Commit a2967a06 by Eric Coissac

Add graph module independent with networkx

parent b9ea3426
......@@ -5,5 +5,5 @@
<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
<path>/OBITools/src</path>
</pydev_pathproperty>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.4</pydev_property>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.5</pydev_property>
</pydev_project>
......@@ -74,55 +74,151 @@
<em class="summary">The most base type</em>
<ul>
<li> <strong class="uidlink">set</strong>:
<em class="summary">set(iterable) --> set object
Build an unordered collection.</em>
<em class="summary">set(iterable) --&gt; set object</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.WrapperSet-class.html">obitools.WrapperSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.tree.Tree-class.html">obitools.tree.Tree</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.table.Table-class.html">obitools.table.Table</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.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.WrapperSetIterator-class.html">obitools.WrapperSetIterator</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.graph.Node-class.html">obitools.graph.Node</a></strong>
<ul>
<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.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>
</ul>
</li>
</ul>
</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.graph.Edge-class.html">obitools.graph.Edge</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.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.fast.Fast-class.html">obitools.fast.Fast</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.tree.TreeNode-class.html">obitools.tree.TreeNode</a></strong>
</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.BioSequence-class.html">obitools.BioSequence</a></strong>:
<em class="summary">BioSequence class is the base class for biological
sequence representation.</em>
<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>
</li>
<li> <strong class="uidlink"><a href="obitools.NucSequence-class.html">obitools.NucSequence</a></strong>
</li>
<li> <strong class="uidlink"><a href="obitools.WrappedBioSequence-class.html">obitools.WrappedBioSequence</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.fast.Fast-class.html">obitools.fast.Fast</a></strong>
<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.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>
<li> <strong class="uidlink"><a href="obitools.utils.ColumnFile-class.html">obitools.utils.ColumnFile</a></strong>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.tree.TreeNode-class.html">obitools.tree.TreeNode</a></strong>
</ul>
</li>
<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>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy.Taxonomy-class.html">obitools.ecopcr.taxonomy.Taxonomy</a></strong>
</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.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>
</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"><a href="obitools.parallel.TaskPool-class.html">obitools.parallel.TaskPool</a></strong>
</li>
<li> <strong class="uidlink">dict</strong>:
<em class="summary">dict() -> new empty dictionary.</em>
<em class="summary">dict() -&gt; new empty dictionary.</em>
<ul>
<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.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.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">list</strong>:
<em class="summary">list() -> new list...</em>
<ul>
<li> <strong class="uidlink"><a href="obitools.align.Alignement-class.html">obitools.align.Alignement</a></strong>
</li>
</ul>
</li>
</ul>
</li>
</ul>
......@@ -158,7 +254,7 @@ sequence representation.</em>
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:42 2007</a>
3.0beta1 on Wed Dec 5 14:21:29 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -257,7 +257,7 @@ page was last updated. </p>
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:42 2007</a>
3.0beta1 on Wed Dec 5 14:21:29 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
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......@@ -62,18 +62,77 @@
<ul class="nomargin-top">
<li> <strong class="uidlink"><a href="obitools-module.html">obitools</a></strong>
<ul>
<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong>
<ul>
<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.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.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.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.ecopcr-module.html">obitools.ecopcr</a></strong>
<ul>
<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.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> </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.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.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.obischemas-module.html">obitools.obischemas</a></strong>
<ul>
<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.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.bioseqfilter-module.html">obitools.options.bioseqfilter</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.sequenceencoder-module.html">obitools.sequenceencoder</a></strong> </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.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>
......@@ -119,7 +178,7 @@ an alignment.</em> </li>
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:42 2007</a>
3.0beta1 on Wed Dec 5 14:21:29 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -79,18 +79,77 @@
</tr>
<tr><td class="summary">
<ul class="nomargin">
<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong> </li>
<li> <strong class="uidlink"><a href="obitools.align-module.html">obitools.align</a></strong>
<ul>
<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.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.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.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.ecopcr-module.html">obitools.ecopcr</a></strong>
<ul>
<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.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> </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.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.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.obischemas-module.html">obitools.obischemas</a></strong>
<ul>
<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.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.bioseqfilter-module.html">obitools.options.bioseqfilter</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.sequenceencoder-module.html">obitools.sequenceencoder</a></strong> </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.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>
......@@ -126,9 +185,23 @@ an alignment.</em> </li>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">&nbsp;</span>
</td><td class="summary">
<a href="obitools.WrapperSetIterator-class.html" class="summary-name">WrapperSetIterator</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.WrapperSet-class.html" class="summary-name">WrapperSet</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" class="summary-name">BioSequence</a><br />
BioSequence class is the base class for biological
sequence representation.
