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        <childnode refid="127" relation="include">
        </childnode>
      </node>
      <node id="128">
        <label>ViennaRNA/probing/basic.h</label>
        <link refid="probing_2basic_8h"/>
        <childnode refid="125" relation="include">
        </childnode>
        <childnode refid="129" relation="include">
        </childnode>
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        </childnode>
        <childnode refid="131" relation="include">
        </childnode>
        <childnode refid="132" relation="include">
        </childnode>
      </node>
      <node id="129">
        <label>ViennaRNA/probing/strategy_deigan.h</label>
        <link refid="strategy__deigan_8h"/>
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      <node id="130">
        <label>ViennaRNA/probing/strategy_eddy.h</label>
        <link refid="strategy__eddy_8h"/>
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      <node id="131">
        <label>ViennaRNA/probing/strategy_nlogp.h</label>
        <link refid="strategy__nlogp_8h"/>
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      <node id="132">
        <label>ViennaRNA/probing/strategy_zarringhalam.h</label>
        <link refid="strategy__zarringhalam_8h"/>
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      <node id="92">
        <label>ViennaRNA/profiledist.h</label>
        <link refid="profiledist_8h"/>
      </node>
      <node id="133">
        <label>ViennaRNA/sampling/basic.h</label>
        <link refid="sampling_2basic_8h"/>
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        </childnode>
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        </childnode>
        <childnode refid="71" relation="include">
        </childnode>
      </node>
      <node id="141">
        <label>ViennaRNA/sequence.h</label>
        <link refid="sequence_8h"/>
      </node>
      <node id="135">
        <label>ViennaRNA/sequences/alignments.h</label>
        <link refid="sequences_2alignments_8h_source"/>
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        </childnode>
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        </childnode>
        <childnode refid="137" relation="include">
        </childnode>
      </node>
      <node id="138">
        <label>ViennaRNA/sequences/alphabet.h</label>
        <link refid="sequences_2alphabet_8h"/>
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        </childnode>
        <childnode refid="46" relation="include">
        </childnode>
        <childnode refid="62" relation="include">
        </childnode>
      </node>
      <node id="140">
        <label>ViennaRNA/sequences/sequence.h</label>
        <link refid="sequences_2sequence_8h"/>
        <childnode refid="1" relation="include">
        </childnode>
        <childnode refid="141" relation="include">
        </childnode>
      </node>
      <node id="93">
        <label>ViennaRNA/snofold.h</label>
        <link refid="snofold_8h_source"/>
      </node>
      <node id="94">
        <label>ViennaRNA/snoop.h</label>
        <link refid="snoop_8h_source"/>
      </node>
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        <label>ViennaRNA/string_utils.h</label>
        <link refid="string__utils_8h"/>
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        <label>ViennaRNA/structure_utils.h</label>
        <link refid="structure__utils_8h"/>
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        <label>ViennaRNA/structures/benchmark.h</label>
        <link refid="benchmark_8h"/>
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        </childnode>
        <childnode refid="97" relation="include">
        </childnode>
      </node>
      <node id="99">
        <label>ViennaRNA/structures/centroid.h</label>
        <link refid="structures_2centroid_8h"/>
        <childnode refid="100" relation="include">
        </childnode>
      </node>
      <node id="76">
        <label>ViennaRNA/structures/mea.h</label>
        <link refid="mea_8h_source"/>
        <childnode refid="77" relation="include">
        </childnode>
      </node>
      <node id="79">
        <label>ViennaRNA/subopt.h</label>
        <link refid="subopt_8h"/>
      </node>
      <node id="142">
        <label>ViennaRNA/subopt/gquad.h</label>
        <link refid="subopt_2gquad_8h"/>
      </node>
      <node id="78">
        <label>ViennaRNA/subopt/wuchty.h</label>
        <link refid="wuchty_8h"/>
        <childnode refid="79" relation="include">
        </childnode>
      </node>
      <node id="143">
        <label>ViennaRNA/subopt/zuker.h</label>
        <link refid="zuker_8h_source"/>
        <childnode refid="144" relation="include">
        </childnode>
      </node>
      <node id="144">
        <label>ViennaRNA/subopt_zuker.h</label>
        <link refid="subopt__zuker_8h"/>
      </node>
      <node id="101">
        <label>ViennaRNA/unstructured_domains.h</label>
        <link refid="unstructured__domains_8h"/>
        <childnode refid="30" relation="include">
        </childnode>
        <childnode refid="1" relation="include">
        </childnode>
      </node>
      <node id="98">
        <label>ViennaRNA/utils.h</label>
        <link refid="utils_8h"/>
      </node>
      <node id="137">
        <label>ViennaRNA/utils/alignments.h</label>
        <link refid="utils_2alignments_8h"/>
      </node>
      <node id="102">
        <label>ViennaRNA/utils/basic.h</label>
        <link refid="utils_2basic_8h"/>
        <childnode refid="15" relation="include">
        </childnode>
        <childnode refid="18" relation="include">
        </childnode>
        <childnode refid="21" relation="include">
        </childnode>
        <childnode refid="47" relation="include">
        </childnode>
        <childnode refid="39" relation="include">
        </childnode>
        <childnode refid="48" relation="include">
        </childnode>
        <childnode refid="63" relation="include">
        </childnode>
        <childnode refid="64" relation="include">
        </childnode>
        <childnode refid="52" relation="include">
