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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 / files.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: File List</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">
+  $(document).ready(initResizable);
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <td style="padding-left: 0.5em;">
+   <div id="projectname">RNAlib-2.1.2
+   </div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+  <div id="navrow1" class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
+      <li><a href="modules.html"><span>Modules</span></a></li>
+      <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+    </ul>
+  </div>
+  <div id="navrow2" class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>Globals</span></a></li>
+    </ul>
+  </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
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+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('files.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="headertitle">
+<div class="title">File List</div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock">Here is a list of all documented files with brief descriptions:</div><div class="directory">
+<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</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_')"/><img id="img_0_" src="ftv2folderopen.png" alt="-" width="24" height="22" onclick="toggleFolder('0_')"/><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html" target="_self">H</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="2Dfold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="2Dfold_8h.html" target="_self">2Dfold.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_" 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 href="2Dpfold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="2Dpfold_8h.html" target="_self">2Dpfold.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="alifold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="alifold_8h.html" target="_self">alifold.h</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_3_" 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 href="cofold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="cofold_8h.html" target="_self">cofold.h</a></td><td class="desc">MFE version of cofolding routines</td></tr>
+<tr id="row_0_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="convert__epars_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="convert__epars_8h.html" target="_self">convert_epars.h</a></td><td class="desc">Functions and definitions for energy parameter file format conversion</td></tr>
+<tr id="row_0_5_" 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 href="data__structures_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="data__structures_8h.html" target="_self">data_structures.h</a></td><td class="desc">All datastructures and typedefs shared among the Vienna RNA Package can be found here</td></tr>
+<tr id="row_0_6_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="dist__vars_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="dist__vars_8h.html" target="_self">dist_vars.h</a></td><td class="desc">Global variables for Distance-Package</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 href="duplex_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="duplex_8h.html" target="_self">duplex.h</a></td><td class="desc">Duplex folding function declarations..</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 href="edit__cost_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="edit__cost_8h.html" target="_self">edit_cost.h</a></td><td class="desc">Global variables for Edit Costs included by treedist.c and stringdist.c</td></tr>
+<tr id="row_0_9_" 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 href="energy__const_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="energy__const_8h.html" target="_self">energy_const.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="findpath_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="findpath_8h.html" target="_self">findpath.h</a></td><td class="desc">Compute direct refolding paths between two secondary structures</td></tr>
+<tr id="row_0_11_" 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 href="fold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="fold_8h.html" target="_self">fold.h</a></td><td class="desc">MFE calculations and energy evaluations for single RNA sequences</td></tr>
+<tr id="row_0_12_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="fold__vars_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="fold__vars_8h.html" target="_self">fold_vars.h</a></td><td class="desc">Here all all declarations of the global variables used throughout RNAlib</td></tr>
+<tr id="row_0_13_" 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 href="gquad_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="gquad_8h.html" target="_self">gquad.h</a></td><td class="desc">Various functions related to G-quadruplex computations</td></tr>
+<tr id="row_0_14_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="inverse_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="inverse_8h.html" target="_self">inverse.h</a></td><td class="desc">Inverse folding routines</td></tr>
+<tr id="row_0_15_" 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 href="Lfold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="Lfold_8h.html" target="_self">Lfold.h</a></td><td class="desc">Predicting local MFE structures of large sequences</td></tr>
+<tr id="row_0_16_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="loop__energies_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="loop__energies_8h.html" target="_self">loop_energies.h</a></td><td class="desc">Energy evaluation for MFE and partition function calculations</td></tr>
+<tr id="row_0_17_" 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 href="LPfold_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="LPfold_8h.html" target="_self">LPfold.h</a></td><td class="desc">Function declarations of partition function variants of the Lfold algorithm</td></tr>
+<tr id="row_0_18_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="MEA_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="MEA_8h.html" target="_self">MEA.h</a></td><td class="desc">Computes a MEA (maximum expected accuracy) structure</td></tr>
+<tr id="row_0_19_" 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 href="mm_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="mm_8h.html" target="_self">mm.h</a></td><td class="desc">Several Maximum Matching implementations</td></tr>
+<tr id="row_0_20_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="naview_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="naview_8h.html" target="_self">naview.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_21_" 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 href="params_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="params_8h.html" target="_self">params.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_22_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="part__func_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="part__func_8h.html" target="_self">part_func.h</a></td><td class="desc">Partition function of single RNA sequences</td></tr>
+<tr id="row_0_23_" 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 href="part__func__co_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="part__func__co_8h.html" target="_self">part_func_co.h</a></td><td class="desc">Partition function for two RNA sequences</td></tr>
+<tr id="row_0_24_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="part__func__up_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="part__func__up_8h.html" target="_self">part_func_up.h</a></td><td class="desc">Partition Function Cofolding as stepwise process</td></tr>
+<tr id="row_0_25_" 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 href="plot__layouts_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="plot__layouts_8h.html" target="_self">plot_layouts.h</a></td><td class="desc">Secondary structure plot layout algorithms</td></tr>
+<tr id="row_0_26_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="profiledist_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="profiledist_8h.html" target="_self">profiledist.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_27_" 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 href="PS__dot_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="PS__dot_8h.html" target="_self">PS_dot.h</a></td><td class="desc">Various functions for plotting RNA secondary structures, dot-plots and other visualizations</td></tr>
+<tr id="row_0_28_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="read__epars_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="read__epars_8h.html" target="_self">read_epars.h</a></td><td class="desc"></td></tr>
+<tr id="row_0_29_" 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 href="RNAstruct_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="RNAstruct_8h.html" target="_self">RNAstruct.h</a></td><td class="desc">Parsing and Coarse Graining of Structures</td></tr>
+<tr id="row_0_30_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="stringdist_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="stringdist_8h.html" target="_self">stringdist.h</a></td><td class="desc">Functions for String Alignment</td></tr>
+<tr id="row_0_31_" 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 href="subopt_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="subopt_8h.html" target="_self">subopt.h</a></td><td class="desc">RNAsubopt and density of states declarations</td></tr>
+<tr id="row_0_32_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><a href="treedist_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="treedist_8h.html" target="_self">treedist.h</a></td><td class="desc">Functions for <a class="el" href="structTree.html">Tree</a> Edit Distances</td></tr>
+<tr id="row_0_33_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a href="utils_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="utils_8h.html" target="_self">utils.h</a></td><td class="desc">Various utility- and helper-functions used throughout the Vienna RNA package</td></tr>
+<tr id="row_1_"><td class="entry"><img id="arr_1_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('1_')"/><img id="img_1_" src="ftv2folderopen.png" alt="-" width="24" height="22" onclick="toggleFolder('1_')"/><a class="el" href="dir_97aefd0d527b934f1d99a682da8fe6a9.html" target="_self">lib</a></td><td class="desc"></td></tr>
+<tr id="row_1_0_" 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 href="1_88_84__epars_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="1_88_84__epars_8h.html" target="_self">1.8.4_epars.h</a></td><td class="desc">Free energy parameters for parameter file conversion</td></tr>
+<tr id="row_1_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a href="1_88_84__intloops_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><a class="el" href="1_88_84__intloops_8h.html" target="_self">1.8.4_intloops.h</a></td><td class="desc">Free energy parameters for interior loop contributions needed by the parameter file conversion functions</td></tr>
+<tr id="row_2_" class="even"><td class="entry"><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><a href="mainpage_8h_source.html"><img src="ftv2doc.png" alt="*" width="24" height="22" /></a><b>mainpage.h</b></td><td class="desc"></td></tr>
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