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    <sectiondef kind="define">
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        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold.h" line="21" column="11" bodyfile="ViennaRNA/fold.h" bodystart="21" bodyend="-1"/>
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    <sectiondef kind="func">
      <member refid="group__mfe__global__deprecated_1ga2bc41df5d71fee6fd8da9904ee65d8fb" kind="function"><name>fold_par</name></member>
      <member refid="group__mfe__global__deprecated_1gaadafcb0f140795ae62e5ca027e335a9b" kind="function"><name>fold</name></member>
      <member refid="group__mfe__global__deprecated_1ga4ac63ab3e8d9a80ced28b8052d94e423" kind="function"><name>circfold</name></member>
      <member refid="group__mfe__global__deprecated_1ga107fdfe5fd641868156bfd849f6866c7" kind="function"><name>free_arrays</name></member>
      <member refid="group__mfe__global__deprecated_1ga41bf8f6fa15b94471f7095cad9f0ccf3" kind="function"><name>update_fold_params</name></member>
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      <member refid="group__mfe__global__deprecated_1ga99641b8dbb40891da5490d3cc271e607" kind="function"><name>export_fold_arrays</name></member>
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      <member refid="group__mfe__global__deprecated_1ga004bb901e7fd2f8d5ae68f9530318ce1" kind="function"><name>export_circfold_arrays_par</name></member>
      <member refid="group__mfe__global__deprecated_1ga2163034a25c6115d894b199e97e03f6c" kind="function"><name>LoopEnergy</name></member>
      <member refid="group__mfe__global__deprecated_1gab327ce11972f5ac069d52c8dedfdb700" kind="function"><name>HairpinE</name></member>
      <member refid="group__mfe__global__deprecated_1gac3f0a28d9cb609d388b155445073fd20" kind="function"><name>initialize_fold</name></member>
      <member refid="group__mfe__global__deprecated_1gad338ea587a5c21b3856ed71b70462c58" kind="function"><name>backtrack_fold_from_pair</name></member>
    </sectiondef>
    <briefdescription>
<para>MFE calculations for single RNA sequences. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_FOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_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">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="params_2basic_8h" kindref="compound">ViennaRNA/params/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="mfe_2global_8h" kindref="compound">ViennaRNA/mfe/global.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="backtrack_2global_8h" kindref="compound">ViennaRNA/backtrack/global.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="eval_2structures_8h" kindref="compound">ViennaRNA/eval/structures.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><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="15"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><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="17"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><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="19"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="78"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="79"><highlight class="normal"><ref refid="group__mfe__global__deprecated_1ga2bc41df5d71fee6fd8da9904ee65d8fb" kindref="member">fold_par</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="80"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure,</highlight></codeline>
<codeline lineno="81"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*parameters,</highlight></codeline>
<codeline lineno="82"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>is_constrained,</highlight></codeline>
<codeline lineno="83"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>is_circular),</highlight></codeline>
<codeline lineno="84" refid="group__mfe__global__deprecated_1ga2bc41df5d71fee6fd8da9904ee65d8fb" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_mfe()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="102"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1gaadafcb0f140795ae62e5ca027e335a9b" kindref="member">fold</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,<sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="103" refid="group__mfe__global__deprecated_1gaadafcb0f140795ae62e5ca027e335a9b" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_fold()<sp/>or<sp/>vrna_mfe()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="104"><highlight class="normal"></highlight></codeline>
<codeline lineno="121"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1ga4ac63ab3e8d9a80ced28b8052d94e423" kindref="member">circfold</ref>(<sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,<sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="122" refid="group__mfe__global__deprecated_1ga4ac63ab3e8d9a80ced28b8052d94e423" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_circfold()<sp/>or<sp/>vrna_mfe()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="123"><highlight class="normal"></highlight></codeline>
<codeline lineno="124"><highlight class="normal"></highlight></codeline>
<codeline lineno="131"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1ga107fdfe5fd641868156bfd849f6866c7" kindref="member">free_arrays</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="132" refid="group__mfe__global__deprecated_1ga107fdfe5fd641868156bfd849f6866c7" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</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></codeline>
