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        <name>BP_pair</name>
        <initializer>=
  
{ { 0, 0, 0, 0, 0, 0, 0, 0 },
  { 0, 0, 0, 0, 5, 0, 0, 5 },
  { 0, 0, 0, 1, 0, 0, 0, 0 },
  { 0, 0, 2, 0, 3, 0, 0, 0 },
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  { 0, 0, 0, 0, 0, 1, 0, 0 },
  { 0, 6, 0, 0, 5, 0, 0, 0 } }</initializer>
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  0, 2, 1, 4, 3, 6, 5, 7
}</initializer>
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        </param>
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          <type>void</type>
        </param>
        <briefdescription>
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          <type>short</type>
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<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PAIR_MAT_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PAIR_MAT_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;ctype.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="utils_2basic_8h" kindref="compound">ViennaRNA/utils/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&quot;<ref refid="log_8h" kindref="compound">ViennaRNA/utils/log.h</ref>&quot;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__vars_8h" kindref="compound">ViennaRNA/fold_vars.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>NBASES<sp/>8</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="comment">/*@notnull@*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>INLINE</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>ifdef<sp/>__GNUC__</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>INLINE<sp/>inline</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>INLINE</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>Law_and_Order[]<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/></highlight><highlight class="stringliteral">&quot;_ACGUTXKI&quot;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>BP_pair[NBASES][NBASES]<sp/>=</highlight></codeline>
<codeline lineno="22"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>_<sp/><sp/>A<sp/><sp/>C<sp/><sp/>G<sp/><sp/>U<sp/><sp/>X<sp/><sp/>K<sp/><sp/>I<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal">{<sp/>{<sp/>0,<sp/>0,<sp/>0,<sp/>0,<sp/>0,<sp/>0,<sp/>0,<sp/>0<sp/>},</highlight></codeline>
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<codeline lineno="31"><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MAXALPHA<sp/>20<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>maximal<sp/>length<sp/>of<sp/>alphabet<sp/>*/</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/>alias[<ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="35"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>pair[<ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>+<sp/>1][<ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>rtype[pair[i][j]]:=pair[j][i]<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>rtype[8]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="38"><highlight class="normal"><sp/><sp/>0,<sp/>2,<sp/>1,<sp/>4,<sp/>3,<sp/>6,<sp/>5,<sp/>7</highlight></codeline>
<codeline lineno="39"><highlight class="normal">};</highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>_OPENMP</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="42"><highlight class="normal"></highlight><highlight class="preprocessor">#pragma<sp/>omp<sp/>threadprivate(Law_and_Order,<sp/>BP_pair,<sp/>alias,<sp/>pair,<sp/>rtype)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="43"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="44"><highlight class="normal"></highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>for<sp/>backward<sp/>compatibility<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>ENCODE(c)<sp/>encode_char(c)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"></highlight></codeline>
<codeline lineno="48"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="49"><highlight class="normal">encode_char(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>c)</highlight></codeline>
<codeline lineno="50"><highlight class="normal">{</highlight></codeline>
<codeline lineno="51"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>return<sp/>numerical<sp/>representation<sp/>of<sp/>base<sp/>used<sp/>e.g.<sp/>in<sp/>pair[][]<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="52"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>code;</highlight></codeline>
<codeline lineno="53"><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"><sp/><sp/>c<sp/>=<sp/>toupper(c);</highlight></codeline>
<codeline lineno="55"><highlight class="normal"></highlight></codeline>
<codeline lineno="56"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kindref="member">energy_set</ref><sp/>&gt;<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="57"><highlight class="normal"><sp/><sp/><sp/><sp/>code<sp/>=<sp/>(int)(c<sp/>-<sp/></highlight><highlight class="charliteral">&apos;A&apos;</highlight><highlight class="normal">)<sp/>+<sp/>1;</highlight></codeline>
<codeline lineno="58"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="59"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*pos;</highlight></codeline>
<codeline lineno="60"><highlight class="normal"><sp/><sp/><sp/><sp/>pos<sp/>=<sp/>strchr(Law_and_Order,<sp/>c);</highlight></codeline>
<codeline lineno="61"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(pos<sp/>==<sp/>NULL)</highlight></codeline>