BioSequence class is the base class for biological sequence
representation.
</td>
</tr>
<tr>
......@@ -145,6 +218,13 @@ sequence representation.
<a href="obitools.AASequence-class.html" class="summary-name">AASequence</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.WrappedBioSequence-class.html" class="summary-name">WrappedBioSequence</a>
</td>
</tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
......@@ -231,7 +311,7 @@ sequence representation.
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:42 2007</a>
3.0beta1 on Wed Dec 5 14:21:29 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -61,6 +61,30 @@
</table>
<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package align</h1><span class="codelink"><a href="obitools.align-pysrc.html">source&nbsp;code</a></span><br /><br />
<!-- ==================== SUBMODULES ==================== -->
<a name="section-Submodules"></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">Submodules</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Submodules"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr><td class="summary">
<ul class="nomargin">
<li> <strong class="uidlink"><a href="obitools.align.ssearch-module.html">obitools.align.ssearch</a></strong> </li>
</ul></td></tr>
</table>
<br />
<!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
<table class="summary" border="1" cellpadding="3"
......@@ -153,7 +177,7 @@
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:42 2007</a>
3.0beta1 on Wed Dec 5 14:21:29 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -80,8 +80,11 @@
<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" 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__"><a title="obitools.BioSequence.__setitem__
obitools.align.Alignement.__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>
<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.graph.Edge.__setitem__()=obitools.graph.Edge-class.html#__setitem__,Method obitools.graph.Node.__setitem__()=obitools.graph.Node-class.html#__setitem__,Method obitools.table.Table.__setitem__()=obitools.table.Table-class.html#__setitem__"><a title="obitools.BioSequence.__setitem__
obitools.align.Alignement.__setitem__
obitools.graph.Edge.__setitem__
obitools.graph.Node.__setitem__
obitools.table.Table.__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>
......@@ -96,8 +99,10 @@ obitools.align.Alignement.__setitem__" class="py-name" href="#" onclick="return
<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-9" class="py-name" targets="Class obitools.align.Alignement=obitools.align.Alignement-class.html"><a title="obitools.align.Alignement" class="py-name" href="#" onclick="return doclink('link-9', 'Alignement', 'link-9');">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-10" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-10', '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="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-10" class="py-name" targets="Variable obitools.BioSequence.seq=obitools.BioSequence-class.html#seq,Variable obitools.WrappedBioSequence.seq=obitools.WrappedBioSequence-class.html#seq"><a title="obitools.BioSequence.seq
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-10', 'seq', 'link-10');">seq</a></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-11" class="py-name"><a title="obitools.align.Alignement.append" class="py-name" href="#" onclick="return doclink('link-11', 'append', 'link-4');">append</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="obitools.BioSequence.seq
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-12', 'seq', 'link-10');">seq</a></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">
<!--
......@@ -138,7 +143,7 @@ expandto(location.href);
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:39:01 2007</a>
3.0beta1 on Wed Dec 5 14:21:41 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -63,22 +63,22 @@
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Alignement</h1><span class="codelink"><a href="obitools.align-pysrc.html#Alignement">source&nbsp;code</a></span><br /><br />
<center>
<center> <map id="uml_class_diagram_for_obitools_4" name="uml_class_diagram_for_obitools_4">
<center> <map id="uml_class_diagram_for_obitools_7" name="uml_class_diagram_for_obitools_7">
<area shape="rect" href="obitools.align.Alignement&#45;class.html" title="obitools.align.Alignement" alt="" coords="16,347,232,467"/>
