--- /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/snofold.h Source File</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('snofold_8h.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+ <div class="headertitle">
+<div class="title">snofold.h</div> </div>
+</div><!--header-->
+<div class="contents">
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/* function from fold.c */</span></div>
+<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span></div>
+<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here.">data_structures.h</a>"</span></div>
+<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> </div>
+<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">/* Normal fold */</span></div>
+<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div>
+<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="keywordtype">int</span> snofold( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
+<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,</div>
+<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> threshold, </div>
+<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
+<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
+<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
+<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);</div>
+<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keywordtype">void</span> snofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length); <span class="comment">/* free arrays for mfe folding */</span></div>
+<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keywordtype">void</span> snoinitialize_fold(<span class="keywordtype">int</span> length); <span class="comment">/* allocate arrays for folding */</span></div>
+<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="keywordtype">void</span> snoupdate_fold_params(<span class="keywordtype">void</span>); <span class="comment">/* recalculate parameters */</span></div>
+<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keywordtype">int</span> snoloop_energy(<span class="keywordtype">short</span> *ptable,</div>
+<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keywordtype">short</span> *s,</div>
+<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordtype">short</span> *s1,</div>
+<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">int</span> i);</div>
+<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keywordtype">void</span> snoexport_fold_arrays( <span class="keywordtype">int</span> **indx_p,</div>
+<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordtype">int</span> **mLoop_p,</div>
+<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordtype">int</span> **cLoop,</div>
+<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <a class="code" href="structfolden.html">folden</a> ***fold_p,</div>
+<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <a class="code" href="structfolden.html">folden</a> ***fold_p_XS);</div>
+<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keywordtype">char</span> * snobacktrack_fold_from_pair( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
+<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordtype">int</span> i,</div>
+<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordtype">int</span> j);</div>
+<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">/* alifold */</span></div>
+<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">float</span> alisnofold( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,</div>
+<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,</div>
+<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
+<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
+<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
+<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
+<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);</div>
+<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keywordtype">void</span> alisnofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length);</div>
+<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keywordtype">char</span> *alisnobacktrack_fold_from_pair(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequence,</div>
+<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">int</span> i,</div>
+<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordtype">int</span> j,</div>
+<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordtype">int</span> *cov);</div>
+<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c" title="This variable controls the weight of the covariance term in the energy function of alignment folding ...">cv_fact</a> <span class="comment">/* =1 */</span>;</div>
+<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61" title="This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...">nc_fact</a> <span class="comment">/* =1 */</span>;</div>
+<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
+<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment">/* max number of mismatch >>>>>..(( )).>>>> */</span></div>
+<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#define MISMATCH 3</span></div>
+<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="preprocessor">#endif</span></div>
+</div><!-- fragment --></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"><b>snofold.h</b></li>
+ <li class="footer">Generated on Wed Jul 24 2013 13:38:56 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