<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/alifold.h Source File</title>
+<title>RNAlib-2.1.2: /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.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 Page</span></a></li>
- <li><a href="pages.html"><span>Related 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 Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
<li><a href="modules.html"><span>Modules</span></a></li>
- <li><a href="annotated.html"><span>Data Structures</span></a></li>
+ <li><a href="annotated.html"><span>Data Structures</span></a></li>
<li class="current"><a href="files.html"><span>Files</span></a></li>
</ul>
</div>
- <div id="navrow2" class="tabs2">
- <ul class="tablist">
- <li><a href="files.html"><span>File List</span></a></li>
+ <div class="tabs">
+ <ul>
+ <li><a href="files.html"><span>File List</span></a></li>
<li><a href="globals.html"><span>Globals</span></a></li>
</ul>
</div>
-</div><!-- top -->
-<div id="side-nav" class="ui-resizable side-nav-resizable">
- <div id="nav-tree">
- <div id="nav-tree-contents">
- </div>
- </div>
- <div id="splitbar" style="-moz-user-select:none;"
- class="ui-resizable-handle">
- </div>
-</div>
-<script type="text/javascript">
-$(document).ready(function(){initNavTree('alifold_8h.html','');});
-</script>
-<div id="doc-content">
-<div class="header">
- <div class="headertitle">
-<div class="title">alifold.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="alifold_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__</span></div>
-<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_ALIFOLD_H__</span></div>
-<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here.">data_structures.h</a>"</span></div>
-<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div>
-<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c" title="This variable controls the weight of the covariance term in the energy function of alignment folding ...">cv_fact</a>;</div>
-<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61" title="This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...">nc_fact</a>;</div>
-<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div>
-<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment">##############################################</span></div>
-<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="comment"># MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #</span></div>
-<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="comment">##############################################</span></div>
-<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div>
-<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keywordtype">void</span> <a class="code" href="alifold_8h.html#ac484c6bd429bafbd353b91044508d8e9" title="Update the energy parameters for alifold function.">update_alifold_params</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
-<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
-<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="keywordtype">float</span> <a class="code" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,</div>
-<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
-<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
-<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <span class="keywordtype">float</span> <a class="code" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96" title="Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...">circalifold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,</div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
-<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="keywordtype">void</span> <a class="code" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e" title="Free the memory occupied by MFE alifold functions.">free_alifold_arrays</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
-<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> <span class="keywordtype">int</span> <a class="code" href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f" title="Get the mean pairwise identity in steps from ?to?(ident)">get_mpi</a>(<span class="keywordtype">char</span> *Alseq[],</div>
-<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordtype">int</span> n_seq,</div>
-<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">int</span> *mini);</div>
-<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
-<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="keywordtype">float</span> **<a class="code" href="group__consensus__fold.html#ga5e125c9586fcd4e2e1559fe76f7289cc" title="Read a ribosum or other user-defined scoring matrix.">readribosum</a>(<span class="keywordtype">char</span> *name);</div>
-<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> </div>
-<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="keywordtype">float</span> <a class="code" href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081" title="Calculate the free energy of a consensus structure given a set of aligned sequences.">energy_of_alistruct</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,</div>
-<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordtype">int</span> n_seq,</div>
-<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordtype">float</span> *energy);</div>
-<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
-<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="keywordtype">float</span> energy_of_ali_gquad_structure(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,</div>
-<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">int</span> n_seq,</div>
-<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordtype">float</span> *energy);</div>
-<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> </div>
-<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="comment">#############################################################</span></div>
-<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="comment"># some helper functions that might be useful in the library #</span></div>
-<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <span class="comment">#############################################################</span></div>
-<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