<area shape="rect" href="obitools.align.Alignement&#45;class.html#isFullGapSite" title="obitools.align.Alignement.isFullGapSite" alt="" coords="17,372,231,391"/>
<area shape="rect" href="obitools.align.Alignement&#45;class.html#getSite" title="obitools.align.Alignement.getSite" alt="" coords="17,391,231,409"/>
<area shape="rect" href="obitools.align.Alignement&#45;class.html#append" title="append object to end" alt="" coords="17,409,231,428"/>
<area shape="rect" href="obitools.align.Alignement&#45;class.html#isGappedSite" title="obitools.align.Alignement.isGappedSite" alt="" coords="17,428,231,447"/>
<area shape="rect" href="obitools.align.Alignement&#45;class.html#__setitem__" title="x[i]=y" alt="" coords="17,447,231,465"/>
<area shape="rect" href="javascript: void(0);" title="list() &#45;&gt; new list..." alt="" coords="52,11,196,317"/>
<area shape="rect" href="javascript: void(0);" title="x[i:j] Use of negative indices is not supported." alt="" coords="53,36,195,55"/>
<area shape="rect" href="javascript: void(0);" title="list() &#45;&gt; new list list(sequence) &#45;&gt; new list initialized from sequence&#39;s items" alt="" coords="52,11,196,317"/>
<area shape="rect" href="javascript: void(0);" title="x[i:j]" alt="" coords="53,36,195,55"/>
<area shape="rect" href="javascript: void(0);" title="x.__getattribute__(&#39;name&#39;) &lt;==&gt; x.name" alt="" coords="53,55,195,73"/>
<area shape="rect" href="javascript: void(0);" title="remove and return item at index (default last)" alt="" coords="53,73,195,92"/>
<area shape="rect" href="javascript: void(0);" title="x+=y" alt="" coords="53,92,195,111"/>
<area shape="rect" href="javascript: void(0);" title="n*x" alt="" coords="53,111,195,129"/>
<area shape="rect" href="javascript: void(0);" title="x&lt;y" alt="" coords="53,129,195,148"/>
<area shape="rect" href="javascript: void(0);" title="L.index(value, [start, [stop]]) &#45;&gt; integer &#45;&#45; return first index of value" alt="" coords="53,148,195,167"/>
<area shape="rect" href="javascript: void(0);" title="del x[i:j] Use of negative indices is not supported." alt="" coords="53,167,195,185"/>
<area shape="rect" href="javascript: void(0);" title="del x[i:j]" alt="" coords="53,167,195,185"/>
<area shape="rect" href="javascript: void(0);" title="Returns: a new object with type S, a subtype of T" alt="" coords="53,185,195,204"/>
<area shape="rect" href="javascript: void(0);" title="y in x" alt="" coords="53,204,195,223"/>
<area shape="rect" href="javascript: void(0);" title="x.__init__(...) initializes x; see x.__class__.__doc__ for signature" alt="" coords="53,223,195,241"/>
......@@ -86,7 +86,7 @@
<area shape="rect" href="javascript: void(0);" title="repr(x)" alt="" coords="53,260,195,279"/>
<area shape="rect" href="javascript: void(0);" title="x&gt;=y" alt="" coords="53,297,195,316"/>
</map>
<img src="uml_class_diagram_for_obitools_4.png" alt='' usemap="#uml_class_diagram_for_obitools_4" ismap="ismap" class="graph-without-title" />
<img src="uml_class_diagram_for_obitools_7.gif" alt='' usemap="#uml_class_diagram_for_obitools_7" ismap="ismap" class="graph-without-title" />
</center></center>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
......@@ -384,7 +384,7 @@
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:53 2007</a>
3.0beta1 on Wed Dec 5 14:21:31 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -80,8 +80,8 @@
</tr>
<tr><td class="summary">
<ul class="nomargin">
<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.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></td></tr>
......@@ -145,7 +145,7 @@ an alignment.</em> </li>
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:38:42 2007</a>
3.0beta1 on Wed Dec 5 14:21:29 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -86,7 +86,8 @@
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">y</tt><tt class="py-op">=</tt><tt class="py-name">z</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matrix</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">x</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">if</tt> <tt class="py-name">rep</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</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">rep</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method obitools.distances.DistanceMatrix.evaluateDist()=obitools.distances.DistanceMatrix-class.html#evaluateDist,Method obitools.distances.observed.PairewiseGapRemoval.evaluateDist()=obitools.distances.observed.PairewiseGapRemoval-class.html#evaluateDist"><a title="obitools.distances.DistanceMatrix.evaluateDist
