<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.15.0" xml:lang="en-US">
  <compounddef id="group__annotation__utils" kind="group">
    <compoundname>annotation_utils</compoundname>
    <title>Annotation</title>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__annotation__utils_1ga48b33b12fd6c1d2580d7666af5514c58" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char **</type>
        <definition>char ** vrna_annotate_covar_db</definition>
        <argsstring>(const char **alignment, const char *structure, vrna_md_t *md_p)</argsstring>
        <name>vrna_annotate_covar_db</name>
        <param>
          <type>const char **</type>
          <declname>alignment</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md_p</declname>
        </param>
        <briefdescription>
<para>Produce covariance annotation for an alignment given a secondary structure. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/utils.h" line="25" column="1" declfile="ViennaRNA/plotting/utils.h" declline="25" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__annotation__utils_1gac53c381303a1fd080d6694c502e9bd3b" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char **</type>
        <definition>char ** vrna_annotate_covar_db_extended</definition>
        <argsstring>(const char **alignment, const char *structure, vrna_md_t *md_p, unsigned int options)</argsstring>
        <name>vrna_annotate_covar_db_extended</name>
        <param>
          <type>const char **</type>
          <declname>alignment</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md_p</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/utils.h" line="31" column="1" declfile="ViennaRNA/plotting/utils.h" declline="31" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__annotation__utils_1gaff9209f0461e6d239e217232ce20f6f0" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>vrna_string_t *</type>
        <definition>vrna_string_t * vrna_annotate_covar_pt</definition>
        <argsstring>(const char **alignment, const short int *pt, vrna_md_t *md_p, double threshold, double min_sat)</argsstring>
        <name>vrna_annotate_covar_pt</name>
        <param>
          <type>const char **</type>
          <declname>alignment</declname>
        </param>
        <param>
          <type>const short int *</type>
          <declname>pt</declname>
        </param>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md_p</declname>
        </param>
        <param>
          <type>double</type>
          <declname>threshold</declname>
        </param>
        <param>
          <type>double</type>
          <declname>min_sat</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/utils.h" line="37" column="1" declfile="ViennaRNA/plotting/utils.h" declline="37" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__annotation__utils_1ga8874ed112d4a6f824f8f3269383cd835" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__data__structures_1gae4fc91141cc69c6d8eaf1332cb991ecc" kindref="member">vrna_cpair_t</ref> *</type>
        <definition>vrna_cpair_t * vrna_annotate_covar_pairs</definition>
        <argsstring>(const char **alignment, vrna_ep_t *pl, vrna_ep_t *mfel, double threshold, vrna_md_t *md)</argsstring>
        <name>vrna_annotate_covar_pairs</name>
        <param>
          <type>const char **</type>
          <declname>alignment</declname>
        </param>
        <param>
          <type><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref> *</type>
          <declname>pl</declname>
        </param>
        <param>
          <type><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref> *</type>
          <declname>mfel</declname>
        </param>
        <param>
          <type>double</type>
          <declname>threshold</declname>
        </param>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <briefdescription>
<para>Produce covariance annotation for an alignment given a set of base pairs. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/utils.h" line="48" column="1" declfile="ViennaRNA/plotting/utils.h" declline="48" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
</doxygen>
