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-<div class="title">LPfold.h</div> </div>
-</div><!--header-->
-<div class="contents">
-<a href="LPfold_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_LPFOLD_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_LPFOLD_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="l00029"></a><span class="lineno"> 29</span> <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga5a019014d37fe6105131dfc2fc447880">update_pf_paramsLP</a>(<span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div>
-<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keywordtype">void</span> update_pf_paramsLP_par(<span class="keywordtype">int</span> length, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters);</div>
-<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div>
-<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *<a class="code" href="group__local__pf__fold.html#gaa1ecd401617ebc748a0220026543c777" title="Compute partition functions for locally stable secondary structures.">pfl_fold</a>(<span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordtype">int</span> winSize,</div>
-<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">int</span> pairSize,</div>
-<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">float</span> cutoffb,</div>
-<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">double</span> **pU,</div>
-<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">struct</span> <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> **dpp2,</div>
-<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  FILE *pUfp,</div>
-<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  FILE *spup);</div>
-<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
-<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *<a class="code" href="group__local__pf__fold.html#gab354507e8028f3e1c52ef96bb1eb9df8" title="Compute partition functions for locally stable secondary structures.">pfl_fold_par</a>(<span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">int</span> winSize,</div>
-<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordtype">int</span> pairSize,</div>
-<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordtype">float</span> cutoffb,</div>
-<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordtype">double</span> **pU,</div>
-<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keyword">struct</span> <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> **dpp2,</div>
-<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  FILE *pUfp,</div>
-<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  FILE *spup,</div>
-<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters);</div>
-<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="keywordtype">void</span> putoutpU_prob_par( <span class="keywordtype">double</span> **pU,</div>
-<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">int</span> ulength,</div>
-<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  FILE *fp,</div>
-<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> energies,</div>
-<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters);</div>
-<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
-<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
-<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga0bcb751860bbf34e3dfee8c2fbdb3ef3" title="Writes the unpaired probabilities (pU) or opening energies into a file.">putoutpU_prob</a>(<span class="keywordtype">double</span> **pU,</div>
-<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">int</span> ulength,</div>
-<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  FILE *fp,</div>
-<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">int</span> energies);</div>
-<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="keywordtype">void</span> putoutpU_prob_bin_par( <span class="keywordtype">double</span> **pU,</div>
-<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordtype">int</span> ulength,</div>
-<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  FILE *fp,</div>
-<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">int</span> energies,</div>
-<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...">pf_paramT</a> *parameters);</div>
-<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
-<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga9acb00ee10e96b1ca4ea394cd8bcec75" title="Writes the unpaired probabilities (pU) or opening energies into a binary file.">putoutpU_prob_bin</a>(<span class="keywordtype">double</span> **pU,</div>
-<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordtype">int</span> length,</div>
-<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordtype">int</span> ulength,</div>
-<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  FILE *fp,</div>
-<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">int</span> energies);</div>
-<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
-<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="LPfold_8h.html#ae85bf55053e9fb295208be322e0fa07a">init_pf_foldLP</a>(<span class="keywordtype">int</span> length));</div>
-<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
-<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="preprocessor">#endif</span></div>
-</div><!-- fragment --></div><!-- contents -->
