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    <innerclass refid="structvrna__sol__TwoD__t" prot="public">vrna_sol_TwoD_t</innerclass>
    <innerclass refid="structTwoDfold__vars" prot="public">TwoDfold_vars</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="2Dfold_8h_1aab347a3c03fbe8e7319551b9fa0cce4a" prot="public" static="no">
        <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/2Dfold.h" line="13" column="11" bodyfile="ViennaRNA/2Dfold.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <member refid="group__kl__neighborhood__mfe_1ga09e71024abb1a2bd19d9137596376e15" kind="define"><name>TwoDfold_solution</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__kl__neighborhood__mfe_1ga264ac71e75add31dfb1fc72a0b2de709" kind="function"><name>vrna_mfe_TwoD</name></member>
      <member refid="group__kl__neighborhood__mfe_1ga1297d34a208f6e3df1670420baaaaead" kind="function"><name>vrna_backtrack5_TwoD</name></member>
      <member refid="group__kl__neighborhood__mfe_1ga9dd36b619bffbbead5735ff5f0d91ee2" kind="function"><name>get_TwoDfold_variables</name></member>
      <member refid="group__kl__neighborhood__mfe_1ga05bf4f31d216b1b160fd2d3d68e9b487" kind="function"><name>destroy_TwoDfold_variables</name></member>
      <member refid="group__kl__neighborhood__mfe_1gad2c0d04ff67eb827b6f4ea78e65a719c" kind="function"><name>TwoDfoldList</name></member>
      <member refid="group__kl__neighborhood__mfe_1ga83816eb31ac4d0d7403354d1916495c0" kind="function"><name>TwoDfold_backtrack_f5</name></member>
      <member refid="group__kl__neighborhood__mfe_1gafcf26281cf10e489b53cbfbe910ef694" kind="function"><name>TwoDfold</name></member>
    </sectiondef>
    <briefdescription>
<para>MFE structures for base pair distance classes. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_TWO_D_FOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_TWO_D_FOLD_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">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><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="7"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><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="9"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><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="11"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><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="29"><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="30"><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="31"><highlight class="normal"></highlight></codeline>
<codeline lineno="46" refid="structvrna__sol__TwoD__t" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="47" refid="structvrna__sol__TwoD__t_1ac111e850bb3b3a11b6b5707912cfa1b8" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="structvrna__sol__TwoD__t_1ac111e850bb3b3a11b6b5707912cfa1b8" kindref="member">k</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="48" refid="structvrna__sol__TwoD__t_1ab8e95cd920901175a2cc8de726ab1d36" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="structvrna__sol__TwoD__t_1ab8e95cd920901175a2cc8de726ab1d36" kindref="member">l</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="49" refid="structvrna__sol__TwoD__t_1a7577863a6a84224dfee39b321c03cab1" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="structvrna__sol__TwoD__t_1a7577863a6a84224dfee39b321c03cab1" kindref="member">en</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
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<codeline lineno="51"><highlight class="normal">}<sp/><ref refid="structvrna__sol__TwoD__t" kindref="compound">vrna_sol_TwoD_t</ref>;</highlight></codeline>
<codeline lineno="52"><highlight class="normal"></highlight></codeline>
<codeline lineno="53"><highlight class="normal"></highlight></codeline>
<codeline lineno="81"><highlight class="normal"><ref refid="structvrna__sol__TwoD__t" kindref="compound">vrna_sol_TwoD_t</ref><sp/>*</highlight></codeline>
<codeline lineno="82" refid="group__kl__neighborhood__mfe_1ga264ac71e75add31dfb1fc72a0b2de709" refkind="member"><highlight class="normal"><ref refid="group__kl__neighborhood__mfe_1ga264ac71e75add31dfb1fc72a0b2de709" kindref="member">vrna_mfe_TwoD</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="83"><highlight class="normal"><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/><sp/>distance1,</highlight></codeline>
<codeline lineno="84"><highlight class="normal"><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/><sp/>distance2);</highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="86"><highlight class="normal"></highlight></codeline>
<codeline lineno="106"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="107" refid="group__kl__neighborhood__mfe_1ga1297d34a208f6e3df1670420baaaaead" refkind="member"><highlight class="normal"><ref refid="group__kl__neighborhood__mfe_1ga1297d34a208f6e3df1670420baaaaead" kindref="member">vrna_backtrack5_TwoD</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="108"><highlight class="normal"><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/>k,</highlight></codeline>
<codeline lineno="109"><highlight class="normal"><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/>l,</highlight></codeline>
