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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 / modules.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: Modules</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>
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+</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 class="current"><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">
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+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('modules.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="headertitle">
+<div class="title">Modules</div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock">Here is a list of all modules:</div><div class="directory">
+<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span>]</div><table class="directory">
+<tr id="row_0_" class="even"><td class="entry"><img id="arr_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_')"/><a class="el" href="group__folding__routines.html" target="_self">RNA Secondary Structure Folding</a></td><td class="desc">This module contains all functions related to thermodynamic folding of RNAs</td></tr>
+<tr id="row_0_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_0_')"/><a class="el" href="group__mfe__fold.html" target="_self">Calculating Minimum Free Energy (MFE) Structures</a></td><td class="desc">This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences</td></tr>
+<tr id="row_0_0_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__mfe__cofold.html" target="_self">MFE Structures of two hybridized Sequences</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__consensus__mfe__fold.html" target="_self">MFE Consensus Structures for Sequence Alignment(s)</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__local__mfe__fold.html" target="_self">Local MFE structure Prediction and Z-scores</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_3_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__kl__neighborhood__mfe.html" target="_self">Calculating MFE representatives of a Distance Based Partitioning</a></td><td class="desc">Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures</td></tr>
+<tr id="row_0_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_1_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_1_')"/><a class="el" href="group__pf__fold.html" target="_self">Calculating Partition Functions and Pair Probabilities</a></td><td class="desc">This section provides information about all functions and variables related to the calculation of the partition function and base pair probabilities</td></tr>
+<tr id="row_0_1_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__mea__fold.html" target="_self">Compute the structure with maximum expected accuracy (MEA)</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__centroid__fold.html" target="_self">Compute the centroid structure</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__pf__cofold.html" target="_self">Partition Function for two hybridized Sequences</a></td><td class="desc">Partition Function Cofolding</td></tr>
+<tr id="row_0_1_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__up__cofold.html" target="_self">Partition Function for two hybridized Sequences as a stepwise Process</a></td><td class="desc">Partition Function Cofolding as a stepwise process</td></tr>
+<tr id="row_0_1_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__consensus__pf__fold.html" target="_self">Partition Function and Base Pair Probabilities for Sequence Alignment(s)</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_5_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__local__pf__fold.html" target="_self">Partition functions for locally stable secondary structures</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_6_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__kl__neighborhood__pf.html" target="_self">Calculate Partition Functions of a Distance Based Partitioning</a></td><td class="desc">Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures</td></tr>
+<tr id="row_0_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_2_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_2_')"/><a class="el" href="group__subopt__fold.html" target="_self">Enumerating Suboptimal Structures</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__subopt__zuker.html" target="_self">Suboptimal structures according to Zuker et al. 1989</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__subopt__wuchty.html" target="_self">Suboptimal structures within an energy band arround the MFE</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_2_2_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('0_2_2_')"/><a class="el" href="group__subopt__stochbt.html" target="_self">Stochastic backtracking in the Ensemble</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_2_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__consensus__stochbt.html" target="_self">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_2_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__kl__neighborhood__stochbt.html" target="_self">Stochastic Backtracking of Structures from Distance Based Partitioning</a></td><td class="desc">Contains functions related to stochastic backtracking from a specified distance class</td></tr>
+<tr id="row_0_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_3_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_3_')"/><a class="el" href="group__cofold.html" target="_self">Calculate Secondary Structures of two RNAs upon Dimerization</a></td><td class="desc">Predict structures formed by two molecules upon hybridization</td></tr>
+<tr id="row_0_3_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__mfe__cofold.html" target="_self">MFE Structures of two hybridized Sequences</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__pf__cofold.html" target="_self">Partition Function for two hybridized Sequences</a></td><td class="desc">Partition Function Cofolding</td></tr>
+<tr id="row_0_3_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__up__cofold.html" target="_self">Partition Function for two hybridized Sequences as a stepwise Process</a></td><td class="desc">Partition Function Cofolding as a stepwise process</td></tr>
+<tr id="row_0_4_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_4_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_4_')"/><a class="el" href="group__consensus__fold.html" target="_self">Predicting Consensus Structures from Alignment(s)</a></td><td class="desc">Compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments</td></tr>
+<tr id="row_0_4_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__consensus__mfe__fold.html" target="_self">MFE Consensus Structures for Sequence Alignment(s)</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__consensus__pf__fold.html" target="_self">Partition Function and Base Pair Probabilities for Sequence Alignment(s)</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__consensus__stochbt.html" target="_self">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__local__consensus__fold.html" target="_self">Local MFE consensus structures for Sequence Alignments</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_5_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_5_')"/><a class="el" href="group__local__fold.html" target="_self">Predicting Locally stable structures of large sequences</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__local__mfe__fold.html" target="_self">Local MFE structure Prediction and Z-scores</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__local__pf__fold.html" target="_self">Partition functions for locally stable secondary structures</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__local__consensus__fold.html" target="_self">Local MFE consensus structures for Sequence Alignments</a></td><td class="desc"></td></tr>
+<tr id="row_0_6_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_6_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_6_')"/><a class="el" href="group__energy__parameters.html" target="_self">Change and Precalculate Energy Parameter Sets and Boltzmann Factors</a></td><td class="desc">All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s)</td></tr>
+<tr id="row_0_6_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_6_0_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('0_6_0_')"/><a class="el" href="group__energy__parameters__rw.html" target="_self">Reading/Writing energy parameter sets from/to File</a></td><td class="desc">Read and Write energy parameter sets from and to text files</td></tr>
+<tr id="row_0_6_0_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__energy__parameters__convert.html" target="_self">Converting energy parameter files</a></td><td class="desc">Convert energy parameter files into the latest format</td></tr>
+<tr id="row_0_7_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__eval.html" target="_self">Energy evaluation</a></td><td class="desc">This module contains all functions and variables related to energy evaluation of sequence/structure pairs</td></tr>
+<tr id="row_0_8_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__inverse__fold.html" target="_self">Searching Sequences for Predefined Structures</a></td><td class="desc"></td></tr>
+<tr id="row_0_9_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_9_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('0_9_')"/><a class="el" href="group__class__fold.html" target="_self">Classified Dynamic Programming</a></td><td class="desc"></td></tr>
+<tr id="row_0_9_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img id="arr_0_9_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_9_0_')"/><a class="el" href="group__kl__neighborhood.html" target="_self">Distance based partitioning of the Secondary Structure Space</a></td><td class="desc">Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space</td></tr>
+<tr id="row_0_9_0_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__kl__neighborhood__mfe.html" target="_self">Calculating MFE representatives of a Distance Based Partitioning</a></td><td class="desc">Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures</td></tr>
+<tr id="row_0_9_0_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a class="el" href="group__kl__neighborhood__pf.html" target="_self">Calculate Partition Functions of a Distance Based Partitioning</a></td><td class="desc">Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures</td></tr>
+<tr id="row_0_9_0_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__kl__neighborhood__stochbt.html" target="_self">Stochastic Backtracking of Structures from Distance Based Partitioning</a></td><td class="desc">Contains functions related to stochastic backtracking from a specified distance class</td></tr>
+<tr id="row_0_9_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__dos.html" target="_self">Compute the Density of States</a></td><td class="desc"></td></tr>
+<tr id="row_1_" class="even"><td class="entry"><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a class="el" href="group__parse.html" target="_self">Parsing and Comparing - Functions to Manipulate Structures</a></td><td class="desc"></td></tr>
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