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    <sectiondef kind="define">
      <member refid="group__command__files_1gac54dec838d7b6bebd5df85f71702d324" kind="define"><name>VRNA_CMD_PARSE_HC</name></member>
      <member refid="group__command__files_1ga8cad3c1f83e6f149829c49a186a83e21" kind="define"><name>VRNA_CMD_PARSE_SC</name></member>
      <member refid="group__command__files_1ga6c6409780698826b04ebfed9151d7649" kind="define"><name>VRNA_CMD_PARSE_UD</name></member>
      <member refid="group__command__files_1gaf5e20210173cdb83bf70256a454f284b" kind="define"><name>VRNA_CMD_PARSE_SD</name></member>
      <member refid="group__command__files_1ga0a6c88e21e366dca14958d69cd024008" kind="define"><name>VRNA_CMD_PARSE_DEFAULTS</name></member>
      <member refid="group__command__files_1ga8d6c5d6d2936464a11f542b843bd1610" kind="define"><name>VRNA_CMD_PARSE_SILENT</name></member>
    </sectiondef>
    <sectiondef kind="typedef">
      <member refid="group__command__files_1gaf31afe4c5f8e4bf44a670ab4c3dcd916" kind="typedef"><name>vrna_cmd_t</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__command__files_1gae5f56400ed43683338f7bf1c1102655a" kind="function"><name>vrna_file_commands_read</name></member>
      <member refid="group__command__files_1ga3118909bd91ecaeb4663b2e3bc2d5edd" kind="function"><name>vrna_file_commands_apply</name></member>
      <member refid="group__command__files_1ga9232cb0efe364086a8a5ee1449e537ba" kind="function"><name>vrna_commands_apply</name></member>
      <member refid="group__command__files_1ga3dc372dcbb43d2c4c91b5ef79b460428" kind="function"><name>vrna_commands_free</name></member>
    </sectiondef>
    <briefdescription>
<para>Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation. </para>
    </briefdescription>
    <detaileddescription>
<para>, , </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_IO_COMMANDS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_IO_COMMANDS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight></codeline>
<codeline lineno="18" refid="group__command__files_1gaf31afe4c5f8e4bf44a670ab4c3dcd916" 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">vrna_command_s<sp/>*<ref refid="group__command__files_1gaf31afe4c5f8e4bf44a670ab4c3dcd916" kindref="member">vrna_cmd_t</ref>;</highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><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="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="28" refid="group__command__files_1gac54dec838d7b6bebd5df85f71702d324" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CMD_PARSE_HC<sp/><sp/><sp/><sp/><sp/><sp/>1U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="34" refid="group__command__files_1ga8cad3c1f83e6f149829c49a186a83e21" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CMD_PARSE_SC<sp/><sp/><sp/><sp/><sp/><sp/>2U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="40" refid="group__command__files_1ga6c6409780698826b04ebfed9151d7649" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CMD_PARSE_UD<sp/><sp/><sp/><sp/><sp/><sp/>4U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="46" refid="group__command__files_1gaf5e20210173cdb83bf70256a454f284b" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CMD_PARSE_SD<sp/><sp/><sp/><sp/><sp/><sp/>8U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="52" refid="group__command__files_1ga0a6c88e21e366dca14958d69cd024008" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CMD_PARSE_DEFAULTS<sp/>(VRNA_CMD_PARSE_HC<sp/>\</highlight></codeline>
<codeline lineno="53"><highlight class="preprocessor"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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_CMD_PARSE_SC<sp/>\</highlight></codeline>
<codeline lineno="54"><highlight class="preprocessor"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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_CMD_PARSE_UD<sp/>\</highlight></codeline>
<codeline lineno="55"><highlight class="preprocessor"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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_CMD_PARSE_SD<sp/>\</highlight></codeline>
<codeline lineno="56"><highlight class="preprocessor"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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="normal"></highlight></codeline>
<codeline lineno="57"><highlight class="normal"></highlight></codeline>
<codeline lineno="58"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CMD_PARSE_SILENT<sp/><sp/><sp/>16U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="59"><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"><ref refid="group__command__files_1gaf31afe4c5f8e4bf44a670ab4c3dcd916" kindref="member">vrna_cmd_t</ref></highlight></codeline>
<codeline lineno="74" refid="group__command__files_1gae5f56400ed43683338f7bf1c1102655a" refkind="member"><highlight class="normal"><ref refid="group__command__files_1gae5f56400ed43683338f7bf1c1102655a" kindref="member">vrna_file_commands_read</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*filename,</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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>options);</highlight></codeline>
<codeline lineno="76"><highlight class="normal"></highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight></codeline>
<codeline lineno="91"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="92" refid="group__command__files_1ga3118909bd91ecaeb4663b2e3bc2d5edd" refkind="member"><highlight class="normal"><ref refid="group__command__files_1ga3118909bd91ecaeb4663b2e3bc2d5edd" kindref="member">vrna_file_commands_apply</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</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/><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/>*filename,</highlight></codeline>
<codeline lineno="94"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight></codeline>
<codeline lineno="96"><highlight class="normal"></highlight></codeline>
<codeline lineno="105"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="106" refid="group__command__files_1ga9232cb0efe364086a8a5ee1449e537ba" refkind="member"><highlight class="normal"><ref refid="group__command__files_1ga9232cb0efe364086a8a5ee1449e537ba" kindref="member">vrna_commands_apply</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="107"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__command__files_1gaf31afe4c5f8e4bf44a670ab4c3dcd916" kindref="member">vrna_cmd_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>commands,</highlight></codeline>
<codeline lineno="108"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="109"><highlight class="normal"></highlight></codeline>
<codeline lineno="110"><highlight class="normal"></highlight></codeline>
<codeline lineno="117"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="118" refid="group__command__files_1ga3dc372dcbb43d2c4c91b5ef79b460428" refkind="member"><highlight class="normal"><ref refid="group__command__files_1ga3dc372dcbb43d2c4c91b5ef79b460428" kindref="member">vrna_commands_free</ref>(<ref refid="group__command__files_1gaf31afe4c5f8e4bf44a670ab4c3dcd916" kindref="member">vrna_cmd_t</ref><sp/>commands);</highlight></codeline>
<codeline lineno="119"><highlight class="normal"></highlight></codeline>
<codeline lineno="120"><highlight class="normal"></highlight></codeline>
<codeline lineno="124"><highlight class="normal"></highlight></codeline>
<codeline lineno="125"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/io/commands.h"/>
  </compounddef>
</doxygen>
