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-<div class="title">2Dfold.h</div> </div>
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-<div class="contents">
-<a href="2Dfold_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="comment">/*</span></div>
-<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> minimum free energy</span></div>
-<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> RNA secondary structure with</span></div>
-<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> basepair distance d to reference structure prediction</span></div>
-<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"></span></div>
-<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">*/</span></div>
-<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__</span></div>
-<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__</span></div>
-<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00032"></a><span class="lineno"> 32</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="l00033"></a><span class="lineno"> 33</span> </div>
-<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#ifdef __GNUC__</span></div>
-<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span></div>
-<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#else</span></div>
-<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span></div>
-<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
-<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *<a class="code" href="group__kl__neighborhood__mfe.html#gac9284f132cf0eaa0a2f43590eda05488" title="Get a structure of type TwoDfold_vars prefilled with current global settings.">get_TwoDfold_variables</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *seq,</div>
-<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure1,</div>
-<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *structure2,</div>
-<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordtype">int</span> circ);</div>
-<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
-<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keywordtype">void</span> <a class="code" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487" title="Destroy a TwoDfold_vars datastructure without memory loss.">destroy_TwoDfold_variables</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *our_variables);</div>
-<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
-<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> DEPRECATED(<a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a> **TwoDfold(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *our_variables,</div>
-<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordtype">int</span> distance1,</div>
-<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">int</span> distance2));</div>
-<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
-<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> <a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a> *<a class="code" href="group__kl__neighborhood__mfe.html#ga47da790166020558d27323aef489703e" title="Compute MFE's and representative for distance partitioning.">TwoDfoldList</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *vars,</div>
-<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordtype">int</span> distance1,</div>
-<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> distance2);</div>
-<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div>
-<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="keywordtype">char</span> *<a class="code" href="group__kl__neighborhood__mfe.html#gaf4dc05bf8fc1ea53acd7aeb798ba80c2" title="Backtrack a minimum free energy structure from a 5' section of specified length.">TwoDfold_backtrack_f5</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j,</div>
-<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordtype">int</span> k,</div>
-<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordtype">int</span> l,</div>
-<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *vars);</div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
-<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> <span class="preprocessor">#endif</span></div>
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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="2Dfold_8h.html">2Dfold.h</a></li>
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- <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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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h</h1><a href="2Dfold_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
+<a name="l00002"></a>00002 <span class="comment"> minimum free energy</span>
+<a name="l00003"></a>00003 <span class="comment"> RNA secondary structure with</span>
+<a name="l00004"></a>00004 <span class="comment"> basepair distance d to reference structure prediction</span>
+<a name="l00005"></a>00005 <span class="comment"></span>
+<a name="l00006"></a>00006 <span class="comment">*/</span>
+<a name="l00007"></a>00007 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__</span>
+<a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__</span>
+<a name="l00009"></a>00009 <span class="preprocessor"></span>
+<a name="l00032"></a>00032 <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="l00033"></a>00033
+<a name="l00034"></a>00034 <span class="preprocessor">#ifdef __GNUC__</span>
+<a name="l00035"></a>00035 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span>
+<a name="l00036"></a>00036 <span class="preprocessor"></span><span class="preprocessor">#else</span>
+<a name="l00037"></a>00037 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span>
+<a name="l00038"></a>00038 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
+<a name="l00039"></a>00039 <span class="preprocessor"></span>
+<a name="l00057"></a>00057 <a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *<a class="code" href="group__kl__neighborhood__mfe.html#gac9284f132cf0eaa0a2f43590eda05488" title="Get a structure of type TwoDfold_vars prefilled with current global settings.">get_TwoDfold_variables</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *seq,
+<a name="l00058"></a>00058 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure1,
+<a name="l00059"></a>00059 <span class="keyword">const</span> <span class="keywordtype">char</span> *structure2,
+<a name="l00060"></a>00060 <span class="keywordtype">int</span> circ);
+<a name="l00061"></a>00061
+<a name="l00071"></a>00071 <span class="keywordtype">void</span> <a class="code" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487" title="Destroy a TwoDfold_vars datastructure without memory loss.">destroy_TwoDfold_variables</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *our_variables);
+<a name="l00072"></a>00072
+<a name="l00076"></a>00076 DEPRECATED(<a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a> **TwoDfold(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *our_variables,
+<a name="l00077"></a>00077 <span class="keywordtype">int</span> distance1,
+<a name="l00078"></a>00078 <span class="keywordtype">int</span> distance2));
+<a name="l00079"></a>00079
+<a name="l00104"></a>00104 <a class="code" href="structTwoDfold__solution.html" title="Solution element returned from TwoDfoldList.">TwoDfold_solution</a> *<a class="code" href="group__kl__neighborhood__mfe.html#ga47da790166020558d27323aef489703e" title="Compute MFE&#39;s and representative for distance partitioning.">TwoDfoldList</a>(<a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *vars,
+<a name="l00105"></a>00105 <span class="keywordtype">int</span> distance1,
+<a name="l00106"></a>00106 <span class="keywordtype">int</span> distance2);
+<a name="l00107"></a>00107
+<a name="l00126"></a>00126 <span class="keywordtype">char</span> *<a class="code" href="group__kl__neighborhood__mfe.html#gaf4dc05bf8fc1ea53acd7aeb798ba80c2" title="Backtrack a minimum free energy structure from a 5&#39; section of specified length...">TwoDfold_backtrack_f5</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j,
+<a name="l00127"></a>00127 <span class="keywordtype">int</span> k,
+<a name="l00128"></a>00128 <span class="keywordtype">int</span> l,
+<a name="l00129"></a>00129 <a class="code" href="structTwoDfold__vars.html" title="Variables compound for 2Dfold MFE folding.">TwoDfold_vars</a> *vars);
+<a name="l00130"></a>00130
+<a name="l00134"></a>00134 <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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