<?xml version='1.0' encoding='UTF-8' standalone='no'?>
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  <compounddef id="group__plotting__utils__deprecated" kind="group">
    <compoundname>plotting_utils_deprecated</compoundname>
    <title>Deprecated Interface for Plotting Utilities</title>
    <innerclass refid="structCOORDINATE" prot="public">COORDINATE</innerclass>
    <sectiondef kind="var">
      <memberdef kind="variable" id="group__plotting__utils__deprecated_1ga5964c4581431b098b80027d6e14dcdd4" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int rna_plot_type</definition>
        <argsstring></argsstring>
        <name>rna_plot_type</name>
        <briefdescription>
<para>Switch for changing the secondary structure layout algorithm. </para>
        </briefdescription>
        <detaileddescription>
<para>Current possibility are 0 for a simple radial drawing or 1 for the modified radial drawing taken from the <emphasis>naview</emphasis> program of  <verbatim>embed:rst:inline  :cite:t:`bruccoleri:1988` </verbatim>.</para>
<para><simplesect kind="note"><para>To provide thread safety please do not rely on this global variable in future implementations but pass a plot type flag directly to the function that decides which layout algorithm it may use!</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__plot__layout__utils_1gae6d17b9f0a53cf5205a9181e0f8422e9" kindref="member">VRNA_PLOT_TYPE_SIMPLE</ref>, <ref refid="group__plot__layout__utils_1ga94d4c863ecac2f220f76658afb92f964" kindref="member">VRNA_PLOT_TYPE_NAVIEW</ref>, <ref refid="group__plot__layout__utils_1ga8c9eac631348da92136c8363ecdd9fb9" kindref="member">VRNA_PLOT_TYPE_CIRCULAR</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/layouts.h" line="480" column="12" declfile="ViennaRNA/plotting/layouts.h" declline="480" declcolumn="12"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__plotting__utils__deprecated_1ga821802c3685e37e15182341f6217470d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int PS_color_aln</definition>
        <argsstring>(const char *structure, const char *filename, const char *seqs[], const char *names[])</argsstring>
        <name>PS_color_aln</name>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>seqs</declname>
          <array>[]</array>
        </param>
        <param>
          <type>const char *</type>
          <declname>names</declname>
          <array>[]</array>
        </param>
        <briefdescription>
<para>Produce PostScript sequence alignment color-annotated by consensus structure. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000199"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use <ref refid="group__alignment__plots_1ga3bb7409f5b73c2273f9f76cf8b754034" kindref="member">vrna_file_PS_aln()</ref> instead!</para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/alignments.h" line="107" column="6" declfile="ViennaRNA/plotting/alignments.h" declline="107" declcolumn="6"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1gaab48d4dac655d688abe921389ac2847c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int aliPS_color_aln</definition>
        <argsstring>(const char *structure, const char *filename, const char *seqs[], const char *names[])</argsstring>
        <name>aliPS_color_aln</name>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>seqs</declname>
          <array>[]</array>
        </param>
        <param>
          <type>const char *</type>
          <declname>names</declname>
          <array>[]</array>
        </param>
        <briefdescription>
<para>PS_color_aln for duplexes. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000200"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use <ref refid="group__alignment__plots_1ga3bb7409f5b73c2273f9f76cf8b754034" kindref="member">vrna_file_PS_aln()</ref> instead!</para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/alignments.h" line="120" column="6" declfile="ViennaRNA/plotting/alignments.h" declline="120" declcolumn="6"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1gaf4b9173e7d3fd361c3c85e6def194123" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int simple_xy_coordinates</definition>
        <argsstring>(short *pair_table, float *X, float *Y)</argsstring>
        <name>simple_xy_coordinates</name>
        <param>
          <type>short *</type>
          <declname>pair_table</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>X</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>Y</declname>
        </param>
        <briefdescription>
<para>Calculate nucleotide coordinates for secondary structure plot the <emphasis>Simple way</emphasis>. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__deprecated_1gab037d0de2e4c3d6a3f1d51b5b22315dc" kindref="member">make_pair_table()</ref>, <ref refid="group__plotting__utils__deprecated_1ga5964c4581431b098b80027d6e14dcdd4" kindref="member">rna_plot_type</ref>, <ref refid="group__plotting__utils__deprecated_1gac4ea13d35308f09940178d2b05a248c2" kindref="member">simple_circplot_coordinates()</ref>, naview_xy_coordinates(), <ref refid="group__plotting__utils_1ga139a31dd0ba9fc6612431f67de901c31" kindref="member">vrna_file_PS_rnaplot_a()</ref>, <ref refid="group__plotting__utils_1gabdc8f6548ba4a3bc3cd868ccbcfdb86a" kindref="member">vrna_file_PS_rnaplot</ref>, <ref refid="group__plotting__utils_1gae7853539b5df98f294b4af434e979304" kindref="member">svg_rna_plot()</ref></para>
</simplesect>
<xrefsect id="deprecated_1_deprecated000201"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Consider switching to <ref refid="group__plot__layout__utils_1ga76788091848e73cfb24b31536e22b7dd" kindref="member">vrna_plot_coords_simple_pt()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>pair_table</parametername>