        </childnode>
        <childnode refid="103" relation="include">
        </childnode>
        <childnode refid="40" relation="include">
        </childnode>
        <childnode refid="72" relation="include">
        </childnode>
        <childnode refid="98" relation="include">
        </childnode>
      </node>
      <node id="104">
        <label>ViennaRNA/utils/strings.h</label>
        <link refid="strings_8h"/>
        <childnode refid="105" relation="include">
        </childnode>
        <childnode refid="98" relation="include">
        </childnode>
      </node>
      <node id="97">
        <label>ViennaRNA/utils/structures.h</label>
        <link refid="utils_2structures_8h"/>
        <childnode refid="98" relation="include">
        </childnode>
      </node>
      <node id="113">
        <label>ViennaRNA/walk.h</label>
        <link refid="walk_8h"/>
      </node>
    </invincdepgraph>
    <innerclass refid="structvrna__fc__s" prot="public">vrna_fc_s</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="fold__compound_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/fold_compound.h" line="13" column="11" bodyfile="ViennaRNA/fold_compound.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <member refid="group__fold__compound_1ga1a5053dc8acbb0111e852988726f07d6" kind="define"><name>VRNA_STATUS_MFE_PRE</name></member>
      <member refid="group__fold__compound_1ga47c900ca76e56e59e2e83a06e0bde641" kind="define"><name>VRNA_STATUS_MFE_POST</name></member>
      <member refid="group__fold__compound_1ga91795d35ebdb6f32be50459f24b3d114" kind="define"><name>VRNA_STATUS_PF_PRE</name></member>
      <member refid="group__fold__compound_1ga1c6fa243533fd026e50f7d595eaaa565" kind="define"><name>VRNA_STATUS_PF_POST</name></member>
      <member refid="group__fold__compound_1gacea5b7ee6181c485f36e2afa0e9089e4" kind="define"><name>VRNA_OPTION_DEFAULT</name></member>
      <member refid="group__fold__compound_1gae63be9127fe7dcc1f9bb14f5bb1064ee" kind="define"><name>VRNA_OPTION_MFE</name></member>
      <member refid="group__fold__compound_1gabfbadcddda3e74ce7f49035ef8f058f7" kind="define"><name>VRNA_OPTION_PF</name></member>
      <member refid="group__fold__compound_1ga8f681fa12b8d4b348bf58415fd1fc82f" kind="define"><name>VRNA_OPTION_HYBRID</name></member>
      <member refid="group__fold__compound_1ga61469c423131552c8483229f8b6c7e0e" kind="define"><name>VRNA_OPTION_EVAL_ONLY</name></member>
      <member refid="group__fold__compound_1ga2b2a8009ccdccc3eb1571556261aee8e" kind="define"><name>VRNA_OPTION_WINDOW</name></member>
      <member refid="group__fold__compound_1ga10fd4c73c91557495f1a41d6cc72e595" kind="define"><name>VRNA_OPTION_F5</name></member>
      <member refid="group__fold__compound_1gabca873cc37c26910db8b37bf864db252" kind="define"><name>VRNA_OPTION_F3</name></member>
      <member refid="group__fold__compound_1gaf4c7bf371bdb153d8c2955a7b4cffe8b" kind="define"><name>VRNA_OPTION_WINDOW_F5</name></member>
      <member refid="group__fold__compound_1ga371ddcb556d7578433661dd7591a787c" kind="define"><name>VRNA_OPTION_WINDOW_F3</name></member>
    </sectiondef>
    <sectiondef kind="enum">
      <member refid="group__fold__compound_1ga01a4ff86fa71deaaa5d1abbd95a1447d" kind="enum"><name>vrna_fc_type_e</name></member>
    </sectiondef>
    <sectiondef kind="typedef">
      <member refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kind="typedef"><name>vrna_fold_compound_t</name></member>
      <member refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kind="typedef"><name>vrna_auxdata_free_f</name></member>
      <member refid="group__fold__compound_1gab78664b2ef71ae6d147d6e74bf2862d3" kind="typedef"><name>vrna_auxdata_prepare_f</name></member>
      <member refid="group__fold__compound_1ga771d6af505144fbfa79af58c5c46f689" kind="typedef"><name>vrna_callback_free_auxdata</name></member>
      <member refid="group__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" kind="typedef"><name>vrna_recursion_status_f</name></member>
      <member refid="group__fold__compound_1ga1edba201472caef00b7cef954341e1b9" kind="typedef"><name>vrna_callback_recursion_status</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kind="function"><name>vrna_fold_compound</name></member>
      <member refid="group__fold__compound_1gabbaffe56b1a37f6ed1a31e9e4f5613f1" kind="function"><name>vrna_fold_compound_comparative</name></member>
      <member refid="group__fold__compound_1ga249143e997e79cec842a2bad2b8bd02e" kind="function"><name>vrna_fold_compound_comparative2</name></member>
      <member refid="group__fold__compound_1ga5186f53af9c11edab6e0269c2c6f6231" kind="function"><name>vrna_fold_compound_TwoD</name></member>
      <member refid="group__fold__compound_1ga051b4bb675cc11b8ced15a6780fd26b7" kind="function"><name>vrna_fold_compound_prepare</name></member>
      <member refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kind="function"><name>vrna_fold_compound_free</name></member>
      <member refid="group__fold__compound_1gad6c0747712712bda6d94702e0de895a7" kind="function"><name>vrna_fold_compound_add_auxdata</name></member>
      <member refid="group__fold__compound_1ga579952cc017127b81e89a186c0d6b9c2" kind="function"><name>vrna_fold_compound_add_callback</name></member>
    </sectiondef>
    <briefdescription>
<para>The Basic Fold Compound API. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_FOLD_COMPOUND_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="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight></codeline>
<codeline lineno="30" refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__fc__s" kindref="compound">vrna_fc_s</ref><sp/><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref>;</highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight></codeline>
<codeline lineno="50" refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>void<sp/>(*<ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f</ref>)(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>*data);</highlight></codeline>
<codeline lineno="51"><highlight class="normal"></highlight></codeline>
