<?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.Compass._Consumer</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.Compass-module.html">Package Compass</a> :: Class _Consumer </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.Compass._Consumer-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class _Consumer</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer">source code</a></span></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></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.__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 href="Bio.Compass._Consumer-class.html#names" class="summary-sig-name">names</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span><br /> Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln...</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.names">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="threshold"></a><span class="summary-sig-name">threshold</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.threshold">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="lengths"></a><span class="summary-sig-name">lengths</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.lengths">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="profilewidth"></a><span class="summary-sig-name">profilewidth</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.profilewidth">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="scores"></a><span class="summary-sig-name">scores</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.scores">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="query_alignment"></a><span class="summary-sig-name">query_alignment</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.query_alignment">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="positive_alignment"></a><span class="summary-sig-name">positive_alignment</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.positive_alignment">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="hit_alignment"></a><span class="summary-sig-name">hit_alignment</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">line</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.hit_alignment">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== CLASS VARIABLES ==================== --> <a name="section-ClassVariables"></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">Class Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-ClassVariables" 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"> <a name="_re_names"></a><span class="summary-name">_re_names</span> = <code title="re.compile(r'Ali1:\s+(\S+)\s+Ali2:\s+(\S+)\s+')">re.compile(r'Ali1:\s<code class="re-op">+</code><code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Ali2:\s<code class="re-op">+</code><code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>')</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Compass._Consumer-class.html#_re_threshold" class="summary-name" onclick="show_private();">_re_threshold</a> = <code title="re.compile(r'Threshold of effective gap content in columns: (\S+)')">re.compile(r'Threshold of effective gap conten<code class="variable-ellipsis">...</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Compass._Consumer-class.html#_re_lengths" class="summary-name" onclick="show_private();">_re_lengths</a> = <code title="re.compile(r'length1=(\S+)\s+filtered_length1=(\S+)\s+length2=(\S+)\s+\ filtered_length2=(\S+)')">re.compile(r'length1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>filtered_length1=<code class="re-group">(</code>\<code class="variable-ellipsis">...</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Compass._Consumer-class.html#_re_profilewidth" class="summary-name" onclick="show_private();">_re_profilewidth</a> = <code title="re.compile(r'Nseqs1=(\S+)\s+Neff1=(\S+)\s+Nseqs2=(\S+)\s+Neff2=(\S+)')">re.compile(r'Nseqs1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Neff1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>N<code class="variable-ellipsis">...</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Compass._Consumer-class.html#_re_scores" class="summary-name" onclick="show_private();">_re_scores</a> = <code title="re.compile(r'Smith-Waterman score = (\S+)\s+Evalue = (\S+)')">re.compile(r'Smith-Waterman score = <code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Evalu<code class="variable-ellipsis">...</code></code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_re_start"></a><span class="summary-name">_re_start</span> = <code title="re.compile(r'(\d+)')">re.compile(r'<code class="re-group">(</code>\d<code class="re-op">+</code><code class="re-group">)</code>')</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_re_align"></a><span class="summary-name">_re_align</span> = <code title="re.compile(r'^.{15}(\S+)')">re.compile(r'^.<code class="re-op">{15}</code><code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>')</code> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="_re_positive_alignment"></a><span class="summary-name">_re_positive_alignment</span> = <code title="re.compile(r'^.{15}(.+)')">re.compile(r'^.<code class="re-op">{15}</code><code class="re-group">(</code>.<code class="re-op">+</code><code class="re-group">)</code>')</code> </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="names"></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">names</span>(<span class="sig-arg">self</span>, <span class="sig-arg">line</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.names">source code</a></span> </td> </tr></table> <pre class="literalblock"> Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln ------query----- -------hit------------- </pre> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== CLASS VARIABLE DETAILS ==================== --> <a name="section-ClassVariableDetails"></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">Class Variable Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-ClassVariableDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="_re_threshold"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_re_threshold</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> re.compile(r'Threshold of effective gap content in columns: <code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>') </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="_re_lengths"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_re_lengths</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> re.compile(r'length1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>filtered_length1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>length2=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span> filtered_length2=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>') </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="_re_profilewidth"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_re_profilewidth</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> re.compile(r'Nseqs1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Neff1=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Nseqs2=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Neff2=<code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>') </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="_re_scores"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">_re_scores</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> re.compile(r'Smith-Waterman score = <code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>\s<code class="re-op">+</code>Evalue = <code class="re-group">(</code>\S<code class="re-op">+</code><code class="re-group">)</code>') </pre></td></tr></table> </dd> </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> 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