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-<div class="title">Predicting Consensus Structures from Alignment(s)</div> </div>
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<div class="contents">
-
+<h1>Predicting Consensus Structures from Alignment(s)<br/>
+<small>
+[<a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a>]</small>
+</h1>
<p>compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
-<a href="#details">More...</a></p>
-<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Predicting Consensus Structures from Alignment(s):</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<center><table><tr><td><img src="group__consensus__fold.png" border="0" alt="" usemap="#group____consensus____fold"/>
-<map name="group____consensus____fold" id="group____consensus____fold">
-<area shape="rect" id="node2" href="group__consensus__pf__fold.html" title="Partition Function\l and Base Pair Probabilities\l for Sequence Alignment(s)" alt="" coords="508,5,705,61"/><area shape="rect" id="node3" href="group__local__consensus__fold.html" title="Local MFE consensus\l structures for Sequence\l Alignments" alt="" coords="517,85,697,141"/><area shape="rect" id="node5" href="group__consensus__stochbt.html" title="Stochastic Backtracking\l of Consensus Structures\l from Sequence Alignment(s)" alt="" coords="501,165,712,221"/><area shape="rect" id="node6" href="group__consensus__mfe__fold.html" title="MFE Consensus Structures\l for Sequence Alignment(s)" alt="" coords="508,245,705,286"/><area shape="rect" id="node4" href="group__folding__routines.html" title="This module contains all functions related to thermodynamic folding of RNAs." alt="" coords="6,133,191,174"/></map>
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+<a href="#_details">More...</a></p>
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+<p><div class="dynheader">
+Collaboration diagram for Predicting Consensus Structures from Alignment(s):</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__consensus__fold.png" border="0" alt="" usemap="#group____consensus____fold_map"/>
+<map name="group____consensus____fold_map" id="group____consensus____fold">
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</div>
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-Modules</h2></td></tr>
-<tr class="memitem:group__consensus__mfe__fold"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html">MFE Consensus Structures for Sequence Alignment(s)</a></td></tr>
-<tr class="memitem:group__consensus__pf__fold"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html">Partition Function and Base Pair Probabilities for Sequence Alignment(s)</a></td></tr>
-<tr class="memitem:group__consensus__stochbt"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__stochbt.html">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td></tr>
-<tr class="memitem:group__local__consensus__fold"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__consensus__fold.html">Local MFE consensus structures for Sequence Alignments</a></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="files"></a>
-Files</h2></td></tr>
-<tr class="memitem:alifold_8h"><td class="memItemLeft" align="right" valign="top">file  </td><td class="memItemRight" valign="bottom"><a class="el" href="alifold_8h.html">alifold.h</a></td></tr>
-<tr class="memdesc:alifold_8h"><td class="mdescLeft"> </td><td class="mdescRight">compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments <br/></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:gaa2d600be90844094ec145ea14a314d2f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f">get_mpi</a> (char *Alseq[], int n_seq, int length, int *mini)</td></tr>
-<tr class="memdesc:gaa2d600be90844094ec145ea14a314d2f"><td class="mdescLeft"> </td><td class="mdescRight">Get the mean pairwise identity in steps from ?to?(ident) <a href="#gaa2d600be90844094ec145ea14a314d2f"></a><br/></td></tr>
-<tr class="memitem:ga5e125c9586fcd4e2e1559fe76f7289cc"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e125c9586fcd4e2e1559fe76f7289cc"></a>
-float ** </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga5e125c9586fcd4e2e1559fe76f7289cc">readribosum</a> (char *name)</td></tr>
-<tr class="memdesc:ga5e125c9586fcd4e2e1559fe76f7289cc"><td class="mdescLeft"> </td><td class="mdescRight">Read a ribosum or other user-defined scoring matrix. <br/></td></tr>
-<tr class="memitem:ga1c48869c03b49a342bf4cbdd61900081"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081">energy_of_alistruct</a> (const char **sequences, const char *structure, int n_seq, float *energy)</td></tr>
-<tr class="memdesc:ga1c48869c03b49a342bf4cbdd61900081"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of a consensus structure given a set of aligned sequences. <a href="#ga1c48869c03b49a342bf4cbdd61900081"></a><br/></td></tr>
-<tr class="memitem:gaa3e40277c837d6f7603afe319884c786"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786">encode_ali_sequence</a> (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
-<tr class="memdesc:gaa3e40277c837d6f7603afe319884c786"><td class="mdescLeft"> </td><td class="mdescRight">Get arrays with encoded sequence of the alignment. <a href="#gaa3e40277c837d6f7603afe319884c786"></a><br/></td></tr>