<codeline lineno="52"><highlight class="normal"></highlight></codeline>
<codeline lineno="62" refid="group__fold__compound_1gab78664b2ef71ae6d147d6e74bf2862d3" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>int<sp/>(*<ref refid="group__fold__compound_1gab78664b2ef71ae6d147d6e74bf2862d3" kindref="member">vrna_auxdata_prepare_f</ref>)(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="63"><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/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data,</highlight></codeline>
<codeline lineno="64"><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/></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/><sp/>event,</highlight></codeline>
<codeline lineno="65"><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/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*event_data);</highlight></codeline>
<codeline lineno="66"><highlight class="normal"></highlight></codeline>
<codeline lineno="67"><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>(<ref refid="group__fold__compound_1ga771d6af505144fbfa79af58c5c46f689" kindref="member">vrna_callback_free_auxdata</ref>)(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>*data),</highlight></codeline>
<codeline lineno="74" refid="group__fold__compound_1ga771d6af505144fbfa79af58c5c46f689" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_auxdata_free_f<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="75"><highlight class="normal"></highlight></codeline>
<codeline lineno="95" refid="group__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>void<sp/>(*<ref refid="group__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" kindref="member">vrna_recursion_status_f</ref>)(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="96"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>status,</highlight></codeline>
<codeline lineno="97"><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">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data);</highlight></codeline>
<codeline lineno="98"><highlight class="normal"></highlight></codeline>
<codeline lineno="99"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>(vrna_callback_recursion_status)(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>status,</highlight></codeline>
<codeline lineno="100"><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/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data),</highlight></codeline>
<codeline lineno="101"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_recursion_status_f<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight></codeline>
<codeline lineno="103"><highlight class="normal"></highlight></codeline>
<codeline lineno="110" refid="group__fold__compound_1ga1a5053dc8acbb0111e852988726f07d6" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_STATUS_MFE_PRE<sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="111"><highlight class="normal"></highlight></codeline>
<codeline lineno="118" refid="group__fold__compound_1ga47c900ca76e56e59e2e83a06e0bde641" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_STATUS_MFE_POST<sp/><sp/><sp/><sp/>(unsigned<sp/>char)2</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="119"><highlight class="normal"></highlight></codeline>
<codeline lineno="125" refid="group__fold__compound_1ga91795d35ebdb6f32be50459f24b3d114" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_STATUS_PF_PRE<sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)3</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="126"><highlight class="normal"></highlight></codeline>
<codeline lineno="132" refid="group__fold__compound_1ga1c6fa243533fd026e50f7d595eaaa565" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_STATUS_PF_POST<sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)4</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="133"><highlight class="normal"></highlight></codeline>
<codeline lineno="134"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="model_8h" kindref="compound">ViennaRNA/model.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="136"><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="137"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="sequences_2sequence_8h" kindref="compound">ViennaRNA/sequences/sequence.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="datastructures_2dp__matrices_8h" kindref="compound">ViennaRNA/datastructures/dp_matrices.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="139"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="hard_8h" kindref="compound">ViennaRNA/constraints/hard.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="140"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="soft_8h" kindref="compound">ViennaRNA/constraints/soft.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="141"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="grammar_2basic_8h" kindref="compound">ViennaRNA/grammar/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="142"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="structured__domains_8h" kindref="compound">ViennaRNA/structured_domains.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="unstructured__domains_8h" kindref="compound">ViennaRNA/unstructured_domains.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="144"><highlight class="normal"></highlight></codeline>
<codeline lineno="145"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WITH_SVM</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="146"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;ViennaRNA/zscore/basic.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="147"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="148"><highlight class="normal"></highlight></codeline>
<codeline lineno="149"><highlight class="normal"></highlight></codeline>
