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-<a href="#func-members">Functions</a> </div>
- <div class="headertitle">
-<div class="title">MFE Structures of two hybridized Sequences</div> </div>
-<div class="ingroups"><a class="el" href="group__cofold.html">Calculate Secondary Structures of two RNAs upon Dimerization</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 Structures of two hybridized Sequences:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+<h1>MFE Structures of two hybridized Sequences<br/>
+<small>
+[<a class="el" href="group__cofold.html">Calculate Secondary Structures of two RNAs upon Dimerization</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 Structures of two hybridized Sequences:</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__mfe__cofold.png" border="0" alt="" usemap="#group____mfe____cofold_map"/>
+<map name="group____mfe____cofold_map" id="group____mfe____cofold">
+<area shape="rect" id="node1" href="group__mfe__fold.html" title="This module contains all functions and variables related to the calculation of global..." alt="" coords="45,5,368,35"/><area shape="rect" id="node3" href="group__cofold.html" title="Predict structures formed by two molecules upon hybridization." alt="" coords="5,58,408,89"/></map></td></tr></table></center>
</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<center><table><tr><td><img src="group__mfe__cofold.png" border="0" alt="" usemap="#group____mfe____cofold"/>
-<map name="group____mfe____cofold" id="group____mfe____cofold">
-<area shape="rect" id="node1" href="group__mfe__fold.html" title="This module contains all functions and variables related to the calculation of global minimum free en..." alt="" coords="6,5,218,46"/><area shape="rect" id="node3" href="group__cofold.html" title="Predict structures formed by two molecules upon hybridization." alt="" coords="25,69,199,125"/></map>
-</td></tr></table></center>
-</div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="files"></a>
-Files</h2></td></tr>
-<tr class="memitem:cofold_8h"><td class="memItemLeft" align="right" valign="top">file  </td><td class="memItemRight" valign="bottom"><a class="el" href="cofold_8h.html">cofold.h</a></td></tr>
-<tr class="memdesc:cofold_8h"><td class="mdescLeft"> </td><td class="mdescRight">MFE version of cofolding routines. <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:gabc8517f22cfe70595ee81fc837910d52"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52">cofold</a> (const char *sequence, char *structure)</td></tr>
-<tr class="memdesc:gabc8517f22cfe70595ee81fc837910d52"><td class="mdescLeft"> </td><td class="mdescRight">Compute the minimum free energy of two interacting RNA molecules. <a href="#gabc8517f22cfe70595ee81fc837910d52"></a><br/></td></tr>
-<tr class="memitem:gafe430060533f14b11fc611f60b3f1f6f"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gafe430060533f14b11fc611f60b3f1f6f"></a>
-float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f">cofold_par</a> (const char *string, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int is_constrained)</td></tr>
-<tr class="memdesc:gafe430060533f14b11fc611f60b3f1f6f"><td class="mdescLeft"> </td><td class="mdescRight">Compute the minimum free energy of two interacting RNA molecules. <br/></td></tr>
-<tr class="memitem:gaafb33d7473eb9af9d1b168ca8761c41a"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaafb33d7473eb9af9d1b168ca8761c41a"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a">free_co_arrays</a> (void)</td></tr>
-<tr class="memdesc:gaafb33d7473eb9af9d1b168ca8761c41a"><td class="mdescLeft"> </td><td class="mdescRight">Free memory occupied by <a class="el" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold()</a> <br/></td></tr>
-<tr class="memitem:ga4fcbf34e77b99bfbb2333d2ab0c41a57"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga4fcbf34e77b99bfbb2333d2ab0c41a57"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57">update_cofold_params</a> (void)</td></tr>
-<tr class="memdesc:ga4fcbf34e77b99bfbb2333d2ab0c41a57"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate parameters. <br/></td></tr>
-<tr class="memitem:ga5f5bf4df35d0554f6ace9579f8744c48"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48">export_cofold_arrays_gq</a> (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)</td></tr>
-<tr class="memdesc:ga5f5bf4df35d0554f6ace9579f8744c48"><td class="mdescLeft"> </td><td class="mdescRight">Export the arrays of partition function cofold (with gquadruplex support) <a href="#ga5f5bf4df35d0554f6ace9579f8744c48"></a><br/></td></tr>
-<tr class="memitem:ga5cb6b59983f1f74ccc00b9b9c4e84482"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482">export_cofold_arrays</a> (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)</td></tr>
-<tr class="memdesc:ga5cb6b59983f1f74ccc00b9b9c4e84482"><td class="mdescLeft"> </td><td class="mdescRight">Export the arrays of partition function cofold. <a href="#ga5cb6b59983f1f74ccc00b9b9c4e84482"></a><br/></td></tr>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Files</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">file </td><td class="memItemRight" valign="bottom"><a class="el" href="cofold_8h.html">cofold.h</a></td></tr>
