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-<div class="title">snofold.h</div> </div>
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-<div class="contents">
-<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/* function from fold.c */</span></div>
-<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span></div>
-<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span></div>
-<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00005"></a><span class="lineno"> 5</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="l00006"></a><span class="lineno"> 6</span> </div>
-<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">/* Normal fold */</span></div>
-<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div>
-<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="keywordtype">int</span> snofold( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  <span class="keywordtype">char</span> *structure,</div>
-<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,</div>
-<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> threshold, </div>
-<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);</div>
-<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keywordtype">void</span> snofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length); <span class="comment">/* free arrays for mfe folding */</span></div>
-<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keywordtype">void</span> snoinitialize_fold(<span class="keywordtype">int</span> length); <span class="comment">/* allocate arrays for folding */</span></div>
-<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="keywordtype">void</span> snoupdate_fold_params(<span class="keywordtype">void</span>); <span class="comment">/* recalculate parameters */</span></div>
-<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keywordtype">int</span> snoloop_energy(<span class="keywordtype">short</span> *ptable,</div>
-<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keywordtype">short</span> *s,</div>
-<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordtype">short</span> *s1,</div>
-<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">int</span> i);</div>
-<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keywordtype">void</span> snoexport_fold_arrays( <span class="keywordtype">int</span> **indx_p,</div>
-<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordtype">int</span> **mLoop_p,</div>
-<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordtype">int</span> **cLoop,</div>
-<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <a class="code" href="structfolden.html">folden</a> ***fold_p,</div>
-<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <a class="code" href="structfolden.html">folden</a> ***fold_p_XS);</div>
-<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keywordtype">char</span> * snobacktrack_fold_from_pair( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,</div>
-<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordtype">int</span> i,</div>
-<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordtype">int</span> j);</div>
-<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">/* alifold */</span></div>
-<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">float</span> alisnofold( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,</div>
-<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,</div>
-<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop, </div>
-<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,</div>
-<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,</div>
-<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,</div>
-<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);</div>
-<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keywordtype">void</span> alisnofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length);</div>
-<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keywordtype">char</span> *alisnobacktrack_fold_from_pair(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequence,</div>
-<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">int</span> i,</div>
-<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordtype">int</span> j,</div>
-<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordtype">int</span> *cov);</div>
-<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c" title="This variable controls the weight of the covariance term in the energy function of alignment folding ...">cv_fact</a> <span class="comment">/* =1 */</span>;</div>
-<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61" title="This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...">nc_fact</a> <span class="comment">/* =1 */</span>;</div>
-<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
-<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="comment">/* max number of mismatch >>>>>..(( )).>>>> */</span></div>
-<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#define MISMATCH 3</span></div>
-<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00058"></a><span class="lineno"> 58</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"><b>snofold.h</b></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/snofold.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/* function from fold.c */</span>
