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    <innerclass refid="structvrna__score__s" prot="public">vrna_score_s</innerclass>
    <sectiondef kind="typedef">
      <member refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kind="typedef"><name>vrna_score_t</name></member>
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    <sectiondef kind="func">
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    </sectiondef>
    <briefdescription>
<para>Various utility- and helper-functions for secondary structure parsing, converting, etc. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_STRUCTURES_BENCHMARK_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_STRUCTURES_BENCHMARK_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;stdio.h&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">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight></codeline>
<codeline lineno="23" refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" 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__score__s" kindref="compound">vrna_score_s</ref><sp/><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref>;</highlight></codeline>
<codeline lineno="24"><highlight class="normal"></highlight></codeline>
<codeline lineno="25"><highlight class="normal"></highlight></codeline>
<codeline lineno="30" refid="structvrna__score__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__score__s" kindref="compound">vrna_score_s</ref><sp/>{</highlight></codeline>
<codeline lineno="31" refid="structvrna__score__s_1acca9e4a5dec48b375e7f5ce15544a71c" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1acca9e4a5dec48b375e7f5ce15544a71c" kindref="member">TP</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="32" refid="structvrna__score__s_1a79de32b42cd83fdf7fc7e76080fe2d14" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1a79de32b42cd83fdf7fc7e76080fe2d14" kindref="member">TN</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="33" refid="structvrna__score__s_1ae1ddf8038685a27253fcb2c0a39fde95" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1ae1ddf8038685a27253fcb2c0a39fde95" kindref="member">FP</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="34" refid="structvrna__score__s_1af3080eb77276c1d30731a8da006ee75f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1af3080eb77276c1d30731a8da006ee75f" kindref="member">FN</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="35" refid="structvrna__score__s_1a22853369d464dc5609bc6b86e2249a6f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1a22853369d464dc5609bc6b86e2249a6f" kindref="member">TPR</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="36" refid="structvrna__score__s_1adc82125a14b5580c8345f8e6bd34287a" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1adc82125a14b5580c8345f8e6bd34287a" kindref="member">PPV</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="37" refid="structvrna__score__s_1ab36bfe221b4a49d3ba640b7a1cc350f6" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1ab36bfe221b4a49d3ba640b7a1cc350f6" kindref="member">FPR</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="38" refid="structvrna__score__s_1a6814036cae1cbe55295512da50ec7846" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1a6814036cae1cbe55295512da50ec7846" kindref="member">FOR</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="39" refid="structvrna__score__s_1ad72ca000cea39feea3ed15a459bc8c1c" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1ad72ca000cea39feea3ed15a459bc8c1c" kindref="member">TNR</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="40" refid="structvrna__score__s_1af99283172ab0399bdb9aea8337f9e66b" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1af99283172ab0399bdb9aea8337f9e66b" kindref="member">FDR</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="41" refid="structvrna__score__s_1abf98844dc1c08a0e5215a379dc451ca2" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1abf98844dc1c08a0e5215a379dc451ca2" kindref="member">FNR</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="42" refid="structvrna__score__s_1a0586733c9eef59fd115b31420de246bc" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1a0586733c9eef59fd115b31420de246bc" kindref="member">NPV</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="43" refid="structvrna__score__s_1a01624a1a3d533179fffb6d2663bdea9f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1a01624a1a3d533179fffb6d2663bdea9f" kindref="member">F1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="44" refid="structvrna__score__s_1aaf197445c80a8379332cc6466b77aa87" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__score__s_1aaf197445c80a8379332cc6466b77aa87" kindref="member">MCC</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="45"><highlight class="normal">};</highlight></codeline>
<codeline lineno="46"><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"></highlight></codeline>
<codeline lineno="57"><highlight class="normal"><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref></highlight></codeline>
<codeline lineno="58" refid="group__struct__utils__benchmark_1gab15a86fd8de27f90e64bae0b6b0ca68d" refkind="member"><highlight class="normal"><ref refid="group__struct__utils__benchmark_1gab15a86fd8de27f90e64bae0b6b0ca68d" kindref="member">vrna_score_from_confusion_matrix</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>TP,</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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>TN,</highlight></codeline>
<codeline lineno="60"><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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>FP,</highlight></codeline>
<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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>FN);</highlight></codeline>
<codeline lineno="62"><highlight class="normal"></highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight></codeline>
<codeline lineno="74"><highlight class="normal"><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref></highlight></codeline>
<codeline lineno="75" refid="group__struct__utils__benchmark_1gafd537fdc762e2f20afabf699e7e74bcf" refkind="member"><highlight class="normal"><ref refid="group__struct__utils__benchmark_1gafd537fdc762e2f20afabf699e7e74bcf" kindref="member">vrna_compare_structure_pt</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*pt_gold,</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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*pt_other,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>fuzzy);</highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight></codeline>
<codeline lineno="89"><highlight class="normal"><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref></highlight></codeline>
<codeline lineno="90" refid="group__struct__utils__benchmark_1ga12495e49a4214b0bdab3fa37f542a9db" refkind="member"><highlight class="normal"><ref refid="group__struct__utils__benchmark_1ga12495e49a4214b0bdab3fa37f542a9db" kindref="member">vrna_compare_structure</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>*structure_gold,</highlight></codeline>
<codeline lineno="91"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>*structure_other,</highlight></codeline>
<codeline lineno="92"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>fuzzy,</highlight></codeline>
<codeline lineno="93"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>options);</highlight></codeline>
<codeline lineno="94"><highlight class="normal"></highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight></codeline>
<codeline lineno="96"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>benchmark<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="98"><highlight class="normal"></highlight></codeline>
<codeline lineno="99"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/structures/benchmark.h"/>
  </compounddef>
</doxygen>