+
+<p><tr><td class="mdescLeft"> </td><td class="mdescRight"><p>MFE version of cofolding routines. </p>
+<br/></td></tr>
+</p>
+<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__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52">cofold</a> (const char *sequence, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute the minimum free energy of two interacting RNA molecules. <a href="#gabc8517f22cfe70595ee81fc837910d52"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gafe430060533f14b11fc611f60b3f1f6f"></a><!-- doxytag: member="mfe_cofold::cofold_par" ref="gafe430060533f14b11fc611f60b3f1f6f" args="(const char *string, char *structure, paramT *parameters, int is_constrained)" -->
+float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f">cofold_par</a> (const char *string, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int is_constrained)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute the minimum free energy of two interacting RNA molecules. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaafb33d7473eb9af9d1b168ca8761c41a"></a><!-- doxytag: member="mfe_cofold::free_co_arrays" ref="gaafb33d7473eb9af9d1b168ca8761c41a" args="(void)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a">free_co_arrays</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free memory occupied by <a class="el" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold()</a>. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga4fcbf34e77b99bfbb2333d2ab0c41a57"></a><!-- doxytag: member="mfe_cofold::update_cofold_params" ref="ga4fcbf34e77b99bfbb2333d2ab0c41a57" args="(void)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57">update_cofold_params</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculate parameters. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48">export_cofold_arrays_gq</a> (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Export the arrays of partition function cofold (with gquadruplex support). <a href="#ga5f5bf4df35d0554f6ace9579f8744c48"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482">export_cofold_arrays</a> (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Export the arrays of partition function cofold. <a href="#ga5cb6b59983f1f74ccc00b9b9c4e84482"></a><br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="gabc8517f22cfe70595ee81fc837910d52"></a>
+<a class="anchor" id="gabc8517f22cfe70595ee81fc837910d52"></a><!-- doxytag: member="cofold.h::cofold" ref="gabc8517f22cfe70595ee81fc837910d52" args="(const char *sequence, char *structure)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float cofold </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">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 the minimum free energy of two interacting RNA molecules. </p>
-<p>The code is analog to 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> function. If <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule within the concat...">cut_point</a> ==-1 results should be the same as with <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>.</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">sequence</td><td>The two sequences concatenated </td></tr>
- <tr><td class="paramname">structure</td><td>Will hold the barcket dot structure of the dimer molecule </td></tr>
+<p>The code is analog to 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> function. If <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule...">cut_point</a> ==-1 results should be the same as with <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>.</p>
+<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 two sequences concatenated </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>Will hold the barcket dot structure of the dimer molecule </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>minimum free energy of the structure </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>minimum free energy of the structure </dd></dl>
</div>
</div>
-<a class="anchor" id="ga5f5bf4df35d0554f6ace9579f8744c48"></a>
+<a class="anchor" id="ga5f5bf4df35d0554f6ace9579f8744c48"></a><!-- doxytag: member="cofold.h::export_cofold_arrays_gq" ref="ga5f5bf4df35d0554f6ace9579f8744c48" args="(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void export_cofold_arrays_gq </td>
<td>(</td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>f5_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>f5_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>c_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>c_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>fML_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>fML_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>fM1_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>fM1_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>fc_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>fc_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>ggg_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>ggg_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>indx_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>indx_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char ** </td>