<codeline lineno="62"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>code<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="63"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="64"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>code<sp/>=<sp/>(int)(pos<sp/>-<sp/>Law_and_Order);</highlight></codeline>
<codeline lineno="65"><highlight class="normal"></highlight></codeline>
<codeline lineno="66"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(code<sp/>&gt;<sp/>5)</highlight></codeline>
<codeline lineno="67"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>code<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight></codeline>
<codeline lineno="69"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(code<sp/>&gt;<sp/>4)</highlight></codeline>
<codeline lineno="70"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>code--;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>make<sp/>T<sp/>and<sp/>U<sp/>equivalent<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="71"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>code;</highlight></codeline>
<codeline lineno="74"><highlight class="normal">}</highlight></codeline>
<codeline lineno="75"><highlight class="normal"></highlight></codeline>
<codeline lineno="76"><highlight class="normal"></highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight><highlight class="comment">/*@+boolint<sp/>+charint@*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight><highlight class="comment">/*@null@*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kindref="member">nonstandards</ref>;</highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight></codeline>
<codeline lineno="81"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/>INLINE<sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="82"><highlight class="normal">make_pair_matrix(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">)</highlight></codeline>
<codeline lineno="83"><highlight class="normal">{</highlight></codeline>
<codeline lineno="84"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>i,<sp/>j;</highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="86"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kindref="member">energy_set</ref><sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="87"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>0;<sp/>i<sp/>&lt;<sp/>5;<sp/>i++)</highlight></codeline>
<codeline lineno="88"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>alias[i]<sp/>=<sp/>(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal">)i;</highlight></codeline>
<codeline lineno="89"><highlight class="normal"><sp/><sp/><sp/><sp/>alias[5]<sp/><sp/>=<sp/>3;<sp/><sp/></highlight><highlight class="comment">/*<sp/>X<sp/>&lt;-&gt;<sp/>G<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="90"><highlight class="normal"><sp/><sp/><sp/><sp/>alias[6]<sp/><sp/>=<sp/>2;<sp/><sp/></highlight><highlight class="comment">/*<sp/>K<sp/>&lt;-&gt;<sp/>C<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="91"><highlight class="normal"><sp/><sp/><sp/><sp/>alias[7]<sp/><sp/>=<sp/>0;<sp/><sp/></highlight><highlight class="comment">/*<sp/>I<sp/>&lt;-&gt;<sp/>default<sp/>base<sp/>&apos;@&apos;<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="92"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>0;<sp/>i<sp/>&lt;<sp/>NBASES;<sp/>i++)</highlight></codeline>
<codeline lineno="93"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(j<sp/>=<sp/>0;<sp/>j<sp/>&lt;<sp/>NBASES;<sp/>j++)</highlight></codeline>
<codeline lineno="94"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][j]<sp/>=<sp/>BP_pair[i][j];</highlight></codeline>
<codeline lineno="95"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1gabf380d09e4f1ab94fc6af57cf0ad5d32" kindref="member">noGU</ref>)</highlight></codeline>
<codeline lineno="96"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>pair[3][4]<sp/>=<sp/>pair[4][3]<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight></codeline>
<codeline lineno="98"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kindref="member">nonstandards</ref><sp/>!=<sp/>NULL)<sp/>{</highlight></codeline>
<codeline lineno="99"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>allow<sp/>nonstandard<sp/>bp&apos;s<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="100"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>0;<sp/>i<sp/>&lt;<sp/>(int)strlen(<ref refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kindref="member">nonstandards</ref>);<sp/>i<sp/>+=<sp/>2)</highlight></codeline>
<codeline lineno="101"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[encode_char(<ref refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kindref="member">nonstandards</ref>[i])]</highlight></codeline>
<codeline lineno="102"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>[encode_char(<ref refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kindref="member">nonstandards</ref>[i<sp/>+<sp/>1])]<sp/>=<sp/>7;</highlight></codeline>
<codeline lineno="103"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="104"><highlight class="normal"></highlight></codeline>
<codeline lineno="105"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>0;<sp/>i<sp/>&lt;<sp/>NBASES;<sp/>i++)</highlight></codeline>
<codeline lineno="106"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(j<sp/>=<sp/>0;<sp/>j<sp/>&lt;<sp/>NBASES;<sp/>j++)</highlight></codeline>
<codeline lineno="107"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>rtype[pair[i][j]]<sp/>=<sp/>pair[j][i];</highlight></codeline>
<codeline lineno="108"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="109"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>0;<sp/>i<sp/>&lt;=<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>i++)</highlight></codeline>