<codeline lineno="110"><highlight class="normal"><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="111"><highlight class="normal"></highlight></codeline>
<codeline lineno="112"><highlight class="normal"></highlight></codeline>
<codeline lineno="113"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="114"><highlight class="normal"></highlight></codeline>
<codeline lineno="115"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>TwoDfold_solution<sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_sol_TwoD_t<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>restore<sp/>compatibility<sp/>of<sp/>struct<sp/>rename<sp/>*/</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="116"><highlight class="normal"></highlight></codeline>
<codeline lineno="124" refid="structTwoDfold__vars" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="125" refid="structTwoDfold__vars_1a70da9e83ad87c37013b4bf0b265dd307" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDfold__vars_1a70da9e83ad87c37013b4bf0b265dd307" kindref="member">P</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="126" refid="structTwoDfold__vars_1ade5c7e9337a458ae20bac75abdc52d64" refkind="member"><highlight class="normal"><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/><sp/><ref refid="structTwoDfold__vars_1ade5c7e9337a458ae20bac75abdc52d64" kindref="member">do_backtrack</ref>;<sp/></highlight></codeline>
<codeline lineno="127" refid="structTwoDfold__vars_1aedf60b8b26dae05ad266d3e098d18208" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDfold__vars_1aedf60b8b26dae05ad266d3e098d18208" kindref="member">ptype</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
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<codeline lineno="156"><highlight class="normal"><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/><sp/>***E_M2;</highlight></codeline>
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<codeline lineno="158"><highlight class="normal"><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/><sp/>**E_Fc;</highlight></codeline>
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<codeline lineno="161"><highlight class="normal"><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/><sp/>**E_FcM;</highlight></codeline>
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<codeline lineno="163"><highlight class="normal"><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/><sp/>**l_min_values;</highlight></codeline>
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<codeline lineno="209"><highlight class="normal"><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/><sp/>*l_max_values_fcM;</highlight></codeline>
<codeline lineno="210"><highlight class="normal"><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/><sp/>k_min_values_fcM;</highlight></codeline>
<codeline lineno="211"><highlight class="normal"><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/><sp/>k_max_values_fcM;</highlight></codeline>
<codeline lineno="212"><highlight class="normal"></highlight></codeline>
<codeline lineno="213"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>auxilary<sp/>arrays<sp/>for<sp/>remaining<sp/>set<sp/>of<sp/>coarse<sp/>graining<sp/>(k,l)<sp/>&gt;<sp/>(k_max,<sp/>l_max)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="214"><highlight class="normal"><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/><sp/>*E_F5_rem;</highlight></codeline>
<codeline lineno="215"><highlight class="normal"><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/><sp/>*E_F3_rem;</highlight></codeline>
<codeline lineno="216"><highlight class="normal"><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/><sp/>*E_C_rem;</highlight></codeline>
<codeline lineno="217"><highlight class="normal"><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/><sp/>*E_M_rem;</highlight></codeline>
<codeline lineno="218"><highlight class="normal"><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/><sp/>*E_M1_rem;</highlight></codeline>
<codeline lineno="219"><highlight class="normal"><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/><sp/>*E_M2_rem;</highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight></codeline>
<codeline lineno="221"><highlight class="normal"><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/><sp/>E_Fc_rem;</highlight></codeline>
<codeline lineno="222"><highlight class="normal"><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/><sp/>E_FcH_rem;</highlight></codeline>
<codeline lineno="223"><highlight class="normal"><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/><sp/>E_FcI_rem;</highlight></codeline>
<codeline lineno="224"><highlight class="normal"><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/><sp/>E_FcM_rem;</highlight></codeline>
<codeline lineno="225"><highlight class="normal"></highlight></codeline>
<codeline lineno="226"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>COUNT_STATES</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="227"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***N_F5;</highlight></codeline>
<codeline lineno="228"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***N_C;</highlight></codeline>
