git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
WSTester updated to work plus hopefully all the other changes that need to go into...
[jabaws.git] / binaries / src / ViennaRNA / doc / html / group__consensus__mfe__fold.html
diff --git a/binaries/src/ViennaRNA/doc/html/group__consensus__mfe__fold.html b/binaries/src/ViennaRNA/doc/html/group__consensus__mfe__fold.html
new file mode 100644 (file)
index 0000000..c645d49
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/html/group__consensus__mfe__fold.html
@@ -0,0 +1,172 @@
+<!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: MFE Consensus Structures for Sequence Alignment(s)</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+  $(document).ready(initResizable);
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <td style="padding-left: 0.5em;">
+   <div id="projectname">RNAlib-2.1.2
+   </div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+  <div id="navrow1" class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
+      <li><a href="modules.html"><span>Modules</span></a></li>
+      <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+    </ul>
+  </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('group__consensus__mfe__fold.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="summary">
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<div class="title">MFE Consensus Structures for Sequence Alignment(s)</div>  </div>
+<div class="ingroups"><a class="el" href="group__consensus__fold.html">Predicting Consensus Structures from Alignment(s)</a> &#124; <a class="el" href="group__mfe__fold.html">Calculating Minimum Free Energy (MFE) 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 MFE Consensus Structures for Sequence Alignment(s):</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<center><table><tr><td><img src="group__consensus__mfe__fold.png" border="0" alt="" usemap="#group____consensus____mfe____fold"/>
+<map name="group____consensus____mfe____fold" id="group____consensus____mfe____fold">
+<area shape="rect" id="node1" href="group__consensus__fold.html" title="compute various properties (consensus MFE structures, partition function, Boltzmann distributed stoch..." alt="" coords="5,5,219,46"/><area shape="rect" id="node2" href="group__mfe__fold.html" title="This module contains all functions and variables related to the calculation of global minimum free en..." alt="" coords="6,70,218,111"/></map>
+</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:ga4cf00f0659e5f0480335d69e797f05b1"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1">alifold</a> (const char **strings, char *structure)</td></tr>
+<tr class="memdesc:ga4cf00f0659e5f0480335d69e797f05b1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute MFE and according consensus structure of an alignment of sequences.  <a href="#ga4cf00f0659e5f0480335d69e797f05b1"></a><br/></td></tr>
+<tr class="memitem:gadbd3b0b1c144cbfb4efe704b2b260f96"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96">circalifold</a> (const char **strings, char *structure)</td></tr>
+<tr class="memdesc:gadbd3b0b1c144cbfb4efe704b2b260f96"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear.  <a href="#gadbd3b0b1c144cbfb4efe704b2b260f96"></a><br/></td></tr>
+<tr class="memitem:ga72095e4554b5d577250ea14c42acc49e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga72095e4554b5d577250ea14c42acc49e"></a>
+void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e">free_alifold_arrays</a> (void)</td></tr>
+<tr class="memdesc:ga72095e4554b5d577250ea14c42acc49e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Free the memory occupied by MFE alifold functions. <br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="ga4cf00f0659e5f0480335d69e797f05b1"></a>
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">float alifold </td>
+          <td>(</td>
+          <td class="paramtype">const char **&#160;</td>
+          <td class="paramname"><em>strings</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">char *&#160;</td>
+          <td class="paramname"><em>structure</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Compute MFE and according consensus structure of an alignment of sequences. </p>
+<p>This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.</p>
+<p>Sufficient space must be allocated for 'structure' before calling <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a>.</p>
+<dl class="params"><dt>Parameters:</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">strings</td><td>A pointer to a NULL terminated array of character arrays </td></tr>
+    <tr><td class="paramname">structure</td><td>A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd>The free energy score in kcal/mol </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="gadbd3b0b1c144cbfb4efe704b2b260f96"></a>
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">float circalifold </td>
+          <td>(</td>
+          <td class="paramtype">const char **&#160;</td>
+          <td class="paramname"><em>strings</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">char *&#160;</td>
+          <td class="paramname"><em>structure</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">strings</td><td>A pointer to a NULL terminated array of character arrays </td></tr>
+    <tr><td class="paramname">structure</td><td>A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd>The free energy score in kcal/mol </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>