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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>
-</div><!-- fragment --></div><!-- contents -->
-</div><!-- doc-content -->
-<!-- start footer part -->
-<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
- <ul>
- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><b>pair_mat.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/pair_mat.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#include <ctype.h></span>
+<a name="l00002"></a>00002 <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>
+<a name="l00003"></a>00003 <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>
+<a name="l00004"></a>00004
+<a name="l00005"></a>00005 <span class="preprocessor">#define NBASES 8</span>
+<a name="l00006"></a>00006 <span class="preprocessor"></span><span class="comment">/*@notnull@*/</span>
+<a name="l00007"></a>00007
+<a name="l00008"></a>00008 <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> Law_and_Order[] = <span class="stringliteral">"_ACGUTXKI"</span>;
+<a name="l00009"></a>00009 <span class="keyword">static</span> <span class="keywordtype">int</span> BP_pair[NBASES][NBASES]=
+<a name="l00010"></a>00010 <span class="comment">/* _ A C G U X K I */</span>
+<a name="l00011"></a>00011 {{ 0, 0, 0, 0, 0, 0, 0, 0},
+<a name="l00012"></a>00012 { 0, 0, 0, 0, 5, 0, 0, 5},
+<a name="l00013"></a>00013 { 0, 0, 0, 1, 0, 0, 0, 0},
+<a name="l00014"></a>00014 { 0, 0, 2, 0, 3, 0, 0, 0},
+<a name="l00015"></a>00015 { 0, 6, 0, 4, 0, 0, 0, 6},
+<a name="l00016"></a>00016 { 0, 0, 0, 0, 0, 0, 2, 0},
+<a name="l00017"></a>00017 { 0, 0, 0, 0, 0, 1, 0, 0},
+<a name="l00018"></a>00018 { 0, 6, 0, 0, 5, 0, 0, 0}};
+<a name="l00019"></a>00019
+<a name="l00020"></a>00020 <span class="preprocessor">#define MAXALPHA 20 </span><span class="comment">/* maximal length of alphabet */</span>
+<a name="l00021"></a>00021
+<a name="l00022"></a>00022 <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];
+<a name="l00023"></a>00023 <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];
+<a name="l00024"></a>00024 <span class="comment">/* rtype[pair[i][j]]:=pair[j][i] */</span>
+<a name="l00025"></a>00025 <span class="keyword">static</span> <span class="keywordtype">int</span> rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};
+<a name="l00026"></a>00026
+<a name="l00027"></a>00027 <span class="preprocessor">#ifdef _OPENMP</span>
+<a name="l00028"></a>00028 <span class="preprocessor"></span><span class="preprocessor">#pragma omp threadprivate(Law_and_Order, BP_pair, alias, pair, rtype)</span>
+<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
+<a name="l00030"></a>00030 <span class="preprocessor"></span>
+<a name="l00031"></a>00031 <span class="comment">/* for backward compatibility */</span>
+<a name="l00032"></a>00032 <span class="preprocessor">#define ENCODE(c) encode_char(c)</span>
+<a name="l00033"></a>00033 <span class="preprocessor"></span>
+<a name="l00034"></a>00034 <span class="keyword">static</span> <span class="keywordtype">int</span> encode_char(<span class="keywordtype">char</span> c) {
+<a name="l00035"></a>00035 <span class="comment">/* return numerical representation of base used e.g. in pair[][] */</span>
+<a name="l00036"></a>00036 <span class="keywordtype">int</span> code;
+<a name="l00037"></a>00037 <span class="keywordflow">if</span> (energy_set>0) code = (int) (c-<span class="charliteral">'A'</span>)+1;
+<a name="l00038"></a>00038 <span class="keywordflow">else</span> {
+<a name="l00039"></a>00039 <span class="keyword">const</span> <span class="keywordtype">char</span> *pos;
+<a name="l00040"></a>00040 pos = strchr(Law_and_Order, c);
+<a name="l00041"></a>00041 <span class="keywordflow">if</span> (pos==NULL) code=0;
+<a name="l00042"></a>00042 <span class="keywordflow">else</span> code = (int) (pos-Law_and_Order);
