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WSTester updated to work plus hopefully all the other changes that need to go into...
[jabaws.git] / binaries / src / ViennaRNA / doc / html / group__subopt__wuchty.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<title>RNAlib-2.1.2: Suboptimal structures within an energy band arround the MFE</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <td style="padding-left: 0.5em;">
+   <div id="projectname">RNAlib-2.1.2
+   </div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+  <div id="navrow1" class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
+      <li><a href="modules.html"><span>Modules</span></a></li>
+      <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+    </ul>
+  </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('group__subopt__wuchty.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="summary">
+<a href="#func-members">Functions</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle">
+<div class="title">Suboptimal structures within an energy band arround the MFE</div>  </div>
+<div class="ingroups"><a class="el" href="group__subopt__fold.html">Enumerating Suboptimal Structures</a></div></div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+  <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Suboptimal structures within an energy band arround the MFE:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
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+</td></tr></table></center>
+</div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:ga700f662506a233e42dd7fda74fafd40e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga700f662506a233e42dd7fda74fafd40e">subopt</a> (char *seq, char *structure, int delta, FILE *fp)</td></tr>
+<tr class="memdesc:ga700f662506a233e42dd7fda74fafd40e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns list of subopt structures or writes to fp.  <a href="#ga700f662506a233e42dd7fda74fafd40e"></a><br/></td></tr>
+<tr class="memitem:ga554dedfcdb249fdf151caade58666e4d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga554dedfcdb249fdf151caade58666e4d"></a>
+<a class="el" href="structSOLUTION.html">SOLUTION</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga554dedfcdb249fdf151caade58666e4d">subopt_par</a> (char *seq, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int delta, int is_constrained, int is_circular, FILE *fp)</td></tr>
+<tr class="memdesc:ga554dedfcdb249fdf151caade58666e4d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns list of subopt structures or writes to fp. <br/></td></tr>
+<tr class="memitem:ga8634516e4740e0b6c9a46d2bae940340"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga8634516e4740e0b6c9a46d2bae940340">subopt_circ</a> (char *seq, char *sequence, int delta, FILE *fp)</td></tr>
+<tr class="memdesc:ga8634516e4740e0b6c9a46d2bae940340"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns list of circular subopt structures or writes to fp.  <a href="#ga8634516e4740e0b6c9a46d2bae940340"></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:ga873cf8ed69e0437f8efa8b1fec854a0e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga873cf8ed69e0437f8efa8b1fec854a0e"></a>
+int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga873cf8ed69e0437f8efa8b1fec854a0e">subopt_sorted</a></td></tr>
+<tr class="memdesc:ga873cf8ed69e0437f8efa8b1fec854a0e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sort output by energy. <br/></td></tr>
+<tr class="memitem:ga5e57d914bcb5feeecdf520e25313fcfe"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e57d914bcb5feeecdf520e25313fcfe"></a>
+double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__wuchty.html#ga5e57d914bcb5feeecdf520e25313fcfe">print_energy</a></td></tr>
+<tr class="memdesc:ga5e57d914bcb5feeecdf520e25313fcfe"><td class="mdescLeft">&#160;</td><td class="mdescRight">printing threshold for use with logML <br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="ga700f662506a233e42dd7fda74fafd40e"></a>
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="structSOLUTION.html">SOLUTION</a>* subopt </td>
+          <td>(</td>
+          <td class="paramtype">char *&#160;</td>
+          <td class="paramname"><em>seq</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">char *&#160;</td>
+          <td class="paramname"><em>structure</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"><em>delta</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">FILE *&#160;</td>
+          <td class="paramname"><em>fp</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Returns list of subopt structures or writes to fp. </p>
+<p>This function produces <b>all</b> suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a <a class="el" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> * list terminated by an entry were the 'structure' pointer is NULL.</p>
+<dl class="params"><dt>Parameters:</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">seq</td><td></td></tr>
+    <tr><td class="paramname">structure</td><td></td></tr>
+    <tr><td class="paramname">delta</td><td></td></tr>
+    <tr><td class="paramname">fp</td><td></td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="ga8634516e4740e0b6c9a46d2bae940340"></a>
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="structSOLUTION.html">SOLUTION</a>* subopt_circ </td>
+          <td>(</td>
+          <td class="paramtype">char *&#160;</td>
+          <td class="paramname"><em>seq</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">char *&#160;</td>
+          <td class="paramname"><em>sequence</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"><em>delta</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">FILE *&#160;</td>
+          <td class="paramname"><em>fp</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Returns list of circular subopt structures or writes to fp. </p>
+<p>This function is similar to <a class="el" href="group__subopt__wuchty.html#ga700f662506a233e42dd7fda74fafd40e" title="Returns list of subopt structures or writes to fp.">subopt()</a> but calculates secondary structures assuming the RNA sequence to be circular instead of linear</p>
+<dl class="params"><dt>Parameters:</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">seq</td><td></td></tr>
+    <tr><td class="paramname">sequence</td><td></td></tr>
+    <tr><td class="paramname">delta</td><td></td></tr>
+    <tr><td class="paramname">fp</td><td></td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="footer">Generated on Wed Jul 24 2013 13:38:59 for RNAlib-2.1.2 by
+    <a href="http://www.doxygen.org/index.html">
+    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
+  </ul>
+</div>
+</body>
+</html>