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    <sectiondef kind="user-defined">
      <header>Basic local (sliding window) MFE prediction interface</header>
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      <member refid="group__mfe__window_1ga5df4a67ce381ed329c289370b0c8adcb" kind="function"><name>vrna_mfe_window_zscore_cb</name></member>
      <member refid="group__mfe__window_1ga17ac221d685bb1e74e2acdbfb02ec86d" kind="function"><name>vrna_backtrack_window</name></member>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Simplified local MFE prediction using sequence(s) or multiple sequence alignment(s)</header>
      <member refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" kind="function"><name>vrna_Lfold</name></member>
      <member refid="group__mfe__window_1ga84dcc36fd88063e1692c2e1e68a5f689" kind="function"><name>vrna_Lfold_cb</name></member>
      <member refid="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" kind="function"><name>vrna_Lfoldz</name></member>
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      <member refid="group__mfe__window_1gaa43d3de352753529a4578cb02cd8bc52" kind="function"><name>vrna_aliLfold</name></member>
      <member refid="group__mfe__window_1gae9b2e312c316961d4a067f9b789cc9d7" kind="function"><name>vrna_aliLfold_cb</name></member>
    </sectiondef>
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        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/mfe/local.h" line="23" column="11" bodyfile="ViennaRNA/mfe/local.h" bodystart="23" bodyend="-1"/>
      </memberdef>
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    <sectiondef kind="typedef">
      <member refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kind="typedef"><name>vrna_mfe_window_f</name></member>
      <member refid="group__mfe__window_1ga215bef80ed74d36daba71ea4fb7d4388" kind="typedef"><name>vrna_mfe_window_callback</name></member>
      <member refid="group__mfe__window_1gad41cef447889684ac02787d6e7ddf670" kind="typedef"><name>vrna_mfe_window_zscore_f</name></member>
      <member refid="group__mfe__window_1ga67e8a2d04140c9220e2b134ed3a08b4e" kind="typedef"><name>vrna_mfe_window_zscore_callback</name></member>
    </sectiondef>
    <briefdescription>
<para>Compute local Minimum Free Energy (MFE) using a sliding window approach. </para>
    </briefdescription>
    <detaileddescription>
<para>, </para>
<para>This file includes the interface to all functions related to predicting locally stable secondary structures. </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_MFE_LOCAL_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_MFE_LOCAL_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;stdio.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WITH_SVM</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;ViennaRNA/zscore/basic.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(DEPRECATED)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/><sp/>undef<sp/>DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</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(&quot;&quot;,<sp/>msg)))</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="18"><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="19"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><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="21"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="24"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="25"><highlight class="normal"></highlight></codeline>
<codeline lineno="35"><highlight class="normal"></highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight></codeline>
<codeline lineno="58" refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>void<sp/>(*<ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref>)(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>start,</highlight></codeline>
<codeline lineno="59"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>end,</highlight></codeline>
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<codeline lineno="61"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>en,</highlight></codeline>
<codeline lineno="62"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data);</highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight></codeline>
<codeline lineno="64"><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_mfe_window_callback)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>start,</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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>end,</highlight></codeline>
<codeline lineno="66"><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/><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/>*structure,</highlight></codeline>
<codeline lineno="67"><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/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>en,</highlight></codeline>
<codeline lineno="68"><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/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>*data),</highlight></codeline>
<codeline lineno="69"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mfe_window_f<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="70"><highlight class="normal"></highlight></codeline>
<codeline lineno="71"><highlight class="normal"></highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WITH_SVM</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>void<sp/>(*vrna_mfe_window_zscore_f)(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>start,</highlight></codeline>
<codeline lineno="74"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>end,</highlight></codeline>
<codeline lineno="75"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="76"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>en,</highlight></codeline>
<codeline lineno="77"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>zscore,</highlight></codeline>
<codeline lineno="78"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data);</highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><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_mfe_window_zscore_callback)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>start,</highlight></codeline>
<codeline lineno="81"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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/>end,</highlight></codeline>
<codeline lineno="82"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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/>*structure,</highlight></codeline>
<codeline lineno="83"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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">float</highlight><highlight class="normal"><sp/>en,</highlight></codeline>
<codeline lineno="84"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>zscore,</highlight></codeline>
<codeline lineno="85"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>*data),</highlight></codeline>
<codeline lineno="86"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mfe_window_zscore_f<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="87"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="88"><highlight class="normal"></highlight></codeline>
<codeline lineno="93"><highlight class="normal"></highlight></codeline>
<codeline lineno="119"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="120" refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="121"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*file);</highlight></codeline>
<codeline lineno="122"><highlight class="normal"></highlight></codeline>
<codeline lineno="123"><highlight class="normal"></highlight></codeline>
<codeline lineno="124"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="125" refid="group__mfe__window_1ga3ade396421340b0f2f989c7936fda3d9" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1ga3ade396421340b0f2f989c7936fda3d9" kindref="member">vrna_mfe_window_cb</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="126"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref><sp/><sp/><sp/><sp/>cb,</highlight></codeline>
<codeline lineno="127"><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">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="128"><highlight class="normal"></highlight></codeline>
<codeline lineno="129"><highlight class="normal"></highlight></codeline>
