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  <compounddef id="group__struct__utils__benchmark" kind="group">
    <compoundname>struct_utils_benchmark</compoundname>
    <title>Benchmark measures for Secondary Structure Predictions</title>
    <innerclass refid="structvrna__score__s" prot="public">vrna_score_s</innerclass>
    <sectiondef kind="typedef">
      <memberdef kind="typedef" id="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" prot="public" static="no">
        <type>struct <ref refid="structvrna__score__s" kindref="compound">vrna_score_s</ref></type>
        <definition>typedef struct vrna_score_s vrna_score_t</definition>
        <argsstring></argsstring>
        <name>vrna_score_t</name>
        <briefdescription>
<para>Typename for the score data structure <ref refid="structvrna__score__s" kindref="compound">vrna_score_s</ref>. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/benchmark.h" line="23" column="27" bodyfile="ViennaRNA/structures/benchmark.h" bodystart="23" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__struct__utils__benchmark_1gab15a86fd8de27f90e64bae0b6b0ca68d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref></type>
        <definition>vrna_score_t vrna_score_from_confusion_matrix</definition>
        <argsstring>(double TP, double TN, double FP, double FN)</argsstring>
        <name>vrna_score_from_confusion_matrix</name>
        <param>
          <type>double</type>
          <declname>TP</declname>
        </param>
        <param>
          <type>double</type>
          <declname>TN</declname>
        </param>
        <param>
          <type>double</type>
          <declname>FP</declname>
        </param>
        <param>
          <type>double</type>
          <declname>FN</declname>
        </param>
        <briefdescription>
<para>Construct score data structure from given confusion matrix. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>TP</parametername>
</parameternamelist>
<parameterdescription>
<para>True positive count </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>TN</parametername>
</parameternamelist>
<parameterdescription>
<para>True negative count </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>FP</parametername>
</parameternamelist>
<parameterdescription>
<para>False positive count </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>FN</parametername>
</parameternamelist>
<parameterdescription>
<para>False negative count </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>The score data structure to write </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/benchmark.h" line="58" column="1" declfile="ViennaRNA/structures/benchmark.h" declline="58" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__struct__utils__benchmark_1gafd537fdc762e2f20afabf699e7e74bcf" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref></type>
        <definition>vrna_score_t vrna_compare_structure_pt</definition>
        <argsstring>(const short *pt_gold, const short *pt_other, int fuzzy)</argsstring>
        <name>vrna_compare_structure_pt</name>
        <param>
          <type>const short *</type>
          <declname>pt_gold</declname>
        </param>
        <param>
          <type>const short *</type>
          <declname>pt_other</declname>
        </param>
        <param>
          <type>int</type>
          <declname>fuzzy</declname>
        </param>
        <briefdescription>
<para>Return statistic of two structure (in pair table) comparaison. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__benchmark_1ga12495e49a4214b0bdab3fa37f542a9db" kindref="member">vrna_compare_structure</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>pt_gold</parametername>
</parameternamelist>
<parameterdescription>
<para>Gold standard structure in pair table </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pt_other</parametername>
</parameternamelist>
<parameterdescription>
<para>Structure to compare in pair table </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>fuzzy</parametername>
</parameternamelist>
<parameterdescription>
<para>Allows for base pair slippage. Hence, for any base pair (i,j) in the gold standard, a base pair (p, q) in the second structure is considered a true positive, if i - fuzzy &lt;= p &lt;= i + fuzzy, and j - fuzzy &lt;= q &lt;= j + fuzzy. </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>The <ref refid="structvrna__score__s" kindref="compound">vrna_score_s</ref> data structure </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/benchmark.h" line="75" column="1" declfile="ViennaRNA/structures/benchmark.h" declline="75" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__struct__utils__benchmark_1ga12495e49a4214b0bdab3fa37f542a9db" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__struct__utils__benchmark_1ga1fb1540256fbcd9543c602b111c3f512" kindref="member">vrna_score_t</ref></type>
        <definition>vrna_score_t vrna_compare_structure</definition>
        <argsstring>(const char *structure_gold, const char *structure_other, int fuzzy, unsigned int options)</argsstring>
        <name>vrna_compare_structure</name>
        <param>
          <type>const char *</type>
          <declname>structure_gold</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure_other</declname>
        </param>
        <param>
          <type>int</type>
          <declname>fuzzy</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
<para>Return statistic of two structure (in dbn) comparaison. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>pt_gold</parametername>
</parameternamelist>
<parameterdescription>
<para>Gold standard structure </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pt_other</parametername>
</parameternamelist>
<parameterdescription>
<para>Structure to compare </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>fuzzy</parametername>
</parameternamelist>
<parameterdescription>
<para>Allows for base pair slippage. Hence, for any base pair (i,j) in the gold standard, a base pair (p, q) in the second structure is considered a true positive, if i - fuzzy &lt;= p &lt;= i + fuzzy, and j - fuzzy &lt;= q &lt;= j + fuzzy. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>options</parametername>
</parameternamelist>
<parameterdescription>
<para>A bitmask to specify which brackets are recognized during conversion to pair table </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>The <ref refid="structvrna__score__s" kindref="compound">vrna_score_s</ref> data structure </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/benchmark.h" line="90" column="1" declfile="ViennaRNA/structures/benchmark.h" declline="90" declcolumn="1"/>
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