git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / html / snoop_8h_source.html
diff --git a/binaries/src/ViennaRNA/doc/html/snoop_8h_source.html b/binaries/src/ViennaRNA/doc/html/snoop_8h_source.html
index c26dd7f..9bf43cd 100644 (file)
--- a/binaries/src/ViennaRNA/doc/html/snoop_8h_source.html
+++ b/binaries/src/ViennaRNA/doc/html/snoop_8h_source.html
@@ -2,313 +2,306 @@
 <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/snoop.h Source File</title>
+<title>RNAlib-2.1.2: /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snoop.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" />
+<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>
+<!-- Generated by Doxygen 1.6.1 -->
+<script type="text/javascript">
+<!--
+function changeDisplayState (e){
+  var num=this.id.replace(/[^[0-9]/g,'');
+  var button=this.firstChild;
+  var sectionDiv=document.getElementById('dynsection'+num);
+  if (sectionDiv.style.display=='none'||sectionDiv.style.display==''){
+    sectionDiv.style.display='block';
+    button.src='open.gif';
+  }else{
+    sectionDiv.style.display='none';
+    button.src='closed.gif';
+  }
+}
+function initDynSections(){
+  var divs=document.getElementsByTagName('div');
+  var sectionCounter=1;
+  for(var i=0;i<divs.length-1;i++){
+    if(divs[i].className=='dynheader'&&divs[i+1].className=='dynsection'){
+      var header=divs[i];
+      var section=divs[i+1];
+      var button=header.firstChild;
+      if (button!='IMG'){
+        divs[i].insertBefore(document.createTextNode(' '),divs[i].firstChild);
+        button=document.createElement('img');
+        divs[i].insertBefore(button,divs[i].firstChild);
+      }
+      header.style.cursor='pointer';
+      header.onclick=changeDisplayState;
+      header.id='dynheader'+sectionCounter;
+      button.src='closed.gif';
+      section.id='dynsection'+sectionCounter;
+      section.style.display='none';
+      section.style.marginLeft='14px';
+      sectionCounter++;
+    }
+  }
+}
+window.onload = initDynSections;
+-->
+</script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul>
+      <li><a href="main.html"><span>Main&nbsp;Page</span></a></li>
+      <li><a href="pages.html"><span>Related&nbsp;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><a href="annotated.html"><span>Data&nbsp;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>
+  <div class="tabs">
+    <ul>
+      <li><a href="files.html"><span>File&nbsp;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('snoop_8h.html','');});
-</script>
-<div id="doc-content">
-<div class="header">
-  <div class="headertitle">
-<div class="title">snoop.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_SNOOP_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_SNOOP_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="l00009"></a><span class="lineno">    9</span>&#160;<a class="code" href="structsnoopT.html">snoopT</a> snoopfold( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">char</span> *s2, </div>
-<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;                  <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;      <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;</div>
-<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<a class="code" href="structsnoopT.html">snoopT</a> *snoop_subopt( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;                      <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;                      <span class="keywordtype">int</span> w,</div>
-<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;                      <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>&#160;                      <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>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;          <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;</div>
-<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="keywordtype">void</span> Lsnoop_subopt( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;                    <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;                    <span class="keywordtype">int</span> w, </div>
-<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
-<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">char</span>* name,</div>
-<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
-<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;<span class="keywordtype">void</span> Lsnoop_subopt_list ( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;                          <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;                          <span class="keywordtype">int</span> w, </div>
-<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
-<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">char</span> *name,</div>
-<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;        <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;</div>
-<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;<span class="keywordtype">void</span> Lsnoop_subopt_list_XS (<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,</div>
-<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;                            <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;                            <span class="keywordtype">int</span> w, </div>
-<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
-<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">char</span> *name,</div>
-<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;          <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
-<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;</div>
-<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;<span class="keywordtype">void</span> snoop_subopt_XS (<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,</div>
-<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;                      <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;                      <span class="keywordtype">int</span> w, </div>
-<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
-<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">char</span> *name,</div>
-<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;          <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;</div>
-<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;<a class="code" href="structsnoopT.html">snoopT</a> *alisnoop_subopt(<span class="keyword">const</span> <span class="keywordtype">char</span> **s1,</div>
-<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">char</span> **s2,</div>
-<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;                        <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;                        <span class="keywordtype">int</span> w,</div>
-<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;                        <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2);</div>
-<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div>
-<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;<a class="code" href="structsnoopT.html">snoopT</a> *aliLsnoop_subopt_list ( <span class="keyword">const</span> <span class="keywordtype">char</span> **s1,</div>
-<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">char</span> **s2,</div>
-<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;                                <span class="keywordtype">int</span> delta,</div>
-<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;                                <span class="keywordtype">int</span> w, </div>
-<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,</div>
-<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,</div>
-<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> distance,</div>
-<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length);</div>
-<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;<a class="code" href="structsnoopT.html">snoopT</a> alisnoopfold(<span class="keyword">const</span> <span class="keywordtype">char</span> **s1,</div>
