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New version of the api documentation

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Eric Coissac
2008-04-15 16:58:36 +00:00
parent eabe06f11b
commit 82e1778714
518 changed files with 21841 additions and 3878 deletions
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@ -81,24 +81,10 @@
<li> <strong class="uidlink">dict</strong>:
<em class="summary">dict() -&gt; new empty dictionary.</em>
<ul>
<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.location.feature.Feature-class.html">obitools.location.feature.Feature</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.TrailingModifier-class.html">obitools.obo.parser.TrailingModifier</a></strong>
</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.tree.layout.TreeLayout-class.html">obitools.tree.layout.TreeLayout</a></strong>:
<em class="summary">Description of a phylogenetic tree layout</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>
@ -107,16 +93,71 @@
</li>
</ul>
</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.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.location.feature.Feature-class.html">obitools.location.feature.Feature</a></strong>
</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.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.ecopcr.EcoPCRDBFile-class.html">obitools.ecopcr.EcoPCRDBFile</a></strong>
<li> <strong class="uidlink"><a href="obitools.distances.DistanceMatrix-class.html">obitools.distances.DistanceMatrix</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html">obitools.ecopcr.sequence.ecoPCRDBSequenceIterator</a></strong>
<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.ecopcr.taxonomy.Taxonomy-class.html">obitools.ecopcr.taxonomy.Taxonomy</a></strong>
<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.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.seqdb.genbank.graph.Edge-class.html">obitools.seqdb.genbank.graph.Edge</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.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.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.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.XrefValue-class.html">obitools.obo.parser.XrefValue</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.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.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.NamespaceValue-class.html">obitools.obo.parser.NamespaceValue</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.RemarkValue-class.html">obitools.obo.parser.RemarkValue</a></strong>
</li>
</ul>
</li>
@ -130,29 +171,77 @@
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.table.UnionIterator-class.html">obitools.table.UnionIterator</a></strong>
<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.TableIterator-class.html">obitools.table.TableIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.blast.BlastResultIterator-class.html">obitools.blast.BlastResultIterator</a></strong>
<li> <strong class="uidlink"><a href="obitools.table.UnionIterator-class.html">obitools.table.UnionIterator</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.graph.Edge-class.html">obitools.graph.Edge</a></strong>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedSequence-class.html">obitools.seqdb.AnnotatedSequence</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.phylogeny.PhylogenicEdge-class.html">obitools.phylogeny.PhylogenicEdge</a></strong>
<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.genbank.graph.Node-class.html">obitools.seqdb.genbank.graph.Node</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.distances.DistanceMatrix-class.html">obitools.distances.DistanceMatrix</a></strong>
<li> <strong class="uidlink"><a href="obitools.seqdb.AnnotatedNucSequence-class.html">obitools.seqdb.AnnotatedNucSequence</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> <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>
<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>
</ul>
</li>
</ul>
</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">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>
@ -180,65 +269,24 @@
</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.parallel.jobqueue.JobIterator-class.html">obitools.parallel.jobqueue.JobIterator</a></strong>
</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.Complement-class.html">obitools.sequenceencoder.Complement</a></strong>
</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.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>
</ul>
</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.NameValue-class.html">obitools.obo.parser.NameValue</a></strong>
<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.obo.parser.SynonymValue-class.html">obitools.obo.parser.SynonymValue</a></strong>:
<em class="summary">A couple 'synonym:value' derived from the class TaggedValue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.RelationshipValue-class.html">obitools.obo.parser.RelationshipValue</a></strong>
</li>
<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' derived from the class TaggedValue.</em>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.XrefValue-class.html">obitools.obo.parser.XrefValue</a></strong>
</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.NamespaceValue-class.html">obitools.obo.parser.NamespaceValue</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.obo.parser.Xref-class.html">obitools.obo.parser.Xref</a></strong>
</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.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> <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.location.Location-class.html">obitools.location.Location</a></strong>:
<em class="summary">Define a location on a sequence.</em>
@ -259,16 +307,16 @@
</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.blast.Blast-class.html">obitools.blast.Blast</a></strong>:
<em class="summary">Run blast</em>
<li> <strong class="uidlink"><a href="obitools.graph.Edge-class.html">obitools.graph.Edge</a></strong>
<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> <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.parallel.TaskPool-class.html">obitools.parallel.TaskPool</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.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>
@ -285,50 +333,15 @@
</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.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.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> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag.DAGNode-class.html">obitools.seqdb.genbank.graph.dag.DAGNode</a></strong>
</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.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> <strong class="uidlink"><a href="obitools.utils.CachedDB-class.html">obitools.utils.CachedDB</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.Task-class.html">obitools.parallel.Task</a></strong>
</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> <strong class="uidlink"><a href="obitools.align.ssearch.SsearchParser-class.html">obitools.align.ssearch.SsearchParser</a></strong>
</li>
<li> <strong class="uidlink">set</strong>:
<em class="summary">set(iterable) --&gt; set object</em>
@ -339,6 +352,8 @@
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue.JobIterator-class.html">obitools.parallel.jobqueue.JobIterator</a></strong>
</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>
@ -353,12 +368,14 @@
</li>
<li> <strong class="uidlink"><a href="obitools.table._Row-class.html">obitools.table._Row</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.align.Alignement-class.html">obitools.align.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.align.Alignement-class.html">obitools.align.Alignement</a></strong>
</li>
</ul>
</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.WrapperSetIterator-class.html">obitools.WrapperSetIterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.BioSequence-class.html">obitools.BioSequence</a></strong>:
@ -393,9 +410,27 @@
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.utils.CachedDB-class.html">obitools.utils.CachedDB</a></strong>
<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>
</li>
<li> <strong class="uidlink"><a href="obitools.table.TableIteratorAsDict-class.html">obitools.table.TableIteratorAsDict</a></strong>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy.Taxonomy-class.html">obitools.ecopcr.taxonomy.Taxonomy</a></strong>
</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.table.TableRow-class.html">obitools.table.TableRow</a></strong>
<ul>
@ -404,45 +439,16 @@
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.align.ssearch.SsearchParser-class.html">obitools.align.ssearch.SsearchParser</a></strong>
<li> <strong class="uidlink"><a href="obitools.tree.TreeNode-class.html">obitools.tree.TreeNode</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>
<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.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> <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.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.parallel.TaskPool-class.html">obitools.parallel.TaskPool</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.parallel.jobqueue.Job-class.html">obitools.parallel.jobqueue.Job</a></strong>
</li>
</ul>
</li>
</ul>
@ -478,7 +484,7 @@
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Tue Apr 15 18:30:34 2008</a>
3.0beta1 on Tue Apr 15 18:53:30 2008</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>

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