+<a name="l00043"></a>00043 <span class="keywordflow">if</span> (code>5) code = 0;
+<a name="l00044"></a>00044 <span class="keywordflow">if</span> (code>4) code--; <span class="comment">/* make T and U equivalent */</span>
+<a name="l00045"></a>00045 }
+<a name="l00046"></a>00046 <span class="keywordflow">return</span> code;
+<a name="l00047"></a>00047 }
+<a name="l00048"></a>00048
+<a name="l00049"></a>00049 <span class="comment">/*@+boolint +charint@*/</span>
+<a name="l00050"></a>00050 <span class="comment">/*@null@*/</span>
+<a name="l00051"></a>00051 <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>;
+<a name="l00052"></a>00052 <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[]);
+<a name="l00053"></a>00053 <span class="keyword">static</span> <span class="keywordtype">void</span> make_pair_matrix(<span class="keywordtype">void</span>)
+<a name="l00054"></a>00054 {
+<a name="l00055"></a>00055 <span class="keywordtype">int</span> i,j;
+<a name="l00056"></a>00056
+<a name="l00057"></a>00057 <span class="keywordflow">if</span> (energy_set==0) {
+<a name="l00058"></a>00058 <span class="keywordflow">for</span> (i=0; i<5; i++) alias[i] = (<span class="keywordtype">short</span>) i;
+<a name="l00059"></a>00059 alias[5] = 3; <span class="comment">/* X <-> G */</span>
+<a name="l00060"></a>00060 alias[6] = 2; <span class="comment">/* K <-> C */</span>
+<a name="l00061"></a>00061 alias[7] = 0; <span class="comment">/* I <-> default base '@' */</span>
+<a name="l00062"></a>00062 <span class="keywordflow">for</span> (i=0; i<NBASES; i++) {
+<a name="l00063"></a>00063 <span class="keywordflow">for</span> (j=0; j<NBASES; j++)
+<a name="l00064"></a>00064 pair[i][j] = BP_pair[i][j];
+<a name="l00065"></a>00065 }
+<a name="l00066"></a>00066 <span class="keywordflow">if</span> (noGU) pair[3][4] = pair[4][3] =0;
+<a name="l00067"></a>00067 <span class="keywordflow">if</span> (nonstandards!=NULL) { <span class="comment">/* allow nonstandard bp's */</span>
+<a name="l00068"></a>00068 <span class="keywordflow">for</span> (i=0; i<(int)strlen(nonstandards); i+=2)
+<a name="l00069"></a>00069 pair[encode_char(nonstandards[i])]
+<a name="l00070"></a>00070 [encode_char(nonstandards[i+1])]=7;
+<a name="l00071"></a>00071 }
+<a name="l00072"></a>00072 <span class="keywordflow">for</span> (i=0; i<NBASES; i++) {
+<a name="l00073"></a>00073 <span class="keywordflow">for</span> (j=0; j<NBASES; j++)
+<a name="l00074"></a>00074 rtype[pair[i][j]] = pair[j][i];
+<a name="l00075"></a>00075 }
+<a name="l00076"></a>00076 } <span class="keywordflow">else</span> {
+<a name="l00077"></a>00077 <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++) {
+<a name="l00078"></a>00078 <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++)
+<a name="l00079"></a>00079 pair[i][j] = 0;
+<a name="l00080"></a>00080 }
+<a name="l00081"></a>00081 <span class="keywordflow">if</span> (energy_set==1) {
+<a name="l00082"></a>00082 <span class="keywordflow">for</span> (i=1; i<<a class="code" href="data__structures_8h.html#a05a5ffe718aa431d97419a12fb082379" title="Maximal length of alphabet.">MAXALPHA</a>;) {
+<a name="l00083"></a>00083 alias[i++] = 3; <span class="comment">/* A <-> G */</span>
+<a name="l00084"></a>00084 alias[i++] = 2; <span class="comment">/* B <-> C */</span>
+<a name="l00085"></a>00085 }
+<a name="l00086"></a>00086 <span class="keywordflow">for</span> (i=1; i<MAXALPHA; i++) {
+<a name="l00087"></a>00087 pair[i][i+1] = 2; <span class="comment">/* AB <-> GC */</span>
+<a name="l00088"></a>00088 i++;
+<a name="l00089"></a>00089 pair[i][i-1] = 1; <span class="comment">/* BA <-> CG */</span>
+<a name="l00090"></a>00090 }
+<a name="l00091"></a>00091 }
+<a name="l00092"></a>00092 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (energy_set==2) {
+<a name="l00093"></a>00093 <span class="keywordflow">for</span> (i=1; i<MAXALPHA;) {