+<a name="l00002"></a>00002 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__</span>
+<a name="l00004"></a>00004 <span class="preprocessor"></span>
+<a name="l00005"></a>00005 <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="l00006"></a>00006
+<a name="l00007"></a>00007 <span class="comment">/* Normal fold */</span>
+<a name="l00008"></a>00008
+<a name="l00012"></a>00012 <span class="keywordtype">int</span> snofold( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00013"></a>00013 <span class="keywordtype">char</span> *structure,
+<a name="l00014"></a>00014 <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,
+<a name="l00015"></a>00015 <span class="keyword">const</span> <span class="keywordtype">int</span> threshold,
+<a name="l00016"></a>00016 <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00017"></a>00017 <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00018"></a>00018 <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00019"></a>00019 <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);
+<a name="l00024"></a>00024 <span class="keywordtype">void</span> snofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length); <span class="comment">/* free arrays for mfe folding */</span>
+<a name="l00025"></a>00025 <span class="keywordtype">void</span> snoinitialize_fold(<span class="keywordtype">int</span> length); <span class="comment">/* allocate arrays for folding */</span>
+<a name="l00026"></a>00026 <span class="keywordtype">void</span> snoupdate_fold_params(<span class="keywordtype">void</span>); <span class="comment">/* recalculate parameters */</span>
+<a name="l00027"></a>00027 <span class="keywordtype">int</span> snoloop_energy(<span class="keywordtype">short</span> *ptable,
+<a name="l00028"></a>00028 <span class="keywordtype">short</span> *s,
+<a name="l00029"></a>00029 <span class="keywordtype">short</span> *s1,
+<a name="l00030"></a>00030 <span class="keywordtype">int</span> i);
+<a name="l00031"></a>00031 <span class="keywordtype">void</span> snoexport_fold_arrays( <span class="keywordtype">int</span> **indx_p,
+<a name="l00032"></a>00032 <span class="keywordtype">int</span> **mLoop_p,
+<a name="l00033"></a>00033 <span class="keywordtype">int</span> **cLoop,
+<a name="l00034"></a>00034 <a class="code" href="structfolden.html">folden</a> ***fold_p,
+<a name="l00035"></a>00035 <a class="code" href="structfolden.html">folden</a> ***fold_p_XS);
+<a name="l00036"></a>00036 <span class="keywordtype">char</span> * snobacktrack_fold_from_pair( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
+<a name="l00037"></a>00037 <span class="keywordtype">int</span> i,
+<a name="l00038"></a>00038 <span class="keywordtype">int</span> j);
+<a name="l00039"></a>00039 <span class="comment">/* alifold */</span>
+<a name="l00040"></a>00040 <span class="keywordtype">float</span> alisnofold( <span class="keyword">const</span> <span class="keywordtype">char</span> **strings,
+<a name="l00041"></a>00041 <span class="keyword">const</span> <span class="keywordtype">int</span> max_assym,
+<a name="l00042"></a>00042 <span class="keyword">const</span> <span class="keywordtype">int</span> threshloop,
+<a name="l00043"></a>00043 <span class="keyword">const</span> <span class="keywordtype">int</span> min_s2,
+<a name="l00044"></a>00044 <span class="keyword">const</span> <span class="keywordtype">int</span> max_s2,
+<a name="l00045"></a>00045 <span class="keyword">const</span> <span class="keywordtype">int</span> half_stem,
+<a name="l00046"></a>00046 <span class="keyword">const</span> <span class="keywordtype">int</span> max_half_stem);
+<a name="l00047"></a>00047 <span class="keywordtype">void</span> alisnofree_arrays(<span class="keyword">const</span> <span class="keywordtype">int</span> length);
+<a name="l00048"></a>00048 <span class="keywordtype">char</span> *alisnobacktrack_fold_from_pair(<span class="keyword">const</span> <span class="keywordtype">char</span> **sequence,
+<a name="l00049"></a>00049 <span class="keywordtype">int</span> i,
+<a name="l00050"></a>00050 <span class="keywordtype">int</span> j,
+<a name="l00051"></a>00051 <span class="keywordtype">int</span> *cov);
+<a name="l00052"></a>00052 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#gaf3cbac6ff5d706d6e414677841ddf94c" title="This variable controls the weight of the covariance term in the energy function of...">cv_fact</a> <span class="comment">/* =1 */</span>;
+<a name="l00053"></a>00053 <span class="keyword">extern</span> <span class="keywordtype">double</span> <a class="code" href="group__consensus__fold.html#ga502948a122a2af5b914355b1f3ea2f61" title="This variable controls the magnitude of the penalty for non-compatible sequences...">nc_fact</a> <span class="comment">/* =1 */</span>;
+<a name="l00054"></a>00054
+<a name="l00055"></a>00055 <span class="comment">/* max number of mismatch >>>>>..(( )).>>>> */</span>
+<a name="l00056"></a>00056 <span class="preprocessor">#define MISMATCH 3</span>
+<a name="l00057"></a>00057 <span class="preprocessor"></span>
+<a name="l00058"></a>00058 <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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