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<?xml version="1.0" encoding="iso-8859-1"?><!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>netconv.gml</title> <link rel="stylesheet" href="epydoc.css" type="text/css"></link></head><body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"><!-- =========== START OF NAVBAR =========== --><table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="center"> <th class="navbar"> <a class="navbar" href="netconv-module.html">Home</a> </th> <th class="navbar"> <a class="navbar" href="trees.html">Trees</a> </th> <th class="navbar"> <a class="navbar" href="indices.html">Index</a> </th> <th class="navbar"> <a class="navbar" 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%"> <font size="-1"><b class="breadcrumbs"> <a href="netconv-module.html">Package netconv</a> :: Module gml </b></font></br> </td> <td><table cellpadding="0" cellspacing="0"> <tr><td align="right"><font size="-2">[show private | <a href="../public/netconv.gml-module.html">hide private</a>]</font></td></tr> <tr><td align="right"><font size="-2">[<a href="frames.html"target="_top">frames</a> | <a href="netconv.gml-module.html" target="_top">no frames</a>]</font></td></tr> </table></td></tr></table><!-- =========== START OF MODULE DESCRIPTION =========== --><h2 class="module">Module netconv.gml</h2>Functions to work with GML files<hr/><p><b>Author:</b> Marcio Rosa da Silva</p><p><b>Contact:</b> mrs@gbf.de</p><p><b>Organization:</b> Systems Biology Group / GBF</p><p><b>License:</b> GPL</p><!-- =========== START OF FUNCTION SUMMARY =========== --><table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"><tr bgcolor="#70b0f0" class="summary"> <th colspan="2">Function Summary</th></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="netconv.gml-module.html#addGMLEdge" class="summary-sig-name"><code>addGMLEdge</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>arq</span>)</span></code><br />Adds GML edge to the the network</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="netconv.gml-module.html#addGMLNode" class="summary-sig-name"><code>addGMLNode</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>arq</span>)</span></code><br />Adds GML node to the the network</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="netconv.gml-module.html#exportGML" class="summary-sig-name"><code>exportGML</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>filename</span>)</span></code><br />Exports network to GML file</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="netconv.gml-module.html#importGML" class="summary-sig-name"><code>importGML</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>filename</span>)</span></code><br />Exports network to GML file</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="../private/netconv.gml-module.html#_bExportGML" class="summary-sig-name"><code>_bExportGML</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>name</span>, <span class=summary-sig-arg>attribs</span>, <span class=summary-sig-arg>indent</span>)</span></code><br />Exports attributes in GML format</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="../private/netconv.gml-module.html#_bImportGML" class="summary-sig-name"><code>_bImportGML</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>arq</span>, <span class=summary-sig-arg>attribs</span>)</span></code><br />Imports the attributes in GML format</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="../private/netconv.gml-module.html#_neExportGML" class="summary-sig-name"><code>_neExportGML</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>name</span>, <span class=summary-sig-arg>attribs</span>, <span class=summary-sig-arg>indent</span>)</span></code><br />Exports the attributes of the node in GML format</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"> </font></td> <td><code><span class="summary-sig"><a href="../private/netconv.gml-module.html#_neImportGML" class="summary-sig-name"><code>_neImportGML</code></a>(<span class=summary-sig-arg>obj</span>, <span class=summary-sig-arg>arq</span>, <span class=summary-sig-arg>attribs</span>)</span></code><br />Imports the attributes of the node in GML format</td></tr></table><br /><!-- =========== START OF VARIABLE SUMMARY =========== --><table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"><tr bgcolor="#70b0f0" class="summary"> <th colspan="2">Variable Summary</th></tr><tr><td align="right" valign="top" width="15%"><font size="-1"><code>str</code></font></td><td><b><a href="netconv.gml-module.html#gml_tab"><code>gml_tab</code></a></b>: used to indent GML file</td></tr><tr><td align="right" valign="top" width="15%"><font size="-1"><code>str</code></font></td><td><b><a href="netconv.gml-module.html#gml_tab_i"><code>gml_tab_i</code></a></b>: internal field separation in GML file</td></tr></table><br /><!