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-<div class="title">MFE Consensus Structures for Sequence Alignment(s)</div> </div>
-<div class="ingroups"><a class="el" href="group__consensus__fold.html">Predicting Consensus Structures from Alignment(s)</a> | <a class="el" href="group__mfe__fold.html">Calculating Minimum Free Energy (MFE) Structures</a></div></div><!--header-->
<div class="contents">
-<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 MFE Consensus Structures for Sequence Alignment(s):</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+<h1>MFE Consensus Structures for Sequence Alignment(s)<br/>
+<small>
+[<a class="el" href="group__consensus__fold.html">Predicting Consensus Structures from Alignment(s)</a>, <a class="el" href="group__mfe__fold.html">Calculating Minimum Free Energy (MFE) Structures</a>]</small>
+</h1>
+<p><div class="dynheader">
+Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__consensus__mfe__fold.png" border="0" alt="" usemap="#group____consensus____mfe____fold_map"/>
+<map name="group____consensus____mfe____fold_map" id="group____consensus____mfe____fold">
+<area shape="rect" id="node1" href="group__consensus__fold.html" title="compute various properties (consensus MFE structures, partition function, Boltzmann..." alt="" coords="5,5,331,35"/><area shape="rect" id="node2" href="group__mfe__fold.html" title="This module contains all functions and variables related to the calculation of global..." alt="" coords="7,58,329,89"/></map></td></tr></table></center>
</div>
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-<center><table><tr><td><img src="group__consensus__mfe__fold.png" border="0" alt="" usemap="#group____consensus____mfe____fold"/>
-<map name="group____consensus____mfe____fold" id="group____consensus____mfe____fold">
-<area shape="rect" id="node1" href="group__consensus__fold.html" title="compute various properties (consensus MFE structures, partition function, Boltzmann distributed stoch..." alt="" coords="5,5,219,46"/><area shape="rect" id="node2" href="group__mfe__fold.html" title="This module contains all functions and variables related to the calculation of global minimum free en..." alt="" coords="6,70,218,111"/></map>
-</td></tr></table></center>
-</div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:ga4cf00f0659e5f0480335d69e797f05b1"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1">alifold</a> (const char **strings, char *structure)</td></tr>
-<tr class="memdesc:ga4cf00f0659e5f0480335d69e797f05b1"><td class="mdescLeft"> </td><td class="mdescRight">Compute MFE and according consensus structure of an alignment of sequences. <a href="#ga4cf00f0659e5f0480335d69e797f05b1"></a><br/></td></tr>
-<tr class="memitem:gadbd3b0b1c144cbfb4efe704b2b260f96"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96">circalifold</a> (const char **strings, char *structure)</td></tr>
-<tr class="memdesc:gadbd3b0b1c144cbfb4efe704b2b260f96"><td class="mdescLeft"> </td><td class="mdescRight">Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. <a href="#gadbd3b0b1c144cbfb4efe704b2b260f96"></a><br/></td></tr>
-<tr class="memitem:ga72095e4554b5d577250ea14c42acc49e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga72095e4554b5d577250ea14c42acc49e"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e">free_alifold_arrays</a> (void)</td></tr>
-<tr class="memdesc:ga72095e4554b5d577250ea14c42acc49e"><td class="mdescLeft"> </td><td class="mdescRight">Free the memory occupied by MFE alifold functions. <br/></td></tr>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1">alifold</a> (const char **strings, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute MFE and according consensus structure of an alignment of sequences. <a href="#ga4cf00f0659e5f0480335d69e797f05b1"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96">circalifold</a> (const char **strings, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. <a href="#gadbd3b0b1c144cbfb4efe704b2b260f96"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga72095e4554b5d577250ea14c42acc49e"></a><!-- doxytag: member="consensus_mfe_fold::free_alifold_arrays" ref="ga72095e4554b5d577250ea14c42acc49e" args="(void)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e">free_alifold_arrays</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free the memory occupied by MFE alifold functions. <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="ga4cf00f0659e5f0480335d69e797f05b1"></a>
+<a class="anchor" id="ga4cf00f0659e5f0480335d69e797f05b1"></a><!-- doxytag: member="alifold.h::alifold" ref="ga4cf00f0659e5f0480335d69e797f05b1" args="(const char **strings, char *structure)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float alifold </td>
<td>(</td>
- <td class="paramtype">const char ** </td>
- <td class="paramname"><em>strings</em>, </td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"> <em>strings</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>structure</em> </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>structure</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>Compute MFE and according consensus structure of an alignment of sequences. </p>
<p>This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.</p>
<p>Sufficient space must be allocated for 'structure' before calling <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1" title="Compute MFE and according consensus structure of an alignment of sequences.">alifold()</a>.</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">strings</td><td>A pointer to a NULL terminated array of character arrays </td></tr>
- <tr><td class="paramname">structure</td><td>A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) </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>strings</em> </td><td>A pointer to a NULL terminated array of character arrays </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The free energy score in kcal/mol </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>The free energy score in kcal/mol </dd></dl>
</div>
</div>
-<a class="anchor" id="gadbd3b0b1c144cbfb4efe704b2b260f96"></a>
+<a class="anchor" id="gadbd3b0b1c144cbfb4efe704b2b260f96"></a><!-- doxytag: member="alifold.h::circalifold" ref="gadbd3b0b1c144cbfb4efe704b2b260f96" args="(const char **strings, char *structure)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float circalifold </td>
<td>(</td>
- <td class="paramtype">const char ** </td>
- <td class="paramname"><em>strings</em>, </td>
+ <td class="paramtype">const char ** </td>
+ <td class="paramname"> <em>strings</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char * </td>
- <td class="paramname"><em>structure</em> </td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"> <em>structure</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>Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. </p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">strings</td><td>A pointer to a NULL terminated array of character arrays </td></tr>
- <tr><td class="paramname">structure</td><td>A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) </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>strings</em> </td><td>A pointer to a NULL terminated array of character arrays </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The free energy score in kcal/mol </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>The free energy score in kcal/mol </dd></dl>
</div>
</div>
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