binaries/src/ViennaRNA/doc/html/group__consensus__pf__fold.html

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   6 <title>RNAlib-2.1.2: Partition Function and Base Pair Probabilities for Sequence Alignment(s)</title>
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  59 <a href="#func-members">Functions</a>  </div>
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  61 <div class="title">Partition Function and Base Pair Probabilities for Sequence Alignment(s)</div>  </div>
  62 <div class="ingroups"><a class="el" href="group__consensus__fold.html">Predicting Consensus Structures from Alignment(s)</a> &#124; <a class="el" href="group__pf__fold.html">Calculating Partition Functions and Pair Probabilities</a></div></div><!--header-->
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  65   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):</div>
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  69 <center><table><tr><td><img src="group__consensus__pf__fold.png" border="0" alt="" usemap="#group____consensus____pf____fold"/>
  70 <map name="group____consensus____pf____fold" id="group____consensus____pf____fold">
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  76 Functions</h2></td></tr>
  77 <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>
  78 <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>
  79 <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>
  80 <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>
  81 <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>
  82 <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>
  83 </table>
  84 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
  85 <hr/><h2>Function Documentation</h2>
  86 <a class="anchor" id="ga4d2ff54d8210fc7cceeeff389d4dbd1d"></a>
  87 <div class="memitem">
  88 <div class="memproto">
  89       <table class="memname">
  90         <tr>
  91           <td class="memname">float alipf_fold_par </td>
  92           <td>(</td>
  93           <td class="paramtype">const char **&#160;</td>
  94           <td class="paramname"><em>sequences</em>, </td>
  95         </tr>
  96         <tr>
  97           <td class="paramkey"></td>
  98           <td></td>
  99           <td class="paramtype">char *&#160;</td>
 100           <td class="paramname"><em>structure</em>, </td>
 101         </tr>
 102         <tr>
 103           <td class="paramkey"></td>
 104           <td></td>
 105           <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&#160;</td>
 106           <td class="paramname"><em>pl</em>, </td>
 107         </tr>
 108         <tr>
 109           <td class="paramkey"></td>
 110           <td></td>
 111           <td class="paramtype"><a class="el" href="structpf__paramT.html">pf_paramT</a> *&#160;</td>
 112           <td class="paramname"><em>parameters</em>, </td>
 113         </tr>
 114         <tr>
 115           <td class="paramkey"></td>
 116           <td></td>
 117           <td class="paramtype">int&#160;</td>
 118           <td class="paramname"><em>calculate_bppm</em>, </td>
 119         </tr>
 120         <tr>
 121           <td class="paramkey"></td>
 122           <td></td>
 123           <td class="paramtype">int&#160;</td>
 124           <td class="paramname"><em>is_constrained</em>, </td>
 125         </tr>
 126         <tr>
 127           <td class="paramkey"></td>
 128           <td></td>
 129           <td class="paramtype">int&#160;</td>
 130           <td class="paramname"><em>is_circular</em>&#160;</td>
 131         </tr>
 132         <tr>
 133           <td></td>
 134           <td>)</td>
 135           <td></td><td></td>
 136         </tr>
 137       </table>
 138 </div><div class="memdoc">
 139 <dl class="params"><dt>Parameters:</dt><dd>
 140   <table class="params">
 141     <tr><td class="paramname">sequences</td><td></td></tr>
 142     <tr><td class="paramname">structure</td><td></td></tr>
 143     <tr><td class="paramname">pl</td><td></td></tr>
 144     <tr><td class="paramname">parameters</td><td></td></tr>
 145     <tr><td class="paramname">calculate_bppm</td><td></td></tr>
 146     <tr><td class="paramname">is_constrained</td><td></td></tr>
 147     <tr><td class="paramname">is_circular</td><td></td></tr>
 148   </table>
 149   </dd>
 150 </dl>
 151 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 152
 153 </div>
 154 </div>
 155 <a class="anchor" id="gad32ded7d753ccaf211ab35782d1f42a9"></a>
 156 <div class="memitem">
 157 <div class="memproto">
 158       <table class="memname">
 159         <tr>
 160           <td class="memname">float alipf_fold </td>
 161           <td>(</td>
 162           <td class="paramtype">const char **&#160;</td>
 163           <td class="paramname"><em>sequences</em>, </td>
 164         </tr>
 165         <tr>
 166           <td class="paramkey"></td>
 167           <td></td>
 168           <td class="paramtype">char *&#160;</td>
 169           <td class="paramname"><em>structure</em>, </td>
 170         </tr>
 171         <tr>
 172           <td class="paramkey"></td>
 173           <td></td>
 174           <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&#160;</td>
 175           <td class="paramname"><em>pl</em>&#160;</td>
 176         </tr>
 177         <tr>
 178           <td></td>
 179           <td>)</td>
 180           <td></td><td></td>
 181         </tr>
 182       </table>
 183 </div><div class="memdoc">
 184
 185 <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>
 186 <dl class="params"><dt>Parameters:</dt><dd>
 187   <table class="params">
 188     <tr><td class="paramname">sequences</td><td></td></tr>
 189     <tr><td class="paramname">structure</td><td></td></tr>
 190     <tr><td class="paramname">pl</td><td></td></tr>
 191   </table>
 192   </dd>
 193 </dl>
 194 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 195
 196 </div>
 197 </div>
 198 <a class="anchor" id="ga6b4dde1d43b79ab3753508c46cf50363"></a>
 199 <div class="memitem">
 200 <div class="memproto">
 201       <table class="memname">
 202         <tr>
 203           <td class="memname">float alipf_circ_fold </td>
 204           <td>(</td>
 205           <td class="paramtype">const char **&#160;</td>
 206           <td class="paramname"><em>sequences</em>, </td>
 207         </tr>
 208         <tr>
 209           <td class="paramkey"></td>
 210           <td></td>
 211           <td class="paramtype">char *&#160;</td>
 212           <td class="paramname"><em>structure</em>, </td>
 213         </tr>
 214         <tr>
 215           <td class="paramkey"></td>
 216           <td></td>
 217           <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&#160;</td>
 218           <td class="paramname"><em>pl</em>&#160;</td>
 219         </tr>
 220         <tr>
 221           <td></td>
 222           <td>)</td>
 223           <td></td><td></td>
 224         </tr>
 225       </table>
 226 </div><div class="memdoc">
 227 <dl class="params"><dt>Parameters:</dt><dd>
 228   <table class="params">
 229     <tr><td class="paramname">sequences</td><td></td></tr>
 230     <tr><td class="paramname">structure</td><td></td></tr>
 231     <tr><td class="paramname">pl</td><td></td></tr>
 232   </table>
 233   </dd>
 234 </dl>
 235 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 236
 237 </div>
 238 </div>
 239 <a class="anchor" id="gadaaf83394216413505e48d913dbc1b4e"></a>
 240 <div class="memitem">
 241 <div class="memproto">
 242       <table class="memname">
 243         <tr>
 244           <td class="memname">double* export_ali_bppm </td>
 245           <td>(</td>
 246           <td class="paramtype">void&#160;</td>
 247           <td class="paramname"></td><td>)</td>
 248           <td></td>
 249         </tr>
 250       </table>
 251 </div><div class="memdoc">
 252
 253 <p>Get a pointer to the base pair probability array. </p>
 254 <p>Accessing the base pair probabilities for a pair (i,j) is achieved by </p>
 255 <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>
 256 <dl class="section return"><dt>Returns:</dt><dd>A pointer to the base pair probability array </dd></dl>
 257
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 266     <a href="http://www.doxygen.org/index.html">
 267     <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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