<codeline lineno="153" refid="group__fold__compound_1ga01a4ff86fa71deaaa5d1abbd95a1447d" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">enum</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="154" refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447da7e264dd3cf2dc9b6448caabcb7763cd6" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447da7e264dd3cf2dc9b6448caabcb7763cd6" kindref="member">VRNA_FC_TYPE_SINGLE</ref>,<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="155" refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447dab821ce46ea3cf665be97df22a76f5023" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447dab821ce46ea3cf665be97df22a76f5023" kindref="member">VRNA_FC_TYPE_COMPARATIVE</ref><sp/><sp/></highlight></codeline>
<codeline lineno="156"><highlight class="normal">}<sp/><ref refid="group__fold__compound_1ga01a4ff86fa71deaaa5d1abbd95a1447d" kindref="member">vrna_fc_type_e</ref>;</highlight></codeline>
<codeline lineno="157"><highlight class="normal"></highlight></codeline>
<codeline lineno="158"><highlight class="normal"></highlight></codeline>
<codeline lineno="171" refid="structvrna__fc__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__fc__s" kindref="compound">vrna_fc_s</ref><sp/>{</highlight></codeline>
<codeline lineno="176" refid="structvrna__fc__s_1a391bcf8ac5997784aaf780cdd251c464" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__fold__compound_1ga01a4ff86fa71deaaa5d1abbd95a1447d" kindref="member">vrna_fc_type_e</ref><sp/><ref refid="structvrna__fc__s_1a391bcf8ac5997784aaf780cdd251c464" kindref="member">type</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="183" refid="structvrna__fc__s_1a95fbfed770b858e50c766505dc4bf998" refkind="member"><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/><sp/><sp/><sp/><sp/><ref refid="structvrna__fc__s_1a95fbfed770b858e50c766505dc4bf998" kindref="member">length</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="184"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="185"><highlight class="normal"><sp/><sp/>DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="structvrna__fc__s_1ae1a7bbff0256577e2b22709bac11fdb4" kindref="member">cutpoint</ref>,</highlight></codeline>
<codeline lineno="186" refid="structvrna__fc__s_1ae1a7bbff0256577e2b22709bac11fdb4" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>strand_*<sp/>members<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="190"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="191" refid="structvrna__fc__s_1a23304c5186dfae97bc69dc19d37f70c3" refkind="member"><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/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a23304c5186dfae97bc69dc19d37f70c3" kindref="member">strand_number</ref>;<sp/></highlight></codeline>
<codeline lineno="192" refid="structvrna__fc__s_1a3bf15e0e44539f9f622fd09227bf3de1" refkind="member"><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/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a3bf15e0e44539f9f622fd09227bf3de1" kindref="member">strand_order</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="193" refid="structvrna__fc__s_1af698d79085056aa9a9075e834b0748ed" refkind="member"><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/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1af698d79085056aa9a9075e834b0748ed" kindref="member">strand_order_uniq</ref>;<sp/></highlight></codeline>
<codeline lineno="194" refid="structvrna__fc__s_1a571ee9a932f633c7d9167ae029573935" refkind="member"><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/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a571ee9a932f633c7d9167ae029573935" kindref="member">strand_start</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="195" refid="structvrna__fc__s_1aaa1b51bc6eb47cc661fea834d7175a54" refkind="member"><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/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1aaa1b51bc6eb47cc661fea834d7175a54" kindref="member">strand_end</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="196"><highlight class="normal"></highlight></codeline>
<codeline lineno="197" refid="structvrna__fc__s_1ad8962b97f5e5e233d9bfb5b16a691d26" refkind="member"><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/><sp/><sp/><sp/><sp/><ref refid="structvrna__fc__s_1ad8962b97f5e5e233d9bfb5b16a691d26" kindref="member">strands</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="198" refid="structvrna__fc__s_1a855b503aefd052430bf463d8518d2ff5" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__alphabet__utils_1gaa35bee3061759495467070b47d0e1f22" kindref="member">vrna_seq_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a855b503aefd052430bf463d8518d2ff5" kindref="member">nucleotides</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="199" refid="structvrna__fc__s_1a0387efd460429ca0847c8009d327c0fb" refkind="member"><highlight class="normal"><sp/><sp/>vrna_msa_t<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a0387efd460429ca0847c8009d327c0fb" kindref="member">alignment</ref>;<sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="200"><highlight class="normal"></highlight></codeline>
<codeline lineno="201" refid="structvrna__fc__s_1aceaa904dbf50092d403ca99422e8f824" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1aceaa904dbf50092d403ca99422e8f824" kindref="member">hc</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="202"><highlight class="normal"></highlight></codeline>
<codeline lineno="203" refid="structvrna__fc__s_1aca8be7bdc65bafe2172c6ee777f18568" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__dp__matrices_1gae5aef35d016475e758f619b7bcb534f9" kindref="member">vrna_mx_mfe_t</ref><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1aca8be7bdc65bafe2172c6ee777f18568" kindref="member">matrices</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="204" refid="structvrna__fc__s_1afc38ed5a1028a2712d2365274bf49727" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__dp__matrices_1ga68729ab3fed26bdd1806fa814f172fc1" kindref="member">vrna_mx_pf_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1afc38ed5a1028a2712d2365274bf49727" kindref="member">exp_matrices</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="205"><highlight class="normal"></highlight></codeline>
