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    <sectiondef kind="func">
      <memberdef kind="function" id="ali__plex_8h_1accff43803f3cc57d8d4cb29c0e008cef" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="structduplexT" kindref="compound">duplexT</ref> **</type>
        <definition>duplexT ** aliLduplexfold</definition>
        <argsstring>(const char *s1[], const char *s2[], const int threshold, const int extension_cost, const int alignment_length, const int delta, const int fast, const int il_a, const int il_b, const int b_a, const int b_b)</argsstring>
        <name>aliLduplexfold</name>
        <param>
          <type>const char *</type>
          <declname>s1</declname>
          <array>[]</array>
        </param>
        <param>
          <type>const char *</type>
          <declname>s2</declname>
          <array>[]</array>
        </param>
        <param>
          <type>const int</type>
          <declname>threshold</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>extension_cost</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>alignment_length</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>delta</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>fast</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>il_a</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>il_b</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>b_a</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>b_b</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>aliLduplexfold computes the duplexes between two alignments </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/ali_plex.h" line="11" column="9" declfile="ViennaRNA/ali_plex.h" declline="11" declcolumn="9"/>
      </memberdef>
      <memberdef kind="function" id="ali__plex_8h_1ab7d6d68942b216c750cd0f92862e0c05" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="structduplexT" kindref="compound">duplexT</ref> **</type>
        <definition>duplexT ** aliLduplexfold_XS</definition>
        <argsstring>(const char *s1[], const char *s2[], const int **access_s1, const int **access_s2, const int threshold, const int alignment_length, const int delta, const int fast, const int il_a, const int il_b, const int b_a, const int b_b)</argsstring>
        <name>aliLduplexfold_XS</name>
        <param>
          <type>const char *</type>
          <declname>s1</declname>
          <array>[]</array>
        </param>
        <param>
          <type>const char *</type>
          <declname>s2</declname>
          <array>[]</array>
        </param>
        <param>
          <type>const int **</type>
          <declname>access_s1</declname>
        </param>
        <param>
          <type>const int **</type>
          <declname>access_s2</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>threshold</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>alignment_length</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>delta</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>fast</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>il_a</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>il_b</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>b_a</declname>
        </param>
        <param>
          <type>const int</type>
          <declname>b_b</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>aliLduplexfold computes the duplexes between two alignments. It also takes the average accessibility into account </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/ali_plex.h" line="27" column="9" declfile="ViennaRNA/ali_plex.h" declline="27" declcolumn="9"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_ALI_PLEX_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_ALI_PLEX_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;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"><ref refid="structduplexT" kindref="compound">duplexT</ref><sp/>**aliLduplexfold(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*s1[],</highlight></codeline>
<codeline lineno="12"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*s2[],</highlight></codeline>
<codeline lineno="13"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>threshold,</highlight></codeline>
<codeline lineno="14"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>extension_cost,</highlight></codeline>
<codeline lineno="15"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>alignment_length,</highlight></codeline>
<codeline lineno="16"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>delta,</highlight></codeline>
<codeline lineno="17"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>fast,</highlight></codeline>
<codeline lineno="18"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>il_a,</highlight></codeline>
<codeline lineno="19"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>il_b,</highlight></codeline>
<codeline lineno="20"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>b_a,</highlight></codeline>
<codeline lineno="21"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>b_b);</highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"><ref refid="structduplexT" kindref="compound">duplexT</ref><sp/>**aliLduplexfold_XS(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*s1[],</highlight></codeline>
<codeline lineno="28"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*s2[],</highlight></codeline>
<codeline lineno="29"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>**access_s1,</highlight></codeline>
<codeline lineno="30"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>**access_s2,</highlight></codeline>
<codeline lineno="31"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>threshold,</highlight></codeline>
<codeline lineno="32"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>alignment_length,</highlight></codeline>
<codeline lineno="33"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>delta,</highlight></codeline>
<codeline lineno="34"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>fast,</highlight></codeline>
<codeline lineno="35"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>il_a,</highlight></codeline>
<codeline lineno="36"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>il_b,</highlight></codeline>
<codeline lineno="37"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>b_a,</highlight></codeline>
<codeline lineno="38"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>b_b);</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="comment">/*</highlight></codeline>
<codeline lineno="42"><highlight class="comment"><sp/>*<sp/>extern<sp/>duplexT<sp/>aliduplexfold(const<sp/>char<sp/>*s1[],<sp/>const<sp/>char<sp/>*s2[],<sp/>const<sp/>int<sp/>extension_cost);</highlight></codeline>
<codeline lineno="43"><highlight class="comment"><sp/>*<sp/>extern<sp/>duplexT<sp/>aliduplexfold_XS(const<sp/>char<sp/>*s1[],<sp/>const<sp/>char<sp/>*s2[],const<sp/>int<sp/>**access_s1,</highlight></codeline>
<codeline lineno="44"><highlight class="comment"><sp/>*<sp/>const<sp/>int<sp/>**access_s2,<sp/>const<sp/>int<sp/>i_pos,<sp/>const<sp/>int<sp/>j_pos,<sp/>const<sp/>int<sp/>threshold);</highlight></codeline>
<codeline lineno="45"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"></highlight></codeline>
<codeline lineno="48"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/ali_plex.h"/>
  </compounddef>
</doxygen>