+<a name="l00094"></a>00094 alias[i++] = 1; <span class="comment">/* A <-> A*/</span>
+<a name="l00095"></a>00095 alias[i++] = 4; <span class="comment">/* B <-> U */</span>
+<a name="l00096"></a>00096 }
+<a name="l00097"></a>00097 <span class="keywordflow">for</span> (i=1; i<MAXALPHA; i++) {
+<a name="l00098"></a>00098 pair[i][i+1] = 5; <span class="comment">/* AB <-> AU */</span>
+<a name="l00099"></a>00099 i++;
+<a name="l00100"></a>00100 pair[i][i-1] = 6; <span class="comment">/* BA <-> UA */</span>
+<a name="l00101"></a>00101 }
+<a name="l00102"></a>00102 }
+<a name="l00103"></a>00103 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (energy_set==3) {
+<a name="l00104"></a>00104 <span class="keywordflow">for</span> (i=1; i<MAXALPHA-2; ) {
+<a name="l00105"></a>00105 alias[i++] = 3; <span class="comment">/* A <-> G */</span>
+<a name="l00106"></a>00106 alias[i++] = 2; <span class="comment">/* B <-> C */</span>
+<a name="l00107"></a>00107 alias[i++] = 1; <span class="comment">/* C <-> A */</span>
+<a name="l00108"></a>00108 alias[i++] = 4; <span class="comment">/* D <-> U */</span>
+<a name="l00109"></a>00109 }
+<a name="l00110"></a>00110 <span class="keywordflow">for</span> (i=1; i<MAXALPHA-2; i++) {
+<a name="l00111"></a>00111 pair[i][i+1] = 2; <span class="comment">/* AB <-> GC */</span>
+<a name="l00112"></a>00112 i++;
+<a name="l00113"></a>00113 pair[i][i-1] = 1; <span class="comment">/* BA <-> CG */</span>
+<a name="l00114"></a>00114 i++;
+<a name="l00115"></a>00115 pair[i][i+1] = 5; <span class="comment">/* CD <-> AU */</span>
+<a name="l00116"></a>00116 i++;
+<a name="l00117"></a>00117 pair[i][i-1] = 6; <span class="comment">/* DC <-> UA */</span>
+<a name="l00118"></a>00118 }
+<a name="l00119"></a>00119 }
+<a name="l00120"></a>00120 <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>);
+<a name="l00121"></a>00121 <span class="keywordflow">for</span> (i=0; i<=MAXALPHA; i++) {
+<a name="l00122"></a>00122 <span class="keywordflow">for</span> (j=0; j<=MAXALPHA; j++)
+<a name="l00123"></a>00123 rtype[pair[i][j]] = pair[j][i];
+<a name="l00124"></a>00124 }
+<a name="l00125"></a>00125 }
+<a name="l00126"></a>00126 }
+<a name="l00127"></a>00127
+<a name="l00128"></a>00128 <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){
+<a name="l00129"></a>00129 <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i,l = (<span class="keywordtype">unsigned</span> int)strlen(sequence);
+<a name="l00130"></a>00130 <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));
+<a name="l00131"></a>00131
+<a name="l00132"></a>00132 <span class="keywordflow">switch</span>(how){
+<a name="l00133"></a>00133 <span class="comment">/* standard encoding as always used for S */</span>
+<a name="l00134"></a>00134 <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>
+<a name="l00135"></a>00135 S[i]= (<span class="keywordtype">short</span>) encode_char(toupper(sequence[i-1]));
+<a name="l00136"></a>00136 S[l+1] = S[1];
+<a name="l00137"></a>00137 S[0] = (short) l;
+<a name="l00138"></a>00138 <span class="keywordflow">break</span>;
+<a name="l00139"></a>00139 <span class="comment">/* encoding for mismatches of nostandard bases (normally used for S1) */</span>
+<a name="l00140"></a>00140 <span class="keywordflow">case</span> 1: <span class="keywordflow">for</span>(i=1; i<=l; i++)
+<a name="l00141"></a>00141 S[i] = alias[(<span class="keywordtype">short</span>) encode_char(toupper(sequence[i-1]))];
+<a name="l00142"></a>00142 S[l+1] = S[1];
+<a name="l00143"></a>00143 S[0] = S[l];
+<a name="l00144"></a>00144 <span class="keywordflow">break</span>;
+<a name="l00145"></a>00145 }
+<a name="l00146"></a>00146
+<a name="l00147"></a>00147 <span class="keywordflow">return</span> S;
+<a name="l00148"></a>00148 }
+</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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