- <td class="paramname"><em>ptype_p</em> </td>
+ <td class="paramtype">char ** </td>
+ <td class="paramname"> <em>ptype_p</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>Export the arrays of partition function cofold (with gquadruplex support) </p>
+<p>Export the arrays of partition function cofold (with gquadruplex support). </p>
<p>Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">f5_p</td><td>A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] </td></tr>
- <tr><td class="paramname">c_p</td><td>A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j </td></tr>
- <tr><td class="paramname">fML_p</td><td>A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem </td></tr>
- <tr><td class="paramname">fM1_p</td><td>A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem </td></tr>
- <tr><td class="paramname">fc_p</td><td>A pointer to the 'fc' array, i.e. array ... </td></tr>
- <tr><td class="paramname">ggg_p</td><td>A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j] </td></tr>
- <tr><td class="paramname">indx_p</td><td>A pointer to the indexing array used for accessing the energy matrices </td></tr>
- <tr><td class="paramname">ptype_p</td><td>A pointer to the ptype array containing the base pair types for each possibility (i,j) </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>f5_p</em> </td><td>A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>c_p</em> </td><td>A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fML_p</em> </td><td>A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fM1_p</em> </td><td>A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fc_p</em> </td><td>A pointer to the 'fc' array, i.e. array ... </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ggg_p</em> </td><td>A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j] </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>indx_p</em> </td><td>A pointer to the indexing array used for accessing the energy matrices </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ptype_p</em> </td><td>A pointer to the ptype array containing the base pair types for each possibility (i,j) </td></tr>
</table>
</dd>
</dl>
</div>
</div>
-<a class="anchor" id="ga5cb6b59983f1f74ccc00b9b9c4e84482"></a>
+<a class="anchor" id="ga5cb6b59983f1f74ccc00b9b9c4e84482"></a><!-- doxytag: member="cofold.h::export_cofold_arrays" ref="ga5cb6b59983f1f74ccc00b9b9c4e84482" args="(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void export_cofold_arrays </td>
<td>(</td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>f5_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>f5_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>c_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>c_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>fML_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>fML_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>fM1_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>fM1_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>fc_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>fc_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int ** </td>
- <td class="paramname"><em>indx_p</em>, </td>
+ <td class="paramtype">int ** </td>
+ <td class="paramname"> <em>indx_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">char ** </td>
- <td class="paramname"><em>ptype_p</em> </td>
+ <td class="paramtype">char ** </td>
+ <td class="paramname"> <em>ptype_p</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>Export the arrays of partition function cofold. </p>
<p>Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">f5_p</td><td>A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] </td></tr>
- <tr><td class="paramname">c_p</td><td>A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j </td></tr>
- <tr><td class="paramname">fML_p</td><td>A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem </td></tr>
- <tr><td class="paramname">fM1_p</td><td>A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem </td></tr>
- <tr><td class="paramname">fc_p</td><td>A pointer to the 'fc' array, i.e. array ... </td></tr>
- <tr><td class="paramname">indx_p</td><td>A pointer to the indexing array used for accessing the energy matrices </td></tr>
- <tr><td class="paramname">ptype_p</td><td>A pointer to the ptype array containing the base pair types for each possibility (i,j) </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>f5_p</em> </td><td>A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>c_p</em> </td><td>A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fML_p</em> </td><td>A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fM1_p</em> </td><td>A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>fc_p</em> </td><td>A pointer to the 'fc' array, i.e. array ... </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>indx_p</em> </td><td>A pointer to the indexing array used for accessing the energy matrices </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ptype_p</em> </td><td>A pointer to the ptype array containing the base pair types for each possibility (i,j) </td></tr>
</table>
</dd>
</dl>
</div>
</div>
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