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JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / html / group__consensus__pf__fold.html
diff --git a/binaries/src/ViennaRNA/doc/html/group__consensus__pf__fold.html b/binaries/src/ViennaRNA/doc/html/group__consensus__pf__fold.html
index cc06af3..32d2f30 100644 (file)
--- a/binaries/src/ViennaRNA/doc/html/group__consensus__pf__fold.html
+++ b/binaries/src/ViennaRNA/doc/html/group__consensus__pf__fold.html
@@ -2,270 +2,269 @@
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-Functions</h2></td></tr>
-<tr class="memitem:ga4d2ff54d8210fc7cceeeff389d4dbd1d"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alipf_fold_par</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
-<tr class="memitem:gad32ded7d753ccaf211ab35782d1f42a9"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9">alipf_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
-<tr class="memdesc:gad32ded7d753ccaf211ab35782d1f42a9"><td class="mdescLeft">&#160;</td><td class="mdescRight">The partition function version of <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a> works in analogy to <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a>. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of <a class="el" href="structpair__info.html" title="A base pair info structure.">pair_info</a> structs. The list is terminated by the first entry with pi.i = 0.  <a href="#gad32ded7d753ccaf211ab35782d1f42a9"></a><br/></td></tr>
-<tr class="memitem:ga6b4dde1d43b79ab3753508c46cf50363"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
-<tr class="memitem:gadaaf83394216413505e48d913dbc1b4e"><td class="memItemLeft" align="right" valign="top">double *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e">export_ali_bppm</a> (void)</td></tr>
-<tr class="memdesc:gadaaf83394216413505e48d913dbc1b4e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get a pointer to the base pair probability array.  <a href="#gadaaf83394216413505e48d913dbc1b4e"></a><br/></td></tr>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alipf_fold_par</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9">alipf_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
+<tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">The partition function version of <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a> works in analogy to <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a>. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of <a class="el" href="structpair__info.html" title="A base pair info structure.">pair_info</a> structs. The list is terminated by the first entry with pi.i = 0.  <a href="#gad32ded7d753ccaf211ab35782d1f42a9"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold</a> (const char **sequences, char *structure, <a class="el" href="structplist.html">plist</a> **pl)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">FLT_OR_DBL *&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html#ga11b6ab8bd9be1821fea352b190a01cab">export_ali_bppm</a> (void)</td></tr>
+<tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Get a pointer to the base pair probability array.  <a href="#ga11b6ab8bd9be1821fea352b190a01cab"></a><br/></td></tr>
 </table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
 <hr/><h2>Function Documentation</h2>
-<a class="anchor" id="ga4d2ff54d8210fc7cceeeff389d4dbd1d"></a>
+<a class="anchor" id="ga4d2ff54d8210fc7cceeeff389d4dbd1d"></a><!-- doxytag: member="alifold.h::alipf_fold_par" ref="ga4d2ff54d8210fc7cceeeff389d4dbd1d" args="(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)" -->
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       <table class="memname">
         <tr>
           <td class="memname">float alipf_fold_par </td>
           <td>(</td>
-          <td class="paramtype">const char **&#160;</td>
-          <td class="paramname"><em>sequences</em>, </td>
+          <td class="paramtype">const char **&nbsp;</td>
+          <td class="paramname"> <em>sequences</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">char *&#160;</td>
-          <td class="paramname"><em>structure</em>, </td>
+          <td class="paramtype">char *&nbsp;</td>
+          <td class="paramname"> <em>structure</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&#160;</td>
-          <td class="paramname"><em>pl</em>, </td>
+          <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&nbsp;</td>
+          <td class="paramname"> <em>pl</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype"><a class="el" href="structpf__paramT.html">pf_paramT</a> *&#160;</td>
-          <td class="paramname"><em>parameters</em>, </td>
+          <td class="paramtype"><a class="el" href="structpf__paramT.html">pf_paramT</a> *&nbsp;</td>
+          <td class="paramname"> <em>parameters</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">int&#160;</td>
-          <td class="paramname"><em>calculate_bppm</em>, </td>
+          <td class="paramtype">int&nbsp;</td>
+          <td class="paramname"> <em>calculate_bppm</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">int&#160;</td>
-          <td class="paramname"><em>is_constrained</em>, </td>
+          <td class="paramtype">int&nbsp;</td>
+          <td class="paramname"> <em>is_constrained</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">int&#160;</td>
-          <td class="paramname"><em>is_circular</em>&#160;</td>
+          <td class="paramtype">int&nbsp;</td>
+          <td class="paramname"> <em>is_circular</em></td><td>&nbsp;</td>
         </tr>
         <tr>
           <td></td>
           <td>)</td>
-          <td></td><td></td>
+          <td></td><td></td><td></td>
         </tr>
       </table>
-</div><div class="memdoc">
-<dl class="params"><dt>Parameters:</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">sequences</td><td></td></tr>
-    <tr><td class="paramname">structure</td><td></td></tr>
-    <tr><td class="paramname">pl</td><td></td></tr>
-    <tr><td class="paramname">parameters</td><td></td></tr>
-    <tr><td class="paramname">calculate_bppm</td><td></td></tr>
-    <tr><td class="paramname">is_constrained</td><td></td></tr>
-    <tr><td class="paramname">is_circular</td><td></td></tr>
+</div>
+<div class="memdoc">
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table border="0" cellspacing="2" cellpadding="0">
+    <tr><td valign="top"></td><td valign="top"><em>sequences</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>pl</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>parameters</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>calculate_bppm</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>is_constrained</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>is_circular</em>&nbsp;</td><td></td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
 
