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 / LPfold_8h.html
diff --git a/binaries/src/ViennaRNA/doc/html/LPfold_8h.html b/binaries/src/ViennaRNA/doc/html/LPfold_8h.html
new file mode 100644 (file)
index 0000000..a5f05f0
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/html/LPfold_8h.html
@@ -0,0 +1,131 @@
+<!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/LPfold.h File Reference</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('LPfold_8h.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">LPfold.h File Reference<div class="ingroups"><a class="el" href="group__local__pf__fold.html">Partition functions for locally stable secondary structures</a></div></div>  </div>
+</div><!--header-->
+<div class="contents">
+
+<p>Function declarations of partition function variants of the Lfold algorithm.  
+<a href="#details">More...</a></p>
+<div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+  <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for LPfold.h:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="LPfold_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2LPfold_8h" alt=""/></div>
+<map name="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2LPfold_8h" id="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2LPfold_8h">
+<area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="19,109,153,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="27,184,147,211"/></map>
+</div>
+</div>
+<p><a href="LPfold_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:ga5a019014d37fe6105131dfc2fc447880"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__pf__fold.html#ga5a019014d37fe6105131dfc2fc447880">update_pf_paramsLP</a> (int length)</td></tr>
+<tr class="memitem:gaa1ecd401617ebc748a0220026543c777"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structplist.html">plist</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__pf__fold.html#gaa1ecd401617ebc748a0220026543c777">pfl_fold</a> (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct <a class="el" href="structplist.html">plist</a> **dpp2, FILE *pUfp, FILE *spup)</td></tr>
+<tr class="memdesc:gaa1ecd401617ebc748a0220026543c777"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute partition functions for locally stable secondary structures.  <a href="group__local__pf__fold.html#gaa1ecd401617ebc748a0220026543c777"></a><br/></td></tr>
+<tr class="memitem:gab354507e8028f3e1c52ef96bb1eb9df8"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gab354507e8028f3e1c52ef96bb1eb9df8"></a>
+<a class="el" href="structplist.html">plist</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__pf__fold.html#gab354507e8028f3e1c52ef96bb1eb9df8">pfl_fold_par</a> (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct <a class="el" href="structplist.html">plist</a> **dpp2, FILE *pUfp, FILE *spup, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
+<tr class="memdesc:gab354507e8028f3e1c52ef96bb1eb9df8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute partition functions for locally stable secondary structures. <br/></td></tr>
+<tr class="memitem:ga0bcb751860bbf34e3dfee8c2fbdb3ef3"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__pf__fold.html#ga0bcb751860bbf34e3dfee8c2fbdb3ef3">putoutpU_prob</a> (double **pU, int length, int ulength, FILE *fp, int energies)</td></tr>
+<tr class="memdesc:ga0bcb751860bbf34e3dfee8c2fbdb3ef3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes the unpaired probabilities (pU) or opening energies into a file.  <a href="group__local__pf__fold.html#ga0bcb751860bbf34e3dfee8c2fbdb3ef3"></a><br/></td></tr>
+<tr class="memitem:ga9acb00ee10e96b1ca4ea394cd8bcec75"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__pf__fold.html#ga9acb00ee10e96b1ca4ea394cd8bcec75">putoutpU_prob_bin</a> (double **pU, int length, int ulength, FILE *fp, int energies)</td></tr>
+<tr class="memdesc:ga9acb00ee10e96b1ca4ea394cd8bcec75"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes the unpaired probabilities (pU) or opening energies into a binary file.  <a href="group__local__pf__fold.html#ga9acb00ee10e96b1ca4ea394cd8bcec75"></a><br/></td></tr>
+<tr class="memitem:ae85bf55053e9fb295208be322e0fa07a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="LPfold_8h.html#ae85bf55053e9fb295208be322e0fa07a">init_pf_foldLP</a> (int length)</td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"><p>Function declarations of partition function variants of the Lfold algorithm. </p>
+</div><hr/><h2>Function Documentation</h2>
+<a class="anchor" id="ae85bf55053e9fb295208be322e0fa07a"></a>
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void init_pf_foldLP </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"><em>length</em></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<p>Dunno if this function was ever used by external programs linking to RNAlib, but it was declared PUBLIC before. Anyway, never use this function as it will be removed soon and does nothing at all </p>
+
+</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="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="LPfold_8h.html">LPfold.h</a></li>
+    <li class="footer">Generated on Wed Jul 24 2013 13:38:58 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>