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      <memberdef kind="define" id="mfe_2gquad_8h_1a2eb6f9e0395b47b8d5e3eeae4fe0c116" prot="public" static="no">
        <name>INLINE</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/gquad.h" line="18" column="11" bodyfile="ViennaRNA/mfe/gquad.h" bodystart="18" bodyend="-1"/>
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        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/gquad.h" line="31" column="11" bodyfile="ViennaRNA/mfe/gquad.h" bodystart="31" bodyend="-1"/>
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      <member refid="group__gquad__dp_1ga3b628f079d9ed1630365b9939ef609d2" kind="function"><name>vrna_mfe_gquad_mx</name></member>
      <member refid="group__gquad__dp_1gaeddca099141903fc4359f740dc3a9a96" kind="function"><name>get_gquad_L_matrix</name></member>
      <member refid="group__gquad__dp_1ga25d7499c49963599c078dc2c93321b8e" kind="function"><name>vrna_gquad_mx_local_update</name></member>
      <member refid="group__gquad__deprecated_1ga2480171f753eed5bf337e283dee16129" kind="function"><name>get_gquad_matrix</name></member>
      <member refid="group__gquad__deprecated_1ga492483d75defad242d59f2fd45fd7b8f" kind="function"><name>get_gquad_ali_matrix</name></member>
      <member refid="group__gquad__deprecated_1gac83ee00ef57784c7efc4572a6cdb90c0" kind="function"><name>E_GQuad_IntLoop_L_comparative</name></member>
      <member refid="group__gquad__deprecated_1gaf2e4be0af1c21ef668307984922f5e09" kind="function"><name>E_GQuad_IntLoop_L</name></member>
    </sectiondef>
    <briefdescription>
<para>G-quadruplexes MFE API. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_GQUAD_MFE_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_GQUAD_MFE_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;string.h&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">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&quot;<ref refid="array_8h" kindref="compound">ViennaRNA/datastructures/array.h</ref>&quot;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&quot;ViennaRNA/datastructures/sparse_mx.h&quot;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="log_8h" kindref="compound">ViennaRNA/utils/log.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="sequences_2alphabet_8h" kindref="compound">ViennaRNA/sequences/alphabet.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="params_2basic_8h" kindref="compound">ViennaRNA/params/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>INLINE</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>__GNUC__</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>INLINE<sp/>inline</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>INLINE</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="24"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(&quot;&quot;,<sp/>msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="25"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal">vrna_mfe_gquad_internal_loop(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="48"><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/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="49"><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/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j);</highlight></codeline>
<codeline lineno="50"><highlight class="normal"></highlight></codeline>
<codeline lineno="51"><highlight class="normal"></highlight></codeline>
<codeline lineno="55"><highlight class="normal"></highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight></codeline>
<codeline lineno="61"><highlight class="normal"></highlight></codeline>
<codeline lineno="62"><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal">vrna_smx_csr_int_t<sp/>*</highlight></codeline>
<codeline lineno="74" refid="group__gquad__dp_1ga3b628f079d9ed1630365b9939ef609d2" refkind="member"><highlight class="normal"><ref refid="group__gquad__dp_1ga3b628f079d9ed1630365b9939ef609d2" kindref="member">vrna_mfe_gquad_mx</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</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="keywordtype">int</highlight><highlight class="normal"><sp/>**</highlight></codeline>
<codeline lineno="78"><highlight class="normal">get_gquad_L_matrix(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*S,</highlight></codeline>
<codeline lineno="79"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>start,</highlight></codeline>
<codeline lineno="80"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxdist,</highlight></codeline>
<codeline lineno="81"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>n,</highlight></codeline>
<codeline lineno="82"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**g,</highlight></codeline>
<codeline lineno="83"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*P);</highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="86"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="87"><highlight class="normal">vrna_gquad_mx_local_update(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="88"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>start);</highlight></codeline>
<codeline lineno="89"><highlight class="normal"></highlight></codeline>
<codeline lineno="90"><highlight class="normal"></highlight></codeline>
<codeline lineno="94"><highlight class="normal"></highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight></codeline>
<codeline lineno="96"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight></codeline>
<codeline lineno="103"><highlight class="normal"></highlight></codeline>
<codeline lineno="120"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="121"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__gquad__deprecated_1ga2480171f753eed5bf337e283dee16129" kindref="member">get_gquad_matrix</ref>(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*S,</highlight></codeline>
<codeline lineno="122"><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/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*<sp/>P),</highlight></codeline>
<codeline lineno="123" refid="group__gquad__deprecated_1ga2480171f753eed5bf337e283dee16129" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mfe_gquad_mx()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="124"><highlight class="normal"></highlight></codeline>
<codeline lineno="125"><highlight class="normal"></highlight></codeline>
<codeline lineno="126"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="127"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>get_gquad_ali_matrix(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n,</highlight></codeline>
<codeline lineno="128"><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/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*S_cons,</highlight></codeline>
<codeline lineno="129"><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/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>**S,</highlight></codeline>
<codeline lineno="130"><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/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**a2s,</highlight></codeline>
<codeline lineno="131"><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/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n_seq,</highlight></codeline>
<codeline lineno="132"><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/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*<sp/>P),</highlight></codeline>
<codeline lineno="133"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mfe_gquad_mx()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="134"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal"></highlight></codeline>
<codeline lineno="136"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="137"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>E_GQuad_IntLoop_L_comparative(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="138"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="139"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*tt,</highlight></codeline>
<codeline lineno="140"><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/><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/><sp/>*S_cons,</highlight></codeline>
<codeline lineno="141"><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/><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/><sp/>**S5,</highlight></codeline>
<codeline lineno="142"><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/><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/><sp/>**S3,</highlight></codeline>
<codeline lineno="143"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**a2s,</highlight></codeline>
<codeline lineno="144"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**ggg,</highlight></codeline>
<codeline lineno="145"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>n_seq,</highlight></codeline>
<codeline lineno="146"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*P),</highlight></codeline>
<codeline lineno="147"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mfe_gquad_internal_loop()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="148"><highlight class="normal"></highlight></codeline>
<codeline lineno="149"><highlight class="normal"></highlight></codeline>
<codeline lineno="150"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="151"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>E_GQuad_IntLoop_L(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="152"><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/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="153"><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/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="154"><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/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*S,</highlight></codeline>
<codeline lineno="155"><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/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**ggg,</highlight></codeline>
<codeline lineno="156"><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/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxdist,</highlight></codeline>
<codeline lineno="157"><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/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*P),</highlight></codeline>
<codeline lineno="158"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mfe_gquad_internal_loop()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="159"><highlight class="normal"></highlight></codeline>
<codeline lineno="163"><highlight class="normal"></highlight></codeline>
<codeline lineno="164"><highlight class="normal"></highlight></codeline>
<codeline lineno="165"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="166"><highlight class="normal"></highlight></codeline>
<codeline lineno="167"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/mfe/gquad.h"/>
  </compounddef>
</doxygen>
