759 lines
42 KiB
HTML
759 lines
42 KiB
HTML
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<center><b>
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[ <a href="module-tree.html">Module Hierarchy</a>
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| <a href="class-tree.html">Class Hierarchy</a> ]
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</b></center><br />
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<h1 class="epydoc">Class Hierarchy</h1>
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<ul class="nomargin-top">
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<li> <strong class="uidlink"><a href="obitools.alignment.AlignedSequence-class.html">obitools.alignment.AlignedSequence</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.svg.Circle-class.html">obitools.svg.Circle</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.gzip.GzipFile-class.html">obitools.gzip.GzipFile</a></strong>:
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<em class="summary">The GzipFile class simulates most of the methods of a file object
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with the exception of the readinto() and truncate() methods.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.svg.Line-class.html">obitools.svg.Line</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.svg.Rectangle-class.html">obitools.svg.Rectangle</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.SVGelement-class.html">obitools.SVGdraw.SVGelement</a></strong>:
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<em class="summary">SVGelement(type,attributes,elements,text,namespace,**args) Creates
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a arbitrary svg element and is intended to be subclassed not used
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on its own.</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.animate-class.html">obitools.SVGdraw.animate</a></strong>:
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<em class="summary">an=animate(attribute,from,to,during,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.animateColor-class.html">obitools.SVGdraw.animateColor</a></strong>:
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<em class="summary">ac=animateColor(attribute,type,from,to,dur,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.animateMotion-class.html">obitools.SVGdraw.animateMotion</a></strong>:
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<em class="summary">an=animateMotion(pathdata,dur,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.animateTransform-class.html">obitools.SVGdraw.animateTransform</a></strong>:
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<em class="summary">antr=animateTransform(type,from,to,dur,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.circle-class.html">obitools.SVGdraw.circle</a></strong>:
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<em class="summary">c=circle(x,y,radius,fill,stroke,stroke_width,**args)</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.point-class.html">obitools.SVGdraw.point</a></strong>:
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<em class="summary">p=point(x,y,color)</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.cursor-class.html">obitools.SVGdraw.cursor</a></strong>:
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<em class="summary">c=cursor(url,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.defs-class.html">obitools.SVGdraw.defs</a></strong>:
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<em class="summary">d=defs(**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.description-class.html">obitools.SVGdraw.description</a></strong>:
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<em class="summary">d=description(text,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.ellipse-class.html">obitools.SVGdraw.ellipse</a></strong>:
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<em class="summary">e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.group-class.html">obitools.SVGdraw.group</a></strong>:
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<em class="summary">g=group(id,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.image-class.html">obitools.SVGdraw.image</a></strong>:
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<em class="summary">im=image(url,width,height,x,y,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.line-class.html">obitools.SVGdraw.line</a></strong>:
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<em class="summary">l=line(x1,y1,x2,y2,stroke,stroke_width,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.lineargradient-class.html">obitools.SVGdraw.lineargradient</a></strong>:
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<em class="summary">lg=lineargradient(x1,y1,x2,y2,id,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.link-class.html">obitools.SVGdraw.link</a></strong>:
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<em class="summary">a=link(url,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.marker-class.html">obitools.SVGdraw.marker</a></strong>:
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<em class="summary">m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.path-class.html">obitools.SVGdraw.path</a></strong>:
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<em class="summary">p=path(path,fill,stroke,stroke_width,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.pattern-class.html">obitools.SVGdraw.pattern</a></strong>:
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<em class="summary">p=pattern(x,y,width,height,patternUnits,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.polygon-class.html">obitools.SVGdraw.polygon</a></strong>:
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<em class="summary">pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.polyline-class.html">obitools.SVGdraw.polyline</a></strong>:
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<em class="summary">pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.radialgradient-class.html">obitools.SVGdraw.radialgradient</a></strong>:
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<em class="summary">rg=radialgradient(cx,cy,r,fx,fy,id,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.rect-class.html">obitools.SVGdraw.rect</a></strong>:
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<em class="summary">r=rect(width,height,x,y,fill,stroke,stroke_width,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.script-class.html">obitools.SVGdraw.script</a></strong>:
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<em class="summary">sc=script(type,type,cdata,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.set-class.html">obitools.SVGdraw.set</a></strong>:
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<em class="summary">st=set(attribute,to,during,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.stop-class.html">obitools.SVGdraw.stop</a></strong>:
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<em class="summary">st=stop(offset,stop_color,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.style-class.html">obitools.SVGdraw.style</a></strong>:
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<em class="summary">st=style(type,cdata=None,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.svg-class.html">obitools.SVGdraw.svg</a></strong>:
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<em class="summary">s=svg(viewbox,width,height,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.switch-class.html">obitools.SVGdraw.switch</a></strong>:
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<em class="summary">sw=switch(**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.symbol-class.html">obitools.SVGdraw.symbol</a></strong>:
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<em class="summary">sy=symbol(id,viewbox,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.text-class.html">obitools.SVGdraw.text</a></strong>:
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<em class="summary">t=text(x,y,text,font_size,font_family,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.textpath-class.html">obitools.SVGdraw.textpath</a></strong>:
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<em class="summary">tp=textpath(text,link,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.title-class.html">obitools.SVGdraw.title</a></strong>:
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<em class="summary">t=title(text,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.tref-class.html">obitools.SVGdraw.tref</a></strong>:
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<em class="summary">tr=tref(link='',**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.tspan-class.html">obitools.SVGdraw.tspan</a></strong>:
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<em class="summary">ts=tspan(text='',**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.use-class.html">obitools.SVGdraw.use</a></strong>:
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<em class="summary">u=use(link,x,y,width,height,**args)</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.view-class.html">obitools.SVGdraw.view</a></strong>:
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<em class="summary">v=view(id,**args)</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.svg.Scene-class.html">obitools.svg.Scene</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.svg.Text-class.html">obitools.svg.Text</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.zipfile.ZipExtFile-class.html" onclick="show_private();">obitools.zipfile.ZipExtFile</a></strong>:
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<em class="summary">File-like object for reading an archive member.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.zipfile.ZipFile-class.html">obitools.zipfile.ZipFile</a></strong>:
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<em class="summary">Class with methods to open, read, write, close, list zip files.</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.zipfile.PyZipFile-class.html">obitools.zipfile.PyZipFile</a></strong>:
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<em class="summary">Class to create ZIP archives with Python library files and
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packages.</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.zipfile._ZipDecrypter-class.html" onclick="show_private();">obitools.zipfile._ZipDecrypter</a></strong>:
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<em class="summary">Class to handle decryption of files stored within a ZIP archive.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SVGdraw.drawing-class.html">obitools.SVGdraw.drawing</a></strong>:
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<em class="summary">d=drawing()</em>
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</li>
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<li> <strong class="uidlink">object</strong>:
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<em class="summary">The most base type</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedSequence-class.html">obitools.seqdb.AnnotatedSequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedAASequence-class.html">obitools.seqdb.AnnotatedAASequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GpepSequence-class.html">obitools.seqdb.genbank.GpepSequence</a></strong>:
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<em class="summary">Class used to represent a peptidic sequence issued from Genpep.</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedNucSequence-class.html">obitools.seqdb.AnnotatedNucSequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.embl.EmblSequence-class.html">obitools.seqdb.embl.EmblSequence</a></strong>:
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<em class="summary">Class used to represent a nucleic sequence issued from EMBL.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GbSequence-class.html">obitools.seqdb.genbank.GbSequence</a></strong>:
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<em class="summary">Class used to represent a nucleic sequence issued from Genbank.</em>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink">exceptions.BaseException</strong>:
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<em class="summary">Common base class for all exceptions</em>
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<ul>
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<li> <strong class="uidlink">exceptions.Exception</strong>:
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<em class="summary">Common base class for all non-exit exceptions.</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.zipfile.BadZipfile-class.html">obitools.zipfile.BadZipfile</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.obo.parser.FileFormatError-class.html">obitools.obo.parser.FileFormatError</a></strong>:
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<em class="summary">An error derived from the class Exception.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.zipfile.LargeZipFile-class.html">obitools.zipfile.LargeZipFile</a></strong>:
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<em class="summary">Raised when writing a zipfile, the zipfile requires ZIP64