 </div>
 </div>
-<a class="anchor" id="gad32ded7d753ccaf211ab35782d1f42a9"></a>
+<a class="anchor" id="gad32ded7d753ccaf211ab35782d1f42a9"></a><!-- doxytag: member="alifold.h::alipf_fold" ref="gad32ded7d753ccaf211ab35782d1f42a9" args="(const char **sequences, char *structure, plist **pl)" -->
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           <td class="memname">float alipf_fold </td>
           <td>(</td>
-          <td class="paramtype">const char **&#160;</td>
-          <td class="paramname"><em>sequences</em>, </td>
+          <td class="paramtype">const char **&nbsp;</td>
+          <td class="paramname"> <em>sequences</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">char *&#160;</td>
-          <td class="paramname"><em>structure</em>, </td>
+          <td class="paramtype">char *&nbsp;</td>
+          <td class="paramname"> <em>structure</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&#160;</td>
-          <td class="paramname"><em>pl</em>&#160;</td>
+          <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&nbsp;</td>
+          <td class="paramname"> <em>pl</em></td><td>&nbsp;</td>
         </tr>
         <tr>
           <td></td>
           <td>)</td>
-          <td></td><td></td>
+          <td></td><td></td><td></td>
         </tr>
       </table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
 
 <p>The partition function version of <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a> works in analogy to <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold()</a>. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of <a class="el" href="structpair__info.html" title="A base pair info structure.">pair_info</a> structs. The list is terminated by the first entry with pi.i = 0. </p>
-<dl class="params"><dt>Parameters:</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">sequences</td><td></td></tr>
-    <tr><td class="paramname">structure</td><td></td></tr>
-    <tr><td class="paramname">pl</td><td></td></tr>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table border="0" cellspacing="2" cellpadding="0">
+    <tr><td valign="top"></td><td valign="top"><em>sequences</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>pl</em>&nbsp;</td><td></td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
 
 </div>
 </div>
-<a class="anchor" id="ga6b4dde1d43b79ab3753508c46cf50363"></a>
+<a class="anchor" id="ga6b4dde1d43b79ab3753508c46cf50363"></a><!-- doxytag: member="alifold.h::alipf_circ_fold" ref="ga6b4dde1d43b79ab3753508c46cf50363" args="(const char **sequences, char *structure, plist **pl)" -->
 <div class="memitem">
 <div class="memproto">
       <table class="memname">
         <tr>
           <td class="memname">float alipf_circ_fold </td>
           <td>(</td>
-          <td class="paramtype">const char **&#160;</td>
-          <td class="paramname"><em>sequences</em>, </td>
+          <td class="paramtype">const char **&nbsp;</td>
+          <td class="paramname"> <em>sequences</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype">char *&#160;</td>
-          <td class="paramname"><em>structure</em>, </td>
+          <td class="paramtype">char *&nbsp;</td>
+          <td class="paramname"> <em>structure</em>, </td>
         </tr>
         <tr>
           <td class="paramkey"></td>
           <td></td>
-          <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&#160;</td>
-          <td class="paramname"><em>pl</em>&#160;</td>
+          <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&nbsp;</td>
+          <td class="paramname"> <em>pl</em></td><td>&nbsp;</td>
         </tr>
         <tr>
           <td></td>
           <td>)</td>
-          <td></td><td></td>
+          <td></td><td></td><td></td>
         </tr>
       </table>
-</div><div class="memdoc">
-<dl class="params"><dt>Parameters:</dt><dd>
-  <table class="params">
-    <tr><td class="paramname">sequences</td><td></td></tr>
-    <tr><td class="paramname">structure</td><td></td></tr>
-    <tr><td class="paramname">pl</td><td></td></tr>
+</div>
+<div class="memdoc">
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table border="0" cellspacing="2" cellpadding="0">
+    <tr><td valign="top"></td><td valign="top"><em>sequences</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td></td></tr>
+    <tr><td valign="top"></td><td valign="top"><em>pl</em>&nbsp;</td><td></td></tr>
   </table>
   </dd>
 </dl>
-<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd></dd></dl>
 
 </div>
 </div>
-<a class="anchor" id="gadaaf83394216413505e48d913dbc1b4e"></a>
+<a class="anchor" id="ga11b6ab8bd9be1821fea352b190a01cab"></a><!-- doxytag: member="alifold.h::export_ali_bppm" ref="ga11b6ab8bd9be1821fea352b190a01cab" args="(void)" -->
 <div class="memitem">
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">double* export_ali_bppm </td>
+          <td class="memname">FLT_OR_DBL* export_ali_bppm </td>
           <td>(</td>
-          <td class="paramtype">void&#160;</td>
-          <td class="paramname"></td><td>)</td>
+          <td class="paramtype">void&nbsp;</td>
+          <td class="paramname"></td>
+          <td>&nbsp;)&nbsp;</td>
           <td></td>
         </tr>
       </table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
 
 <p>Get a pointer to the base pair probability array. </p>
 <p>Accessing the base pair probabilities for a pair (i,j) is achieved by </p>
-<pre class="fragment">FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; </pre><dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397" title="Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...">get_iindx()</a> </dd></dl>
-<dl class="section return"><dt>Returns:</dt><dd>A pointer to the base pair probability array </dd></dl>
+<div class="fragment"><pre class="fragment">FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; </pre></div><dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397" title="Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition...">get_iindx()</a> </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>A pointer to the base pair probability array </dd></dl>
 
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 </div>
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-    <a href="http://www.doxygen.org/index.html">
-    <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
-  </ul>
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+<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>
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