315 lines
17 KiB
HTML
315 lines
17 KiB
HTML
<?xml version="1.0" encoding="ascii"?>
|
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
"DTD/xhtml1-transitional.dtd">
|
|
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
<head>
|
|
<title>Module Hierarchy</title>
|
|
<link rel="stylesheet" href="epydoc.css" type="text/css" />
|
|
<script type="text/javascript" src="epydoc.js"></script>
|
|
</head>
|
|
|
|
<body bgcolor="white" text="black" link="blue" vlink="#204080"
|
|
alink="#204080">
|
|
<!-- ==================== NAVIGATION BAR ==================== -->
|
|
<table class="navbar" border="0" width="100%" cellpadding="0"
|
|
bgcolor="#a0c0ff" cellspacing="0">
|
|
<tr valign="middle">
|
|
<!-- Home link -->
|
|
<th> <a
|
|
href="obitools-module.html">Home</a> </th>
|
|
|
|
<!-- Tree link -->
|
|
<th bgcolor="#70b0f0" class="navbar-select"
|
|
> Trees </th>
|
|
|
|
<!-- Index link -->
|
|
<th> <a
|
|
href="identifier-index.html">Indices</a> </th>
|
|
|
|
<!-- Help link -->
|
|
<th> <a
|
|
href="help.html">Help</a> </th>
|
|
|
|
<!-- Project homepage -->
|
|
<th class="navbar" align="right" width="100%">
|
|
<table border="0" cellpadding="0" cellspacing="0">
|
|
<tr><th class="navbar" align="center"
|
|
><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
|
|
</tr></table></th>
|
|
</tr>
|
|
</table>
|
|
<table width="100%" cellpadding="0" cellspacing="0">
|
|
<tr valign="top">
|
|
<td width="100%"> </td>
|
|
<td>
|
|
<table cellpadding="0" cellspacing="0">
|
|
<!-- hide/show private -->
|
|
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
|
|
onclick="toggle_private();">hide private</a>]</span></td></tr>
|
|
<tr><td align="right"><span class="options"
|
|
>[<a href="frames.html" target="_top">frames</a
|
|
>] | <a href="module-tree.html"
|
|
target="_top">no frames</a>]</span></td></tr>
|
|
</table>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<center><b>
|
|
[ <a href="module-tree.html">Module Hierarchy</a>
|
|
| <a href="class-tree.html">Class Hierarchy</a> ]
|
|
</b></center><br />
|
|
<h1 class="epydoc">Module Hierarchy</h1>
|
|
<ul class="nomargin-top">
|
|
<li> <strong class="uidlink"><a href="obitools-module.html">obitools</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.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.alignment-module.html">obitools.alignment</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.alignment.ace-module.html">obitools.alignment.ace</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.blast-module.html">obitools.blast</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.cns-module.html">obitools.cns</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.cns.fasta-module.html">obitools.cns.fasta</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.cns.quality-module.html">obitools.cns.quality</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.decorator-module.html">obitools.decorator</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.distances-module.html">obitools.distances</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.distances.observed-module.html">obitools.distances.observed</a></strong>: <em class="summary">Module dedicated to compute observed divergeances from an
|
|
alignment.</em> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.distances.phylip-module.html">obitools.distances.phylip</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.distances.r-module.html">obitools.distances.r</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.dnahash-module.html">obitools.dnahash</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.ecopcr-module.html">obitools.ecopcr</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.ecopcr.sequence-module.html">obitools.ecopcr.sequence</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.ecopcr.taxonomy-module.html">obitools.ecopcr.taxonomy</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.eutils-module.html">obitools.eutils</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.fast-module.html">obitools.fast</a></strong>: <em class="summary">implement fastn/fastp sililarity search algorithm for
|
|
BioSequence.</em> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.fasta-module.html">obitools.fasta</a></strong>: <em class="summary">fasta module provides functions to read and write sequences in
|
|
fasta format.</em> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.format-module.html">obitools.format</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.format.genericparser-module.html">obitools.format.genericparser</a></strong>: <em class="summary"><center><table border="0" cellpadding="0" cellspacing="0"
|
|
class="graph">
|
|
<tr><td align="center">
|
|
<map id="package_tree_for_format" name="package_tree_for_format">
|
|
<area shape="rect"
|
|
href="obitools.format.genericparser-module.html"
|
|
title="obitools.format.genericparser" alt=""
|
|
coords="25,76,117,119"/>
|
|
<area shape="rect"
|
|
href="obitools.format.ontology.obo-module.html"
|
|
title="obitools.format.ontology.obo" alt=""
|
|
coords="135,88,268,110"/>
|
|
<area shape="rect" href="obitools.format.ontology-module.html"
|
|
title="obitools.format.ontology" alt="" coords="125,55,277,119"/>
|
|
<area shape="rect"
|
|
href="obitools.format.sequence.fasta-module.html"
|
|
title="obitools.format.sequence.fasta" alt=""
|
|
coords="295,88,349,110"/>
|
|
<area shape="rect"
|
|
href="obitools.format.sequence.genbank-module.html"
|
|
title="obitools.format.sequence.genbank" alt=""
|
|
coords="357,88,435,110"/>
|
|
<area shape="rect" href="obitools.format.sequence-module.html"
|
|
title="obitools.format.sequence" alt="" coords="285,55,444,119"/>
|
|
<area shape="rect" href="obitools.format-module.html"
|
|
title="obitools.format" alt="" coords="16,22,453,128"/>
|
|
<area shape="rect" href="obitools.format-module.html"
|
|
title="obitools.format" alt="" coords="16,11,453,128"/>
|
|
</map>
|
|
<img src="package_tree_for_format.gif" alt='Package Tree for
|
|
format' usemap="#package_tree_for_format" ismap="ismap"
|
|
class="graph-with-title" />
|
|
</td></tr>
|
|
<tr><td align='center'>
|
|
<span class="graph-title">Package Tree for format</span>
|
|
</td></tr>
|
|