-<tr class="memitem:ga8a560930f7f2582cc3967723a86cfdfa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa">alloc_sequence_arrays</a> (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
-<tr class="memdesc:ga8a560930f7f2582cc3967723a86cfdfa"><td class="mdescLeft"> </td><td class="mdescRight">Allocate memory for sequence array used to deal with aligned sequences. <a href="#ga8a560930f7f2582cc3967723a86cfdfa"></a><br/></td></tr>
-<tr class="memitem:ga298a420a8c879202e2617b3f724fde38"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38">free_sequence_arrays</a> (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)</td></tr>
-<tr class="memdesc:ga298a420a8c879202e2617b3f724fde38"><td class="mdescLeft"> </td><td class="mdescRight">Free the memory of the sequence arrays used to deal with aligned sequences. <a href="#ga298a420a8c879202e2617b3f724fde38"></a><br/></td></tr>
-<tr class="memitem:ga0cc49457fd79eeb04d4a7f97c868b09b"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga0cc49457fd79eeb04d4a7f97c868b09b">get_alipf_arrays</a> (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p, short **pscore)</td></tr>
-<tr class="memdesc:ga0cc49457fd79eeb04d4a7f97c868b09b"><td class="mdescLeft"> </td><td class="mdescRight">Get pointers to (almost) all relavant arrays used in alifold's partition function computation. <a href="#ga0cc49457fd79eeb04d4a7f97c868b09b"></a><br/></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
-Variables</h2></td></tr>
-<tr class="memitem:gaf3cbac6ff5d706d6e414677841ddf94c"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c">cv_fact</a></td></tr>
-<tr class="memdesc:gaf3cbac6ff5d706d6e414677841ddf94c"><td class="mdescLeft"> </td><td class="mdescRight">This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. <a href="#gaf3cbac6ff5d706d6e414677841ddf94c"></a><br/></td></tr>
-<tr class="memitem:ga502948a122a2af5b914355b1f3ea2f61"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61">nc_fact</a></td></tr>
-<tr class="memdesc:ga502948a122a2af5b914355b1f3ea2f61"><td class="mdescLeft"> </td><td class="mdescRight">This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. <a href="#ga502948a122a2af5b914355b1f3ea2f61"></a><br/></td></tr>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Modules</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html">MFE Consensus Structures for Sequence Alignment(s)</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__pf__fold.html">Partition Function and Base Pair Probabilities for Sequence Alignment(s)</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__stochbt.html">Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__local__consensus__fold.html">Local MFE consensus structures for Sequence Alignments</a></td></tr>
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f">get_mpi</a> (char *Alseq[], int n_seq, int length, int *mini)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the mean pairwise identity in steps from ?to?(ident). <a href="#gaa2d600be90844094ec145ea14a314d2f"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga5e125c9586fcd4e2e1559fe76f7289cc"></a><!-- doxytag: member="consensus_fold::readribosum" ref="ga5e125c9586fcd4e2e1559fe76f7289cc" args="(char *name)" -->
+float ** </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga5e125c9586fcd4e2e1559fe76f7289cc">readribosum</a> (char *name)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Read a ribosum or other user-defined scoring matrix. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081">energy_of_alistruct</a> (const char **sequences, const char *structure, int n_seq, float *energy)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of a consensus structure given a set of aligned sequences. <a href="#ga1c48869c03b49a342bf4cbdd61900081"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786">encode_ali_sequence</a> (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get arrays with encoded sequence of the alignment. <a href="#gaa3e40277c837d6f7603afe319884c786"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa">alloc_sequence_arrays</a> (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Allocate memory for sequence array used to deal with aligned sequences. <a href="#ga8a560930f7f2582cc3967723a86cfdfa"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38">free_sequence_arrays</a> (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free the memory of the sequence arrays used to deal with aligned sequences. <a href="#ga298a420a8c879202e2617b3f724fde38"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga5349960075b1847720a2e9df021e2675">get_alipf_arrays</a> (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get pointers to (almost) all relavant arrays used in alifold's partition function computation. <a href="#ga5349960075b1847720a2e9df021e2675"></a><br/></td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c">cv_fact</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. <a href="#gaf3cbac6ff5d706d6e414677841ddf94c"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61">nc_fact</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. <a href="#ga502948a122a2af5b914355b1f3ea2f61"></a><br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments </p>
