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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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