binaries/src/ViennaRNA/doc/html/plot__layouts_8h.html

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  70 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot_layouts.h File Reference</h1>
  71 <p>Secondary structure plot layout algorithms.
  72 <a href="#_details">More...</a></p>
  73 <div class="dynheader">
  74 Include dependency graph for plot_layouts.h:</div>
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  85 <area shape="rect" id="node3" href="PS__dot_8h.html" title="Various functions for plotting RNA secondary structures, dot&#45;plots and other visualizations..." alt="" coords="19,86,523,117"/></map>
  86 </div>
  87
  88 <p><a href="plot__layouts_8h_source.html">Go to the source code of this file.</a></p>
  89 <table border="0" cellpadding="0" cellspacing="0">
  90 <tr><td colspan="2"><h2>Defines</h2></td></tr>
  91 <tr><td class="memItemLeft" align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#ae6d17b9f0a53cf5205a9181e0f8422e9">VRNA_PLOT_TYPE_SIMPLE</a>&nbsp;&nbsp;&nbsp;0</td></tr>
  92 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Definition of Plot type <em>simple</em>.  <a href="#ae6d17b9f0a53cf5205a9181e0f8422e9"></a><br/></td></tr>
  93 <tr><td class="memItemLeft" align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#a94d4c863ecac2f220f76658afb92f964">VRNA_PLOT_TYPE_NAVIEW</a>&nbsp;&nbsp;&nbsp;1</td></tr>
  94 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Definition of Plot type <em>Naview</em>.  <a href="#a94d4c863ecac2f220f76658afb92f964"></a><br/></td></tr>
  95 <tr><td class="memItemLeft" align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#a8c9eac631348da92136c8363ecdd9fb9">VRNA_PLOT_TYPE_CIRCULAR</a>&nbsp;&nbsp;&nbsp;2</td></tr>
  96 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Definition of Plot type <em>Circular</em>.  <a href="#a8c9eac631348da92136c8363ecdd9fb9"></a><br/></td></tr>
  97 <tr><td colspan="2"><h2>Functions</h2></td></tr>
  98 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</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>
  99 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate nucleotide coordinates for secondary structure plot the <em>Simple way</em>.  <a href="#af4b9173e7d3fd361c3c85e6def194123"></a><br/></td></tr>
 100 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</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>
 101 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate nucleotide coordinates for <em>Circular Plot</em>.  <a href="#ac4ea13d35308f09940178d2b05a248c2"></a><br/></td></tr>
 102 <tr><td colspan="2"><h2>Variables</h2></td></tr>
 103 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4">rna_plot_type</a></td></tr>
 104 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Switch for changing the secondary structure layout algorithm.  <a href="#a5964c4581431b098b80027d6e14dcdd4"></a><br/></td></tr>
 105 </table>
 106 <hr/><a name="_details"></a><h2>Detailed Description</h2>
 107 <p>Secondary structure plot layout algorithms. </p>
 108 <p>c Ronny Lorenz The ViennaRNA Package </p>
 109 <hr/><h2>Define Documentation</h2>
 110 <a class="anchor" id="ae6d17b9f0a53cf5205a9181e0f8422e9"></a><!-- doxytag: member="plot_layouts.h::VRNA_PLOT_TYPE_SIMPLE" ref="ae6d17b9f0a53cf5205a9181e0f8422e9" args="" -->
 111 <div class="memitem">
 112 <div class="memproto">
 113       <table class="memname">
 114         <tr>
 115           <td class="memname">#define VRNA_PLOT_TYPE_SIMPLE&nbsp;&nbsp;&nbsp;0</td>
 116         </tr>
 117       </table>
 118 </div>
 119 <div class="memdoc">
 120
 121 <p>Definition of Plot type <em>simple</em>. </p>
 122 <p>This is the plot type definition for several RNA structure plotting functions telling them to use <b>Simple</b> plotting algorithm</p>
 123 <dl class="see"><dt><b>See also:</b></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...">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 &#39;filename&#39;...">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...">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>
 124
 125 </div>
 126 </div>
 127 <a class="anchor" id="a94d4c863ecac2f220f76658afb92f964"></a><!-- doxytag: member="plot_layouts.h::VRNA_PLOT_TYPE_NAVIEW" ref="a94d4c863ecac2f220f76658afb92f964" args="" -->
 128 <div class="memitem">
 129 <div class="memproto">
 130       <table class="memname">
 131         <tr>
 132           <td class="memname">#define VRNA_PLOT_TYPE_NAVIEW&nbsp;&nbsp;&nbsp;1</td>
 133         </tr>
 134       </table>
 135 </div>
 136 <div class="memdoc">
 137
 138 <p>Definition of Plot type <em>Naview</em>. </p>
 139 <p>This is the plot type definition for several RNA structure plotting functions telling them to use <b>Naview</b> plotting algorithm</p>
 140 <dl class="see"><dt><b>See also:</b></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...">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 &#39;filename&#39;...">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...">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>
 141
 142 </div>
 143 </div>
 144 <a class="anchor" id="a8c9eac631348da92136c8363ecdd9fb9"></a><!-- doxytag: member="plot_layouts.h::VRNA_PLOT_TYPE_CIRCULAR" ref="a8c9eac631348da92136c8363ecdd9fb9" args="" -->
 145 <div class="memitem">
 146 <div class="memproto">
