class.html">SimpleFeature</a></li><li>, <a href="obitools.carto.MultiPartFeature-class.html">MultiPartFeature</a></li><li>, <a href="obitools.carto.TagFeature-class.html">TagFeature</a></li> </ul>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__init__</code>,
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;Level
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Level</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#Level">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Level</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.carto.Level-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">level</span>,
<span class="summary-sig-arg">map</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
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<span class="codelink"><a href="obitools.carto-pysrc.html#Level.__init__">source&nbsp;code</a></span>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sublevel</span>)</span><br />
retourne le niveau *sublevel* du niveau en le creant s'il n'existe
pas</td>
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<span class="codelink"><a href="obitools.carto-pysrc.html#Level.__getitem__">source&nbsp;code</a></span>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getBase"></a><span class="summary-sig-name">getBase</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Level.getBase">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
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<td><span class="summary-sig"><a name="getElement"></a><span class="summary-sig-name">getElement</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Level.getElement">source&nbsp;code</a></span>
</td>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getHeight"></a><span class="summary-sig-name">getHeight</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Level.getHeight">source&nbsp;code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">level</span>,
<span class="sig-arg">map</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#Level.__init__">source&nbsp;code</a></span>&nbsp;
</td>
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<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;Map
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<!-- hide/show private -->
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Map</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#Map">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Map</strong>
</pre>
<hr />
<p>Map represente une instance d'une carte genetique physique. Une telle
carte est definie par la longueur de la sequence qui lui est associe.</p>
<p>A une carte est associe un certain nombre de niveaux (Level) eux meme
decoupe en sous-niveau (SubLevel) Les sous niveaux contiennent eux des
features</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type">&nbsp;</span>
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<tr>
<td><span class="summary-sig"><a href="obitools.carto.Map-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">seqlength</span>,
<span class="summary-sig-arg">scale</span>=<span class="summary-sig-default">1</span>)</span><br />
Constructeur d'une nouvelle carte</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.carto.Map-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
str(x)</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.__str__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">level</span>)</span><br />
retourne le niveau *level* de la carte et le cree s'il n'existe pas</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.__getitem__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getBasicHSize"></a><span class="summary-sig-name">getBasicHSize</span>(<span class="summary-sig-arg">self</span>)</span><br />
retourne la hauteur de base d'un element de cartographie exprimee en
pixel</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.getBasicHSize">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getScale"></a><span class="summary-sig-name">getScale</span>(<span class="summary-sig-arg">self</span>)</span><br />
Retourne l'echelle de la carte en nombre de pixels par unite physique
de la carte</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.getScale">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getNegativeBase"></a><span class="summary-sig-name">getNegativeBase</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.getNegativeBase">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getPositiveBase"></a><span class="summary-sig-name">getPositiveBase</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.getPositiveBase">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getHeight"></a><span class="summary-sig-name">getHeight</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.getHeight">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="toXML"></a><span class="summary-sig-name">toXML</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">begin</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">end</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#Map.toXML">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
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<td align="left"><span class="table-header">Method Details</span></td>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
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<a name="__init__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">seqlength</span>,
<span class="sig-arg">scale</span>=<span class="sig-default">1</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#Map.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<pre class="literalblock">
Constructeur d'une nouvelle carte
*Param*:
name
nom de la carte
seqlength
longueur de la sequence associee a la carte
scale
echelle de la carte indicant combien de pixel
correspondent a une unite de la carte
</pre>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#Map.__str__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>str(x)</p>
<dl class="fields">
<dt>Overrides:
object.__str__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
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<?xml version="1.0" encoding="ascii"?>
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>obitools.carto.MultiPartFeature</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
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href="obitools-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>
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<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;MultiPartFeature
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>]&nbsp;|&nbsp;<a href="obitools.carto.MultiPartFeature-class.html"
target="_top">no&nbsp;frames</a>]</span></td></tr>
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class MultiPartFeature</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#MultiPartFeature">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.carto.Feature-class.html">Feature</a> --+
|
<strong class="uidshort">MultiPartFeature</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.carto.MultiPartFeature-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">*args</span>,
<span class="summary-sig-arg">**kargs</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#MultiPartFeature.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getHeight"></a><span class="summary-sig-name">getHeight</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#MultiPartFeature.getHeight">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getElement"></a><span class="summary-sig-name">getElement</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">base</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#MultiPartFeature.getElement">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
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<td align="left"><span class="table-header">Method Details</span></td>
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><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
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</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">*args</span>,
<span class="sig-arg">**kargs</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#MultiPartFeature.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
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View File