<codeline lineno="206" refid="structvrna__fc__s_1a19b8720c2c5321c1b97c830bd17566ea" 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/>*<ref refid="structvrna__fc__s_1a19b8720c2c5321c1b97c830bd17566ea" kindref="member">params</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="207" refid="structvrna__fc__s_1a7052a5d24f6091b9c5f79edcc9456a12" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/><sp/>*<ref refid="structvrna__fc__s_1a7052a5d24f6091b9c5f79edcc9456a12" kindref="member">exp_params</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="208"><highlight class="normal"></highlight></codeline>
<codeline lineno="209" refid="structvrna__fc__s_1afdead4cf55c882d3497e779573e17e03" 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/>*<ref refid="structvrna__fc__s_1afdead4cf55c882d3497e779573e17e03" kindref="member">iindx</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="210" refid="structvrna__fc__s_1a5037235dee512efd85ca543780bbca1a" 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/>*<ref refid="structvrna__fc__s_1a5037235dee512efd85ca543780bbca1a" kindref="member">jindx</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="211"><highlight class="normal"></highlight></codeline>
<codeline lineno="218" refid="structvrna__fc__s_1aef282a5d126e0038f3855e59a99ef360" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" kindref="member">vrna_recursion_status_f</ref><sp/><sp/><sp/><ref refid="structvrna__fc__s_1aef282a5d126e0038f3855e59a99ef360" kindref="member">stat_cb</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="222"><highlight class="normal"></highlight></codeline>
<codeline lineno="223" refid="structvrna__fc__s_1a20048e0c369e9f24b55423d600037c68" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><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/>*<ref refid="structvrna__fc__s_1a20048e0c369e9f24b55423d600037c68" kindref="member">auxdata</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="226"><highlight class="normal"></highlight></codeline>
<codeline lineno="227" refid="structvrna__fc__s_1a02b2bfc9d563b4748f933308de09791c" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__fc__s_1a02b2bfc9d563b4748f933308de09791c" kindref="member">free_auxdata</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="230"><highlight class="normal"></highlight></codeline>
<codeline lineno="237"><highlight class="normal"></highlight></codeline>
<codeline lineno="238"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>data<sp/>structure<sp/>to<sp/>adjust<sp/>additional<sp/>structural<sp/>domains,<sp/>such<sp/>as<sp/>G-quadruplexes<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="239" refid="structvrna__fc__s_1ac25a84f2658de0d7a54cd710c16198b1" refkind="member"><highlight class="normal"><sp/><sp/>vrna_sd_t<sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1ac25a84f2658de0d7a54cd710c16198b1" kindref="member">domains_struc</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="240"><highlight class="normal"></highlight></codeline>
<codeline lineno="241"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>data<sp/>structure<sp/>to<sp/>adjust<sp/>additional<sp/>contributions<sp/>to<sp/>unpaired<sp/>stretches,<sp/>e.g.<sp/>due<sp/>to<sp/>protein<sp/>binding<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="242" refid="structvrna__fc__s_1a4f70b6d32681fc8ca061236f21819ae7" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__domains__up_1ga0009117b14d29143e8b18ab891f48c2d" kindref="member">vrna_ud_t</ref><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a4f70b6d32681fc8ca061236f21819ae7" kindref="member">domains_up</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="243"><highlight class="normal"></highlight></codeline>
<codeline lineno="244"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>auxiliary<sp/>(user-defined)<sp/>extension<sp/>to<sp/>the<sp/>folding<sp/>grammar<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="245" refid="structvrna__fc__s_1a4dbcba59425e0d4b222adae148e3041a" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__grammar_1gab771519c88455091fff89211cc8b1f97" kindref="member">vrna_gr_aux_t</ref><sp/><ref refid="structvrna__fc__s_1a4dbcba59425e0d4b222adae148e3041a" kindref="member">aux_grammar</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="246"><highlight class="normal"></highlight></codeline>
<codeline lineno="250"><highlight class="normal"></highlight></codeline>
<codeline lineno="251"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_C11_FEATURES</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="252"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>C11<sp/>support<sp/>for<sp/>unnamed<sp/>unions/structs<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="253"><highlight class="normal"><sp/><sp/></highlight><highlight class="keyword">union<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="254"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="255"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="256"><highlight class="normal"></highlight></codeline>
<codeline lineno="261" refid="structvrna__fc__s_1a87f6abcda89cfb7a486c97e1f5371525" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="structvrna__fc__s_1a87f6abcda89cfb7a486c97e1f5371525" kindref="member">sequence</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="264" refid="structvrna__fc__s_1a9934bdb695d35a3544285cbcc19f9763" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*<ref refid="structvrna__fc__s_1a9934bdb695d35a3544285cbcc19f9763" kindref="member">sequence_encoding</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="268"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*encoding5;</highlight></codeline>
<codeline lineno="269"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*encoding3;</highlight></codeline>
<codeline lineno="270"><highlight class="normal"></highlight></codeline>
<codeline lineno="271"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*sequence_encoding2;</highlight></codeline>
<codeline lineno="272"><highlight class="normal"></highlight></codeline>
<codeline lineno="273"><highlight class="normal"></highlight></codeline>
