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-<div class="title">cofold.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="cofold_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__</span></div>
-<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_COFOLD_H__</span></div>
-<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here.">data_structures.h</a>"</span></div>
-<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div>
-<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
-<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
-<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
-<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
-<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
-<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordtype">char</span> *structure);</div>
-<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
-<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f" title="Compute the minimum free energy of two interacting RNA molecules.">cofold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,</div>
-<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">int</span> is_constrained);</div>
-<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
-<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a" title="Free memory occupied by cofold()">free_co_arrays</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
-<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57" title="Recalculate parameters.">update_cofold_params</a>(<span class="keywordtype">void</span>);</div>
-<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
-<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="keywordtype">void</span> update_cofold_params_par(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);</div>
-<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
-<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
-<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48" title="Export the arrays of partition function cofold (with gquadruplex support)">export_cofold_arrays_gq</a>( <span class="keywordtype">int</span> **f5_p,</div>
-<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> **c_p,</div>
-<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">int</span> **fML_p,</div>
-<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordtype">int</span> **fM1_p,</div>
-<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">int</span> **fc_p,</div>
-<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">int</span> **ggg_p,</div>
-<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">char</span> **ptype_p);</div>
-<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
-<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482" title="Export the arrays of partition function cofold.">export_cofold_arrays</a>(<span class="keywordtype">int</span> **f5_p,</div>
-<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">int</span> **c_p,</div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">int</span> **fML_p,</div>
-<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">int</span> **fM1_p,</div>
-<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">int</span> **fc_p,</div>
-<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">char</span> **ptype_p);</div>
-<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
-<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
-<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> *<a class="code" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90" title="Compute Zuker type suboptimal structures.">zukersubopt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>);</div>
-<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
-<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> *<a class="code" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c" title="Compute Zuker type suboptimal structures.">zukersubopt_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
-<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);</div>
-<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
-<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> <span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79" title="get_monomer_free_energies">get_monomere_mfes</a>( <span class="keywordtype">float</span> *e1,</div>
-<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordtype">float</span> *e2);</div>
-<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
-<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div>
-<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a>(<span class="keywordtype">int</span> length));</div>
-<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
-<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="preprocessor">#endif</span></div>
-</div><!-- fragment --></div><!-- contents -->
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- <ul>
- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="cofold_8h.html">cofold.h</a></li>
- <li class="footer">Generated on Wed Jul 24 2013 13:38:55 for RNAlib-2.1.2 by
- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
- </ul>
-</div>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h</h1><a href="cofold_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_COFOLD_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00004"></a>00004 <span class="preprocessor">#include "<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found...">data_structures.h</a>"</span>
+<a name="l00005"></a>00005
+<a name="l00006"></a>00006 <span class="preprocessor">#ifdef __GNUC__</span>
+<a name="l00007"></a>00007 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span>
+<a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#else</span>
+<a name="l00009"></a>00009 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span>
+<a name="l00010"></a>00010 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
+<a name="l00011"></a>00011 <span class="preprocessor"></span>
+<a name="l00065"></a>00065 <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00066"></a>00066 <span class="keywordtype">char</span> *structure);
+<a name="l00067"></a>00067
+<a name="l00072"></a>00072 <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f" title="Compute the minimum free energy of two interacting RNA molecules.">cofold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00073"></a>00073 <span class="keywordtype">char</span> *structure,
+<a name="l00074"></a>00074 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,
+<a name="l00075"></a>00075 <span class="keywordtype">int</span> is_constrained);
+<a name="l00076"></a>00076
+<a name="l00080"></a>00080 <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a" title="Free memory occupied by cofold().">free_co_arrays</a>(<span class="keywordtype">void</span>);
+<a name="l00081"></a>00081
+<a name="l00085"></a>00085 <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57" title="Recalculate parameters.">update_cofold_params</a>(<span class="keywordtype">void</span>);
+<a name="l00086"></a>00086
+<a name="l00087"></a>00087 <span class="keywordtype">void</span> update_cofold_params_par(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);
+<a name="l00088"></a>00088
+<a name="l00089"></a>00089
+<a name="l00105"></a>00105 <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48" title="Export the arrays of partition function cofold (with gquadruplex support).">export_cofold_arrays_gq</a>( <span class="keywordtype">int</span> **f5_p,
+<a name="l00106"></a>00106 <span class="keywordtype">int</span> **c_p,
+<a name="l00107"></a>00107 <span class="keywordtype">int</span> **fML_p,
+<a name="l00108"></a>00108 <span class="keywordtype">int</span> **fM1_p,
+<a name="l00109"></a>00109 <span class="keywordtype">int</span> **fc_p,
+<a name="l00110"></a>00110 <span class="keywordtype">int</span> **ggg_p,
+<a name="l00111"></a>00111 <span class="keywordtype">int</span> **indx_p,
+<a name="l00112"></a>00112 <span class="keywordtype">char</span> **ptype_p);
+<a name="l00113"></a>00113
+<a name="l00128"></a>00128 <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482" title="Export the arrays of partition function cofold.">export_cofold_arrays</a>(<span class="keywordtype">int</span> **f5_p,
+<a name="l00129"></a>00129 <span class="keywordtype">int</span> **c_p,
+<a name="l00130"></a>00130 <span class="keywordtype">int</span> **fML_p,
+<a name="l00131"></a>00131 <span class="keywordtype">int</span> **fM1_p,
+<a name="l00132"></a>00132 <span class="keywordtype">int</span> **fc_p,
+<a name="l00133"></a>00133 <span class="keywordtype">int</span> **indx_p,
+<a name="l00134"></a>00134 <span class="keywordtype">char</span> **ptype_p);
+<a name="l00135"></a>00135
+<a name="l00136"></a>00136
+<a name="l00153"></a>00153 <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> *<a class="code" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90" title="Compute Zuker type suboptimal structures.">zukersubopt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>);
+<a name="l00154"></a>00154
+<a name="l00161"></a>00161 <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a> *<a class="code" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c" title="Compute Zuker type suboptimal structures.">zukersubopt_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
+<a name="l00162"></a>00162 <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);
+<a name="l00163"></a>00163
+<a name="l00172"></a>00172 <span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79" title="get_monomer_free_energies">get_monomere_mfes</a>( <span class="keywordtype">float</span> *e1,
+<a name="l00173"></a>00173 <span class="keywordtype">float</span> *e2);
+<a name="l00174"></a>00174
+<a name="l00175"></a>00175
+<a name="l00180"></a>00180 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a>(<span class="keywordtype">int</span> length));
+<a name="l00181"></a>00181
+<a name="l00182"></a>00182 <span class="preprocessor">#endif</span>
+</pre></div></div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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