<codeline lineno="229"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***N_M;</highlight></codeline>
<codeline lineno="230"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***N_M1;</highlight></codeline>
<codeline lineno="231"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="232"><highlight class="normal"></highlight></codeline>
<codeline lineno="233"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*compatibility;</highlight></codeline>
<codeline lineno="234"><highlight class="normal">}<sp/><ref refid="structTwoDfold__vars" kindref="compound">TwoDfold_vars</ref>;</highlight></codeline>
<codeline lineno="235"><highlight class="normal"></highlight></codeline>
<codeline lineno="254"><highlight class="normal">DEPRECATED(<ref refid="structTwoDfold__vars" kindref="compound">TwoDfold_vars</ref><sp/>*</highlight></codeline>
<codeline lineno="255"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__kl__neighborhood__mfe_1ga9dd36b619bffbbead5735ff5f0d91ee2" kindref="member">get_TwoDfold_variables</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*seq,</highlight></codeline>
<codeline lineno="256"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*structure1,</highlight></codeline>
<codeline lineno="257"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*structure2,</highlight></codeline>
<codeline lineno="258"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" kindref="member">circ</ref>),</highlight></codeline>
<codeline lineno="259" refid="group__kl__neighborhood__mfe_1ga9dd36b619bffbbead5735ff5f0d91ee2" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>corresponding<sp/>functions<sp/>vrna_fold_compound_TwoD(),<sp/>etc.<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="260"><highlight class="normal"></highlight></codeline>
<codeline lineno="271"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="272"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__kl__neighborhood__mfe_1ga05bf4f31d216b1b160fd2d3d68e9b487" kindref="member">destroy_TwoDfold_variables</ref>(<ref refid="structTwoDfold__vars" kindref="compound">TwoDfold_vars</ref><sp/>*our_variables),</highlight></codeline>
<codeline lineno="273" refid="group__kl__neighborhood__mfe_1ga05bf4f31d216b1b160fd2d3d68e9b487" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_fold_compound_free()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="274"><highlight class="normal"></highlight></codeline>
<codeline lineno="300"><highlight class="normal">DEPRECATED(TwoDfold_solution<sp/>*</highlight></codeline>
<codeline lineno="301"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__kl__neighborhood__mfe_1gad2c0d04ff67eb827b6f4ea78e65a719c" kindref="member">TwoDfoldList</ref>(<ref refid="structTwoDfold__vars" kindref="compound">TwoDfold_vars</ref><sp/>*vars,</highlight></codeline>
<codeline lineno="302"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>distance1,</highlight></codeline>
<codeline lineno="303"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>distance2),</highlight></codeline>
<codeline lineno="304" refid="group__kl__neighborhood__mfe_1gad2c0d04ff67eb827b6f4ea78e65a719c" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_mfe_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="305"><highlight class="normal"></highlight></codeline>
<codeline lineno="327"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__kl__neighborhood__mfe_1ga83816eb31ac4d0d7403354d1916495c0" kindref="member">TwoDfold_backtrack_f5</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="328"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k,</highlight></codeline>
<codeline lineno="329"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>l,</highlight></codeline>
<codeline lineno="330"><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/><ref refid="structTwoDfold__vars" kindref="compound">TwoDfold_vars</ref><sp/><sp/>*vars),</highlight></codeline>
<codeline lineno="331" refid="group__kl__neighborhood__mfe_1ga83816eb31ac4d0d7403354d1916495c0" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_backtrack5_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="332"><highlight class="normal"></highlight></codeline>
<codeline lineno="336"><highlight class="normal">DEPRECATED(TwoDfold_solution<sp/>**TwoDfold(<ref refid="structTwoDfold__vars" kindref="compound">TwoDfold_vars</ref><sp/>*our_variables,</highlight></codeline>
<codeline lineno="337"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>distance1,</highlight></codeline>
<codeline lineno="338"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>distance2),</highlight></codeline>
<codeline lineno="339"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_mfe_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="340"><highlight class="normal"></highlight></codeline>
<codeline lineno="341"><highlight class="normal"></highlight></codeline>
<codeline lineno="342"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="343"><highlight class="normal"></highlight></codeline>
<codeline lineno="347"><highlight class="normal"></highlight></codeline>
<codeline lineno="348"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/2Dfold.h"/>
  </compounddef>
</doxygen>