</parameternamelist>
<parameterdescription>
<para>The pair table of the secondary structure </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>X</parametername>
</parameternamelist>
<parameterdescription>
<para>a pointer to an array with enough allocated space to hold the x coordinates </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>Y</parametername>
</parameternamelist>
<parameterdescription>
<para>a pointer to an array with enough allocated space to hold the y coordinates </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>length of sequence on success, 0 otherwise </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/layouts.h" line="500" column="17" declfile="ViennaRNA/plotting/layouts.h" declline="500" declcolumn="17"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1gac4ea13d35308f09940178d2b05a248c2" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int simple_circplot_coordinates</definition>
        <argsstring>(short *pair_table, float *x, float *y)</argsstring>
        <name>simple_circplot_coordinates</name>
        <param>
          <type>short *</type>
          <declname>pair_table</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>x</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>y</declname>
        </param>
        <briefdescription>
<para>Calculate nucleotide coordinates for <emphasis>Circular Plot</emphasis>. </para>
        </briefdescription>
        <detaileddescription>
<para>This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.</para>
<para><simplesect kind="note"><para>In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate a second tangential point <formula id="139">$P^t$</formula> in addition to the actual R<superscript>2</superscript> coordinates. the simplest way to do so may be to compute a radius scaling factor <formula id="140">$rs$</formula> in the interval <formula id="141">$[0,1]$</formula> that weights the proportion of base pair span to the actual length of the sequence. This scaling factor can then be used to calculate the coordinates for <formula id="139">$P^t$</formula>, i.e. <formula id="144">$ P^{t}_x[i] = X[i] * rs$</formula> and <formula id="145">$P^{t}_y[i] = Y[i] * rs$</formula>.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__struct__utils__deprecated_1gab037d0de2e4c3d6a3f1d51b5b22315dc" kindref="member">make_pair_table()</ref>, <ref refid="group__plotting__utils__deprecated_1ga5964c4581431b098b80027d6e14dcdd4" kindref="member">rna_plot_type</ref>, <ref refid="group__plotting__utils__deprecated_1gaf4b9173e7d3fd361c3c85e6def194123" kindref="member">simple_xy_coordinates()</ref>, naview_xy_coordinates(), <ref refid="group__plotting__utils_1ga139a31dd0ba9fc6612431f67de901c31" kindref="member">vrna_file_PS_rnaplot_a()</ref>, <ref refid="group__plotting__utils_1gabdc8f6548ba4a3bc3cd868ccbcfdb86a" kindref="member">vrna_file_PS_rnaplot</ref>, <ref refid="group__plotting__utils_1gae7853539b5df98f294b4af434e979304" kindref="member">svg_rna_plot()</ref></para>
</simplesect>
<xrefsect id="deprecated_1_deprecated000202"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Consider switching to <ref refid="group__plot__layout__utils_1gaeec80faa235f3ca489bc5e50adc41460" kindref="member">vrna_plot_coords_circular_pt()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>pair_table</parametername>
</parameternamelist>
<parameterdescription>
<para>The pair table of the secondary structure </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>x</parametername>
</parameternamelist>
<parameterdescription>
<para>a pointer to an array with enough allocated space to hold the x coordinates </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>y</parametername>
</parameternamelist>
<parameterdescription>
<para>a pointer to an array with enough allocated space to hold the y coordinates </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>length of sequence on success, 0 otherwise </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/layouts.h" line="529" column="17" declfile="ViennaRNA/plotting/layouts.h" declline="529" declcolumn="17"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1gaa88c6a2455d08cecdb9d58ec2a366c46" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int PS_color_dot_plot</definition>
        <argsstring>(char *string, vrna_cpair_t *pi, char *filename)</argsstring>
        <name>PS_color_dot_plot</name>
        <param>
          <type>char *</type>
          <declname>string</declname>
        </param>
        <param>
          <type><ref refid="group__data__structures_1gae4fc91141cc69c6d8eaf1332cb991ecc" kindref="member">vrna_cpair_t</ref> *</type>
          <declname>pi</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>filename</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/probabilities.h" line="172" column="1" declfile="ViennaRNA/plotting/probabilities.h" declline="172" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1ga3afb175db9396ea4f7f7dd25950509fa" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int PS_color_dot_plot_turn</definition>
        <argsstring>(char *seq, vrna_cpair_t *pi, char *filename, int winSize)</argsstring>
        <name>PS_color_dot_plot_turn</name>
        <param>
          <type>char *</type>
          <declname>seq</declname>
        </param>
        <param>
          <type><ref refid="group__data__structures_1gae4fc91141cc69c6d8eaf1332cb991ecc" kindref="member">vrna_cpair_t</ref> *</type>
          <declname>pi</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>int</type>