-<p>Consensus structures can be predicted by a modified version of the <a class="el" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence.">fold()</a> algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see <a class="el" href="citelist.html#CITEREF_hofacker:2002">[6]</a> and <a class="el" href="citelist.html#CITEREF_bernhart:2008">[2]</a>. </p>
+<p>Consensus structures can be predicted by a modified version of the <a class="el" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence...">fold()</a> algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see hofacker:2002 and bernhart:2008. </p>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="gaa2d600be90844094ec145ea14a314d2f"></a>
+<a class="anchor" id="gaa2d600be90844094ec145ea14a314d2f"></a><!-- doxytag: member="alifold.h::get_mpi" ref="gaa2d600be90844094ec145ea14a314d2f" args="(char *Alseq[], int n_seq, int length, int *mini)" -->
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<td class="memname">int get_mpi </td>
<td>(</td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>Alseq</em>[], </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>Alseq</em>[], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>n_seq</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>n_seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int * </td>
- <td class="paramname"><em>mini</em> </td>
+ <td class="paramtype">int * </td>
+ <td class="paramname"> <em>mini</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
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-</div><div class="memdoc">
+</div>
+<div class="memdoc">
-<p>Get the mean pairwise identity in steps from ?to?(ident) </p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">Alseq</td><td></td></tr>
- <tr><td class="paramname">n_seq</td><td>The number of sequences in the alignment </td></tr>
- <tr><td class="paramname">length</td><td>The length of the alignment </td></tr>
- <tr><td class="paramname">mini</td><td></td></tr>
+<p>Get the mean pairwise identity in steps from ?to?(ident). </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>Alseq</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>n_seq</em> </td><td>The number of sequences in the alignment </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>length</em> </td><td>The length of the alignment </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>mini</em> </td><td></td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The mean pairwise identity </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>The mean pairwise identity </dd></dl>
</div>
</div>
-<a class="anchor" id="ga1c48869c03b49a342bf4cbdd61900081"></a>
+<a class="anchor" id="ga1c48869c03b49a342bf4cbdd61900081"></a><!-- doxytag: member="alifold.h::energy_of_alistruct" ref="ga1c48869c03b49a342bf4cbdd61900081" args="(const char **sequences, const char *structure, int n_seq, float *energy)" -->
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<td class="memname">float energy_of_alistruct </td>
<td>(</td>
- <td class="paramtype">const char ** </td>
- <td class="paramname"><em>sequences</em>, </td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"> <em>sequences</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>structure</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>structure</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>n_seq</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>n_seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">float * </td>
- <td class="paramname"><em>energy</em> </td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"> <em>energy</em></td><td> </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>Calculate the free energy of a consensus structure given a set of aligned sequences. </p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">sequences</td><td>The NULL terminated array of sequences </td></tr>
- <tr><td class="paramname">structure</td><td>The consensus structure </td></tr>
- <tr><td class="paramname">n_seq</td><td>The number of sequences in the alignment </td></tr>
- <tr><td class="paramname">energy</td><td>A pointer to an array of at least two floats that will hold the free energies (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term) </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> </td><td>The NULL terminated array of sequences </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>The consensus structure </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>n_seq</em> </td><td>The number of sequences in the alignment </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>energy</em> </td><td>A pointer to an array of at least two floats that will hold the free energies (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term) </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>free energy in kcal/mol </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>free energy in kcal/mol </dd></dl>
</div>
</div>
-<a class="anchor" id="gaa3e40277c837d6f7603afe319884c786"></a>
+<a class="anchor" id="gaa3e40277c837d6f7603afe319884c786"></a><!-- doxytag: member="alifold.h::encode_ali_sequence" ref="gaa3e40277c837d6f7603afe319884c786" args="(const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)" -->
