<?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.Nexus.Nodes.Chain</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.Nexus-module.html">Package Nexus</a> :: <a href="Bio.Nexus.Nodes-module.html">Module Nodes</a> :: Class Chain </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.Nexus.Nodes.Chain-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Chain</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain">source code</a></span></p> <dl><dt>Known Subclasses:</dt> <dd> <ul class="subclass-list"> <li><a href="Bio.Nexus.Trees.Tree-class.html">Trees.Tree</a></li> </ul> </dd></dl> <hr /> <p>Stores a list of nodes that are linked together.</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><br /> Initiates a node chain: (self).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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="_get_id"></a><span class="summary-sig-name">_get_id</span>(<span class="summary-sig-arg">self</span>)</span><br /> Gets a new id for a node in the chain.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain._get_id">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"></a><span class="summary-sig-name">add</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">node</span>, <span class="summary-sig-arg">prev</span>=<span class="summary-sig-default">None</span>)</span><br /> Attaches node to another: (self, node, prev).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.add">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="all_ids"></a><span class="summary-sig-name">all_ids</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return a list of all node ids.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.all_ids">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="collapse"></a><span class="summary-sig-name">collapse</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Deletes node from chain and relinks successors to predecessor: collapse(self, id).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.collapse">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="is_parent_of"></a><span class="summary-sig-name">is_parent_of</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">parent</span>, <span class="summary-sig-arg">grandchild</span>)</span><br /> Check if grandchild is a subnode of parent: is_parent_of(self,parent,grandchild).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.is_parent_of">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="kill"></a><span class="summary-sig-name">kill</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Kills a node from chain without caring to what it is connected: kill(self,id).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.kill">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="link"></a><span class="summary-sig-name">link</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">parent</span>, <span class="summary-sig-arg">child</span>)</span><br /> Connects son to parent: link(self,son,parent).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.link">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="trace"></a><span class="summary-sig-name">trace</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">start</span>, <span class="summary-sig-arg">finish</span>)</span><br /> Returns a list of all node_ids between two nodes (excluding start, including end): trace(start,end).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.trace">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="unlink"></a><span class="summary-sig-name">unlink</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">id</span>)</span><br /> Disconnects node from his predecessor: unlink(self,id).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nodes-pysrc.html#Chain.unlink">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 09:26:36 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 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