-<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> <span class="keywordtype">void</span> <a class="code" href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786" title="Get arrays with encoded sequence of the alignment.">encode_ali_sequence</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordtype">short</span> *S,</div>
-<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordtype">short</span> *s5,</div>
-<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordtype">short</span> *s3,</div>
-<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordtype">char</span> *ss,</div>
-<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> *as,</div>
-<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordtype">int</span> circ);</div>
-<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
-<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="keywordtype">void</span> <a class="code" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa" title="Allocate memory for sequence array used to deal with aligned sequences.">alloc_sequence_arrays</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,</div>
-<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordtype">short</span> ***S,</div>
-<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordtype">short</span> ***S5,</div>
-<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordtype">short</span> ***S3,</div>
-<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> ***a2s,</div>
-<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordtype">char</span> ***Ss,</div>
-<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordtype">int</span> circ);</div>
-<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
-<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> <span class="keywordtype">void</span> <a class="code" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38" title="Free the memory of the sequence arrays used to deal with aligned sequences.">free_sequence_arrays</a>( <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n_seq,</div>
-<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="keywordtype">short</span> ***S,</div>
-<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keywordtype">short</span> ***S5,</div>
-<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordtype">short</span> ***S3,</div>
-<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> ***a2s,</div>
-<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordtype">char</span> ***Ss);</div>
-<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div>
-<div class="line"><a name="l00236"></a><span class="lineno"> 236</span> <span class="comment">/*</span></div>
-<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> <span class="comment">#############################################################</span></div>
-<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> <span class="comment"># PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #</span></div>
-<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> <span class="comment">#############################################################</span></div>
-<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00241"></a><span class="lineno"> 241</span> </div>
-<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div>
-<div class="line"><a name="l00265"></a><span class="lineno"> 265</span> <span class="keywordtype">float</span> <a class="code" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alipf_fold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,</div>
-<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> **pl,</div>
-<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters,</div>
-<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordtype">int</span> calculate_bppm,</div>
-<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordtype">int</span> is_constrained,</div>
-<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keywordtype">int</span> is_circular);</div>
-<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> </div>
-<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> <span class="keywordtype">float</span> <a class="code" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9" title="The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...">alipf_fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,</div>
-<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> **pl);</div>
-<div class="line"><a name="l00292"></a><span class="lineno"> 292</span> </div>
-<div class="line"><a name="l00303"></a><span class="lineno"> 303</span> <span class="keywordtype">float</span> <a class="code" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,</div>
-<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> **pl);</div>
-<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> </div>
-<div class="line"><a name="l00307"></a><span class="lineno"> 307</span> </div>
-<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> FLT_OR_DBL *<a class="code" href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e" title="Get a pointer to the base pair probability array.">export_ali_bppm</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00320"></a><span class="lineno"> 320</span> </div>
-<div class="line"><a name="l00327"></a><span class="lineno"> 327</span> <span class="keywordtype">void</span> free_alipf_arrays(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div>
-<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> <span class="keywordtype">char</span> *<a class="code" href="group__consensus__stochbt.html#ga0df40248788f0fb17ebdc59d74116d1c" title="Sample a consensus secondary structure from the Boltzmann ensemble according its probability ...">alipbacktrack</a>(<span class="keywordtype">double</span> *prob);</div>
-<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
-<div class="line"><a name="l00346"></a><span class="lineno"> 346</span> </div>
-<div class="line"><a name="l00367"></a><span class="lineno"> 367</span> <span class="keywordtype">int</span> <a class="code" href="group__consensus__fold.html#ga0cc49457fd79eeb04d4a7f97c868b09b" title="Get pointers to (almost) all relavant arrays used in alifold's partition function computation...">get_alipf_arrays</a>(<span class="keywordtype">short</span> ***S_p,</div>