@ -1,285 +0,0 @@
<?xml version="1.0" encoding="ascii"?>
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<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;SimpleFeature
</span>
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<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
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target="_top">no&nbsp;frames</a>]</span></td></tr>
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</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SimpleFeature</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#SimpleFeature">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.carto.Feature-class.html">Feature</a> --+
|
<strong class="uidshort">SimpleFeature</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="obitools.carto.BoxFeature-class.html">BoxFeature</a></li> </ul>
</dd></dl>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.carto.SimpleFeature-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">begin</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">visiblename</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">color</span>=<span class="summary-sig-default">0</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SimpleFeature.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getHeight"></a><span class="summary-sig-name">getHeight</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SimpleFeature.getHeight">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getElement"></a><span class="summary-sig-name">getElement</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">base</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SimpleFeature.getElement">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">begin</span>,
<span class="sig-arg">end</span>,
<span class="sig-arg">visiblename</span>=<span class="sig-default">False</span>,
<span class="sig-arg">color</span>=<span class="sig-default">0</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#SimpleFeature.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<br />
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@ -1,303 +0,0 @@
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"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>obitools.carto.SubLevel</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
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alink="#204080">
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<table class="navbar" border="0" width="100%" cellpadding="0"
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href="obitools-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>
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<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;SubLevel
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
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</td>
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</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SubLevel</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">SubLevel</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.carto.SubLevel-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sublevel</span>,
<span class="summary-sig-arg">level</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getHeight"></a><span class="summary-sig-name">getHeight</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel.getHeight">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getBase"></a><span class="summary-sig-name">getBase</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel.getBase">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getElement"></a><span class="summary-sig-name">getElement</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel.getElement">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="add"></a><span class="summary-sig-name">add</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">feature</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel.add">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
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<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sublevel</span>,
<span class="sig-arg">level</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#SubLevel.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
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View File

@ -1,281 +0,0 @@
<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>obitools.carto.TagFeature</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
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<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
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<!-- Home link -->
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<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.carto-module.html">Package&nbsp;carto</a> ::
Class&nbsp;TagFeature
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>]&nbsp;|&nbsp;<a href="obitools.carto.TagFeature-class.html"
target="_top">no&nbsp;frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class TagFeature</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.carto-pysrc.html#TagFeature">source&nbsp;code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="obitools.carto.Feature-class.html">Feature</a> --+
|
<strong class="uidshort">TagFeature</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
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<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="obitools.carto.TagFeature-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">begin</span>,
<span class="summary-sig-arg">length</span>,
<span class="summary-sig-arg">ratio</span>,
<span class="summary-sig-arg">visiblename</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">color</span>=<span class="summary-sig-default">0</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#TagFeature.__init__">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getHeight"></a><span class="summary-sig-name">getHeight</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#TagFeature.getHeight">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="getElement"></a><span class="summary-sig-name">getElement</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">base</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="obitools.carto-pysrc.html#TagFeature.getElement">source&nbsp;code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">begin</span>,
<span class="sig-arg">length</span>,
<span class="sig-arg">ratio</span>,
<span class="sig-arg">visiblename</span>=<span class="sig-default">False</span>,
<span class="sig-arg">color</span>=<span class="sig-default">0</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="obitools.carto-pysrc.html#TagFeature.__init__">source&nbsp;code</a></span>&nbsp;
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<br />
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View File

@ -1,161 +0,0 @@
<?xml version="1.0" encoding="ascii"?>
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<title>obitools.cns</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Package&nbsp;cns
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<!-- hide/show private -->
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package cns</h1><p class="nomargin-top"><span class="codelink"><a href="obitools.cns-pysrc.html">source&nbsp;code</a></span></p>
<!-- ==================== SUBMODULES ==================== -->
<a name="section-Submodules"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<td align="right" valign="top"
><span class="options">[<a href="#section-Submodules"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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<tr><td class="summary">
<ul class="nomargin">
<li> <strong class="uidlink"><a href="obitools.cns.fasta-module.html">obitools.cns.fasta</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.cns.quality-module.html">obitools.cns.quality</a></strong> </li>
</ul></td></tr>
</table>
<br />
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="cnsTag"></a><span class="summary-name">cnsTag</span> = <code title="re.compile(r'([a-zA-Z]\w*) *= *([^\s]+)')">re.compile(r'<code class="re-group">(</code><code class="re-group">[</code>a<code class="re-op">-</code>zA<code class="re-op">-</code>Z<code class="re-group">]</code>\w<code class="re-op">*</code><code class="re-group">)</code> <code class="re-op">*</code>= <code class="re-op">*</code><code class="re-group">(</code><code class="re-group">[</code><code class="re-op">^</code>\s<code class="re-group">]</code><code class="re-op">+</code><code class="re-group">)</code>')</code>
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<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'obitools.cns'"><code class="variable-quote">'</code><code class="variable-string">obitools.cns</code><code class="variable-quote">'</code></code>
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@ -1,114 +0,0 @@
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<a href="obitools-module.html">Package&nbsp;obitools</a> ::
Package&nbsp;cns
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>[<a href="frames.html" target="_top">frames</a
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<h1 class="epydoc">Source Code for <a href="obitools.cns-module.html">Package obitools.cns</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L2"></a><tt class="py-lineno">2</tt> <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno">3</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable obitools.cns.cnsTag=obitools.cns-module.html#cnsTag"><a title="obitools.cns.cnsTag" class="py-name" href="#" onclick="return doclink('link-0', 'cnsTag', 'link-0');">cnsTag</a></tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'([a-zA-Z]\w*) *= *([^\s]+)'</tt><tt class="py-op">)</tt> </tt>
<a name="L4"></a><tt class="py-lineno">4</tt> <tt class="py-line"> </tt><script type="text/javascript">
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