<codeline lineno="274" refid="structvrna__fc__s_1a3fbea559f1d1976b2d67c215cdeee0b2" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="structvrna__fc__s_1a3fbea559f1d1976b2d67c215cdeee0b2" kindref="member">ptype</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="283" refid="structvrna__fc__s_1a7fe1235ce3d41287695f1ae1e283e8fc" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="structvrna__fc__s_1a7fe1235ce3d41287695f1ae1e283e8fc" kindref="member">ptype_pf_compat</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="288" refid="structvrna__fc__s_1ac7089e90460ad3990a308808c8044c9f" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/>*<ref refid="structvrna__fc__s_1ac7089e90460ad3990a308808c8044c9f" kindref="member">sc</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="291"><highlight class="normal"></highlight></codeline>
<codeline lineno="295"><highlight class="normal"></highlight></codeline>
<codeline lineno="296"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_C11_FEATURES</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="297"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>C11<sp/>support<sp/>for<sp/>unnamed<sp/>unions/structs<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="298"><highlight class="normal">};</highlight></codeline>
<codeline lineno="299"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="300"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="301"><highlight class="normal"></highlight></codeline>
<codeline lineno="306" refid="structvrna__fc__s_1a965dbb42f2e13cace5aa3bbab4396530" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**<ref refid="structvrna__fc__s_1a965dbb42f2e13cace5aa3bbab4396530" kindref="member">sequences</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="310" refid="structvrna__fc__s_1a614702ab74478e786272be44f8cebfe3" refkind="member"><highlight class="normal"><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/><ref refid="structvrna__fc__s_1a614702ab74478e786272be44f8cebfe3" kindref="member">n_seq</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="313" refid="structvrna__fc__s_1ac472afde64d8b3c8b84e4809fda7d814" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1ac472afde64d8b3c8b84e4809fda7d814" kindref="member">cons_seq</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="316" refid="structvrna__fc__s_1aa3fab7ae38ebfed2028375221d295686" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1aa3fab7ae38ebfed2028375221d295686" kindref="member">S_cons</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="319" refid="structvrna__fc__s_1aebb37297f92c7bd22aac6343f8f61d61" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**<ref refid="structvrna__fc__s_1aebb37297f92c7bd22aac6343f8f61d61" kindref="member">S</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="322" refid="structvrna__fc__s_1a78d089b475e2230bd536b9a6ed8bb17c" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**<ref refid="structvrna__fc__s_1a78d089b475e2230bd536b9a6ed8bb17c" kindref="member">S5</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="325" refid="structvrna__fc__s_1af6ab2a25b84d2308ee23f6b11b5fd52d" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**<ref refid="structvrna__fc__s_1af6ab2a25b84d2308ee23f6b11b5fd52d" kindref="member">S3</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="328"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**Ss;</highlight></codeline>
<codeline lineno="329"><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/>**a2s;</highlight></codeline>
<codeline lineno="330" refid="structvrna__fc__s_1a14dc7755af6019ddbd0cf94b209e89dd" refkind="member"><highlight class="normal"><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/>*<ref refid="structvrna__fc__s_1a14dc7755af6019ddbd0cf94b209e89dd" kindref="member">pscore</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="333" refid="structvrna__fc__s_1ad966c15907e6c2e32b0910c7a3154509" refkind="member"><highlight class="normal"><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/>**<ref refid="structvrna__fc__s_1ad966c15907e6c2e32b0910c7a3154509" kindref="member">pscore_local</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="336" refid="structvrna__fc__s_1abf5e82d14649b6179ae60ed7da6e4fc0" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1abf5e82d14649b6179ae60ed7da6e4fc0" kindref="member">pscore_pf_compat</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="340" refid="structvrna__fc__s_1ac2b047fddabc51a76a96511174e47db1" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/>**<ref refid="structvrna__fc__s_1ac2b047fddabc51a76a96511174e47db1" kindref="member">scs</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="343"><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/>oldAliEn;</highlight></codeline>
<codeline lineno="344"><highlight class="normal"></highlight></codeline>
<codeline lineno="348"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_C11_FEATURES</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="349"><highlight class="normal">};</highlight></codeline>
<codeline lineno="350"><highlight class="normal">};</highlight></codeline>
<codeline lineno="351"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="352"><highlight class="normal"></highlight></codeline>
<codeline lineno="359" refid="structvrna__fc__s_1a426305721b16023f2f3247f7354d2c46" refkind="member"><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/><ref refid="structvrna__fc__s_1a426305721b16023f2f3247f7354d2c46" kindref="member">maxD1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="360" refid="structvrna__fc__s_1a38695774fd396c892f9a70d39978b231" refkind="member"><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/><ref refid="structvrna__fc__s_1a38695774fd396c892f9a70d39978b231" kindref="member">maxD2</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="361" refid="structvrna__fc__s_1aa279ba4bd0ff541d435d3a049687f3ac" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1aa279ba4bd0ff541d435d3a049687f3ac" kindref="member">reference_pt1</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="362" refid="structvrna__fc__s_1a926ad253f5f0eed642bc227493d0278d" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__fc__s_1a926ad253f5f0eed642bc227493d0278d" kindref="member">reference_pt2</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="363"><highlight class="normal"></highlight></codeline>
