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<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.15.0" xml:lang="en-US">
  <compounddef id="plots" kind="page">
    <compoundname>plots</compoundname>
    <title>Plotting</title>
    <tableofcontents>
      <tocsect>
        <name>Producing secondary structure graphs</name>
        <docs><para>Producing secondary structure graphs </para>
</docs>
        <reference>plots_1utils_ss</reference>
      </tocsect>
      <tocsect>
        <name>Producing (colored) dot plots for base pair probabilities</name>
        <docs><para>Producing (colored) dot plots for base pair probabilities </para>
</docs>
        <reference>plots_1utils_dot</reference>
      </tocsect>
      <tocsect>
        <name>Producing (colored) alignments</name>
        <docs><para>Producing (colored) alignments </para>
</docs>
        <reference>plots_1utils_aln</reference>
      </tocsect>
    </tableofcontents>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
<para>Create Plots of Secondary Structures, Feature Motifs, and Sequence Alignments</para>
<sect1 id="plots_1utils_ss">
<title>Producing secondary structure graphs</title><para><verbatim>int PS_rna_plot ( char *string,
                  char *structure,
                  char *file)
</verbatim>   Produce a secondary structure graph in PostScript and write it to &apos;filename&apos;.   </para>
<para><verbatim>int PS_rna_plot_a (
            char *string,
            char *structure,
            char *file,
            char *pre,
            char *post)
</verbatim>   Produce a secondary structure graph in PostScript including additional annotation macros and write it to &apos;filename&apos;.   </para>
<para><verbatim>int gmlRNA (char *string,
            char *structure,
            char *ssfile,
            char option)
</verbatim>   Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.   </para>
<para><verbatim>int ssv_rna_plot (char *string,
                  char *structure,
                  char *ssfile)
</verbatim>   Produce a secondary structure graph in SStructView format.   </para>
<para><verbatim>int svg_rna_plot (char *string,
                  char *structure,
                  char *ssfile)
</verbatim>   Produce a secondary structure plot in SVG format and write it to a file.   </para>
<para><verbatim>int xrna_plot ( char *string,
                char *structure,
                char *ssfile)
</verbatim>   Produce a secondary structure plot for further editing in XRNA.   </para>
<para><verbatim>int rna_plot_type
</verbatim>   Switch for changing the secondary structure layout algorithm.   </para>
<para>Two low-level functions provide direct access to the graph lauyouting algorithms:</para>
<para><verbatim>int simple_xy_coordinates ( short *pair_table,
                            float *X,
                            float *Y)
</verbatim>   Calculate nucleotide coordinates for secondary structure plot the <emphasis>Simple way</emphasis>.   </para>
<para><verbatim>int naview_xy_coordinates ( short *pair_table,
                            float *X,
                            float *Y)
</verbatim></para>
<para><simplesect kind="see"><para><ref refid="PS__dot_8h" kindref="compound">PS_dot.h</ref> and <ref refid="naview_8h" kindref="compound">naview.h</ref> for more detailed descriptions.</para>
</simplesect>
<htmlonly> 
&lt;hr&gt;
&lt;a href=&quot;#toc&quot;&gt;Table of Contents&lt;/a&gt;
&lt;hr&gt;
</htmlonly></para>
</sect1>
<sect1 id="plots_1utils_dot">
<title>Producing (colored) dot plots for base pair probabilities</title><para><verbatim>int PS_color_dot_plot ( char *string,
                        cpair *pi,
                        char *filename)
</verbatim>  </para>
<para><verbatim>int PS_color_dot_plot_turn (char *seq,
                            cpair *pi,
                            char *filename,
                            int winSize)
</verbatim>  </para>
<para><verbatim>int PS_dot_plot_list (char *seq,
                      char *filename,
                      plist *pl,
                      plist *mf,
                      char *comment)
</verbatim>   Produce a postscript dot-plot from two pair lists.   </para>
<para><verbatim>int PS_dot_plot_turn (char *seq,
                      struct plist *pl,
                      char *filename,
                      int winSize)
</verbatim>  </para>
<para><simplesect kind="see"><para><ref refid="PS__dot_8h" kindref="compound">PS_dot.h</ref> for more detailed descriptions.</para>
</simplesect>
</para>
</sect1>
<sect1 id="plots_1utils_aln">
<title>Producing (colored) alignments</title><para><verbatim>int PS_color_aln (
            const char *structure,
            const char *filename,
            const char *seqs[],
            const char *names[])
</verbatim>   Produce PostScript sequence alignment color-annotated by consensus structure.    </para>
</sect1>
    </detaileddescription>
    <location file="doc/doxygen/refman.include/plotting.dox"/>
  </compounddef>
</doxygen>
