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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Compass-module.html">Package Compass</a> ::
Class _Consumer
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<!-- ==================== 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 ==================== -->
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<span class="summary-type"> </span>
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<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>
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<span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.__init__">source code</a></span>
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<span class="summary-type"> </span>
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<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>
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<span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.names">source code</a></span>
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<span class="summary-type"> </span>
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<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>
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<span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.threshold">source code</a></span>
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<span class="summary-type"> </span>
</td><td class="summary">
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<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>
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<span class="codelink"><a href="Bio.Compass-pysrc.html#_Consumer.lengths">source code</a></span>
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<span class="summary-type"> </span>
</td><td class="summary">
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<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>
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<span class="summary-type"> </span>
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<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>
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<span class="summary-type"> </span>
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<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>
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<span class="summary-type"> </span>
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<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>
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<span class="summary-type"> </span>
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<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>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<span class="summary-type"> </span>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<span class="summary-type"> </span>
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<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>
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<span class="summary-type"> </span>
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<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>
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<a name="names"></a>
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<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>
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<pre class="literalblock">
Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln
------query----- -------hit-------------
</pre>
<dl class="fields">
</dl>
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<br />
<!-- ==================== CLASS VARIABLE DETAILS ==================== -->
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<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>
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<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>
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<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>
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<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>')
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