<codeline lineno="110"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(j<sp/>=<sp/>0;<sp/>j<sp/>&lt;=<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>j++)</highlight></codeline>
<codeline lineno="111"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][j]<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="112"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kindref="member">energy_set</ref><sp/>==<sp/>1)<sp/>{</highlight></codeline>
<codeline lineno="113"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>)<sp/>{</highlight></codeline>
<codeline lineno="114"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>3;<sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>A<sp/>&lt;-&gt;<sp/>G<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="115"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>2;<sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>B<sp/>&lt;-&gt;<sp/>C<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="116"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="117"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>i++)<sp/>{</highlight></codeline>
<codeline lineno="118"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>+<sp/>1]<sp/>=<sp/>2;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>AB<sp/>&lt;-&gt;<sp/>GC<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="119"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i++;</highlight></codeline>
<codeline lineno="120"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>-<sp/>1]<sp/>=<sp/>1;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>BA<sp/>&lt;-&gt;<sp/>CG<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="121"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="122"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kindref="member">energy_set</ref><sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="123"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>)<sp/>{</highlight></codeline>
<codeline lineno="124"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>1;<sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>A<sp/>&lt;-&gt;<sp/>A*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="125"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>4;<sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>B<sp/>&lt;-&gt;<sp/>U<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="126"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="127"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>i++)<sp/>{</highlight></codeline>
<codeline lineno="128"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>+<sp/>1]<sp/>=<sp/>5;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>AB<sp/>&lt;-&gt;<sp/>AU<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="129"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i++;</highlight></codeline>
<codeline lineno="130"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>-<sp/>1]<sp/>=<sp/>6;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>BA<sp/>&lt;-&gt;<sp/>UA<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="131"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="132"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kindref="member">energy_set</ref><sp/>==<sp/>3)<sp/>{</highlight></codeline>
<codeline lineno="133"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>-<sp/>2;<sp/>)<sp/>{</highlight></codeline>
<codeline lineno="134"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>3;<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>A<sp/>&lt;-&gt;<sp/>G<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>2;<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>B<sp/>&lt;-&gt;<sp/>C<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="136"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>1;<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>C<sp/>&lt;-&gt;<sp/>A<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="137"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alias[i++]<sp/><sp/>=<sp/>4;<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>D<sp/>&lt;-&gt;<sp/>U<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="139"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>-<sp/>2;<sp/>i++)<sp/>{</highlight></codeline>
<codeline lineno="140"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>+<sp/>1]<sp/>=<sp/>2;<sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>AB<sp/>&lt;-&gt;<sp/>GC<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="141"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i++;</highlight></codeline>
<codeline lineno="142"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>-<sp/>1]<sp/>=<sp/>1;<sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>BA<sp/>&lt;-&gt;<sp/>CG<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i++;</highlight></codeline>
<codeline lineno="144"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>+<sp/>1]<sp/>=<sp/>5;<sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>CD<sp/>&lt;-&gt;<sp/>AU<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="145"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i++;</highlight></codeline>