<codeline lineno="364" refid="structvrna__fc__s_1a62a8d4ab8dadffbf09da917adff6c71e" refkind="member"><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/>*<ref refid="structvrna__fc__s_1a62a8d4ab8dadffbf09da917adff6c71e" kindref="member">referenceBPs1</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="365" refid="structvrna__fc__s_1a19187f33433e84683730dedff8544f71" refkind="member"><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/>*<ref refid="structvrna__fc__s_1a19187f33433e84683730dedff8544f71" kindref="member">referenceBPs2</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="366" refid="structvrna__fc__s_1a5c53e55583ce096148075bc240fc2bce" refkind="member"><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/>*<ref refid="structvrna__fc__s_1a5c53e55583ce096148075bc240fc2bce" kindref="member">bpdist</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="367"><highlight class="normal"></highlight></codeline>
<codeline lineno="368" refid="structvrna__fc__s_1a0af5a888bac2ae32107da32776144504" refkind="member"><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/>*<ref refid="structvrna__fc__s_1a0af5a888bac2ae32107da32776144504" kindref="member">mm1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="369" refid="structvrna__fc__s_1a54c0b979274b285a7e093ed54aa3252e" refkind="member"><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/>*<ref refid="structvrna__fc__s_1a54c0b979274b285a7e093ed54aa3252e" kindref="member">mm2</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="370"><highlight class="normal"></highlight></codeline>
<codeline lineno="374"><highlight class="normal"></highlight></codeline>
<codeline lineno="381" refid="structvrna__fc__s_1adacbf7cdfb47d3072683ab509de735f6" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="structvrna__fc__s_1adacbf7cdfb47d3072683ab509de735f6" kindref="member">window_size</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="382" refid="structvrna__fc__s_1a2ecb8ff5e21190936a8a146be7a251ff" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>**<ref refid="structvrna__fc__s_1a2ecb8ff5e21190936a8a146be7a251ff" kindref="member">ptype_local</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="383"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WITH_SVM</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="384" refid="structvrna__fc__s_1ab9e9e3fd24c960c6e2390be1a070e4c5" refkind="member"><highlight class="normal"><sp/><sp/>vrna_zsc_dat_t<sp/><sp/><ref refid="structvrna__fc__s_1ab9e9e3fd24c960c6e2390be1a070e4c5" kindref="member">zscore_data</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="385"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="386"><highlight class="normal"></highlight></codeline>
<codeline lineno="390"><highlight class="normal">};</highlight></codeline>
<codeline lineno="391"><highlight class="normal"></highlight></codeline>
<codeline lineno="392"><highlight class="normal"></highlight></codeline>
<codeline lineno="393"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>the<sp/>definitions<sp/>below<sp/>should<sp/>be<sp/>used<sp/>for<sp/>functions<sp/>that<sp/>return/receive/destroy<sp/>fold<sp/>compound<sp/>data<sp/>structures<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="394"><highlight class="normal"></highlight></codeline>
<codeline lineno="398" refid="group__fold__compound_1gacea5b7ee6181c485f36e2afa0e9089e4" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_DEFAULT<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="399"><highlight class="normal"></highlight></codeline>
<codeline lineno="406" refid="group__fold__compound_1gae63be9127fe7dcc1f9bb14f5bb1064ee" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_MFE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>0)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="407"><highlight class="normal"></highlight></codeline>
<codeline lineno="414" refid="group__fold__compound_1gabfbadcddda3e74ce7f49035ef8f058f7" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_PF<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>1)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="415"><highlight class="normal"></highlight></codeline>
<codeline lineno="419" refid="group__fold__compound_1ga8f681fa12b8d4b348bf58415fd1fc82f" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_HYBRID<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>2)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="420"><highlight class="normal"></highlight></codeline>
<codeline lineno="430" refid="group__fold__compound_1ga61469c423131552c8483229f8b6c7e0e" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_EVAL_ONLY<sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>3)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="431"><highlight class="normal"></highlight></codeline>
<codeline lineno="435" refid="group__fold__compound_1ga2b2a8009ccdccc3eb1571556261aee8e" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_WINDOW<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>4)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="436"><highlight class="normal"></highlight></codeline>
<codeline lineno="437"><highlight class="normal"></highlight></codeline>
<codeline lineno="438"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_F5<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>5)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="439"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_F3<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>6)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="440"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_WINDOW_F5<sp/><sp/><sp/><sp/><sp/><sp/><sp/>(VRNA_OPTION_WINDOW<sp/>|<sp/>VRNA_OPTION_F5)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="441"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OPTION_WINDOW_F3<sp/><sp/><sp/><sp/><sp/><sp/><sp/>(VRNA_OPTION_WINDOW<sp/>|<sp/>VRNA_OPTION_F3)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="442"><highlight class="normal"></highlight></codeline>
