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 / 2Dfold_8h_source.html
diff --git a/binaries/src/ViennaRNA/doc/html/2Dfold_8h_source.html b/binaries/src/ViennaRNA/doc/html/2Dfold_8h_source.html
new file mode 100644 (file)
index 0000000..b158a2c
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/html/2Dfold_8h_source.html
@@ -0,0 +1,118 @@
+<!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: /home/mescalin/ronny/public_html/programs/ViennaRNA/H/2Dfold.h Source File</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">
+  $(document).ready(initResizable);
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <td style="padding-left: 0.5em;">
+   <div id="projectname">RNAlib-2.1.2
+   </div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+  <div id="navrow1" class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
+      <li><a href="modules.html"><span>Modules</span></a></li>
+      <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+    </ul>
+  </div>
+  <div id="navrow2" class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>Globals</span></a></li>
+    </ul>
+  </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('2Dfold_8h.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="headertitle">
+<div class="title">2Dfold.h</div>  </div>
+</div><!--header-->
+<div class="contents">
+<a href="2Dfold_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
+<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">      minimum free energy</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">      RNA secondary structure with</span></div>
+<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">      basepair distance d to reference structure prediction</span></div>
+<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment"></span></div>
+<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">*/</span></div>
+<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__</span></div>
+<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__</span></div>
+<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="preprocessor"></span></div>
+<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here.">data_structures.h</a>&quot;</span></div>
+<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;</div>
+<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="preprocessor">#ifdef __GNUC__</span></div>
+<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
+<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#else</span></div>
+<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
+<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor"></span></div>
+<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *<a class="code" href="group__kl__neighborhood__mfe.html#gac9284f132cf0eaa0a2f43590eda05488" title="Get a structure of type TwoDfold_vars prefilled with current global settings.">get_TwoDfold_variables</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *seq,</div>
+<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">char</span> *structure1,</div>
+<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">char</span> *structure2,</div>
+<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;                                      <span class="keywordtype">int</span> circ);</div>
+<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;</div>
+<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="keywordtype">void</span>          <a class="code" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487" title="Destroy a TwoDfold_vars datastructure without memory loss.">destroy_TwoDfold_variables</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *our_variables);</div>
+<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
+<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;DEPRECATED(<a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a> **TwoDfold(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *our_variables,</div>
+<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;                                        <span class="keywordtype">int</span> distance1,</div>
+<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;                                        <span class="keywordtype">int</span> distance2));</div>
+<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
+<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;<a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a> *<a class="code" href="group__kl__neighborhood__mfe.html#ga47da790166020558d27323aef489703e" title="Compute MFE&#39;s and representative for distance partitioning.">TwoDfoldList</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *vars,</div>
+<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;                                <span class="keywordtype">int</span> distance1,</div>
+<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;                                <span class="keywordtype">int</span> distance2);</div>
+<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;</div>
+<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;<span class="keywordtype">char</span> *<a class="code" href="group__kl__neighborhood__mfe.html#gaf4dc05bf8fc1ea53acd7aeb798ba80c2" title="Backtrack a minimum free energy structure from a 5&#39; section of specified length.">TwoDfold_backtrack_f5</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j,</div>
+<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;                            <span class="keywordtype">int</span> k,</div>
+<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;                            <span class="keywordtype">int</span> l,</div>
+<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;                            <a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *vars);</div>
+<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
+<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;<span class="preprocessor">#endif</span></div>
+</div><!-- fragment --></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="2Dfold_8h.html">2Dfold.h</a></li>
+    <li class="footer">Generated on Wed Jul 24 2013 13:38:55 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>