-<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordtype">short</span> ***S5_p,</div>
-<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <span class="keywordtype">short</span> ***S3_p,</div>
-<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> ***a2s_p,</div>
-<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keywordtype">char</span> ***Ss_p,</div>
-<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  FLT_OR_DBL **qb_p,</div>
-<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  FLT_OR_DBL **qm_p,</div>
-<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  FLT_OR_DBL **q1k_p,</div>
-<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  FLT_OR_DBL **qln_p,</div>
-<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordtype">short</span> **pscore);</div>
-<div class="line"><a name="l00377"></a><span class="lineno"> 377</span> </div>
-<div class="line"><a name="l00378"></a><span class="lineno"> 378</span> <span class="preprocessor">#endif</span></div>
-</div><!-- fragment --></div><!-- contents -->
-</div><!-- doc-content -->
-<!-- start footer part -->
-<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
- <ul>
- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="alifold_8h.html">alifold.h</a></li>
- <li class="footer">Generated on Wed Jul 24 2013 13:38:55 for RNAlib-2.1.2 by
- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
- </ul>
-</div>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h</h1><a href="alifold_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_ALIFOLD_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00004"></a>00004 <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found...">data_structures.h</a>"</span>
+<a name="l00005"></a>00005
+<a name="l00043"></a>00043 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c" title="This variable controls the weight of the covariance term in the energy function of...">cv_fact</a>;
+<a name="l00052"></a>00052 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61" title="This variable controls the magnitude of the penalty for non-compatible sequences...">nc_fact</a>;
+<a name="l00053"></a>00053
+<a name="l00054"></a>00054 <span class="comment">/*</span>
+<a name="l00055"></a>00055 <span class="comment">##############################################</span>
+<a name="l00056"></a>00056 <span class="comment"># MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #</span>
+<a name="l00057"></a>00057 <span class="comment">##############################################</span>
+<a name="l00058"></a>00058 <span class="comment">*/</span>
+<a name="l00059"></a>00059
+<a name="l00066"></a>00066 <span class="keywordtype">void</span> <a class="code" href="alifold_8h.html#ac484c6bd429bafbd353b91044508d8e9" title="Update the energy parameters for alifold function.">update_alifold_params</a>(<span class="keywordtype">void</span>);
+<a name="l00067"></a>00067
+<a name="l00068"></a>00068
+<a name="l00086"></a>00086 <span class="keywordtype">float</span> <a class="code" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,
+<a name="l00087"></a>00087 <span class="keywordtype">char</span> *structure);
+<a name="l00088"></a>00088
+<a name="l00089"></a>00089
+<a name="l00100"></a>00100 <span class="keywordtype">float</span> <a class="code" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96" title="Compute MFE and according structure of an alignment of sequences assuming the sequences...">circalifold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,
+<a name="l00101"></a>00101 <span class="keywordtype">char</span> *structure);
+<a name="l00102"></a>00102
+<a name="l00109"></a>00109 <span class="keywordtype">void</span> <a class="code" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e" title="Free the memory occupied by MFE alifold functions.">free_alifold_arrays</a>(<span class="keywordtype">void</span>);
+<a name="l00110"></a>00110
+<a name="l00122"></a>00122 <span class="keywordtype">int</span> <a class="code" href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f" title="Get the mean pairwise identity in steps from ?to?(ident).">get_mpi</a>(<span class="keywordtype">char</span> *Alseq[],
+<a name="l00123"></a>00123 <span class="keywordtype">int</span> n_seq,
+<a name="l00124"></a>00124 <span class="keywordtype">int</span> length,
+<a name="l00125"></a>00125 <span class="keywordtype">int</span> *mini);
+<a name="l00126"></a>00126
+<a name="l00133"></a>00133 <span class="keywordtype">float</span> **<a class="code" href="group__consensus__fold.html#ga5e125c9586fcd4e2e1559fe76f7289cc" title="Read a ribosum or other user-defined scoring matrix.">readribosum</a>(<span class="keywordtype">char</span> *name);
+<a name="l00134"></a>00134
+<a name="l00148"></a>00148 <span class="keywordtype">float</span> <a class="code" href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081" title="Calculate the free energy of a consensus structure given a set of aligned sequences...">energy_of_alistruct</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,
+<a name="l00149"></a>00149 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00150"></a>00150 <span class="keywordtype">int</span> n_seq,
+<a name="l00151"></a>00151 <span class="keywordtype">float</span> *energy);
+<a name="l00152"></a>00152
+<a name="l00153"></a>00153 <span class="keywordtype">float</span> energy_of_ali_gquad_structure(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,
+<a name="l00154"></a>00154 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure,
+<a name="l00155"></a>00155 <span class="keywordtype">int</span> n_seq,
+<a name="l00156"></a>00156 <span class="keywordtype">float</span> *energy);
+<a name="l00157"></a>00157
+<a name="l00158"></a>00158 <span class="comment">/*</span>
+<a name="l00159"></a>00159 <span class="comment">#############################################################</span>
+<a name="l00160"></a>00160 <span class="comment"># some helper functions that might be useful in the library #</span>
+<a name="l00161"></a>00161 <span class="comment">#############################################################</span>
+<a name="l00162"></a>00162 <span class="comment">*/</span>
+<a name="l00163"></a>00163