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<td class="memname">void encode_ali_sequence </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>sequence</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>sequence</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>S</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>S</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>s5</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>s5</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>s3</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>s3</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>ss</em>, </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>ss</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">unsigned short * </td>
- <td class="paramname"><em>as</em>, </td>
+ <td class="paramtype">unsigned short * </td>
+ <td class="paramname"> <em>as</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>circ</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>circ</em></td><td> </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>Get arrays with encoded sequence of the alignment. </p>
<p>this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">sequence</td><td>The gapped sequence from the alignment </td></tr>
- <tr><td class="paramname">S</td><td>pointer to an array that holds encoded sequence </td></tr>
- <tr><td class="paramname">s5</td><td>pointer to an array that holds the next base 5' of alignment position i </td></tr>
- <tr><td class="paramname">s3</td><td>pointer to an array that holds the next base 3' of alignment position i </td></tr>
- <tr><td class="paramname">ss</td><td></td></tr>
- <tr><td class="paramname">as</td><td></td></tr>
- <tr><td class="paramname">circ</td><td>assume the molecules to be circular instead of linear (circ=0) </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>sequence</em> </td><td>The gapped sequence from the alignment </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S</em> </td><td>pointer to an array that holds encoded sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s5</em> </td><td>pointer to an array that holds the next base 5' of alignment position i </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s3</em> </td><td>pointer to an array that holds the next base 3' of alignment position i </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ss</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>as</em> </td><td></td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>circ</em> </td><td>assume the molecules to be circular instead of linear (circ=0) </td></tr>
</table>
</dd>
</dl>
</div>
</div>
-<a class="anchor" id="ga8a560930f7f2582cc3967723a86cfdfa"></a>
+<a class="anchor" id="ga8a560930f7f2582cc3967723a86cfdfa"></a><!-- doxytag: member="alifold.h::alloc_sequence_arrays" ref="ga8a560930f7f2582cc3967723a86cfdfa" args="(const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)" -->
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<td class="memname">void alloc_sequence_arrays </td>
<td>(</td>
- <td class="paramtype">const char ** </td>
- <td class="paramname"><em>sequences</em>, </td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"> <em>sequences</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S5</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S5</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S3</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S3</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">unsigned short *** </td>
- <td class="paramname"><em>a2s</em>, </td>
+ <td class="paramtype">unsigned short *** </td>
+ <td class="paramname"> <em>a2s</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char *** </td>
- <td class="paramname"><em>Ss</em>, </td>
+ <td class="paramtype">char *** </td>
+ <td class="paramname"> <em>Ss</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>circ</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>circ</em></td><td> </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>Allocate memory for sequence array used to deal with aligned sequences. </p>
<p>Note that these arrays will also be initialized according to the sequence alignment given</p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38" title="Free the memory of the sequence arrays used to deal with aligned sequences.">free_sequence_arrays()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">sequences</td><td>The aligned sequences </td></tr>
- <tr><td class="paramname">S</td><td>A pointer to the array of encoded sequences </td></tr>
- <tr><td class="paramname">S5</td><td>A pointer to the array that contains the next 5' nucleotide of a sequence position </td></tr>
- <tr><td class="paramname">S3</td><td>A pointer to the array that contains the next 3' nucleotide of a sequence position </td></tr>
- <tr><td class="paramname">a2s</td><td>A pointer to the array that contains the alignment to sequence position mapping </td></tr>
- <tr><td class="paramname">Ss</td><td>A pointer to the array that contains the ungapped sequence </td></tr>
- <tr><td class="paramname">circ</td><td>assume the molecules to be circular instead of linear (circ=0) </td></tr>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38" title="Free the memory of the sequence arrays used to deal with aligned sequences.">free_sequence_arrays()</a></dd></dl>