<codeline lineno="146"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pair[i][i<sp/>-<sp/>1]<sp/>=<sp/>6;<sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>DC<sp/>&lt;-&gt;<sp/>UA<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="147"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="148"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="149"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__utils__log_1ga8da5560f12f62e4afc523e3ee26e8017" kindref="member">vrna_log_error</ref>(</highlight><highlight class="stringliteral">&quot;What<sp/>energy_set<sp/>are<sp/>YOU<sp/>using??&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="150"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="151"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="152"><highlight class="normal"></highlight></codeline>
<codeline lineno="153"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>0;<sp/>i<sp/>&lt;=<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>i++)</highlight></codeline>
<codeline lineno="154"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(j<sp/>=<sp/>0;<sp/>j<sp/>&lt;=<sp/><ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref>;<sp/>j++)</highlight></codeline>
<codeline lineno="155"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>rtype[pair[i][j]]<sp/>=<sp/>pair[j][i];</highlight></codeline>
<codeline lineno="156"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="157"><highlight class="normal">}</highlight></codeline>
<codeline lineno="158"><highlight class="normal"></highlight></codeline>
<codeline lineno="159"><highlight class="normal"></highlight></codeline>
<codeline lineno="160"><highlight class="normal"></highlight><highlight class="keyword">static</highlight><highlight class="normal"><sp/>INLINE<sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="161"><highlight class="normal">encode_sequence(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="162"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>how)</highlight></codeline>
<codeline lineno="163"><highlight class="normal">{</highlight></codeline>
<codeline lineno="164"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>i,<sp/>l<sp/>=<sp/>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/>int)strlen(sequence);</highlight></codeline>
<codeline lineno="165"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*S<sp/>=<sp/>(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*)<ref refid="group__utils_1ga33cfc8d12ab976aa34025ce53b643f77" kindref="member">vrna_alloc</ref>(</highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal">)<sp/>*<sp/>(l<sp/>+<sp/>2));</highlight></codeline>
<codeline lineno="166"><highlight class="normal"></highlight></codeline>
<codeline lineno="167"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">switch</highlight><highlight class="normal"><sp/>(how)<sp/>{</highlight></codeline>
<codeline lineno="168"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>standard<sp/>encoding<sp/>as<sp/>always<sp/>used<sp/>for<sp/>S<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="169"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">case</highlight><highlight class="normal"><sp/>0:</highlight></codeline>
<codeline lineno="170"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;=<sp/>l;<sp/>i++)<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>make<sp/>numerical<sp/>encoding<sp/>of<sp/>sequence<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="171"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>S[i]<sp/>=<sp/>(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal">)encode_char(sequence[i<sp/>-<sp/>1]);</highlight></codeline>
<codeline lineno="172"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>S[l<sp/>+<sp/>1]<sp/><sp/>=<sp/>S[1];</highlight></codeline>
<codeline lineno="173"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>S[0]<sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>(short)l;</highlight></codeline>
<codeline lineno="174"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">break</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="175"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>encoding<sp/>for<sp/>mismatches<sp/>of<sp/>nostandard<sp/>bases<sp/>(normally<sp/>used<sp/>for<sp/>S1)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="176"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">case</highlight><highlight class="normal"><sp/>1:</highlight></codeline>
<codeline lineno="177"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">for</highlight><highlight class="normal"><sp/>(i<sp/>=<sp/>1;<sp/>i<sp/>&lt;=<sp/>l;<sp/>i++)</highlight></codeline>
<codeline lineno="178"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>S[i]<sp/>=<sp/>alias[(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal">)encode_char(sequence[i<sp/>-<sp/>1])];</highlight></codeline>
<codeline lineno="179"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>S[l<sp/>+<sp/>1]<sp/><sp/>=<sp/>S[1];</highlight></codeline>
<codeline lineno="180"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>S[0]<sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>S[l];</highlight></codeline>
<codeline lineno="181"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">break</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="182"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="183"><highlight class="normal"></highlight></codeline>
<codeline lineno="184"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>S;</highlight></codeline>
<codeline lineno="185"><highlight class="normal">}</highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="187"><highlight class="normal"></highlight></codeline>
<codeline lineno="188"><highlight class="normal"></highlight><highlight class="preprocessor">#endif<sp/></highlight><highlight class="comment">/*<sp/>VIENNA_RNA_PACKAGE_PAIR_MAT_H<sp/>*/</highlight><highlight class="preprocessor"></highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/pair_mat.h"/>
  </compounddef>
</doxygen>
