--- /dev/null
+<!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/MEA.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">
+ $(document).ready(initResizable);
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">RNAlib-2.1.2
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="modules.html"><span>Modules</span></a></li>
+ <li><a href="annotated.html"><span>Data Structures</span></a></li>
+ <li class="current"><a href="files.html"><span>Files</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="files.html"><span>File List</span></a></li>
+ <li><a href="globals.html"><span>Globals</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('MEA_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">MEA.h File Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>Computes a MEA (maximum expected accuracy) structure.
+<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 MEA.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="MEA_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2MEA_8h" alt=""/></div>
+<map name="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2MEA_8h" id="_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2MEA_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="MEA_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:a396ec6144c6a74fcbab4cea6b42d76c3"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="MEA_8h.html#a396ec6144c6a74fcbab4cea6b42d76c3">MEA</a> (<a class="el" href="structplist.html">plist</a> *p, char *structure, double gamma)</td></tr>
+<tr class="memdesc:a396ec6144c6a74fcbab4cea6b42d76c3"><td class="mdescLeft"> </td><td class="mdescRight">Computes a MEA (maximum expected accuracy) structure. <a href="#a396ec6144c6a74fcbab4cea6b42d76c3"></a><br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"><p>Computes a MEA (maximum expected accuracy) structure. </p>
+</div><hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a396ec6144c6a74fcbab4cea6b42d76c3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">float MEA </td>
+ <td>(</td>
+ <td class="paramtype"><a class="el" href="structplist.html">plist</a> * </td>
+ <td class="paramname"><em>p</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"><em>structure</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">double </td>
+ <td class="paramname"><em>gamma</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Computes a MEA (maximum expected accuracy) structure. </p>
+<p>The algorithm maximizes the expected accuracy </p>
+<p class="formulaDsp">
+<img class="formulaDsp" alt="\[ A(S) = \sum_{(i,j) \in S} 2 \gamma p_{ij} + \sum_{i \notin S} p^u_i \]" src="form_15.png"/>
+</p>
+<p> Higher values of <img class="formulaInl" alt="$\gamma$" src="form_16.png"/> result in more base pairs of lower probability and thus higher sensitivity. Low values of <img class="formulaInl" alt="$\gamma$" src="form_16.png"/> result in structures containing only highly likely pairs (high specificity). The code of the MEA function also demonstrates the use of sparse dynamic programming scheme to reduce the time and memory complexity of folding. </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="MEA_8h.html">MEA.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>
git://source.jalview.org / jabaws.git / blobdiff