<?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>Bio.Pathway.Network</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">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Pathway-module.html">Package Pathway</a> ::
Class Network
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.Pathway.Network-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Network</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Pathway-pysrc.html#Network">source code</a></span></p>
<p>A set of species that are explicitly linked by interactions.</p>
<p>The network is a directed multigraph with labeled edges. The nodes in
the graph are the biochemical species involved. The edges represent an
interaction between two species, and the edge label is a reference to the
associated Interaction object.</p>
<p>Attributes:</p>
<p>None</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">species</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span><br />
Initializes a new Network object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.__init__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a debugging string representation of this network.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.__repr__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a string representation of this network.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.__str__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="add_species"></a><span class="summary-sig-name">add_species</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">species</span>)</span><br />
Adds species to this network.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.add_species">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="add_interaction"></a><span class="summary-sig-name">add_interaction</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">source</span>,
<span class="summary-sig-arg">sink</span>,
<span class="summary-sig-arg">interaction</span>)</span><br />
Adds interaction to this network.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.add_interaction">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="source"></a><span class="summary-sig-name">source</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">species</span>)</span><br />
Returns list of unique sources for species.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.source">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="source_interactions"></a><span class="summary-sig-name">source_interactions</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">species</span>)</span><br />
Returns list of (source, interaction) pairs for species.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.source_interactions">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="sink"></a><span class="summary-sig-name">sink</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">species</span>)</span><br />
Returns list of unique sinks for species.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.sink">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="sink_interactions"></a><span class="summary-sig-name">sink_interactions</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">species</span>)</span><br />
Returns list of (sink, interaction) pairs for species.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.sink_interactions">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="species"></a><span class="summary-sig-name">species</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns list of the species in this network.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.species">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="interactions"></a><span class="summary-sig-name">interactions</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns list of the unique interactions in this network.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Pathway-pysrc.html#Network.interactions">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:37 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" 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>