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extensions and those extensions are disabled.</em>
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</li>
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<li> <strong class="uidlink">exceptions.StandardError</strong>:
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<em class="summary">Base class for all standard Python exceptions that do not represent
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interpreter exiting.</em>
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<ul>
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<li> <strong class="uidlink"><a href="exceptions.AssertionError-class.html">exceptions.AssertionError</a></strong>:
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<em class="summary">Assertion failed.</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.dnaparser.UnknownFormatError-class.html">obitools.seqdb.dnaparser.UnknownFormatError</a></strong>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.BioSequence-class.html">obitools.BioSequence</a></strong>:
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<em class="summary">BioSequence class is the base class for biological sequence
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representation.</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.AASequence-class.html">obitools.AASequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedAASequence-class.html">obitools.seqdb.AnnotatedAASequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GpepSequence-class.html">obitools.seqdb.genbank.GpepSequence</a></strong>:
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<em class="summary">Class used to represent a peptidic sequence issued from Genpep.</em>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.NucSequence-class.html">obitools.NucSequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedNucSequence-class.html">obitools.seqdb.AnnotatedNucSequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.seqdb.embl.EmblSequence-class.html">obitools.seqdb.embl.EmblSequence</a></strong>:
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<em class="summary">Class used to represent a nucleic sequence issued from EMBL.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.GbSequence-class.html">obitools.seqdb.genbank.GbSequence</a></strong>:
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<em class="summary">Class used to represent a nucleic sequence issued from Genbank.</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.solexa.SolexaSequence-class.html">obitools.solexa.SolexaSequence</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.tagmatcher.TagMatcherSequence-class.html">obitools.tagmatcher.TagMatcherSequence</a></strong>:
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<em class="summary">Class used to represent a nucleic sequence issued mapped on a
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genome by the tagMatcher software.</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.WrappedBioSequence-class.html">obitools.WrappedBioSequence</a></strong>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.DNAComplementSequence-class.html">obitools.DNAComplementSequence</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.align.homopolymere.HomoNucBioSeq-class.html">obitools.align.homopolymere.HomoNucBioSeq</a></strong>:
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<em class="summary">classdocs</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.SubSequence-class.html">obitools.SubSequence</a></strong>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.blast.Blast-class.html">obitools.blast.Blast</a></strong>:
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<em class="summary">Run blast</em>
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<ul>
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<li> <strong class="uidlink"><a href="obitools.blast.NetBlast-class.html">obitools.blast.NetBlast</a></strong>:
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<em class="summary">Run blast on ncbi servers</em>
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</li>
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</ul>
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</li>
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<li> <strong class="uidlink"><a href="obitools.utils.CachedDB-class.html">obitools.utils.CachedDB</a></strong>
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</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() -> new empty dictionary.</em>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.ecotag.EcoTagResult-class.html">obitools.ecotag.EcoTagResult</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.location.feature.Feature-class.html">obitools.location.feature.Feature</a></strong>
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</li>
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<li> <strong class="uidlink"><a href="obitools.graph.Indexer-class.html">obitools.graph.Indexer</a></strong>:
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<em class="summary">Allow to manage convertion between an arbitrarly hashable python
|
|
value and an unique integer key</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.Indexer-class.html">obitools.seqdb.genbank.graph.Indexer</a></strong>:
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<em class="summary">Allow to manage convertion between an arbitrarly hashable python
|
|
value and an unique integer key</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue.JobPool-class.html">obitools.parallel.jobqueue.JobPool</a></strong>:
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<em class="summary">JobPool is dedicated to manage a job queue.</em>
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</li>
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<li> <strong class="uidlink"><a href="obitools.tree.layout.NodeLayout-class.html">obitools.tree.layout.NodeLayout</a></strong>:
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<em class="summary">Layout data associated to a tree node.</em>
|
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</li>
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|
<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>
|
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</ul>
|
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</li>
|
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<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() -> new list list(sequence) -> 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) --> 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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