</table><br/></center></em> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.format.ontology-module.html">obitools.format.ontology</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.format.ontology.obo-module.html">obitools.format.ontology.obo</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.format.sequence-module.html">obitools.format.sequence</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.format.sequence.fasta-module.html">obitools.format.sequence.fasta</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.format.sequence.genbank-module.html">obitools.format.sequence.genbank</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.graph-module.html">obitools.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.graph.algorithms-module.html">obitools.graph.algorithms</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.clique-module.html">obitools.graph.algorithms.clique</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.graph.algorithms.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.gzip-module.html">obitools.gzip</a></strong>: <em class="summary">Functions that read and write gzipped files.</em> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.location-module.html">obitools.location</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.location.feature-module.html">obitools.location.feature</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.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.obo-module.html">obitools.obo</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.obo.parser-module.html">obitools.obo.parser</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.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.seqdb-module.html">obitools.seqdb</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.blastdb-module.html">obitools.seqdb.blastdb</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank-module.html">obitools.seqdb.genbank</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph-module.html">obitools.seqdb.genbank.graph</a></strong>: <em class="summary">This module offert classes to manipulate graphs</em>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms-module.html">obitools.seqdb.genbank.graph.algorithms</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.clique-module.html">obitools.seqdb.genbank.graph.algorithms.clique</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.algorithms.component-module.html">obitools.seqdb.genbank.graph.algorithms.component</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.dag-module.html">obitools.seqdb.genbank.graph.dag</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.rootedtree-module.html">obitools.seqdb.genbank.graph.rootedtree</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.graph.tree-module.html">obitools.seqdb.genbank.graph.tree</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.ncbi-module.html">obitools.seqdb.genbank.ncbi</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.seqdb.genbank.parser-module.html">obitools.seqdb.genbank.parser</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.sequenceencoder-module.html">obitools.sequenceencoder</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.solexa-module.html">obitools.solexa</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.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>
|
|
<li> <strong class="uidlink"><a href="obitools.tree.layout-module.html">obitools.tree.layout</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.tree.newick-module.html">obitools.tree.newick</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.tree.svg-module.html">obitools.tree.svg</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.tree.unrooted-module.html">obitools.tree.unrooted</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.unit-module.html">obitools.unit</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.unit.obitools-module.html">obitools.unit.obitools</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.utils-module.html">obitools.utils</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.utils.bioseq-module.html">obitools.utils.bioseq</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.word-module.html">obitools.word</a></strong>
|
|
<ul>
|
|
<li> <strong class="uidlink"><a href="obitools.word.options-module.html">obitools.word.options</a></strong> </li>
|
|
<li> <strong class="uidlink"><a href="obitools.word.predicat-module.html">obitools.word.predicat</a></strong> </li>
|
|
</ul>
|
|
</li>
|
|
<li> <strong class="uidlink"><a href="obitools.zipfile-module.html">obitools.zipfile</a></strong>: <em class="summary">Read and write ZIP files.</em> </li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<!-- ==================== NAVIGATION BAR ==================== -->
|
|
<table class="navbar" border="0" width="100%" cellpadding="0"
|
|
bgcolor="#a0c0ff" cellspacing="0">
|
|
<tr valign="middle">
|
|
<!-- Home link -->
|
|
<th> <a
|
|
href="obitools-module.html">Home</a> </th>
|
|
|
|
<!-- Tree link -->
|
|
<th bgcolor="#70b0f0" class="navbar-select"
|
|
> Trees </th>
|
|
|
|
<!-- Index link -->
|
|
<th> <a
|
|
href="identifier-index.html">Indices</a> </th>
|
|
|
|
<!-- Help link -->
|
|
<th> <a
|
|
href="help.html">Help</a> </th>
|
|
|
|
<!-- Project homepage -->
|
|
<th class="navbar" align="right" width="100%">
|
|
<table border="0" cellpadding="0" cellspacing="0">
|
|
<tr><th class="navbar" align="center"
|
|
><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
|
|
</tr></table></th>
|
|
</tr>
|
|
</table>
|
|
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
|
|
<tr>
|
|
<td align="left" class="footer">
|
|
<a href="epydoc-log.html">Generated by Epydoc
|
|
3.0beta1 on Tue Apr 29 13:03:43 2008</a>
|
|
</td>
|
|
<td align="right" class="footer">
|
|
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
<script type="text/javascript">
|
|
<!--
|
|
// Private objects are initially displayed (because if
|
|
// javascript is turned off then we want them to be
|
|
// visible); but by default, we want to hide them. So hide
|
|
// them unless we have a cookie that says to show them.
|
|
checkCookie()
|
|
// -->
|
|
</script>
|
|
|
|
</body>
|
|
</html>
|