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  <compounddef id="group__alignment__plots" kind="group">
    <compoundname>alignment_plots</compoundname>
    <title>Alignment Plots</title>
    <innerclass refid="structvrna__aln__opt__t" prot="public">vrna_aln_opt_t</innerclass>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__alignment__plots_1ga3bb7409f5b73c2273f9f76cf8b754034" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_file_PS_aln</definition>
        <argsstring>(const char *filename, const char **seqs, const char **names, const char *structure, unsigned int columns)</argsstring>
        <name>vrna_file_PS_aln</name>
        <param>
          <type>const char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>seqs</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>names</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>columns</declname>
        </param>
        <briefdescription>
<para>Create an annotated PostScript alignment plot. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__alignment__plots_1ga2b132dddeb2044e52dc39cf0ad8afaee" kindref="member">vrna_file_PS_aln_slice()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>filename</parametername>
</parameternamelist>
<parameterdescription>
<para>The output file name </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>seqs</parametername>
</parameternamelist>
<parameterdescription>
<para>The aligned sequences </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>names</parametername>
</parameternamelist>
<parameterdescription>
<para>The names of the sequences </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>structure</parametername>
</parameternamelist>
<parameterdescription>
<para>The consensus structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>columns</parametername>
</parameternamelist>
<parameterdescription>
<para>The number of columns before the alignment is wrapped as a new block (a value of 0 indicates no wrapping)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<xrefsect id="wrappers_1_wrappers000163"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput>file_PS_aln()</computeroutput> with three additional parameters <computeroutput>start</computeroutput>, <computeroutput>end</computeroutput>, and <computeroutput>offset</computeroutput> before the <computeroutput>columns</computeroutput> argument. Thus, it resembles the <computeroutput><ref refid="group__alignment__plots_1ga2b132dddeb2044e52dc39cf0ad8afaee" kindref="member">vrna_file_PS_aln_slice()</ref></computeroutput> function. The last four arguments may be omitted, indicating the default of <computeroutput>start</computeroutput> = <emphasis>0</emphasis>, <computeroutput>end</computeroutput> = <emphasis>0</emphasis>, <computeroutput>offset</computeroutput> = <emphasis>0</emphasis>, and <computeroutput>columns</computeroutput> = <emphasis>60</emphasis>. See, e.g.  <verbatim>embed:rst:inline :py:func:`RNA.file_PS_aln()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/alignments.h" line="48" column="1" declfile="ViennaRNA/plotting/alignments.h" declline="48" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__alignment__plots_1ga2b132dddeb2044e52dc39cf0ad8afaee" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_file_PS_aln_slice</definition>
        <argsstring>(const char *filename, const char **seqs, const char **names, const char *structure, unsigned int start, unsigned int end, int offset, unsigned int columns)</argsstring>
        <name>vrna_file_PS_aln_slice</name>
        <param>
          <type>const char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>seqs</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>names</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>start</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>end</declname>
        </param>
        <param>
          <type>int</type>
          <declname>offset</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>columns</declname>
        </param>
        <briefdescription>
<para>Create an annotated PostScript alignment plot. </para>
        </briefdescription>
        <detaileddescription>
<para>Similar to <ref refid="group__alignment__plots_1ga3bb7409f5b73c2273f9f76cf8b754034" kindref="member">vrna_file_PS_aln()</ref> but allows the user to print a particular slice of the alignment by specifying a <computeroutput>start</computeroutput> and <computeroutput>end</computeroutput> position. The additional <computeroutput>offset</computeroutput> parameter allows for adjusting the alignment position ruler value.</para>
<para><simplesect kind="see"><para><ref refid="group__alignment__plots_1ga2b132dddeb2044e52dc39cf0ad8afaee" kindref="member">vrna_file_PS_aln_slice()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>filename</parametername>
</parameternamelist>
<parameterdescription>
<para>The output file name </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>seqs</parametername>
</parameternamelist>
<parameterdescription>
<para>The aligned sequences </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>names</parametername>
</parameternamelist>
<parameterdescription>
<para>The names of the sequences </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>structure</parametername>
</parameternamelist>
<parameterdescription>
<para>The consensus structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>start</parametername>
</parameternamelist>
<parameterdescription>
<para>The start of the alignment slice (a value of 0 indicates the first position of the alignment, i.e. no slicing at 5&apos; side) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>end</parametername>
</parameternamelist>
<parameterdescription>
<para>The end of the alignment slice (a value of 0 indicates the last position of the alignment, i.e. no slicing at 3&apos; side) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>offset</parametername>
</parameternamelist>
<parameterdescription>
<para>The alignment coordinate offset for the position ruler. </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>columns</parametername>
</parameternamelist>
<parameterdescription>
<para>The number of columns before the alignment is wrapped as a new block (a value of 0 indicates no wrapping)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<xrefsect id="wrappers_1_wrappers000164"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as overloaded function <computeroutput>file_PS_aln()</computeroutput> where the last four parameter may be omitted, indicating <computeroutput>start</computeroutput> = <emphasis>0</emphasis>, <computeroutput>end</computeroutput> = <emphasis>0</emphasis>, <computeroutput>offset</computeroutput> = <emphasis>0</emphasis>, and <computeroutput>columns</computeroutput> = <emphasis>60</emphasis>. See, e.g.  <verbatim>embed:rst:inline :py:func:`RNA.file_PS_aln()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/alignments.h" line="74" column="1" declfile="ViennaRNA/plotting/alignments.h" declline="74" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__alignment__plots_1gacad3969b2155a95809e1d492f8a95385" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_file_PS_aln_opt</definition>
        <argsstring>(const char *filename, const char **seqs, const char **names, const char *structure, vrna_aln_opt_t options)</argsstring>
        <name>vrna_file_PS_aln_opt</name>
        <param>
          <type>const char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>seqs</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>names</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type><ref refid="structvrna__aln__opt__t" kindref="compound">vrna_aln_opt_t</ref></type>
          <declname>options</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/alignments.h" line="84" column="1" declfile="ViennaRNA/plotting/alignments.h" declline="84" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
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