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-<div class="title">cofold.h File Reference<div class="ingroups"><a class="el" href="group__mfe__cofold.html">MFE Structures of two hybridized Sequences</a></div></div> </div>
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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h File Reference</h1>
<p>MFE version of cofolding routines.
-<a href="#details">More...</a></p>
-<div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for cofold.h:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<div class="center"><img src="cofold_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2cofold_8h" alt=""/></div>
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-<area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="19,109,153,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="27,184,147,211"/></map>
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+
<p><a href="cofold_8h_source.html">Go to the source code of this file.</a></p>
-<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="group__mfe__cofold.html#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="group__mfe__cofold.html#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="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482"></a><br/></td></tr>
-<tr class="memitem:ga0d5104e3ecf119d8eabd40aa5fe47f90"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90">zukersubopt</a> (const char *string)</td></tr>
-<tr class="memdesc:ga0d5104e3ecf119d8eabd40aa5fe47f90"><td class="mdescLeft"> </td><td class="mdescRight">Compute Zuker type suboptimal structures. <a href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90"></a><br/></td></tr>
-<tr class="memitem:ga6d98a9450d1affadf144ac79f543da8c"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga6d98a9450d1affadf144ac79f543da8c"></a>
-<a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c">zukersubopt_par</a> (const char *string, <a class="el" href="structparamT.html">paramT</a> *parameters)</td></tr>
-<tr class="memdesc:ga6d98a9450d1affadf144ac79f543da8c"><td class="mdescLeft"> </td><td class="mdescRight">Compute Zuker type suboptimal structures. <br/></td></tr>
-<tr class="memitem:a4958b517c613e4d2afd5bce6c1060a79"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79">get_monomere_mfes</a> (float *e1, float *e2)</td></tr>
-<tr class="memdesc:a4958b517c613e4d2afd5bce6c1060a79"><td class="mdescLeft"> </td><td class="mdescRight">get_monomer_free_energies <a href="#a4958b517c613e4d2afd5bce6c1060a79"></a><br/></td></tr>
-<tr class="memitem:afee0c32208aa2ac97338b6e3fbad7fa5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a> (int length)</td></tr>
+<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__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="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gafe430060533f14b11fc611f60b3f1f6f"></a><!-- doxytag: member="cofold.h::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="cofold.h::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="cofold.h::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="group__mfe__cofold.html#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="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90">zukersubopt</a> (const char *string)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute Zuker type suboptimal structures. <a href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga6d98a9450d1affadf144ac79f543da8c"></a><!-- doxytag: member="cofold.h::zukersubopt_par" ref="ga6d98a9450d1affadf144ac79f543da8c" args="(const char *string, paramT *parameters)" -->
+<a class="el" href="structSOLUTION.html">SOLUTION</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c">zukersubopt_par</a> (const char *string, <a class="el" href="structparamT.html">paramT</a> *parameters)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute Zuker type suboptimal structures. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79">get_monomere_mfes</a> (float *e1, float *e2)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">get_monomer_free_energies <a href="#a4958b517c613e4d2afd5bce6c1060a79"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a> (int length)</td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>MFE version of cofolding routines. </p>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>MFE version of cofolding routines. </p>
<p>This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines. </p>
-</div><hr/><h2>Function Documentation</h2>
-<a class="anchor" id="a4958b517c613e4d2afd5bce6c1060a79"></a>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a4958b517c613e4d2afd5bce6c1060a79"></a><!-- doxytag: member="cofold.h::get_monomere_mfes" ref="a4958b517c613e4d2afd5bce6c1060a79" args="(float *e1, float *e2)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void get_monomere_mfes </td>
<td>(</td>
- <td class="paramtype">float * </td>
- <td class="paramname"><em>e1</em>, </td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"> <em>e1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">float * </td>
- <td class="paramname"><em>e2</em> </td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"> <em>e2</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_monomer_free_energies </p>
<p>Export monomer free energies out of cofold arrays</p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">e1</td><td>A pointer to a variable where the energy of molecule A will be written to </td></tr>
- <tr><td class="paramname">e2</td><td>A pointer to a variable where the energy of molecule B will be written to </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>e1</em> </td><td>A pointer to a variable where the energy of molecule A will be written to </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>e2</em> </td><td>A pointer to a variable where the energy of molecule B will be written to </td></tr>
</table>
</dd>
</dl>
</div>
</div>
-<a class="anchor" id="afee0c32208aa2ac97338b6e3fbad7fa5"></a>
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<td class="memname">void initialize_cofold </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em></td><td>)</td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em></td>
+ <td> ) </td>
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<p>allocate arrays for folding </p>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000001">Deprecated:</a></b></dt><dd>{This function is obsolete and will be removed soon!} </dd></dl>
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