          <declname>winSize</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/probabilities.h" line="178" column="1" declfile="ViennaRNA/plotting/probabilities.h" declline="178" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1gaabe8e6cb31a52763c8549861b1022a96" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int PS_dot_plot_turn</definition>
        <argsstring>(char *seq, vrna_ep_t *pl, char *filename, int winSize)</argsstring>
        <name>PS_dot_plot_turn</name>
        <param>
          <type>char *</type>
          <declname>seq</declname>
        </param>
        <param>
          <type><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref> *</type>
          <declname>pl</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>filename</declname>
        </param>
        <param>
          <type>int</type>
          <declname>winSize</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/probabilities.h" line="185" column="1" declfile="ViennaRNA/plotting/probabilities.h" declline="185" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1ga4d3a807be24a9a60a90a82dbc3225f02" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int PS_dot_plot_list</definition>
        <argsstring>(char *seq, char *filename, vrna_ep_t *pl, vrna_ep_t *mf, char *comment)</argsstring>
        <name>PS_dot_plot_list</name>
        <param>
          <type>char *</type>
          <declname>seq</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>filename</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>mf</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>comment</declname>
        </param>
        <briefdescription>
<para>Produce a postscript dot-plot from two pair lists. </para>
        </briefdescription>
        <detaileddescription>
<para>This function reads two plist structures (e.g. base pair probabilities and a secondary structure) as produced by <ref refid="group__part__func__global__deprecated_1ga1cc05aaa9b0e7df2d3887e98321c2030" kindref="member">assign_plist_from_pr()</ref> and <ref refid="group__part__func__global__deprecated_1gab61df77cf7949cd516181fce0c3d7d78" kindref="member">assign_plist_from_db()</ref> and produces a postscript &quot;dot plot&quot; that is written to &apos;filename&apos;.<linebreak/>
Using base pair probabilities in the first and mfe structure in the second plist, the resulting &quot;dot plot&quot; represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy structure.</para>
<para><simplesect kind="see"><para><ref refid="group__part__func__global__deprecated_1ga1cc05aaa9b0e7df2d3887e98321c2030" kindref="member">assign_plist_from_pr()</ref>, <ref refid="group__part__func__global__deprecated_1gab61df77cf7949cd516181fce0c3d7d78" kindref="member">assign_plist_from_db()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>seq</parametername>
</parameternamelist>
<parameterdescription>
<para>The RNA sequence </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>filename</parametername>
</parameternamelist>
<parameterdescription>
<para>A filename for the postscript output </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pl</parametername>
</parameternamelist>
<parameterdescription>
<para>The base pair probability pairlist </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>mf</parametername>
</parameternamelist>
<parameterdescription>
<para>The mfe secondary structure pairlist </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>comment</parametername>
</parameternamelist>
<parameterdescription>
<para>A comment </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>1 if postscript was successfully written, 0 otherwise </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/probabilities.h" line="215" column="6" declfile="ViennaRNA/plotting/probabilities.h" declline="215" declcolumn="6"/>
      </memberdef>
      <memberdef kind="function" id="group__plotting__utils__deprecated_1ga689a97a7e3b8a2df14728b8204d9d57b" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int PS_dot_plot</definition>
        <argsstring>(char *string, char *file)</argsstring>
        <name>PS_dot_plot</name>
        <param>
          <type>char *</type>
          <declname>string</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>file</declname>
        </param>
        <briefdescription>
<para>Produce postscript dot-plot. </para>
        </briefdescription>
        <detaileddescription>
<para>Wrapper to PS_dot_plot_list</para>
<para>Reads base pair probabilities produced by <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> from the global array <ref refid="fold__vars_8h_1ac98ec419070aee6831b44e5c700f090f" kindref="member">pr</ref> and the pair list <ref refid="fold__vars_8h_1a0244a629b5ab4f58b77590c3dfd130dc" kindref="member">base_pair</ref> produced by <ref refid="group__mfe__global__deprecated_1gaadafcb0f140795ae62e5ca027e335a9b" kindref="member">fold()</ref> and produces a postscript &quot;dot plot&quot; that is written to &apos;filename&apos;. The &quot;dot plot&quot; represents each base pairing probability by a square of corresponding area in a upper triangle matrix. The lower part of the matrix contains the minimum free energy <simplesect kind="note"><para>DO NOT USE THIS FUNCTION ANYMORE SINCE IT IS NOT THREADSAFE</para>
</simplesect>
<xrefsect id="deprecated_1_deprecated000203"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This function is deprecated and will be removed soon! Use <ref refid="group__plotting__utils__deprecated_1ga4d3a807be24a9a60a90a82dbc3225f02" kindref="member">PS_dot_plot_list()</ref> instead! </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/plotting/probabilities.h" line="235" column="6" declfile="ViennaRNA/plotting/probabilities.h" declline="235" declcolumn="6"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
</doxygen>
