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-<div class="title">part_func_up.h</div> </div>
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-<a href="part__func__up_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_PART_FUNC_UP_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_PART_FUNC_UP_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">#define RNA_UP_MODE_1 1U</span></div>
-<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor"></span><span class="preprocessor">#define RNA_UP_MODE_2 2U</span></div>
-<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define RNA_UP_MODE_3 4U</span></div>
-<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *<a class="code" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf" title="Calculate the partition function over all unpaired regions of a maximal length.">pf_unstru</a>(<span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordtype">int</span> max_w);</div>
-<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
-<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <a class="code" href="structinteract.html">interact</a> *<a class="code" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00" title="Calculates the probability of a local interaction between two sequences.">pf_interact</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
-<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,</div>
-<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c,</div>
-<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c2,</div>
-<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">int</span> max_w,</div>
-<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordtype">char</span> *cstruc,</div>
-<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> incr3,</div>
-<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">int</span> incr5);</div>
-<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
-<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="keywordtype">void</span> <a class="code" href="group__up__cofold.html#gadde308fd5f696dc271b1532aa96fd12f" title="Frees the output of function pf_interact().">free_interact</a>(<a class="code" href="structinteract.html">interact</a> *pin);</div>
-<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
-<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="keywordtype">int</span> Up_plot(<a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c,</div>
-<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c_sh,</div>
-<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <a class="code" href="structinteract.html">interact</a> *pint,</div>
-<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordtype">char</span> *ofile,</div>
-<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordtype">int</span> **unpaired_values,</div>
-<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordtype">char</span> *select_contrib,</div>
-<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordtype">char</span> *head,</div>
-<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> mode);</div>
-<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div>
-<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *get_pu_contrib_struct( <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n,</div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> w);</div>
-<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
-<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="keywordtype">void</span> <a class="code" href="group__up__cofold.html#gac20bd61824981d45ce0dc9934aa56df8" title="Frees the output of function pf_unstru().">free_pu_contrib_struct</a>(<a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *pu);</div>
-<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
-<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="preprocessor">#endif</span></div>
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- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="part__func__up_8h.html">part_func_up.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>
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-</div>
+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_up.h</h1><a href="part__func__up_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_PART_FUNC_UP_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_PART_FUNC_UP_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">#define RNA_UP_MODE_1 1U</span>
+<a name="l00007"></a>00007 <span class="preprocessor"></span><span class="preprocessor">#define RNA_UP_MODE_2 2U</span>
+<a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#define RNA_UP_MODE_3 4U</span>
+<a name="l00009"></a>00009 <span class="preprocessor"></span>
+<a name="l00055"></a>00055 <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *<a class="code" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf" title="Calculate the partition function over all unpaired regions of a maximal length.">pf_unstru</a>(<span class="keywordtype">char</span> *sequence,
+<a name="l00056"></a>00056 <span class="keywordtype">int</span> max_w);
+<a name="l00057"></a>00057
+<a name="l00100"></a>00100 <a class="code" href="structinteract.html">interact</a> *<a class="code" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00" title="Calculates the probability of a local interaction between two sequences.">pf_interact</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *s1,
+<a name="l00101"></a>00101 <span class="keyword">const</span> <span class="keywordtype">char</span> *s2,
+<a name="l00102"></a>00102 <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c,
+<a name="l00103"></a>00103 <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c2,
+<a name="l00104"></a>00104 <span class="keywordtype">int</span> max_w,
+<a name="l00105"></a>00105 <span class="keywordtype">char</span> *cstruc,
+<a name="l00106"></a>00106 <span class="keywordtype">int</span> incr3,
+<a name="l00107"></a>00107 <span class="keywordtype">int</span> incr5);
+<a name="l00108"></a>00108
+<a name="l00112"></a>00112 <span class="keywordtype">void</span> <a class="code" href="group__up__cofold.html#gadde308fd5f696dc271b1532aa96fd12f" title="Frees the output of function pf_interact().">free_interact</a>(<a class="code" href="structinteract.html">interact</a> *pin);
+<a name="l00113"></a>00113
+<a name="l00117"></a>00117 <span class="keywordtype">int</span> Up_plot(<a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c,
+<a name="l00118"></a>00118 <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *p_c_sh,
+<a name="l00119"></a>00119 <a class="code" href="structinteract.html">interact</a> *pint,
+<a name="l00120"></a>00120 <span class="keywordtype">char</span> *ofile,
+<a name="l00121"></a>00121 <span class="keywordtype">int</span> **unpaired_values,
+<a name="l00122"></a>00122 <span class="keywordtype">char</span> *select_contrib,
+<a name="l00123"></a>00123 <span class="keywordtype">char</span> *head,
+<a name="l00124"></a>00124 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> mode);
+<a name="l00125"></a>00125
+<a name="l00129"></a>00129 <a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *get_pu_contrib_struct( <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> n,
+<a name="l00130"></a>00130 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> w);
+<a name="l00131"></a>00131
+<a name="l00135"></a>00135 <span class="keywordtype">void</span> <a class="code" href="group__up__cofold.html#gac20bd61824981d45ce0dc9934aa56df8" title="Frees the output of function pf_unstru().">free_pu_contrib_struct</a>(<a class="code" href="structpu__contrib.html" title="contributions to p_u">pu_contrib</a> *pu);
+<a name="l00136"></a>00136
+<a name="l00141"></a>00141 <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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