<codeline lineno="142"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1ga41bf8f6fa15b94471f7095cad9f0ccf3" kindref="member">update_fold_params</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="143" refid="group__mfe__global__deprecated_1ga41bf8f6fa15b94471f7095cad9f0ccf3" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="144"><highlight class="normal"></highlight></codeline>
<codeline lineno="151"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1gae66dc422efb8f5d56717d92d6002a9f8" kindref="member">update_fold_params_par</ref>(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*parameters),</highlight></codeline>
<codeline lineno="152" refid="group__mfe__global__deprecated_1gae66dc422efb8f5d56717d92d6002a9f8" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="153"><highlight class="normal"></highlight></codeline>
<codeline lineno="159"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="160"><highlight class="normal"><ref refid="group__mfe__global__deprecated_1ga99641b8dbb40891da5490d3cc271e607" kindref="member">export_fold_arrays</ref>(<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**f5_p,</highlight></codeline>
<codeline lineno="161"><highlight class="normal"><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/>**c_p,</highlight></codeline>
<codeline lineno="162"><highlight class="normal"><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/>**fML_p,</highlight></codeline>
<codeline lineno="163"><highlight class="normal"><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/>**fM1_p,</highlight></codeline>
<codeline lineno="164"><highlight class="normal"><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/>**indx_p,</highlight></codeline>
<codeline lineno="165"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**ptype_p),</highlight></codeline>
<codeline lineno="166" refid="group__mfe__global__deprecated_1ga99641b8dbb40891da5490d3cc271e607" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="167"><highlight class="normal"></highlight></codeline>
<codeline lineno="173"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="174"><highlight class="normal"><ref refid="group__mfe__global__deprecated_1ga6606ec0ec964ea506fdadb997a1a5328" kindref="member">export_fold_arrays_par</ref>(<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**f5_p,</highlight></codeline>
<codeline lineno="175"><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/>**c_p,</highlight></codeline>
<codeline lineno="176"><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/>**fML_p,</highlight></codeline>
<codeline lineno="177"><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/>**fM1_p,</highlight></codeline>
<codeline lineno="178"><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/>**indx_p,</highlight></codeline>
<codeline lineno="179"><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">char</highlight><highlight class="normal"><sp/>**ptype_p,</highlight></codeline>
<codeline lineno="180"><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__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>**P_p),</highlight></codeline>
<codeline lineno="181" refid="group__mfe__global__deprecated_1ga6606ec0ec964ea506fdadb997a1a5328" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="188"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="189"><highlight class="normal"><ref refid="group__mfe__global__deprecated_1ga04d5d639fd4473ca766436a9bae5665c" kindref="member">export_circfold_arrays</ref>(<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*Fc_p,</highlight></codeline>
<codeline lineno="190"><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/>*FcH_p,</highlight></codeline>
<codeline lineno="191"><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/>*FcI_p,</highlight></codeline>
<codeline lineno="192"><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/>*FcM_p,</highlight></codeline>
<codeline lineno="193"><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/>**fM2_p,</highlight></codeline>
<codeline lineno="194"><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/>**f5_p,</highlight></codeline>
<codeline lineno="195"><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/>**c_p,</highlight></codeline>
<codeline lineno="196"><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/>**fML_p,</highlight></codeline>
<codeline lineno="197"><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/>**fM1_p,</highlight></codeline>
<codeline lineno="198"><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/>**indx_p,</highlight></codeline>
<codeline lineno="199"><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">char</highlight><highlight class="normal"><sp/>**ptype_p),</highlight></codeline>
<codeline lineno="200" refid="group__mfe__global__deprecated_1ga04d5d639fd4473ca766436a9bae5665c" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="201"><highlight class="normal"></highlight></codeline>
<codeline lineno="207"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="208"><highlight class="normal"><ref refid="group__mfe__global__deprecated_1ga004bb901e7fd2f8d5ae68f9530318ce1" kindref="member">export_circfold_arrays_par</ref>(<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*Fc_p,</highlight></codeline>
<codeline lineno="209"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*FcH_p,</highlight></codeline>
<codeline lineno="210"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*FcI_p,</highlight></codeline>
<codeline lineno="211"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>*FcM_p,</highlight></codeline>
<codeline lineno="212"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**fM2_p,</highlight></codeline>
<codeline lineno="213"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**f5_p,</highlight></codeline>
<codeline lineno="214"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**c_p,</highlight></codeline>