-</div><!-- doc-content -->
-<!-- start footer part -->
-<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
- <ul>
- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="LPfold_8h.html">LPfold.h</a></li>
- <li class="footer">Generated on Wed Jul 24 2013 13:38:56 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/LPfold.h</h1><a href="LPfold_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_LPFOLD_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_LPFOLD_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="l00029"></a>00029 <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga5a019014d37fe6105131dfc2fc447880">update_pf_paramsLP</a>(<span class="keywordtype">int</span> length);
+<a name="l00030"></a>00030
+<a name="l00037"></a>00037 <span class="keywordtype">void</span> update_pf_paramsLP_par(<span class="keywordtype">int</span> length, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters);
+<a name="l00038"></a>00038
+<a name="l00076"></a>00076 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> *<a class="code" href="group__local__pf__fold.html#gaa1ecd401617ebc748a0220026543c777" title="Compute partition functions for locally stable secondary structures.">pfl_fold</a>(<span class="keywordtype">char</span> *sequence,
+<a name="l00077"></a>00077 <span class="keywordtype">int</span> winSize,
+<a name="l00078"></a>00078 <span class="keywordtype">int</span> pairSize,
+<a name="l00079"></a>00079 <span class="keywordtype">float</span> cutoffb,
+<a name="l00080"></a>00080 <span class="keywordtype">double</span> **pU,
+<a name="l00081"></a>00081 <span class="keyword">struct</span> <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **dpp2,
+<a name="l00082"></a>00082 FILE *pUfp,
+<a name="l00083"></a>00083 FILE *spup);
+<a name="l00084"></a>00084
+<a name="l00091"></a>00091 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> *<a class="code" href="group__local__pf__fold.html#gab354507e8028f3e1c52ef96bb1eb9df8" title="Compute partition functions for locally stable secondary structures.">pfl_fold_par</a>(<span class="keywordtype">char</span> *sequence,
+<a name="l00092"></a>00092 <span class="keywordtype">int</span> winSize,
+<a name="l00093"></a>00093 <span class="keywordtype">int</span> pairSize,
+<a name="l00094"></a>00094 <span class="keywordtype">float</span> cutoffb,
+<a name="l00095"></a>00095 <span class="keywordtype">double</span> **pU,
+<a name="l00096"></a>00096 <span class="keyword">struct</span> <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **dpp2,
+<a name="l00097"></a>00097 FILE *pUfp,
+<a name="l00098"></a>00098 FILE *spup,
+<a name="l00099"></a>00099 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters);
+<a name="l00100"></a>00100
+<a name="l00101"></a>00101
+<a name="l00102"></a>00102 <span class="keywordtype">void</span> putoutpU_prob_par( <span class="keywordtype">double</span> **pU,
+<a name="l00103"></a>00103 <span class="keywordtype">int</span> length,
+<a name="l00104"></a>00104 <span class="keywordtype">int</span> ulength,
+<a name="l00105"></a>00105 FILE *fp,
+<a name="l00106"></a>00106 <span class="keywordtype">int</span> energies,
+<a name="l00107"></a>00107 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters);
+<a name="l00108"></a>00108
+<a name="l00109"></a>00109
+<a name="l00124"></a>00124 <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga0bcb751860bbf34e3dfee8c2fbdb3ef3" title="Writes the unpaired probabilities (pU) or opening energies into a file.">putoutpU_prob</a>(<span class="keywordtype">double</span> **pU,
+<a name="l00125"></a>00125 <span class="keywordtype">int</span> length,
+<a name="l00126"></a>00126 <span class="keywordtype">int</span> ulength,
+<a name="l00127"></a>00127 FILE *fp,
+<a name="l00128"></a>00128 <span class="keywordtype">int</span> energies);
+<a name="l00129"></a>00129
+<a name="l00130"></a>00130 <span class="keywordtype">void</span> putoutpU_prob_bin_par( <span class="keywordtype">double</span> **pU,
+<a name="l00131"></a>00131 <span class="keywordtype">int</span> length,
+<a name="l00132"></a>00132 <span class="keywordtype">int</span> ulength,
+<a name="l00133"></a>00133 FILE *fp,
+<a name="l00134"></a>00134 <span class="keywordtype">int</span> energies,
+<a name="l00135"></a>00135 <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters);
+<a name="l00136"></a>00136
+<a name="l00151"></a>00151 <span class="keywordtype">void</span> <a class="code" href="group__local__pf__fold.html#ga9acb00ee10e96b1ca4ea394cd8bcec75" title="Writes the unpaired probabilities (pU) or opening energies into a binary file.">putoutpU_prob_bin</a>(<span class="keywordtype">double</span> **pU,
+<a name="l00152"></a>00152 <span class="keywordtype">int</span> length,
+<a name="l00153"></a>00153 <span class="keywordtype">int</span> ulength,
+<a name="l00154"></a>00154 FILE *fp,
+<a name="l00155"></a>00155 <span class="keywordtype">int</span> energies);
+<a name="l00156"></a>00156
+<a name="l00162"></a>00162 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="LPfold_8h.html#ae85bf55053e9fb295208be322e0fa07a">init_pf_foldLP</a>(<span class="keywordtype">int</span> length));
+<a name="l00163"></a>00163
+<a name="l00164"></a>00164 <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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