git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
WSTester updated to work plus hopefully all the other changes that need to go into...
[jabaws.git] / binaries / src / ViennaRNA / doc / html / ali__plex_8h_source.html
diff --git a/binaries/src/ViennaRNA/doc/html/ali__plex_8h_source.html b/binaries/src/ViennaRNA/doc/html/ali__plex_8h_source.html
new file mode 100644 (file)
index 0000000..cd432e0
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/html/ali__plex_8h_source.html
@@ -0,0 +1,114 @@
+<!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/ali_plex.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">
+  $(document).ready(initResizable);
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <td style="padding-left: 0.5em;">
+   <div id="projectname">RNAlib-2.1.2
+   </div>
+  </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.1.1 -->
+  <div id="navrow1" class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
+      <li><a href="modules.html"><span>Modules</span></a></li>
+      <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+    </ul>
+  </div>
+  <div id="navrow2" class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>Globals</span></a></li>
+    </ul>
+  </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+  <div id="nav-tree">
+    <div id="nav-tree-contents">
+    </div>
+  </div>
+  <div id="splitbar" style="-moz-user-select:none;" 
+       class="ui-resizable-handle">
+  </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('ali__plex_8h.html','');});
+</script>
+<div id="doc-content">
+<div class="header">
+  <div class="headertitle">
+<div class="title">ali_plex.h</div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_ALI_PLEX_H__</span></div>
+<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_ALI_PLEX_H__</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="preprocessor"></span></div>
+<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#include &quot;<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>&quot;</span></div>
+<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<a class="code" href="structduplexT.html">duplexT</a>** aliLduplexfold( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1[],</div>
+<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">char</span> *s2[],</div>
+<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshold,</div>
+<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> extension_cost,</div>
+<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
+<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> delta,</div>
+<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> fast,</div>
+<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> il_a,</div>
+<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> il_b,</div>
+<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> b_a,</div>
+<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> b_b);</div>
+<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<a class="code" href="structduplexT.html">duplexT</a>** aliLduplexfold_XS(<span class="keyword">const</span> <span class="keywordtype">char</span>* s1[],</div>
+<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">char</span>* s2[],</div>
+<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,</div>
+<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s2, </div>
+<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshold,</div>
+<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
+<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> delta,</div>
+<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> fast,</div>
+<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> il_a,</div>
+<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> il_b,</div>
+<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> b_a,</div>
+<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> b_b);</div>
+<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
+<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="comment">/*</span></div>
+<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="comment">extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);</span></div>
+<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="comment">extern duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1, </span></div>
+<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="comment">const int **access_s2, const int i_pos, const int j_pos, const int threshold);</span></div>
+<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="comment">*/</span></div>
+<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<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>ali_plex.h</b></li>
+    <li class="footer">Generated on Wed Jul 24 2013 13:38:55 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>