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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 / annotated.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: Data Structures</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"/>
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+</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 class="current"><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+    </ul>
+  </div>
+  <div id="navrow2" class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li><a href="classes.html"><span>Data&#160;Structure&#160;Index</span></a></li>
+      <li><a href="functions.html"><span>Data&#160;Fields</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('annotated.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="headertitle">
+<div class="title">Data Structures</div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock">Here are the data structures with brief descriptions:</div><div class="directory">
+<table class="directory">
+<tr id="row_0_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structbondT.html" target="_self">bondT</a></td><td class="desc">Base pair</td></tr>
+<tr id="row_1_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structbondTEn.html" target="_self">bondTEn</a></td><td class="desc">Base pair with associated energy</td></tr>
+<tr id="row_2_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structcofoldF.html" target="_self">cofoldF</a></td><td class="desc"></td></tr>
+<tr id="row_3_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structConcEnt.html" target="_self">ConcEnt</a></td><td class="desc"></td></tr>
+<tr id="row_4_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structconstrain.html" target="_self">constrain</a></td><td class="desc">Constraints for cofolding</td></tr>
+<tr id="row_5_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structCOORDINATE.html" target="_self">COORDINATE</a></td><td class="desc">This is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type <a class="el" href="structCOORDINATE.html" title="this is a workarround for the SWIG Perl Wrapper RNA plot function that returns an array of type COORD...">COORDINATE</a></td></tr>
+<tr id="row_6_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structcpair.html" target="_self">cpair</a></td><td class="desc">This datastructure is used as input parameter in functions of PS_dot.c</td></tr>
+<tr id="row_7_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structduplexT.html" target="_self">duplexT</a></td><td class="desc"></td></tr>
+<tr id="row_8_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structdupVar.html" target="_self">dupVar</a></td><td class="desc"></td></tr>
+<tr id="row_9_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structfolden.html" target="_self">folden</a></td><td class="desc"></td></tr>
+<tr id="row_10_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structinteract.html" target="_self">interact</a></td><td class="desc"></td></tr>
+<tr id="row_11_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structintermediate__t.html" target="_self">intermediate_t</a></td><td class="desc"></td></tr>
+<tr id="row_12_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structINTERVAL.html" target="_self">INTERVAL</a></td><td class="desc">Sequence interval stack element used in subopt.c</td></tr>
+<tr id="row_13_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structLIST.html" target="_self">LIST</a></td><td class="desc"></td></tr>
+<tr id="row_14_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structLST__BUCKET.html" target="_self">LST_BUCKET</a></td><td class="desc"></td></tr>
+<tr id="row_15_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structmodel__detailsT.html" target="_self">model_detailsT</a></td><td class="desc">The data structure that contains the complete model details used throughout the calculations</td></tr>
+<tr id="row_16_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structmove__t.html" target="_self">move_t</a></td><td class="desc"></td></tr>
+<tr id="row_17_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structPAIR.html" target="_self">PAIR</a></td><td class="desc">Base pair data structure used in subopt.c</td></tr>
+<tr id="row_18_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structpair__info.html" target="_self">pair_info</a></td><td class="desc">A base pair info structure</td></tr>
+<tr id="row_19_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structpairpro.html" target="_self">pairpro</a></td><td class="desc"></td></tr>
+<tr id="row_20_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structparamT.html" target="_self">paramT</a></td><td class="desc">The datastructure that contains temperature scaled energy parameters</td></tr>
+<tr id="row_21_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structpath__t.html" target="_self">path_t</a></td><td class="desc"></td></tr>
+<tr id="row_22_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structpf__paramT.html" target="_self">pf_paramT</a></td><td class="desc">The datastructure that contains temperature scaled Boltzmann weights of the energy parameters</td></tr>
+<tr id="row_23_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structplist.html" target="_self">plist</a></td><td class="desc">This datastructure is used as input parameter in functions of <a class="el" href="PS__dot_8h.html" title="Various functions for plotting RNA secondary structures, dot-plots and other visualizations.">PS_dot.h</a> and others</td></tr>
+<tr id="row_24_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structPostorder__list.html" target="_self">Postorder_list</a></td><td class="desc"></td></tr>
+<tr id="row_25_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structpu__contrib.html" target="_self">pu_contrib</a></td><td class="desc">Contributions to p_u</td></tr>
+<tr id="row_26_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structpu__out.html" target="_self">pu_out</a></td><td class="desc">Collection of all free_energy of beeing unpaired values for output</td></tr>
+<tr id="row_27_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structsect.html" target="_self">sect</a></td><td class="desc">Stack of partial structures for backtracking</td></tr>
+<tr id="row_28_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structsnoopT.html" target="_self">snoopT</a></td><td class="desc"></td></tr>
+<tr id="row_29_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structSOLUTION.html" target="_self">SOLUTION</a></td><td class="desc">Solution element from subopt.c</td></tr>
+<tr id="row_30_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structstruct__en.html" target="_self">struct_en</a></td><td class="desc"></td></tr>
+<tr id="row_31_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structsvm__model.html" target="_self">svm_model</a></td><td class="desc"></td></tr>
+<tr id="row_32_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structswString.html" target="_self">swString</a></td><td class="desc"></td></tr>
+<tr id="row_33_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structTree.html" target="_self">Tree</a></td><td class="desc"></td></tr>
+<tr id="row_34_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structTwoDfold__solution.html" target="_self">TwoDfold_solution</a></td><td class="desc">Solution element returned from TwoDfoldList</td></tr>
+<tr id="row_35_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structTwoDfold__vars.html" target="_self">TwoDfold_vars</a></td><td class="desc">Variables compound for 2Dfold MFE folding</td></tr>
+<tr id="row_36_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structTwoDpfold__solution.html" target="_self">TwoDpfold_solution</a></td><td class="desc">Solution element returned from TwoDpfoldList</td></tr>
+<tr id="row_37_"><td class="entry"><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structTwoDpfold__vars.html" target="_self">TwoDpfold_vars</a></td><td class="desc">Variables compound for 2Dfold partition function folding</td></tr>
+</table>
+</div><!-- directory -->
+</div><!-- contents -->
+</div><!-- doc-content -->
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+    <li class="footer">Generated on Wed Jul 24 2013 13:39:00 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>
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