<?xml version='1.0' encoding='UTF-8' standalone='no'?>
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  <compounddef id="io_2file__formats__msa_8h" kind="file" language="C++">
    <compoundname>file_formats_msa.h</compoundname>
    <includes local="no">stdio.h</includes>
    <includedby refid="file__formats_8h" local="no">ViennaRNA/file_formats.h</includedby>
    <includedby refid="file__formats__msa_8h" local="no">ViennaRNA/file_formats_msa.h</includedby>
    <incdepgraph>
      <node id="1">
        <label>ViennaRNA/io/file_formats_msa.h</label>
        <link refid="io_2file__formats__msa_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
      </node>
      <node id="2">
        <label>stdio.h</label>
      </node>
    </incdepgraph>
    <invincdepgraph>
      <node id="2">
        <label>ViennaRNA/file_formats.h</label>
        <link refid="file__formats_8h"/>
      </node>
      <node id="3">
        <label>ViennaRNA/file_formats_msa.h</label>
        <link refid="file__formats__msa_8h"/>
      </node>
      <node id="1">
        <label>ViennaRNA/io/file_formats_msa.h</label>
        <link refid="io_2file__formats__msa_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="3" relation="include">
        </childnode>
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    </invincdepgraph>
    <sectiondef kind="define">
      <member refid="group__file__formats__msa_1ga79a23de2c7249f2cccd762e475c81859" kind="define"><name>VRNA_FILE_FORMAT_MSA_CLUSTAL</name></member>
      <member refid="group__file__formats__msa_1ga62be992445cd8ab2ad7a8fded944338b" kind="define"><name>VRNA_FILE_FORMAT_MSA_STOCKHOLM</name></member>
      <member refid="group__file__formats__msa_1gacf6274a2c825f34e4131404665b00604" kind="define"><name>VRNA_FILE_FORMAT_MSA_FASTA</name></member>
      <member refid="group__file__formats__msa_1gab3186d774c01570d2a47d0308eec4927" kind="define"><name>VRNA_FILE_FORMAT_MSA_MAF</name></member>
      <member refid="group__file__formats__msa_1ga494488a771aa0c602fb4cf445be34d47" kind="define"><name>VRNA_FILE_FORMAT_MSA_MIS</name></member>
      <member refid="group__file__formats__msa_1ga4acc255373831856a8417b68de8a94c0" kind="define"><name>VRNA_FILE_FORMAT_MSA_DEFAULT</name></member>
      <member refid="group__file__formats__msa_1ga229fb3778ecabea4782902b69fa48fd1" kind="define"><name>VRNA_FILE_FORMAT_MSA_NOCHECK</name></member>
      <member refid="group__file__formats__msa_1gabdc948f547e550125de3e7c65878400c" kind="define"><name>VRNA_FILE_FORMAT_MSA_UNKNOWN</name></member>
      <member refid="group__file__formats__msa_1ga1577ea0f497d9c501549c863a4f2c089" kind="define"><name>VRNA_FILE_FORMAT_MSA_APPEND</name></member>
      <member refid="group__file__formats__msa_1ga73aa3701a22c5acfcb2e8927287a0554" kind="define"><name>VRNA_FILE_FORMAT_MSA_QUIET</name></member>
      <member refid="group__file__formats__msa_1gad98ca08968d19f221f29d2a1faf26887" kind="define"><name>VRNA_FILE_FORMAT_MSA_SILENT</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__file__formats__msa_1gad02d5d12bda54611c915a1019323b7be" kind="function"><name>vrna_file_msa_read</name></member>
      <member refid="group__file__formats__msa_1gad4203a438622b2df7bc2f16578d54799" kind="function"><name>vrna_file_msa_read_record</name></member>
      <member refid="group__file__formats__msa_1gade4fa8136ebb2d0f7eb3f8b59a8658e3" kind="function"><name>vrna_file_msa_detect_format</name></member>
      <member refid="group__file__formats__msa_1gaccca55b71d34def88e18ed9a51ccb2bf" kind="function"><name>vrna_file_msa_write</name></member>
    </sectiondef>
    <briefdescription>
<para>Functions dealing with file formats for Multiple Sequence Alignments (MSA). </para>
    </briefdescription>
    <detaileddescription>
<para>, , </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_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="16"><highlight class="normal"></highlight></codeline>
<codeline lineno="22" refid="group__file__formats__msa_1ga79a23de2c7249f2cccd762e475c81859" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_CLUSTAL<sp/><sp/><sp/><sp/><sp/><sp/>1U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight></codeline>
<codeline lineno="29" refid="group__file__formats__msa_1ga62be992445cd8ab2ad7a8fded944338b" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_STOCKHOLM<sp/><sp/><sp/><sp/>2U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight></codeline>
<codeline lineno="36" refid="group__file__formats__msa_1gacf6274a2c825f34e4131404665b00604" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_FASTA<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>4U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight></codeline>
<codeline lineno="43" refid="group__file__formats__msa_1gab3186d774c01570d2a47d0308eec4927" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_MAF<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>8U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="44"><highlight class="normal"></highlight></codeline>
<codeline lineno="53" refid="group__file__formats__msa_1ga494488a771aa0c602fb4cf445be34d47" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_MIS<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>16U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"></highlight></codeline>
<codeline lineno="60" refid="group__file__formats__msa_1ga4acc255373831856a8417b68de8a94c0" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_DEFAULT<sp/><sp/><sp/><sp/><sp/><sp/>(<sp/>\</highlight></codeline>
<codeline lineno="61"><highlight class="preprocessor"><sp/><sp/><sp/><sp/>VRNA_FILE_FORMAT_MSA_CLUSTAL<sp/>\</highlight></codeline>
<codeline lineno="62"><highlight class="preprocessor"><sp/><sp/><sp/><sp/>|<sp/>VRNA_FILE_FORMAT_MSA_STOCKHOLM<sp/>\</highlight></codeline>
<codeline lineno="63"><highlight class="preprocessor"><sp/><sp/><sp/><sp/>|<sp/>VRNA_FILE_FORMAT_MSA_FASTA<sp/>\</highlight></codeline>
