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-<div class="title">Stochastic backtracking in the Ensemble</div> </div>
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- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Stochastic backtracking in the Ensemble:</div>
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-</td></tr></table></center>
+<h1>Stochastic backtracking in the Ensemble<br/>
+<small>
+[<a class="el" href="group__subopt__fold.html">Enumerating Suboptimal Structures</a>]</small>
+</h1>
+<p><div class="dynheader">
+Collaboration diagram for Stochastic backtracking in the Ensemble:</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__subopt__stochbt.png" border="0" alt="" usemap="#group____subopt____stochbt_map"/>
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+<area shape="rect" id="node1" href="group__kl__neighborhood__stochbt.html" title="Contains functions related to stochastic backtracking from a specified distance class..." alt="" coords="619,5,1061,35"/><area shape="rect" id="node2" href="group__subopt__fold.html" title="Enumerating Suboptimal Structures" alt="" coords="7,31,233,62"/><area shape="rect" id="node4" href="group__consensus__stochbt.html" title="Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)" alt="" coords="595,58,1085,89"/></map></td></tr></table></center>
</div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="groups"></a>
-Modules</h2></td></tr>
-<tr class="memitem:group__consensus__stochbt"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__stochbt.html">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td></tr>
-<tr class="memitem:group__kl__neighborhood__stochbt"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html">Stochastic Backtracking of Structures from Distance Based Partitioning</a></td></tr>
-<tr class="memdesc:group__kl__neighborhood__stochbt"><td class="mdescLeft"> </td><td class="mdescRight">Contains functions related to stochastic backtracking from a specified distance class. <br/></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack</a> (char *sequence)</td></tr>
-<tr class="memdesc:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Modules</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__stochbt.html">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html">Stochastic Backtracking of Structures from Distance Based Partitioning</a></td></tr>
+
+<p><tr><td class="mdescLeft"> </td><td class="mdescRight"><p>Contains functions related to stochastic backtracking from a specified distance class. </p>
+<br/></td></tr>
+</p>
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack</a> (char *sequence)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
. <a href="#gac03ca6db186bb3bf0a2a326d7fb3ba03"></a><br/></td></tr>
-<tr class="memitem:ga00474051204ac9ad576b3e45174d03ff"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">pbacktrack_circ</a> (char *sequence)</td></tr>
-<tr class="memdesc:ga00474051204ac9ad576b3e45174d03ff"><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. <a href="#ga00474051204ac9ad576b3e45174d03ff"></a><br/></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
-Variables</h2></td></tr>
-<tr class="memitem:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td></tr>
-<tr class="memdesc:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="mdescLeft"> </td><td class="mdescRight">Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. <a href="#gacd79b1a570e6ad9be24cb11fe8cae30a"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">pbacktrack_circ</a> (char *sequence)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. <a href="#ga00474051204ac9ad576b3e45174d03ff"></a><br/></td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. <a href="#gacd79b1a570e6ad9be24cb11fe8cae30a"></a><br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="gac03ca6db186bb3bf0a2a326d7fb3ba03"></a>
+<a class="anchor" id="gac03ca6db186bb3bf0a2a326d7fb3ba03"></a><!-- doxytag: member="part_func.h::pbacktrack" ref="gac03ca6db186bb3bf0a2a326d7fb3ba03" args="(char *sequence)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">char* pbacktrack </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>sequence</em></td><td>)</td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>sequence</em></td>
+ <td> ) </td>
<td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
. </p>
-<dl class="section pre"><dt>Precondition:</dt><dd><a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function for a given RNA sequence.">pf_fold_par()</a> or <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> have to be called first to fill the partition function matrices</dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">sequence</td><td>The RNA sequence </td></tr>
+<dl class="pre"><dt><b>Precondition:</b></dt><dd><a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function for a given RNA sequence.">pf_fold_par()</a> or <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> have to be called first to fill the partition function matrices</dd></dl>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>sequence</em> </td><td>The RNA sequence </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
</div>
</div>
-<a class="anchor" id="ga00474051204ac9ad576b3e45174d03ff"></a>
+<a class="anchor" id="ga00474051204ac9ad576b3e45174d03ff"></a><!-- doxytag: member="part_func.h::pbacktrack_circ" ref="ga00474051204ac9ad576b3e45174d03ff" args="(char *sequence)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">char* pbacktrack_circ </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>sequence</em></td><td>)</td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>sequence</em></td>
+ <td> ) </td>
<td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. </p>
<p>This function does the same as <a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack()</a> but assumes the RNA molecule to be circular</p>
-<pre class="fragment">\pre pf_fold_par() or pf_fold_circ() have to be called first to fill the partition function matrices
+<dl class="pre"><dt><b>Precondition:</b></dt><dd><a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function for a given RNA sequence.">pf_fold_par()</a> or pf_fold_circ() have to be called first to fill the partition function matrices</dd></dl>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>sequence</em> </td><td>The RNA sequence </td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>A sampled secondary structure in dot-bracket notation </dd></dl>
-\param sequence The RNA sequence
-\return A sampled secondary structure in dot-bracket notation</pre>
</div>
</div>
<hr/><h2>Variable Documentation</h2>
-<a class="anchor" id="gacd79b1a570e6ad9be24cb11fe8cae30a"></a>
+<a class="anchor" id="gacd79b1a570e6ad9be24cb11fe8cae30a"></a><!-- doxytag: member="part_func.h::st_back" ref="gacd79b1a570e6ad9be24cb11fe8cae30a" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
- <td class="memname">int st_back</td>
+ <td class="memname">int <a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. </p>
<p>Set this variable to 1 prior to a call of <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions</p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03" title="Sample a secondary structure from the Boltzmann ensemble according its probability ...">pbacktrack()</a>, <a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff" title="Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability...">pbacktrack_circ</a> </dd></dl>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03" title="Sample a secondary structure from the Boltzmann ensemble according its probability...">pbacktrack()</a>, <a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff" title="Sample a secondary structure of a circular RNA from the Boltzmann ensemble according...">pbacktrack_circ</a> </dd></dl>
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