-<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">char</span> **s2, </div>
-<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop,</div>
-<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2);</div>
-<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;<a class="code" href="structsnoopT.html">snoopT</a> snoopfold_XS(<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,</div>
-<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> pos,</div>
-<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_pos_j,</div>
-<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,</div>
-<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,</div>
-<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,</div>
-<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,</div>
-<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,</div>
-<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,</div>
-<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,</div>
-<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,</div>
-<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,</div>
-<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;                    <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,</div>
-<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;        <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);</div>
-<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;</div>
-<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;</div>
-<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;</div>
-<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;</div>
-<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;<span class="keyword">extern</span> <span class="keywordtype">int</span> snoop_subopt_sorted;</div>
-<div class="line"><a name="l00284"></a><span class="lineno">  284</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>snoop.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>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/snoop.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_SNOOP_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_SNOOP_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00004"></a>00004 <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...">data_structures.h</a>&quot;</span>
+<a name="l00009"></a>00009 <a class="code" href="structsnoopT.html">snoopT</a> snoopfold( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00010"></a>00010                   <span class="keyword">const</span> <span class="keywordtype">char</span> *s2, 
+<a name="l00011"></a>00011                   <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00012"></a>00012                   <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00013"></a>00013                   <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00014"></a>00014                   <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00015"></a>00015                   <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00016"></a>00016                   <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00017"></a>00017                   <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00018"></a>00018                   <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00019"></a>00019                   <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00020"></a>00020                   <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00021"></a>00021                   <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00022"></a>00022                   <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00023"></a>00023                   <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00024"></a>00024                   <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00025"></a>00025       <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00026"></a>00026 
+<a name="l00032"></a>00032 <a class="code" href="structsnoopT.html">snoopT</a> *snoop_subopt( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00033"></a>00033                       <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00034"></a>00034                       <span class="keywordtype">int</span> delta,
+<a name="l00035"></a>00035                       <span class="keywordtype">int</span> w,
+<a name="l00036"></a>00036                       <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00037"></a>00037                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00038"></a>00038                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00039"></a>00039                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00040"></a>00040                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00041"></a>00041                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00042"></a>00042                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00043"></a>00043                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00044"></a>00044                       <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00045"></a>00045                       <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00046"></a>00046                       <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00047"></a>00047                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00048"></a>00048                       <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00049"></a>00049                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00050"></a>00050                       <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00051"></a>00051                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00052"></a>00052                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00053"></a>00053           <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00054"></a>00054 
+<a name="l00061"></a>00061 <span class="keywordtype">void</span> Lsnoop_subopt( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00062"></a>00062                     <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00063"></a>00063                     <span class="keywordtype">int</span> delta,
+<a name="l00064"></a>00064                     <span class="keywordtype">int</span> w, 
+<a name="l00065"></a>00065                     <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00066"></a>00066                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00067"></a>00067                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00068"></a>00068                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00069"></a>00069                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00070"></a>00070                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00071"></a>00071                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00072"></a>00072                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00073"></a>00073                     <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00074"></a>00074                     <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00075"></a>00075                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00076"></a>00076                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00077"></a>00077                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00078"></a>00078                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00079"></a>00079                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00080"></a>00080                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00081"></a>00081                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00082"></a>00082                     <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,
