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+<div class="title">pair_mat.h</div> </div>
+</div><!--header-->
+<div class="contents">
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include <ctype.h></span></div>
+<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#include "<a class="code" href="utils_8h.html" title="Various utility- and helper-functions used throughout the Vienna RNA package.">utils.h</a>"</span></div>
+<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include "<a class="code" href="fold__vars_8h.html" title="Here all all declarations of the global variables used throughout RNAlib.">fold_vars.h</a>"</span></div>
+<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> </div>
+<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#define NBASES 8</span></div>
+<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor"></span><span class="comment">/*@notnull@*/</span></div>
+<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> </div>
+<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> Law_and_Order[] = <span class="stringliteral">"_ACGUTXKI"</span>;</div>
+<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="keyword">static</span> <span class="keywordtype">int</span> BP_pair[NBASES][NBASES]=</div>
+<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">/* _ A C G U X K I */</span></div>
+<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> {{ 0, 0, 0, 0, 0, 0, 0, 0},</div>
+<div class="line"><a name="l00012"></a><span class="lineno"> 12</span>  { 0, 0, 0, 0, 5, 0, 0, 5},</div>
+<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  { 0, 0, 0, 1, 0, 0, 0, 0},</div>
+<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  { 0, 0, 2, 0, 3, 0, 0, 0},</div>
+<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  { 0, 6, 0, 4, 0, 0, 0, 6},</div>
+<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  { 0, 0, 0, 0, 0, 0, 2, 0},</div>
+<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  { 0, 0, 0, 0, 0, 1, 0, 0},</div>
+<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  { 0, 6, 0, 0, 5, 0, 0, 0}};</div>
+<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div>
+<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#define MAXALPHA 20 </span><span class="comment">/* maximal length of alphabet */</span><span class="preprocessor"></span></div>
+<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">static</span> <span class="keywordtype">short</span> alias[<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>+1];</div>
+<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">static</span> <span class="keywordtype">int</span> pair[<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>+1][<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>+1];</div>
+<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">/* rtype[pair[i][j]]:=pair[j][i] */</span></div>
+<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">static</span> <span class="keywordtype">int</span> rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};</div>
+<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div>
+<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#ifdef _OPENMP</span></div>
+<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor"></span><span class="preprocessor">#pragma omp threadprivate(Law_and_Order, BP_pair, alias, pair, rtype)</span></div>
+<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
+<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">/* for backward compatibility */</span></div>
+<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#define ENCODE(c) encode_char(c)</span></div>
+<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor"></span></div>
+<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">static</span> <span class="keywordtype">int</span> encode_char(<span class="keywordtype">char</span> c) {</div>
+<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="comment">/* return numerical representation of base used e.g. in pair[][] */</span></div>
+<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordtype">int</span> code;</div>
+<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">if</span> (energy_set>0) code = (int) (c-<span class="charliteral">'A'</span>)+1;</div>
+<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">else</span> {</div>
+<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *pos;</div>
+<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  pos = strchr(Law_and_Order, c);</div>
+<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">if</span> (pos==NULL) code=0;</div>
+<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">else</span> code = (int) (pos-Law_and_Order);</div>
+<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordflow">if</span> (code>5) code = 0;</div>
+<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordflow">if</span> (code>4) code--; <span class="comment">/* make T and U equivalent */</span></div>
+<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  }</div>
+<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordflow">return</span> code;</div>
+<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> }</div>
+<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
+<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="comment">/*@+boolint +charint@*/</span></div>
+<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="comment">/*@null@*/</span></div>
+<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">extern</span> <span class="keywordtype">char</span> *<a class="code" href="fold__vars_8h.html#a2695d91cc535d09c2eae5c3884e2ec64" title="contains allowed non standard base pairs">nonstandards</a>;</div>
+<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a127ce946e56b5a5773781cabe68e38c5" title="Die with an error message.">nrerror</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> message[]);</div>
+<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">static</span> <span class="keywordtype">void</span> make_pair_matrix(<span class="keywordtype">void</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="keywordtype">int</span> i,j;</div>
+<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div>
+<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordflow">if</span> (energy_set==0) {</div>
+<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">for</span> (i=0; i<5; i++) alias[i] = (<span class="keywordtype">short</span>) i;</div>
+<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  alias[5] = 3; <span class="comment">/* X <-> G */</span></div>
+<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  alias[6] = 2; <span class="comment">/* K <-> C */</span></div>
+<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  alias[7] = 0; <span class="comment">/* I <-> default base '@' */</span></div>
+<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordflow">for</span> (i=0; i<NBASES; i++) {</div>
+<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordflow">for</span> (j=0; j<NBASES; j++)</div>
+<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  pair[i][j] = BP_pair[i][j];</div>
+<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  }</div>
+<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordflow">if</span> (noGU) pair[3][4] = pair[4][3] =0;</div>
+<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordflow">if</span> (nonstandards!=NULL) { <span class="comment">/* allow nonstandard bp's */</span></div>
+<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordflow">for</span> (i=0; i<(int)strlen(nonstandards); i+=2)</div>
+<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  pair[encode_char(nonstandards[i])]</div>
+<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  [encode_char(nonstandards[i+1])]=7;</div>
+<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  }</div>
+<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordflow">for</span> (i=0; i<NBASES; i++) {</div>
+<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordflow">for</span> (j=0; j<NBASES; j++)</div>
+<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  rtype[pair[i][j]] = pair[j][i];</div>
