<?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.KDTree.KDTree</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.KDTree-module.html">Package KDTree</a> :: Module KDTree </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.KDTree.KDTree-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module KDTree</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.KDTree.KDTree-pysrc.html">source code</a></span></p> <p>The KD tree data structure can be used for all kinds of searches that involve N-dimensional vectors, e.g. neighbor searches (find all points within a radius of a given point) or finding all point pairs in a set that are within a certain radius of each other. See "Computational Geometry: Algorithms and Applications" (Mark de Berg, Marc van Kreveld, Mark Overmars, Otfried Schwarzkopf). Author: Thomas Hamelryck.</p> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></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">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" 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"> <a href="Bio.KDTree.KDTree.KDTree-class.html" class="summary-name">KDTree</a><br /> KD tree implementation (C++, SWIG python wrapper) </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></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">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</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="_dist"></a><span class="summary-sig-name">_dist</span>(<span class="summary-sig-arg">p</span>, <span class="summary-sig-arg">q</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.KDTree.KDTree-pysrc.html#_dist">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 href="Bio.KDTree.KDTree-module.html#_neighbor_test" class="summary-sig-name" onclick="show_private();">_neighbor_test</a>(<span class="summary-sig-arg">nr_points</span>, <span class="summary-sig-arg">dim</span>, <span class="summary-sig-arg">bucket_size</span>, <span class="summary-sig-arg">radius</span>)</span><br /> Test all fixed radius neighbor search.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.KDTree.KDTree-pysrc.html#_neighbor_test">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 href="Bio.KDTree.KDTree-module.html#_test" class="summary-sig-name" onclick="show_private();">_test</a>(<span class="summary-sig-arg">nr_points</span>, <span class="summary-sig-arg">dim</span>, <span class="summary-sig-arg">bucket_size</span>, <span class="summary-sig-arg">radius</span>)</span><br /> Test neighbor search.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.KDTree.KDTree-pysrc.html#_test">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" 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">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="_neighbor_test"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_neighbor_test</span>(<span class="sig-arg">nr_points</span>, <span class="sig-arg">dim</span>, <span class="sig-arg">bucket_size</span>, <span class="sig-arg">radius</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.KDTree.KDTree-pysrc.html#_neighbor_test">source code</a></span> </td> </tr></table> <p>Test all fixed radius neighbor search.</p> <p>Test all fixed radius neighbor search using the KD tree C module.</p> <p>o nr_points - number of points used in test o dim - dimension of coords o bucket_size - nr of points per tree node o radius - radius of search (typically 0.05 or so)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_test"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_test</span>(<span class="sig-arg">nr_points</span>, <span class="sig-arg">dim</span>, <span class="sig-arg">bucket_size</span>, <span class="sig-arg">radius</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.KDTree.KDTree-pysrc.html#_test">source code</a></span> </td> </tr></table> <p>Test neighbor search.</p> <p>Test neighbor search using the KD tree C module.</p> <p>o nr_points - number of points used in test o dim - dimension of coords o bucket_size - nr of points per tree node o radius - radius of search (typically 0.05 or so)</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== 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 09:26:24 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"> 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