+<a name="l00083"></a>00083                     <span class="keyword">const</span> <span class="keywordtype">char</span>* name,
+<a name="l00084"></a>00084         <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00085"></a>00085 
+<a name="l00092"></a>00092 <span class="keywordtype">void</span> Lsnoop_subopt_list ( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00093"></a>00093                           <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00094"></a>00094                           <span class="keywordtype">int</span> delta,
+<a name="l00095"></a>00095                           <span class="keywordtype">int</span> w, 
+<a name="l00096"></a>00096                           <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00097"></a>00097                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00098"></a>00098                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00099"></a>00099                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00100"></a>00100                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00101"></a>00101                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00102"></a>00102                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00103"></a>00103                           <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00104"></a>00104                           <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00105"></a>00105                           <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00106"></a>00106                           <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00107"></a>00107                           <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00108"></a>00108                           <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00109"></a>00109                           <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00110"></a>00110                           <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00111"></a>00111                           <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00112"></a>00112                           <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00113"></a>00113                           <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,
+<a name="l00114"></a>00114                           <span class="keyword">const</span> <span class="keywordtype">char</span> *name,
+<a name="l00115"></a>00115         <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00116"></a>00116 
+<a name="l00122"></a>00122 <span class="keywordtype">void</span> Lsnoop_subopt_list_XS (<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00123"></a>00123                             <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00124"></a>00124                             <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,
+<a name="l00125"></a>00125                             <span class="keywordtype">int</span> delta,
+<a name="l00126"></a>00126                             <span class="keywordtype">int</span> w, 
+<a name="l00127"></a>00127                             <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00128"></a>00128                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00129"></a>00129                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00130"></a>00130                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00131"></a>00131                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00132"></a>00132                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00133"></a>00133                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00134"></a>00134                             <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00135"></a>00135                             <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00136"></a>00136                             <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00137"></a>00137                             <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00138"></a>00138                             <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00139"></a>00139                             <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00140"></a>00140                             <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00141"></a>00141                             <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00142"></a>00142                             <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00143"></a>00143                             <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00144"></a>00144                             <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,
+<a name="l00145"></a>00145                             <span class="keyword">const</span> <span class="keywordtype">char</span> *name,
+<a name="l00146"></a>00146           <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00147"></a>00147 
+<a name="l00148"></a>00148 
+<a name="l00154"></a>00154 <span class="keywordtype">void</span> snoop_subopt_XS (<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00155"></a>00155                       <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00156"></a>00156                       <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,
+<a name="l00157"></a>00157                       <span class="keywordtype">int</span> delta,
+<a name="l00158"></a>00158                       <span class="keywordtype">int</span> w, 
+<a name="l00159"></a>00159                       <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00160"></a>00160                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00161"></a>00161                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00162"></a>00162                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00163"></a>00163                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00164"></a>00164                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00165"></a>00165                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00166"></a>00166                       <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00167"></a>00167                       <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00168"></a>00168                       <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00169"></a>00169                       <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00170"></a>00170                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00171"></a>00171                       <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00172"></a>00172                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00173"></a>00173                       <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00174"></a>00174                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00175"></a>00175                       <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00176"></a>00176                       <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,
+<a name="l00177"></a>00177                       <span class="keyword">const</span> <span class="keywordtype">char</span> *name,
+<a name="l00178"></a>00178           <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00179"></a>00179 
+<a name="l00184"></a>00184 <a class="code" href="structsnoopT.html">snoopT</a> *alisnoop_subopt(<span class="keyword">const</span> <span class="keywordtype">char</span> **s1,
+<a name="l00185"></a>00185                         <span class="keyword">const</span> <span class="keywordtype">char</span> **s2,
+<a name="l00186"></a>00186                         <span class="keywordtype">int</span> delta,
+<a name="l00187"></a>00187                         <span class="keywordtype">int</span> w,
