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+<a href="#func-members">Functions</a> |
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+<div class="title">plot_layouts.h File Reference</div> </div>
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+<div class="contents">
+
+<p>Secondary structure plot layout algorithms.
+<a href="#details">More...</a></p>
+<div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for plot_layouts.h:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="plot__layouts_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2plot__layouts_8h" alt=""/></div>
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+<area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="5,109,139,136"/><area shape="rect" id="node9" href="naview_8h.html" title="naview.h" alt="" coords="163,109,239,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="12,184,132,211"/></map>
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+</div>
+</div>
+<p><a href="plot__layouts_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="define-members"></a>
+Macros</h2></td></tr>
+<tr class="memitem:ae6d17b9f0a53cf5205a9181e0f8422e9"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#ae6d17b9f0a53cf5205a9181e0f8422e9">VRNA_PLOT_TYPE_SIMPLE</a>   0</td></tr>
+<tr class="memdesc:ae6d17b9f0a53cf5205a9181e0f8422e9"><td class="mdescLeft"> </td><td class="mdescRight">Definition of Plot type <em>simple</em> <a href="#ae6d17b9f0a53cf5205a9181e0f8422e9"></a><br/></td></tr>
+<tr class="memitem:a94d4c863ecac2f220f76658afb92f964"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#a94d4c863ecac2f220f76658afb92f964">VRNA_PLOT_TYPE_NAVIEW</a>   1</td></tr>
+<tr class="memdesc:a94d4c863ecac2f220f76658afb92f964"><td class="mdescLeft"> </td><td class="mdescRight">Definition of Plot type <em>Naview</em> <a href="#a94d4c863ecac2f220f76658afb92f964"></a><br/></td></tr>
+<tr class="memitem:a8c9eac631348da92136c8363ecdd9fb9"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#a8c9eac631348da92136c8363ecdd9fb9">VRNA_PLOT_TYPE_CIRCULAR</a>   2</td></tr>
+<tr class="memdesc:a8c9eac631348da92136c8363ecdd9fb9"><td class="mdescLeft"> </td><td class="mdescRight">Definition of Plot type <em>Circular</em> <a href="#a8c9eac631348da92136c8363ecdd9fb9"></a><br/></td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:af4b9173e7d3fd361c3c85e6def194123"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#af4b9173e7d3fd361c3c85e6def194123">simple_xy_coordinates</a> (short *pair_table, float *X, float *Y)</td></tr>
+<tr class="memdesc:af4b9173e7d3fd361c3c85e6def194123"><td class="mdescLeft"> </td><td class="mdescRight">Calculate nucleotide coordinates for secondary structure plot the <em>Simple way</em> <a href="#af4b9173e7d3fd361c3c85e6def194123"></a><br/></td></tr>
+<tr class="memitem:ac4ea13d35308f09940178d2b05a248c2"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#ac4ea13d35308f09940178d2b05a248c2">simple_circplot_coordinates</a> (short *pair_table, float *x, float *y)</td></tr>
+<tr class="memdesc:ac4ea13d35308f09940178d2b05a248c2"><td class="mdescLeft"> </td><td class="mdescRight">Calculate nucleotide coordinates for <em>Circular Plot</em> <a href="#ac4ea13d35308f09940178d2b05a248c2"></a><br/></td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr class="memitem:a5964c4581431b098b80027d6e14dcdd4"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4">rna_plot_type</a></td></tr>
+<tr class="memdesc:a5964c4581431b098b80027d6e14dcdd4"><td class="mdescLeft"> </td><td class="mdescRight">Switch for changing the secondary structure layout algorithm. <a href="#a5964c4581431b098b80027d6e14dcdd4"></a><br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"><p>Secondary structure plot layout algorithms. </p>
+<p>c Ronny Lorenz The ViennaRNA Package </p>
+</div><hr/><h2>Macro Definition Documentation</h2>
+<a class="anchor" id="ae6d17b9f0a53cf5205a9181e0f8422e9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_PLOT_TYPE_SIMPLE   0</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Definition of Plot type <em>simple</em> </p>
+<p>This is the plot type definition for several RNA structure plotting functions telling them to use <b>Simple</b> plotting algorithm</p>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4" title="Switch for changing the secondary structure layout algorithm.">rna_plot_type</a>, <a class="el" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a()</a>, <a class="el" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#a70834bc8c0aad4fe6824ff76ccb8f329" title="Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file...">gmlRNA()</a>, <a class="el" href="PS__dot_8h.html#add368528755f9a830727b680243541df" title="Produce a secondary structure graph in SStructView format.">ssv_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#a2f6d5953e6a323df898896b8d6614483" title="Produce a secondary structure plot for further editing in XRNA.">xrna_plot()</a> </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a94d4c863ecac2f220f76658afb92f964"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_PLOT_TYPE_NAVIEW   1</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Definition of Plot type <em>Naview</em> </p>
+<p>This is the plot type definition for several RNA structure plotting functions telling them to use <b>Naview</b> plotting algorithm</p>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4" title="Switch for changing the secondary structure layout algorithm.">rna_plot_type</a>, <a class="el" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a()</a>, <a class="el" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#a70834bc8c0aad4fe6824ff76ccb8f329" title="Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file...">gmlRNA()</a>, <a class="el" href="PS__dot_8h.html#add368528755f9a830727b680243541df" title="Produce a secondary structure graph in SStructView format.">ssv_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#a2f6d5953e6a323df898896b8d6614483" title="Produce a secondary structure plot for further editing in XRNA.">xrna_plot()</a> </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a8c9eac631348da92136c8363ecdd9fb9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">#define VRNA_PLOT_TYPE_CIRCULAR   2</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Definition of Plot type <em>Circular</em> </p>