+<a name="l00180"></a>00180 <span class="keywordtype">void</span> <a class="code" href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786" title="Get arrays with encoded sequence of the alignment.">encode_ali_sequence</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00181"></a>00181 <span class="keywordtype">short</span> *S,
+<a name="l00182"></a>00182 <span class="keywordtype">short</span> *s5,
+<a name="l00183"></a>00183 <span class="keywordtype">short</span> *s3,
+<a name="l00184"></a>00184 <span class="keywordtype">char</span> *ss,
+<a name="l00185"></a>00185 <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> *as,
+<a name="l00186"></a>00186 <span class="keywordtype">int</span> circ);
+<a name="l00187"></a>00187
+<a name="l00205"></a>00205 <span class="keywordtype">void</span> <a class="code" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa" title="Allocate memory for sequence array used to deal with aligned sequences.">alloc_sequence_arrays</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,
+<a name="l00206"></a>00206 <span class="keywordtype">short</span> ***S,
+<a name="l00207"></a>00207 <span class="keywordtype">short</span> ***S5,
+<a name="l00208"></a>00208 <span class="keywordtype">short</span> ***S3,
+<a name="l00209"></a>00209 <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> ***a2s,
+<a name="l00210"></a>00210 <span class="keywordtype">char</span> ***Ss,
+<a name="l00211"></a>00211 <span class="keywordtype">int</span> circ);
+<a name="l00212"></a>00212
+<a name="l00229"></a>00229 <span class="keywordtype">void</span> <a class="code" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38" title="Free the memory of the sequence arrays used to deal with aligned sequences.">free_sequence_arrays</a>( <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n_seq,
+<a name="l00230"></a>00230 <span class="keywordtype">short</span> ***S,
+<a name="l00231"></a>00231 <span class="keywordtype">short</span> ***S5,
+<a name="l00232"></a>00232 <span class="keywordtype">short</span> ***S3,
+<a name="l00233"></a>00233 <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> ***a2s,
+<a name="l00234"></a>00234 <span class="keywordtype">char</span> ***Ss);
+<a name="l00235"></a>00235
+<a name="l00236"></a>00236 <span class="comment">/*</span>
+<a name="l00237"></a>00237 <span class="comment">#############################################################</span>
+<a name="l00238"></a>00238 <span class="comment"># PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #</span>
+<a name="l00239"></a>00239 <span class="comment">#############################################################</span>
+<a name="l00240"></a>00240 <span class="comment">*/</span>
+<a name="l00241"></a>00241
+<a name="l00242"></a>00242
+<a name="l00265"></a>00265 <span class="keywordtype">float</span> <a class="code" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alipf_fold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,
+<a name="l00266"></a>00266 <span class="keywordtype">char</span> *structure,
+<a name="l00267"></a>00267 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **pl,
+<a name="l00268"></a>00268 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters,
+<a name="l00269"></a>00269 <span class="keywordtype">int</span> calculate_bppm,
+<a name="l00270"></a>00270 <span class="keywordtype">int</span> is_constrained,
+<a name="l00271"></a>00271 <span class="keywordtype">int</span> is_circular);
+<a name="l00272"></a>00272
+<a name="l00289"></a>00289 <span class="keywordtype">float</span> <a class="code" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9" title="The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities...">alipf_fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,
+<a name="l00290"></a>00290 <span class="keywordtype">char</span> *structure,
+<a name="l00291"></a>00291 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **pl);
+<a name="l00292"></a>00292
+<a name="l00303"></a>00303 <span class="keywordtype">float</span> <a class="code" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequences,
+<a name="l00304"></a>00304 <span class="keywordtype">char</span> *structure,
+<a name="l00305"></a>00305 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **pl);
+<a name="l00306"></a>00306
+<a name="l00307"></a>00307
+<a name="l00319"></a>00319 FLT_OR_DBL *<a class="code" href="group__consensus__pf__fold.html#ga11b6ab8bd9be1821fea352b190a01cab" title="Get a pointer to the base pair probability array.">export_ali_bppm</a>(<span class="keywordtype">void</span>);
+<a name="l00320"></a>00320
+<a name="l00327"></a>00327 <span class="keywordtype">void</span> free_alipf_arrays(<span class="keywordtype">void</span>);
+<a name="l00328"></a>00328
+<a name="l00344"></a>00344 <span class="keywordtype">char</span> *<a class="code" href="group__consensus__stochbt.html#ga0df40248788f0fb17ebdc59d74116d1c" title="Sample a consensus secondary structure from the Boltzmann ensemble according its...">alipbacktrack</a>(<span class="keywordtype">double</span> *prob);
+<a name="l00345"></a>00345
+<a name="l00346"></a>00346
+<a name="l00367"></a>00367 <span class="keywordtype">int</span> <a class="code" href="group__consensus__fold.html#ga5349960075b1847720a2e9df021e2675" title="Get pointers to (almost) all relavant arrays used in alifold&#39;s partition function...">get_alipf_arrays</a>(<span class="keywordtype">short</span> ***S_p,
+<a name="l00368"></a>00368 <span class="keywordtype">short</span> ***S5_p,
+<a name="l00369"></a>00369 <span class="keywordtype">short</span> ***S3_p,
+<a name="l00370"></a>00370 <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> ***a2s_p,
+<a name="l00371"></a>00371 <span class="keywordtype">char</span> ***Ss_p,
+<a name="l00372"></a>00372 FLT_OR_DBL **qb_p,
+<a name="l00373"></a>00373 FLT_OR_DBL **qm_p,
+<a name="l00374"></a>00374 FLT_OR_DBL **q1k_p,
+<a name="l00375"></a>00375 FLT_OR_DBL **qln_p,
+<a name="l00376"></a>00376 <span class="keywordtype">short</span> **pscore);
+<a name="l00377"></a>00377
+<a name="l00378"></a>00378 <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
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
</body>
</html>
git://source.jalview.org / jabaws.git / blobdiff