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  65 <div class="title">ali_plex.h</div>  </div>
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  67 <div class="contents">
  68 <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_ALI_PLEX_H__</span></div>
  69 <div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_ALI_PLEX_H__</span></div>
  70 <div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="preprocessor"></span></div>
  71 <div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#include &quot;<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>&quot;</span></div>
  72 <div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<a class="code" href="structduplexT.html">duplexT</a>** aliLduplexfold( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1[],</div>
  73 <div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">char</span> *s2[],</div>
  74 <div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> threshold,</div>
  75 <div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> extension_cost,</div>
  76 <div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
  77 <div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> delta,</div>
  78 <div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> fast,</div>
  79 <div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> il_a,</div>
  80 <div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> il_b,</div>
  81 <div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> b_a,</div>
  82 <div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span> b_b);</div>
  83 <div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<a class="code" href="structduplexT.html">duplexT</a>** aliLduplexfold_XS(<span class="keyword">const</span> <span class="keywordtype">char</span>* s1[],</div>
  84 <div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">char</span>* s2[],</div>
  85 <div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s1,</div>
  86 <div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> **access_s2, </div>
  87 <div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> threshold,</div>
  88 <div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> alignment_length,</div>
  89 <div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> delta,</div>
  90 <div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> fast,</div>
  91 <div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> il_a,</div>
  92 <div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> il_b,</div>
  93 <div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> b_a,</div>
  94 <div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;                            <span class="keyword">const</span> <span class="keywordtype">int</span> b_b);</div>
  95 <div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
  96 <div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="comment">/*</span></div>
  97 <div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="comment">extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);</span></div>
  98 <div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="comment">extern duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1, </span></div>
  99 <div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="comment">const int **access_s2, const int i_pos, const int j_pos, const int threshold);</span></div>
 100 <div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="comment">*/</span></div>
 101 <div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#endif</span></div>
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