<codeline lineno="64"><highlight class="preprocessor"><sp/><sp/><sp/><sp/>|<sp/>VRNA_FILE_FORMAT_MSA_MAF<sp/>\</highlight></codeline>
<codeline lineno="65"><highlight class="preprocessor"><sp/><sp/><sp/><sp/>)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="66"><highlight class="normal"></highlight></codeline>
<codeline lineno="72" refid="group__file__formats__msa_1ga229fb3778ecabea4782902b69fa48fd1" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_NOCHECK<sp/><sp/><sp/><sp/><sp/><sp/>4096U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"></highlight></codeline>
<codeline lineno="79" refid="group__file__formats__msa_1gabdc948f547e550125de3e7c65878400c" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_UNKNOWN<sp/><sp/><sp/><sp/><sp/><sp/>8192U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight></codeline>
<codeline lineno="86" refid="group__file__formats__msa_1ga1577ea0f497d9c501549c863a4f2c089" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_APPEND<sp/><sp/><sp/><sp/><sp/><sp/><sp/>16384U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="87"><highlight class="normal"></highlight></codeline>
<codeline lineno="93" refid="group__file__formats__msa_1ga73aa3701a22c5acfcb2e8927287a0554" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_QUIET<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>32768U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="94"><highlight class="normal"></highlight></codeline>
<codeline lineno="100" refid="group__file__formats__msa_1gad98ca08968d19f221f29d2a1faf26887" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_FILE_FORMAT_MSA_SILENT<sp/><sp/><sp/><sp/><sp/><sp/><sp/>65536U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="101"><highlight class="normal"></highlight></codeline>
<codeline lineno="153"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="154" refid="group__file__formats__msa_1gad02d5d12bda54611c915a1019323b7be" refkind="member"><highlight class="normal"><ref refid="group__file__formats__msa_1gad02d5d12bda54611c915a1019323b7be" kindref="member">vrna_file_msa_read</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>*filename,</highlight></codeline>
<codeline lineno="155"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***names,</highlight></codeline>
<codeline lineno="156"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***aln,</highlight></codeline>
<codeline lineno="157"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**</highlight><highlight class="keywordtype">id</highlight><highlight class="normal">,</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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**structure,</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/></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="160"><highlight class="normal"></highlight></codeline>
<codeline lineno="161"><highlight class="normal"></highlight></codeline>
<codeline lineno="217"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="218" refid="group__file__formats__msa_1gad4203a438622b2df7bc2f16578d54799" refkind="member"><highlight class="normal"><ref refid="group__file__formats__msa_1gad4203a438622b2df7bc2f16578d54799" kindref="member">vrna_file_msa_read_record</ref>(FILE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*fp,</highlight></codeline>
<codeline lineno="219"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***names,</highlight></codeline>
<codeline lineno="220"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***aln,</highlight></codeline>
<codeline lineno="221"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**</highlight><highlight class="keywordtype">id</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="222"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**structure,</highlight></codeline>
<codeline lineno="223"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>options);</highlight></codeline>
<codeline lineno="224"><highlight class="normal"></highlight></codeline>
<codeline lineno="225"><highlight class="normal"></highlight></codeline>
<codeline lineno="251"><highlight class="normal"></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="252" refid="group__file__formats__msa_1gade4fa8136ebb2d0f7eb3f8b59a8658e3" refkind="member"><highlight class="normal"><ref refid="group__file__formats__msa_1gade4fa8136ebb2d0f7eb3f8b59a8658e3" kindref="member">vrna_file_msa_detect_format</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="253"><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/></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="254"><highlight class="normal"></highlight></codeline>
<codeline lineno="255"><highlight class="normal"></highlight></codeline>
<codeline lineno="273"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="274" refid="group__file__formats__msa_1gaccca55b71d34def88e18ed9a51ccb2bf" refkind="member"><highlight class="normal"><ref refid="group__file__formats__msa_1gaccca55b71d34def88e18ed9a51ccb2bf" kindref="member">vrna_file_msa_write</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="275"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>**names,</highlight></codeline>
<codeline lineno="276"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>**aln,</highlight></codeline>
<codeline lineno="277"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*</highlight><highlight class="keywordtype">id</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="278"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="279"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*source,</highlight></codeline>
<codeline lineno="280"><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/>options);</highlight></codeline>
<codeline lineno="281"><highlight class="normal"></highlight></codeline>
<codeline lineno="282"><highlight class="normal"></highlight></codeline>
<codeline lineno="286"><highlight class="normal"></highlight></codeline>
<codeline lineno="287"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/io/file_formats_msa.h"/>
  </compounddef>
</doxygen>