+<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> </td><td>The aligned sequences </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S</em> </td><td>A pointer to the array of encoded sequences </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S5</em> </td><td>A pointer to the array that contains the next 5' nucleotide of a sequence position </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S3</em> </td><td>A pointer to the array that contains the next 3' nucleotide of a sequence position </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>a2s</em> </td><td>A pointer to the array that contains the alignment to sequence position mapping </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>Ss</em> </td><td>A pointer to the array that contains the ungapped sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>circ</em> </td><td>assume the molecules to be circular instead of linear (circ=0) </td></tr>
</table>
</dd>
</dl>
</div>
</div>
-<a class="anchor" id="ga298a420a8c879202e2617b3f724fde38"></a>
+<a class="anchor" id="ga298a420a8c879202e2617b3f724fde38"></a><!-- doxytag: member="alifold.h::free_sequence_arrays" ref="ga298a420a8c879202e2617b3f724fde38" args="(unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)" -->
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<td class="memname">void free_sequence_arrays </td>
<td>(</td>
- <td class="paramtype">unsigned int </td>
- <td class="paramname"><em>n_seq</em>, </td>
+ <td class="paramtype">unsigned int </td>
+ <td class="paramname"> <em>n_seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S5</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S5</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S3</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S3</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">unsigned short *** </td>
- <td class="paramname"><em>a2s</em>, </td>
+ <td class="paramtype">unsigned short *** </td>
+ <td class="paramname"> <em>a2s</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char *** </td>
- <td class="paramname"><em>Ss</em> </td>
+ <td class="paramtype">char *** </td>
+ <td class="paramname"> <em>Ss</em></td><td> </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>Free the memory of the sequence arrays used to deal with aligned sequences. </p>
<p>This function frees the memory previously allocated with <a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa" title="Allocate memory for sequence array used to deal with aligned sequences.">alloc_sequence_arrays()</a></p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa" title="Allocate memory for sequence array used to deal with aligned sequences.">alloc_sequence_arrays()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">n_seq</td><td>The number of aligned sequences </td></tr>
- <tr><td class="paramname">S</td><td>A pointer to the array of encoded sequences </td></tr>
- <tr><td class="paramname">S5</td><td>A pointer to the array that contains the next 5' nucleotide of a sequence position </td></tr>
- <tr><td class="paramname">S3</td><td>A pointer to the array that contains the next 3' nucleotide of a sequence position </td></tr>
- <tr><td class="paramname">a2s</td><td>A pointer to the array that contains the alignment to sequence position mapping </td></tr>
- <tr><td class="paramname">Ss</td><td>A pointer to the array that contains the ungapped sequence </td></tr>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa" title="Allocate memory for sequence array used to deal with aligned sequences.">alloc_sequence_arrays()</a></dd></dl>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>n_seq</em> </td><td>The number of aligned sequences </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S</em> </td><td>A pointer to the array of encoded sequences </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S5</em> </td><td>A pointer to the array that contains the next 5' nucleotide of a sequence position </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S3</em> </td><td>A pointer to the array that contains the next 3' nucleotide of a sequence position </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>a2s</em> </td><td>A pointer to the array that contains the alignment to sequence position mapping </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>Ss</em> </td><td>A pointer to the array that contains the ungapped sequence </td></tr>
</table>
</dd>
</dl>
</div>
</div>
-<a class="anchor" id="ga0cc49457fd79eeb04d4a7f97c868b09b"></a>
+<a class="anchor" id="ga5349960075b1847720a2e9df021e2675"></a><!-- doxytag: member="alifold.h::get_alipf_arrays" ref="ga5349960075b1847720a2e9df021e2675" args="(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)" -->
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<td class="memname">int get_alipf_arrays </td>
<td>(</td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S_p</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S5_p</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S5_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short *** </td>
- <td class="paramname"><em>S3_p</em>, </td>
+ <td class="paramtype">short *** </td>
+ <td class="paramname"> <em>S3_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">unsigned short *** </td>
- <td class="paramname"><em>a2s_p</em>, </td>
+ <td class="paramtype">unsigned short *** </td>
+ <td class="paramname"> <em>a2s_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char *** </td>
- <td class="paramname"><em>Ss_p</em>, </td>