-- =========== START OF FUNCTION DETAILS =========== --><table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"><tr bgcolor="#70b0f0" class="details"> <th colspan="2">Function Details</th></tr></table><a name="addGMLEdge"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">addGMLEdge</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>arq</span>)</span> </h3> Adds GML edge to the the network <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - edge <dd><code><b>arq</b></code> - .gml file </dd> </dl> </dd></dl></td></tr></table><a name="addGMLNode"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">addGMLNode</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>arq</span>)</span> </h3> Adds GML node to the the network <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - node <dd><code><b>arq</b></code> - .gml file </dd> </dl> </dd></dl></td></tr></table><a name="exportGML"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">exportGML</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>filename</span>=<span class=sig-default>'-'</span>)</span> </h3> Exports network to GML file <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - network <dd><code><b>filename</b></code> - .gml file </dd> </dl> </dd></dl></td></tr></table><a name="importGML"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">importGML</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>filename</span>=<span class=sig-default>'-'</span>)</span> </h3> Exports network to GML file <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - network <dd><code><b>filename</b></code> - .gml file </dd> </dl> </dd></dl></td></tr></table><a name="_bExportGML"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">_bExportGML</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>name</span>, <span class=sig-arg>attribs</span>, <span class=sig-arg>indent</span>)</span> </h3> Exports attributes in GML format <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - network <dd><code><b>name</b></code> - name of the group being exported <dd><code><b>attribs</b></code> - attribute to export (use recursively to work on dictionary attributes) <dd><code><b>indent</b></code> - level of indentation (tabs) </dd> </dl> </dd></dl></td></tr></table><a name="_bImportGML"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">_bImportGML</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>arq</span>, <span class=sig-arg>attribs</span>)</span> </h3> Imports the attributes in GML format <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - network <dd><code><b>arq</b></code> - .gml file <dd><code><b>attribs</b></code> - attributes dict (used recursively) </dd> </dl> </dd></dl></td></tr></table><a name="_neExportGML"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">_neExportGML</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>name</span>=<span class=sig-default>None</span>, <span class=sig-arg>attribs</span>=<span class=sig-default>None</span>, <span class=sig-arg>indent</span>=<span class=sig-default>0</span>)</span> </h3> Exports the attributes of the node in GML format <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - node/edge <dd><code><b>name</b></code> - name of the group being exported <dd><code><b>attribs</b></code> - attribute to export (use recursively to work on dictionary attributes) <dd><code><b>indent</b></code> - level of indentation (tabs) </dd> </dl> </dd></dl></td></tr></table><a name="_neImportGML"></a><table width="100%" class="func-details" bgcolor="#e0e0e0"><tr><td> <h3><span class="sig"><span class="sig-name">_neImportGML</span>(<span class=sig-arg>obj</span>, <span class=sig-arg>arq</span>, <span class=sig-arg>attribs</span>=<span class=sig-default>None</span>)</span> </h3> Imports the attributes of the node in GML format <dl><dt></dt><dd> <dl><dt><b>Parameters:</b></dt> <dd><code><b>obj</b></code> - node/edge <dd><code><b>arq</b></code> - .gml file <dd><code><b>attribs</b></code> - attributes list (used recursively) </dd> </dl> </dd></dl></td></tr></table><br /><!-- =========== START OF VARIABLE DETAILS =========== --><table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"><tr bgcolor="#70b0f0" class="details"> <th colspan="2">Variable Details</th></tr></table><table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td><a name="gml_tab"></a><h3>gml_tab</h3>used to indent GML file<dl> <dt></dt> <dd> <dl> <dt><b>Type:</b></dt> <dd> <code>str</code> </dd><span title="'\t'"> <dt><b>Value:</b></dt> <dd><table><tr><td><pre class="variable"><span class="variable-quote">'</span>\t<span class="variable-quote">'</span> </pre> </td></tr></table></dd></span> </dl> </dd></dl></td></tr></table><table width="100%" class="var-details" bgcolor="#e0e0e0"><tr><td><a name="gml_tab_i"></a><h3>gml_tab_i</h3>internal field separation in GML file<dl> <dt></dt> <dd> <dl> <dt><b>Type:</b></dt> <dd> <code>str</code> </dd><span title="'\t'"> <dt><b>Value:</b></dt> <dd><table><tr><td><pre class="variable"><span class="variable-quote">'</span>\t<span class="variable-quote">'</span> </pre> </td></tr></table></dd></span> </dl> </dd></dl></td></tr></table><br /><!-- =========== START OF NAVBAR =========== --><table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="center"> <th 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