<codeline lineno="480"><highlight class="normal"><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*</highlight></codeline>
<codeline lineno="481" refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" refkind="member"><highlight class="normal"><ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="482"><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="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>*md_p,</highlight></codeline>
<codeline lineno="483"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="484"><highlight class="normal"></highlight></codeline>
<codeline lineno="485"><highlight class="normal"></highlight></codeline>
<codeline lineno="523"><highlight class="normal"><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*</highlight></codeline>
<codeline lineno="524" refid="group__fold__compound_1gabbaffe56b1a37f6ed1a31e9e4f5613f1" refkind="member"><highlight class="normal"><ref refid="group__fold__compound_1gabbaffe56b1a37f6ed1a31e9e4f5613f1" kindref="member">vrna_fold_compound_comparative</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>**sequences,</highlight></codeline>
<codeline lineno="525"><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/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/>*md_p,</highlight></codeline>
<codeline lineno="526"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>options);</highlight></codeline>
<codeline lineno="527"><highlight class="normal"></highlight></codeline>
<codeline lineno="528"><highlight class="normal"></highlight></codeline>
<codeline lineno="529"><highlight class="normal"><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*</highlight></codeline>
<codeline lineno="530"><highlight class="normal">vrna_fold_compound_comparative2(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><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/>**sequences,</highlight></codeline>
<codeline lineno="531"><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="keyword">const</highlight><highlight class="normal"><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/>**names,</highlight></codeline>
<codeline lineno="532"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*orientation,</highlight></codeline>
<codeline lineno="533"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/>*start,</highlight></codeline>
<codeline lineno="534"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/>*genome_size,</highlight></codeline>
<codeline lineno="535"><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__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*md_p,</highlight></codeline>
<codeline lineno="536"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="537"><highlight class="normal"></highlight></codeline>
<codeline lineno="538"><highlight class="normal"></highlight></codeline>
<codeline lineno="539"><highlight class="normal"><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*</highlight></codeline>
<codeline lineno="540"><highlight class="normal">vrna_fold_compound_TwoD(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="541"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*s1,</highlight></codeline>
<codeline lineno="542"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*s2,</highlight></codeline>
<codeline lineno="543"><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/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/>*md_p,</highlight></codeline>
<codeline lineno="544"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>options);</highlight></codeline>
<codeline lineno="545"><highlight class="normal"></highlight></codeline>
<codeline lineno="546"><highlight class="normal"></highlight></codeline>
<codeline lineno="547"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="548"><highlight class="normal">vrna_fold_compound_prepare(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="549"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="550"><highlight class="normal"></highlight></codeline>
<codeline lineno="551"><highlight class="normal"></highlight></codeline>
<codeline lineno="559"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="560" refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" refkind="member"><highlight class="normal"><ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="561"><highlight class="normal"></highlight></codeline>
<codeline lineno="562"><highlight class="normal"></highlight></codeline>
<codeline lineno="580"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="581" refid="group__fold__compound_1gad6c0747712712bda6d94702e0de895a7" refkind="member"><highlight class="normal"><ref refid="group__fold__compound_1gad6c0747712712bda6d94702e0de895a7" kindref="member">vrna_fold_compound_add_auxdata</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="582"><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/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data,</highlight></codeline>
<codeline lineno="583"><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/><ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f</ref><sp/><sp/>f);</highlight></codeline>
<codeline lineno="584"><highlight class="normal"></highlight></codeline>
<codeline lineno="585"><highlight class="normal"></highlight></codeline>
<codeline lineno="601"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="602" refid="group__fold__compound_1ga579952cc017127b81e89a186c0d6b9c2" refkind="member"><highlight class="normal"><ref refid="group__fold__compound_1ga579952cc017127b81e89a186c0d6b9c2" kindref="member">vrna_fold_compound_add_callback</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="603"><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__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" kindref="member">vrna_recursion_status_f</ref><sp/>f);</highlight></codeline>
<codeline lineno="604"><highlight class="normal"></highlight></codeline>
<codeline lineno="605"><highlight class="normal"></highlight></codeline>
<codeline lineno="609"><highlight class="normal"></highlight></codeline>
<codeline lineno="610"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/fold_compound.h"/>
  </compounddef>
</doxygen>