+ <td class="paramtype">char *** </td>
+ <td class="paramname"> <em>Ss_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">double ** </td>
- <td class="paramname"><em>qb_p</em>, </td>
+ <td class="paramtype">FLT_OR_DBL ** </td>
+ <td class="paramname"> <em>qb_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">double ** </td>
- <td class="paramname"><em>qm_p</em>, </td>
+ <td class="paramtype">FLT_OR_DBL ** </td>
+ <td class="paramname"> <em>qm_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">double ** </td>
- <td class="paramname"><em>q1k_p</em>, </td>
+ <td class="paramtype">FLT_OR_DBL ** </td>
+ <td class="paramname"> <em>q1k_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">double ** </td>
- <td class="paramname"><em>qln_p</em>, </td>
+ <td class="paramtype">FLT_OR_DBL ** </td>
+ <td class="paramname"> <em>qln_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short ** </td>
- <td class="paramname"><em>pscore</em> </td>
+ <td class="paramtype">short ** </td>
+ <td class="paramname"> <em>pscore</em></td><td> </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>Get pointers to (almost) all relavant arrays used in alifold's partition function computation. </p>
-<dl class="section note"><dt>Note:</dt><dd>To obtain meaningful pointers, call alipf_fold first!</dd></dl>
-<dl class="section see"><dt>See also:</dt><dd>pf_alifold(), <a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">S_p</td><td>A pointer to the 'S' array (integer representation of nucleotides) </td></tr>
- <tr><td class="paramname">S5_p</td><td>A pointer to the 'S5' array </td></tr>
- <tr><td class="paramname">S3_p</td><td>A pointer to the 'S3' array </td></tr>
- <tr><td class="paramname">a2s_p</td><td>A pointer to the pair type matrix </td></tr>
- <tr><td class="paramname">Ss_p</td><td>A pointer to the 'Ss' array </td></tr>
- <tr><td class="paramname">qb_p</td><td>A pointer to the Q<sup>B</sup> matrix </td></tr>
- <tr><td class="paramname">qm_p</td><td>A pointer to the Q<sup>M</sup> matrix </td></tr>
- <tr><td class="paramname">q1k_p</td><td>A pointer to the 5' slice of the Q matrix ( <img class="formulaInl" alt="$q1k(k) = Q(1, k)$" src="form_0.png"/>) </td></tr>
- <tr><td class="paramname">qln_p</td><td>A pointer to the 3' slice of the Q matrix ( <img class="formulaInl" alt="$qln(l) = Q(l, n)$" src="form_1.png"/>) </td></tr>
+<dl class="note"><dt><b>Note:</b></dt><dd>To obtain meaningful pointers, call alipf_fold first!</dd></dl>
+<dl class="see"><dt><b>See also:</b></dt><dd>pf_alifold(), <a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alipf_circ_fold()</a></dd></dl>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>S_p</em> </td><td>A pointer to the 'S' array (integer representation of nucleotides) </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S5_p</em> </td><td>A pointer to the 'S5' array </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>S3_p</em> </td><td>A pointer to the 'S3' array </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>a2s_p</em> </td><td>A pointer to the pair type matrix </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>Ss_p</em> </td><td>A pointer to the 'Ss' array </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>qb_p</em> </td><td>A pointer to the Q<sup>B</sup> matrix </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>qm_p</em> </td><td>A pointer to the Q<sup>M</sup> matrix </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>q1k_p</em> </td><td>A pointer to the 5' slice of the Q matrix (<img class="formulaInl" alt="$q1k(k) = Q(1, k)$" src="form_0.png"/>) </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>qln_p</em> </td><td>A pointer to the 3' slice of the Q matrix (<img class="formulaInl" alt="$qln(l) = Q(l, n)$" src="form_1.png"/>) </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>Non Zero if everything went fine, 0 otherwise </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>Non Zero if everything went fine, 0 otherwise </dd></dl>
</div>
</div>
<hr/><h2>Variable Documentation</h2>
-<a class="anchor" id="gaf3cbac6ff5d706d6e414677841ddf94c"></a>
+<a class="anchor" id="gaf3cbac6ff5d706d6e414677841ddf94c"></a><!-- doxytag: member="alifold.h::cv_fact" ref="gaf3cbac6ff5d706d6e414677841ddf94c" args="" -->
<div class="memitem">
<div class="memproto">
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<tr>
- <td class="memname">double cv_fact</td>
+ <td class="memname">double <a class="el" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c">cv_fact</a></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. </p>
<p>Default is 1. </p>
</div>
</div>
-<a class="anchor" id="ga502948a122a2af5b914355b1f3ea2f61"></a>
+<a class="anchor" id="ga502948a122a2af5b914355b1f3ea2f61"></a><!-- doxytag: member="alifold.h::nc_fact" ref="ga502948a122a2af5b914355b1f3ea2f61" args="" -->
<div class="memitem">
<div class="memproto">
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<tr>
- <td class="memname">double nc_fact</td>
+ <td class="memname">double <a class="el" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61">nc_fact</a></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. </p>
<p>Default is 1. </p>
</div>
</div>
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-</div><!-- doc-content -->
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