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method obitools.distances.DistanceMatrix.evaluateDist()=obitools.distances.DistanceMatrix-class.html#evaluateDist,Method obitools.distances.observed.Pairewise.evaluateDist()=obitools.distances.observed.Pairewise-class.html#evaluateDist,Method obitools.distances.observed.PairewiseGapRemoval.evaluateDist()=obitools.distances.observed.PairewiseGapRemoval-class.html#evaluateDist"><a title="obitools.distances.DistanceMatrix.evaluateDist
obitools.distances.observed.Pairewise.evaluateDist
obitools.distances.observed.PairewiseGapRemoval.evaluateDist" class="py-name" href="#" onclick="return doclink('link-0', 'evaluateDist', 'link-0');">evaluateDist</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>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matrix</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">x</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">rep</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> </tt>
......@@ -130,7 +131,7 @@ expandto(location.href);
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Fri Jun 29 14:39:01 2007</a>
3.0beta1 on Wed Dec 5 14:21:40 2007</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
......
......@@ -63,14 +63,15 @@
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DistanceMatrix</h1><span class="codelink"><a href="obitools.distances-pysrc.html#DistanceMatrix">source&nbsp;code</a></span><br /><br />
<center>
<center> <map id="uml_class_diagram_for_obitools_5" name="uml_class_diagram_for_obitools_5">
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html" title="obitools.distances.DistanceMatrix" alt="" coords="51,11,227,93"/>
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html#__getitem__" title="obitools.distances.DistanceMatrix.__getitem__" alt="" coords="52,36,225,55"/>
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html#evaluateDist" title="obitools.distances.DistanceMatrix.evaluateDist" alt="" coords="52,55,225,73"/>
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html#__init__" title="DistanceMatrix constructor." alt="" coords="52,73,225,92"/>
<area shape="rect" href="obitools.distances.observed.PairewiseGapRemoval&#45;class.html" title="Observed divergeance matrix from an alignment." alt="" coords="16,123,261,149"/>
<center> <map id="uml_class_diagram_for_obitools_9" name="uml_class_diagram_for_obitools_9">
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html" title="obitools.distances.DistanceMatrix" alt="" coords="128,11,304,93"/>
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html#__getitem__" title="obitools.distances.DistanceMatrix.__getitem__" alt="" coords="129,36,303,55"/>
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html#evaluateDist" title="obitools.distances.DistanceMatrix.evaluateDist" alt="" coords="129,55,303,73"/>
<area shape="rect" href="obitools.distances.DistanceMatrix&#45;class.html#__init__" title="DistanceMatrix constructor." alt="" coords="129,73,303,92"/>
<area shape="rect" href="obitools.distances.observed.Pairewise&#45;class.html" title="Observed divergeance matrix from an alignment." alt="" coords="16,123,168,149"/>
<area shape="rect" href="obitools.distances.observed.PairewiseGapRemoval&#45;class.html" title="Observed divergeance matrix from an alignment." alt="" coords="219,123,464,149"/>
</map>
<img src="uml_class_diagram_for_obitools_5.png" alt='' usemap="#uml_class_diagram_for_obitools_5" ismap="ismap" class="graph-without-title" />
<img src="uml_class_diagram_for_obitools_9.gif" alt='' usemap="#uml_class_diagram_for_obitools_9" ismap="ismap" class="graph-without-title" />
</center></center>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
......@@ -218,12 +219,10 @@
</td>
</table>
DistanceMatrix constructor.
<p>DistanceMatrix constructor.</p>
@param alignment aligment used to compute distance matrix @type
alignment obitools.align.Alignment
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>alignment</code></strong> (obitools.align.Alignment) - aligment used to compute distance matrix</li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
......@@ -263,7 +262,7 @@
<tr>
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