<?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.Blast.NCBIStandalone._Scanner</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.Blast-module.html">Package Blast</a> :: <a href="Bio.Blast.NCBIStandalone-module.html">Module NCBIStandalone</a> :: Class _Scanner </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.Blast.NCBIStandalone._Scanner-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class _Scanner</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner">source code</a></span></p> <p>Scan BLAST output from blastall or blastpgp.</p> <p>Tested with blastall and blastpgp v2.0.10, v2.0.11</p> <p>Methods: feed Feed data into the scanner.</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 href="Bio.Blast.NCBIStandalone._Scanner-class.html#feed" class="summary-sig-name">feed</a>(<span class="summary-sig-arg">S</span>, <span class="summary-sig-arg">handle</span>, <span class="summary-sig-arg">consumer</span>)</span><br /> Feed in a BLAST report for scanning.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner.feed">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="_scan_header"></a><span class="summary-sig-name">_scan_header</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_header">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="_scan_rounds"></a><span class="summary-sig-name">_scan_rounds</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_rounds">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="_scan_descriptions"></a><span class="summary-sig-name">_scan_descriptions</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_descriptions">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="_scan_alignments"></a><span class="summary-sig-name">_scan_alignments</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_alignments">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="_scan_pairwise_alignments"></a><span class="summary-sig-name">_scan_pairwise_alignments</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_pairwise_alignments">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="_scan_one_pairwise_alignment"></a><span class="summary-sig-name">_scan_one_pairwise_alignment</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_one_pairwise_alignment">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="_scan_alignment_header"></a><span class="summary-sig-name">_scan_alignment_header</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_alignment_header">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="_scan_hsp"></a><span class="summary-sig-name">_scan_hsp</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_hsp">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="_scan_hsp_header"></a><span class="summary-sig-name">_scan_hsp_header</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_hsp_header">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="_scan_hsp_alignment"></a><span class="summary-sig-name">_scan_hsp_alignment</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_hsp_alignment">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="_scan_masterslave_alignment"></a><span class="summary-sig-name">_scan_masterslave_alignment</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_masterslave_alignment">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="_scan_database_report"></a><span class="summary-sig-name">_scan_database_report</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_database_report">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="_scan_parameters"></a><span class="summary-sig-name">_scan_parameters</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">uhandle</span>, <span class="summary-sig-arg">consumer</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner._scan_parameters">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></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">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="feed"></a> <div> <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">feed</span>(<span class="sig-arg">S</span>, <span class="sig-arg">handle</span>, <span class="sig-arg">consumer</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Blast.NCBIStandalone-pysrc.html#_Scanner.feed">source code</a></span> </td> </tr></table> <p>Feed in a BLAST report for scanning. handle is a file-like object that contains the BLAST report. consumer is a Consumer object that will receive events as the report is scanned.</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 09:26:30 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. 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