+<p>This is the plot type definition for several RNA structure plotting functions telling them to produce a <b>Circular plot</b></p>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4" title="Switch for changing the secondary structure layout algorithm.">rna_plot_type</a>, <a class="el" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a()</a>, <a class="el" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#a70834bc8c0aad4fe6824ff76ccb8f329" title="Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file...">gmlRNA()</a>, <a class="el" href="PS__dot_8h.html#add368528755f9a830727b680243541df" title="Produce a secondary structure graph in SStructView format.">ssv_rna_plot()</a>, <a class="el" href="PS__dot_8h.html#a2f6d5953e6a323df898896b8d6614483" title="Produce a secondary structure plot for further editing in XRNA.">xrna_plot()</a> </dd></dl>
+
+</div>
+</div>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="af4b9173e7d3fd361c3c85e6def194123"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">int simple_xy_coordinates </td>
+ <td>(</td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"><em>pair_table</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"><em>X</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"><em>Y</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Calculate nucleotide coordinates for secondary structure plot the <em>Simple way</em> </p>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table()</a>, <a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4" title="Switch for changing the secondary structure layout algorithm.">rna_plot_type</a>, <a class="el" href="plot__layouts_8h.html#ac4ea13d35308f09940178d2b05a248c2" title="Calculate nucleotide coordinates for Circular Plot">simple_circplot_coordinates()</a>, naview_xy_coordinates(), <a class="el" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a()</a>, <a class="el" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot</a>, <a class="el" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot()</a></dd></dl>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">pair_table</td><td>The pair table of the secondary structure </td></tr>
+ <tr><td class="paramname">X</td><td>a pointer to an array with enough allocated space to hold the x coordinates </td></tr>
+ <tr><td class="paramname">Y</td><td>a pointer to an array with enough allocated space to hold the y coordinates </td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd>length of sequence on success, 0 otherwise </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="ac4ea13d35308f09940178d2b05a248c2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">int simple_circplot_coordinates </td>
+ <td>(</td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"><em>pair_table</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"><em>x</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">float * </td>
+ <td class="paramname"><em>y</em> </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Calculate nucleotide coordinates for <em>Circular Plot</em> </p>
+<p>This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.</p>
+<dl class="section note"><dt>Note:</dt><dd>In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate a second tangential point <img class="formulaInl" alt="$P^t$" src="form_25.png"/> in addition to the actual R<sup>2</sup> coordinates. the simplest way to do so may be to compute a radius scaling factor <img class="formulaInl" alt="$rs$" src="form_26.png"/> in the interval <img class="formulaInl" alt="$[0,1]$" src="form_27.png"/> 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 <img class="formulaInl" alt="$P^t$" src="form_25.png"/>, i.e. <img class="formulaInl" alt="$ P^{t}_x[i] = X[i] * rs$" src="form_28.png"/> and <img class="formulaInl" alt="$P^{t}_y[i] = Y[i] * rs$" src="form_29.png"/>.</dd></dl>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table()</a>, <a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4" title="Switch for changing the secondary structure layout algorithm.">rna_plot_type</a>, <a class="el" href="plot__layouts_8h.html#af4b9173e7d3fd361c3c85e6def194123" title="Calculate nucleotide coordinates for secondary structure plot the Simple way">simple_xy_coordinates()</a>, naview_xy_coordinates(), <a class="el" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a()</a>, <a class="el" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot</a>, <a class="el" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot()</a></dd></dl>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">pair_table</td><td>The pair table of the secondary structure </td></tr>
+ <tr><td class="paramname">x</td><td>a pointer to an array with enough allocated space to hold the x coordinates </td></tr>
+ <tr><td class="paramname">y</td><td>a pointer to an array with enough allocated space to hold the y coordinates </td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd>length of sequence on success, 0 otherwise </dd></dl>
+
+</div>
+</div>
+<hr/><h2>Variable Documentation</h2>
+<a class="anchor" id="a5964c4581431b098b80027d6e14dcdd4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">int rna_plot_type</td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Switch for changing the secondary structure layout algorithm. </p>
+<p>Current possibility are 0 for a simple radial drawing or 1 for the modified radial drawing taken from the <em>naview</em> program of Bruccoleri & Heinrich (1988).</p>
+<dl class="section note"><dt>Note:</dt><dd>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!</dd></dl>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="plot__layouts_8h.html#ae6d17b9f0a53cf5205a9181e0f8422e9" title="Definition of Plot type simple">VRNA_PLOT_TYPE_SIMPLE</a>, <a class="el" href="plot__layouts_8h.html#a94d4c863ecac2f220f76658afb92f964" title="Definition of Plot type Naview">VRNA_PLOT_TYPE_NAVIEW</a>, <a class="el" href="plot__layouts_8h.html#a8c9eac631348da92136c8363ecdd9fb9" title="Definition of Plot type Circular">VRNA_PLOT_TYPE_CIRCULAR</a> </dd></dl>
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