+<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  }</div>
+<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  } <span class="keywordflow">else</span> {</div>
+<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">for</span> (i=0; i<=<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>; i++) {</div>
+<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordflow">for</span> (j=0; j<=<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>; j++)</div>
+<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  pair[i][j] = 0;</div>
+<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  }</div>
+<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">if</span> (energy_set==1) {</div>
+<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordflow">for</span> (i=1; i<<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>;) {</div>
+<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  alias[i++] = 3; <span class="comment">/* A <-> G */</span></div>
+<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  alias[i++] = 2; <span class="comment">/* B <-> C */</span></div>
+<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  }</div>
+<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordflow">for</span> (i=1; i<<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>; i++) {</div>
+<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  pair[i][i+1] = 2; <span class="comment">/* AB <-> GC */</span></div>
+<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  i++;</div>
+<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  pair[i][i-1] = 1; <span class="comment">/* BA <-> CG */</span></div>
+<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  }</div>
+<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  }</div>
+<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (energy_set==2) {</div>
+<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordflow">for</span> (i=1; i<<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>;) {</div>
+<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  alias[i++] = 1; <span class="comment">/* A <-> A*/</span></div>
+<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  alias[i++] = 4; <span class="comment">/* B <-> U */</span></div>
+<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  }</div>
+<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordflow">for</span> (i=1; i<<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>; i++) {</div>
+<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  pair[i][i+1] = 5; <span class="comment">/* AB <-> AU */</span></div>
+<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  i++;</div>
+<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  pair[i][i-1] = 6; <span class="comment">/* BA <-> UA */</span></div>
+<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  }</div>
+<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  }</div>
+<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (energy_set==3) {</div>
+<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordflow">for</span> (i=1; i<MAXALPHA-2; ) {</div>
+<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  alias[i++] = 3; <span class="comment">/* A <-> G */</span></div>
+<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  alias[i++] = 2; <span class="comment">/* B <-> C */</span></div>
+<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  alias[i++] = 1; <span class="comment">/* C <-> A */</span></div>
+<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  alias[i++] = 4; <span class="comment">/* D <-> U */</span></div>
+<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  }</div>
+<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordflow">for</span> (i=1; i<MAXALPHA-2; i++) {</div>
+<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  pair[i][i+1] = 2; <span class="comment">/* AB <-> GC */</span></div>
+<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  i++;</div>
+<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  pair[i][i-1] = 1; <span class="comment">/* BA <-> CG */</span></div>
+<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  i++;</div>
+<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  pair[i][i+1] = 5; <span class="comment">/* CD <-> AU */</span></div>
+<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  i++;</div>
+<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  pair[i][i-1] = 6; <span class="comment">/* DC <-> UA */</span></div>
+<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  }</div>
+<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  }</div>
+<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordflow">else</span> <a class="code" href="utils_8h.html#a127ce946e56b5a5773781cabe68e38c5" title="Die with an error message.">nrerror</a>(<span class="stringliteral">"What energy_set are YOU using??"</span>);</div>
+<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">for</span> (i=0; i<=<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>; i++) {</div>
+<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">for</span> (j=0; j<=<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>; j++)</div>
+<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  rtype[pair[i][j]] = pair[j][i];</div>
+<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  }</div>
+<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  }</div>
+<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> }</div>
+<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
+<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> <span class="keyword">static</span> <span class="keywordtype">short</span> *encode_sequence(<span class="keyword">const</span> <span class="keywordtype">char</span> *sequence, <span class="keywordtype">short</span> how){</div>
+<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i,l = (<span class="keywordtype">unsigned</span> int)strlen(sequence);</div>
+<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">short</span> *S = (<span class="keywordtype">short</span> *) <a class="code" href="utils_8h.html#ad7e1e137b3bf1f7108933d302a7f0177" title="Allocate space safely.">space</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">short</span>)*(l+2));</div>
+<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
+<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">switch</span>(how){</div>
+<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="comment">/* standard encoding as always used for S */</span></div>
+<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordflow">case</span> 0: <span class="keywordflow">for</span>(i=1; i<=l; i++) <span class="comment">/* make numerical encoding of sequence */</span></div>
+<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  S[i]= (<span class="keywordtype">short</span>) encode_char(toupper(sequence[i-1]));</div>
+<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  S[l+1] = S[1];</div>
+<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  S[0] = (short) l;</div>
+<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordflow">break</span>;</div>
+<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">/* encoding for mismatches of nostandard bases (normally used for S1) */</span></div>
+<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordflow">case</span> 1: <span class="keywordflow">for</span>(i=1; i<=l; i++)</div>
+<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  S[i] = alias[(<span class="keywordtype">short</span>) encode_char(toupper(sequence[i-1]))];</div>
+<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  S[l+1] = S[1];</div>
+<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  S[0] = S[l];</div>
+<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordflow">break</span>;</div>
+<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  }</div>
+<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> </div>
+<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">return</span> S;</div>
+<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> }</div>
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