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csb.apps.buildhmm.ProfileBuilder-class.html
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<?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>csb.apps.buildhmm.ProfileBuilder</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">
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<!-- Home link -->
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href="csb-module.html">Home</a> </th>
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</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="csb-module.html">Package csb</a> ::
<a href="csb.apps-module.html">Package apps</a> ::
<a href="csb.apps.buildhmm-module.html">Module buildhmm</a> ::
Class ProfileBuilder
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="csb.apps.buildhmm.ProfileBuilder-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class ProfileBuilder</h1><p class="nomargin-top"><span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">ProfileBuilder</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="csb.apps.buildhmm.FASTAProfileBuilder-class.html">FASTAProfileBuilder</a></li><li>, <a href="csb.apps.buildhmm.PDBProfileBuilder-class.html">PDBProfileBuilder</a></li> </ul>
</dd></dl>
<hr />
<!-- ==================== NESTED CLASSES ==================== -->
<a name="section-NestedClasses"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Nested Classes</span></td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="abc.ABCMeta-class.html" class="summary-name">__metaclass__</a><br />
Metaclass for defining Abstract Base Classes (ABCs).
</td>
</tr>
</table>
<!-- ==================== 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 align="left" colspan="2" class="table-header">
<span class="table-header">Instance Methods</span></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="csb.apps.buildhmm.ProfileBuilder-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">query</span>,
<span class="summary-sig-arg">target_id</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">tk_root</span>,
<span class="summary-sig-arg">tk_config</span>,
<span class="summary-sig-arg">pseudo</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">ss</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">cpu</span>=<span class="summary-sig-default">1</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.__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 name="build_alignment"></a><span class="summary-sig-name">build_alignment</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.build_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="calibrate_hmm"></a><span class="summary-sig-name">calibrate_hmm</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.calibrate_hmm">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="configure_input"></a><span class="summary-sig-name">configure_input</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.configure_input">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="make_hmm"></a><span class="summary-sig-name">make_hmm</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.make_hmm">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="run"></a><span class="summary-sig-name">run</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.run">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== STATIC METHODS ==================== -->
<a name="section-StaticMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Static Methods</span></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="create"></a><span class="summary-sig-name">create</span>(<span class="summary-sig-arg">query</span>,
<span class="summary-sig-arg">target_id</span>,
<span class="summary-sig-arg">database</span>,
<span class="summary-sig-arg">tk_root</span>,
<span class="summary-sig-arg">tk_config</span>,
<span class="summary-sig-arg">pseudo</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">ss</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">cpu</span>=<span class="summary-sig-default">1</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.create">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 align="left" colspan="2" class="table-header">
<span class="table-header">Class Variables</span></td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="EMISSION_PSEUDO"></a><span class="summary-name">EMISSION_PSEUDO</span> = <code title="'-pcm 4 -pca 2.5 -pcb 0.5 -pcc 1.0'"><code class="variable-quote">'</code><code class="variable-string">-pcm 4 -pca 2.5 -pcb 0.5 -pcc 1.0</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="csb.apps.buildhmm.ProfileBuilder-class.html#TRANSITION_PSEUDO" class="summary-name">TRANSITION_PSEUDO</a> = <code title="'-gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 -gapg 0.6 -gapi 0.6'"><code class="variable-quote">'</code><code class="variable-string">-gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 </code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="__abstractmethods__"></a><span class="summary-name">__abstractmethods__</span> = <code title="frozenset(['configure_input'])"><code class="variable-group">frozenset([</code><code class="variable-quote">'</code><code class="variable-string">configure_input</code><code class="variable-quote">'</code><code class="variable-group">])</code></code>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Properties</span></td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="csb.apps.buildhmm.ProfileBuilder-class.html#target_id" class="summary-name">target_id</a>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</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 align="left" colspan="2" class="table-header">
<span class="table-header">Method Details</span></td>
</tr>
</table>
<a name="__init__"></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">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">query</span>,
<span class="sig-arg">target_id</span>,
<span class="sig-arg">database</span>,
<span class="sig-arg">tk_root</span>,
<span class="sig-arg">tk_config</span>,
<span class="sig-arg">pseudo</span>=<span class="sig-default">True</span>,
<span class="sig-arg">ss</span>=<span class="sig-default">True</span>,
<span class="sig-arg">cpu</span>=<span class="sig-default">1</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="csb.apps.buildhmm-pysrc.html#ProfileBuilder.__init__">source code</a></span>
</td>
</tr></table>
<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</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 align="left" colspan="2" class="table-header">
<span class="table-header">Class Variable Details</span></td>
</tr>
</table>
<a name="TRANSITION_PSEUDO"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">TRANSITION_PSEUDO</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-quote">'</code><code class="variable-string">-gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 -gapg 0.6 -gapi 0.6</code><code class="variable-quote">'</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
<a name="section-PropertyDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Property Details</span></td>
</tr>
</table>
<a name="target_id"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">target_id</h3>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><i>unreachable</i>.target_id(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
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