<codeline lineno="215"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**fML_p,</highlight></codeline>
<codeline lineno="216"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**fM1_p,</highlight></codeline>
<codeline lineno="217"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**indx_p,</highlight></codeline>
<codeline lineno="218"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>**ptype_p,</highlight></codeline>
<codeline lineno="219"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>**P_p),</highlight></codeline>
<codeline lineno="220" refid="group__mfe__global__deprecated_1ga004bb901e7fd2f8d5ae68f9530318ce1" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>datastructure<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="221"><highlight class="normal"></highlight></codeline>
<codeline lineno="222"><highlight class="normal"></highlight></codeline>
<codeline lineno="223"><highlight class="normal"></highlight></codeline>
<codeline lineno="224"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>finally<sp/>moved<sp/>the<sp/>loop<sp/>energy<sp/>function<sp/>declarations<sp/>to<sp/>this<sp/>header...<sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="225"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>BUT:<sp/>The<sp/>functions<sp/>only<sp/>exist<sp/>for<sp/>backward<sp/>compatibility<sp/>reasons!<sp/><sp/><sp/><sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="226"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>You<sp/>better<sp/>include<sp/>&quot;loop_energies.h&quot;<sp/>and<sp/>call<sp/>the<sp/>functions:<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="227"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>vrna_E_hairpin()<sp/>and<sp/>E_IntLoop()<sp/>which<sp/>are<sp/>(almost)<sp/>threadsafe<sp/>as<sp/>they<sp/>get<sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="228"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>a<sp/>pointer<sp/>to<sp/>the<sp/>energy<sp/>parameter<sp/>data<sp/>structure<sp/>as<sp/>additional<sp/>argument<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="229"><highlight class="normal"></highlight></codeline>
<codeline lineno="234"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1ga2163034a25c6115d894b199e97e03f6c" kindref="member">LoopEnergy</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n1,</highlight></codeline>
<codeline lineno="235"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n2,</highlight></codeline>
<codeline lineno="236"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>type,</highlight></codeline>
<codeline lineno="237"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>type_2,</highlight></codeline>
<codeline lineno="238"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>si1,</highlight></codeline>
<codeline lineno="239"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>sj1,</highlight></codeline>
<codeline lineno="240"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>sp1,</highlight></codeline>
<codeline lineno="241"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>sq1),</highlight></codeline>
<codeline lineno="242" refid="group__mfe__global__deprecated_1ga2163034a25c6115d894b199e97e03f6c" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="243"><highlight class="normal"></highlight></codeline>
<codeline lineno="248"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1gab327ce11972f5ac069d52c8dedfdb700" kindref="member">HairpinE</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>size,</highlight></codeline>
<codeline lineno="249"><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/>type,</highlight></codeline>
<codeline lineno="250"><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/>si1,</highlight></codeline>
<codeline lineno="251"><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/>sj1,</highlight></codeline>
<codeline lineno="252"><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/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="253" refid="group__mfe__global__deprecated_1gab327ce11972f5ac069d52c8dedfdb700" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_E_hairpin()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="254"><highlight class="normal"></highlight></codeline>
<codeline lineno="260"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__mfe__global__deprecated_1gac3f0a28d9cb609d388b155445073fd20" kindref="member">initialize_fold</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),</highlight></codeline>
<codeline lineno="261" refid="group__mfe__global__deprecated_1gac3f0a28d9cb609d388b155445073fd20" refkind="member"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="262"><highlight class="normal"></highlight></codeline>
<codeline lineno="266"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*backtrack_fold_from_pair(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="267"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>i,</highlight></codeline>
<codeline lineno="268"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>j),</highlight></codeline>
<codeline lineno="269"><highlight class="normal"></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete.<sp/>Consider<sp/>using<sp/>vrna_backtrack_from_intervals()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="270"><highlight class="normal"></highlight></codeline>
<codeline lineno="271"><highlight class="normal"></highlight></codeline>
<codeline lineno="272"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="273"><highlight class="normal"></highlight></codeline>
<codeline lineno="277"><highlight class="normal"></highlight></codeline>
<codeline lineno="278"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/fold.h"/>
  </compounddef>
</doxygen>