+<a name="l00188"></a>00188                         <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00189"></a>00189                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00190"></a>00190                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00191"></a>00191                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00192"></a>00192                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00193"></a>00193                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00194"></a>00194                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00195"></a>00195                         <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00196"></a>00196                         <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00197"></a>00197                         <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00198"></a>00198                         <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00199"></a>00199                         <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00200"></a>00200                         <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00201"></a>00201                         <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00202"></a>00202                         <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00203"></a>00203                         <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00204"></a>00204                         <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2);
+<a name="l00205"></a>00205 
+<a name="l00212"></a>00212 <a class="code" href="structsnoopT.html">snoopT</a> *aliLsnoop_subopt_list ( <span class="keyword">const</span> <span class="keywordtype">char</span> **s1,
+<a name="l00213"></a>00213                                 <span class="keyword">const</span> <span class="keywordtype">char</span> **s2,
+<a name="l00214"></a>00214                                 <span class="keywordtype">int</span> delta,
+<a name="l00215"></a>00215                                 <span class="keywordtype">int</span> w, 
+<a name="l00216"></a>00216                                 <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00217"></a>00217                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00218"></a>00218                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00219"></a>00219                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00220"></a>00220                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00221"></a>00221                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshTE,
+<a name="l00222"></a>00222                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshSE,
+<a name="l00223"></a>00223                                 <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00224"></a>00224                                 <span class="keyword">const</span> <span class="keywordtype">int</span> distance,
+<a name="l00225"></a>00225                                 <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00226"></a>00226                                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00227"></a>00227                                 <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00228"></a>00228                                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00229"></a>00229                                 <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00230"></a>00230                                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00231"></a>00231                                 <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00232"></a>00232                                 <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00233"></a>00233                                 <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length);
+<a name="l00239"></a>00239 <a class="code" href="structsnoopT.html">snoopT</a> alisnoopfold(<span class="keyword">const</span> <span class="keywordtype">char</span> **s1,
+<a name="l00240"></a>00240                     <span class="keyword">const</span> <span class="keywordtype">char</span> **s2, 
+<a name="l00241"></a>00241                     <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00242"></a>00242                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop,
+<a name="l00243"></a>00243                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00244"></a>00244                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00245"></a>00245                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00246"></a>00246                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00247"></a>00247                     <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00248"></a>00248                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00249"></a>00249                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00250"></a>00250                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00251"></a>00251                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00252"></a>00252                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00253"></a>00253                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00254"></a>00254                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2);
+<a name="l00259"></a>00259 <a class="code" href="structsnoopT.html">snoopT</a> snoopfold_XS(<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00260"></a>00260                     <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00261"></a>00261                     <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,
+<a name="l00262"></a>00262                     <span class="keyword">const</span> <span class="keywordtype">int</span> pos,
+<a name="l00263"></a>00263                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_pos_j,
+<a name="l00264"></a>00264                     <span class="keyword">const</span> <span class="keywordtype">int</span> penalty,
+<a name="l00265"></a>00265                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, 
+<a name="l00266"></a>00266                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshLE,
+<a name="l00267"></a>00267                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshRE,
+<a name="l00268"></a>00268                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshDE,
+<a name="l00269"></a>00269                     <span class="keyword">const</span> <span class="keywordtype">int</span> threshD,
+<a name="l00270"></a>00270                     <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00271"></a>00271                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem,
+<a name="l00272"></a>00272                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00273"></a>00273                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00274"></a>00274                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_s1,
+<a name="l00275"></a>00275                     <span class="keyword">const</span> <span class="keywordtype">int</span> max_s1,
+<a name="l00276"></a>00276                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_d1,
+<a name="l00277"></a>00277                     <span class="keyword">const</span> <span class="keywordtype">int</span> min_d2,
+<a name="l00278"></a>00278         <span class="keyword">const</span> <span class="keywordtype">int</span> fullStemEnergy);
+<a name="l00279"></a>00279 
+<a name="l00280"></a>00280 
+<a name="l00281"></a>00281 
+<a name="l00282"></a>00282 
+<a name="l00283"></a>00283 <span class="keyword">extern</span> <span class="keywordtype">int</span> snoop_subopt_sorted;
+<a name="l00284"></a>00284 <span class="preprocessor">#endif</span>
+</pre></div></div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>
 </html>