<codeline lineno="130"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WITH_SVM</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="156"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="157" refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="158"><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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>min_z,</highlight></codeline>
<codeline lineno="159"><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/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*file);</highlight></codeline>
<codeline lineno="160"><highlight class="normal"></highlight></codeline>
<codeline lineno="161"><highlight class="normal"></highlight></codeline>
<codeline lineno="162"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="163" refid="group__mfe__window_1ga5df4a67ce381ed329c289370b0c8adcb" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1ga5df4a67ce381ed329c289370b0c8adcb" kindref="member">vrna_mfe_window_zscore_cb</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*fc,</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/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>min_z,</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/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_mfe_window_zscore_f<sp/><sp/>cb,</highlight></codeline>
<codeline lineno="166"><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">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/>*data);</highlight></codeline>
<codeline lineno="167"><highlight class="normal"></highlight></codeline>
<codeline lineno="168"><highlight class="normal"></highlight></codeline>
<codeline lineno="169"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="170"><highlight class="normal"></highlight></codeline>
<codeline lineno="171"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="172"><highlight class="normal">vrna_backtrack_window(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="173"><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/></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/>*Lfold_filename,</highlight></codeline>
<codeline lineno="174"><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/></highlight><highlight class="keywordtype">long</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>file_pos,</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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**structure,</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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>mfe);</highlight></codeline>
<codeline lineno="177"><highlight class="normal"></highlight></codeline>
<codeline lineno="178"><highlight class="normal"></highlight></codeline>
<codeline lineno="179"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>basic<sp/>local<sp/>MFE<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="181"><highlight class="normal"></highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="207"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="208" refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1ga4918cce52bf69c1913cda503b2ac75d8" kindref="member">vrna_Lfold</ref>(</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="209"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>window_size,</highlight></codeline>
<codeline lineno="210"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/>*file);</highlight></codeline>
<codeline lineno="211"><highlight class="normal"></highlight></codeline>
<codeline lineno="212"><highlight class="normal"></highlight></codeline>
<codeline lineno="213"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="214" refid="group__mfe__window_1ga84dcc36fd88063e1692c2e1e68a5f689" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1ga84dcc36fd88063e1692c2e1e68a5f689" kindref="member">vrna_Lfold_cb</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/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="215"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>window_size,</highlight></codeline>
<codeline lineno="216"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref><sp/>cb,</highlight></codeline>
<codeline lineno="217"><highlight class="normal"><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/>*data);</highlight></codeline>
<codeline lineno="218"><highlight class="normal"></highlight></codeline>
<codeline lineno="219"><highlight class="normal"></highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WITH_SVM</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="245"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="246" refid="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1ga27fddda5fc63eb49c861e38845fc34b4" kindref="member">vrna_Lfoldz</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="247"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>window_size,</highlight></codeline>
<codeline lineno="248"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>min_z,</highlight></codeline>
<codeline lineno="249"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*file);</highlight></codeline>
<codeline lineno="250"><highlight class="normal"></highlight></codeline>
<codeline lineno="251"><highlight class="normal"></highlight></codeline>
<codeline lineno="252"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="253" refid="group__mfe__window_1gae982184f119219b616f3e5a8b3f558ec" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1gae982184f119219b616f3e5a8b3f558ec" kindref="member">vrna_Lfoldz_cb</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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="254"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>window_size,</highlight></codeline>
<codeline lineno="255"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>min_z,</highlight></codeline>
<codeline lineno="256"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_mfe_window_zscore_f<sp/>cb,</highlight></codeline>
<codeline lineno="257"><highlight class="normal"><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/><sp/><sp/><sp/>*data);</highlight></codeline>
<codeline lineno="258"><highlight class="normal"></highlight></codeline>
<codeline lineno="259"><highlight class="normal"></highlight></codeline>
<codeline lineno="260"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="261"><highlight class="normal"></highlight></codeline>
<codeline lineno="262"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="263" refid="group__mfe__window_1gaa43d3de352753529a4578cb02cd8bc52" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1gaa43d3de352753529a4578cb02cd8bc52" kindref="member">vrna_aliLfold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="264"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxdist,</highlight></codeline>
<codeline lineno="265"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*fp);</highlight></codeline>
<codeline lineno="266"><highlight class="normal"></highlight></codeline>
<codeline lineno="267"><highlight class="normal"></highlight></codeline>
<codeline lineno="268"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="269" refid="group__mfe__window_1gae9b2e312c316961d4a067f9b789cc9d7" refkind="member"><highlight class="normal"><ref refid="group__mfe__window_1gae9b2e312c316961d4a067f9b789cc9d7" kindref="member">vrna_aliLfold_cb</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/><sp/><sp/>**alignment,</highlight></codeline>
<codeline lineno="270"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxdist,</highlight></codeline>
<codeline lineno="271"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__mfe__window_1gaa97863c328b909d7da26d618e0c83fb9" kindref="member">vrna_mfe_window_f</ref><sp/><sp/>cb,</highlight></codeline>
<codeline lineno="272"><highlight class="normal"><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/>*data);</highlight></codeline>
<codeline lineno="273"><highlight class="normal"></highlight></codeline>
<codeline lineno="274"><highlight class="normal"></highlight></codeline>
<codeline lineno="275"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>simplified<sp/>local<sp/>MFE<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="277"><highlight class="normal"></highlight></codeline>
<codeline lineno="278"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>group<sp/>mfe_fold_window<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="280"><highlight class="normal"></highlight></codeline>
<codeline lineno="281"><highlight class="normal"></highlight></codeline>
<codeline lineno="282"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/mfe/local.h"/>
  </compounddef>
</doxygen>