 147       <table class="memname">
 148         <tr>
 149           <td class="memname">#define VRNA_PLOT_TYPE_CIRCULAR&nbsp;&nbsp;&nbsp;2</td>
 150         </tr>
 151       </table>
 152 </div>
 153 <div class="memdoc">
 154
 155 <p>Definition of Plot type <em>Circular</em>. </p>
 156 <p>This is the plot type definition for several RNA structure plotting functions telling them to produce a <b>Circular plot</b></p>
 157 <dl class="see"><dt><b>See also:</b></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...">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 &#39;filename&#39;...">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...">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>
 158
 159 </div>
 160 </div>
 161 <hr/><h2>Function Documentation</h2>
 162 <a class="anchor" id="af4b9173e7d3fd361c3c85e6def194123"></a><!-- doxytag: member="plot_layouts.h::simple_xy_coordinates" ref="af4b9173e7d3fd361c3c85e6def194123" args="(short *pair_table, float *X, float *Y)" -->
 163 <div class="memitem">
 164 <div class="memproto">
 165       <table class="memname">
 166         <tr>
 167           <td class="memname">int simple_xy_coordinates </td>
 168           <td>(</td>
 169           <td class="paramtype">short *&nbsp;</td>
 170           <td class="paramname"> <em>pair_table</em>, </td>
 171         </tr>
 172         <tr>
 173           <td class="paramkey"></td>
 174           <td></td>
 175           <td class="paramtype">float *&nbsp;</td>
 176           <td class="paramname"> <em>X</em>, </td>
 177         </tr>
 178         <tr>
 179           <td class="paramkey"></td>
 180           <td></td>
 181           <td class="paramtype">float *&nbsp;</td>
 182           <td class="paramname"> <em>Y</em></td><td>&nbsp;</td>
 183         </tr>
 184         <tr>
 185           <td></td>
 186           <td>)</td>
 187           <td></td><td></td><td></td>
 188         </tr>
 189       </table>
 190 </div>
 191 <div class="memdoc">
 192
 193 <p>Calculate nucleotide coordinates for secondary structure plot the <em>Simple way</em>. </p>
 194 <dl class="see"><dt><b>See also:</b></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...">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 &#39;filename&#39;...">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>
 195 <dl><dt><b>Parameters:</b></dt><dd>
 196   <table border="0" cellspacing="2" cellpadding="0">
 197     <tr><td valign="top"></td><td valign="top"><em>pair_table</em>&nbsp;</td><td>The pair table of the secondary structure </td></tr>
 198     <tr><td valign="top"></td><td valign="top"><em>X</em>&nbsp;</td><td>a pointer to an array with enough allocated space to hold the x coordinates </td></tr>
 199     <tr><td valign="top"></td><td valign="top"><em>Y</em>&nbsp;</td><td>a pointer to an array with enough allocated space to hold the y coordinates </td></tr>
 200   </table>
 201   </dd>
 202 </dl>
 203 <dl class="return"><dt><b>Returns:</b></dt><dd>length of sequence on success, 0 otherwise </dd></dl>
 204
 205 </div>
 206 </div>
 207 <a class="anchor" id="ac4ea13d35308f09940178d2b05a248c2"></a><!-- doxytag: member="plot_layouts.h::simple_circplot_coordinates" ref="ac4ea13d35308f09940178d2b05a248c2" args="(short *pair_table, float *x, float *y)" -->
 208 <div class="memitem">
 209 <div class="memproto">
 210       <table class="memname">
 211         <tr>
 212           <td class="memname">int simple_circplot_coordinates </td>
 213           <td>(</td>
 214           <td class="paramtype">short *&nbsp;</td>
 215           <td class="paramname"> <em>pair_table</em>, </td>
 216         </tr>
 217         <tr>
 218           <td class="paramkey"></td>
 219           <td></td>
 220           <td class="paramtype">float *&nbsp;</td>
 221           <td class="paramname"> <em>x</em>, </td>
 222         </tr>
 223         <tr>
 224           <td class="paramkey"></td>
 225           <td></td>
 226           <td class="paramtype">float *&nbsp;</td>
 227           <td class="paramname"> <em>y</em></td><td>&nbsp;</td>
 228         </tr>
 229         <tr>
 230           <td></td>
 231           <td>)</td>
 232           <td></td><td></td><td></td>
 233         </tr>
 234       </table>
 235 </div>
 236 <div class="memdoc">
 237
 238 <p>Calculate nucleotide coordinates for <em>Circular Plot</em>. </p>
 239 <p>This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.</p>
 240 <dl class="note"><dt><b>Note:</b></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>
 241 <dl class="see"><dt><b>See also:</b></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...">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 &#39;filename&#39;...">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>
 242 <dl><dt><b>Parameters:</b></dt><dd>
 243   <table border="0" cellspacing="2" cellpadding="0">
 244     <tr><td valign="top"></td><td valign="top"><em>pair_table</em>&nbsp;</td><td>The pair table of the secondary structure </td></tr>
 245     <tr><td valign="top"></td><td valign="top"><em>x</em>&nbsp;</td><td>a pointer to an array with enough allocated space to hold the x coordinates </td></tr>
 246     <tr><td valign="top"></td><td valign="top"><em>y</em>&nbsp;</td><td>a pointer to an array with enough allocated space to hold the y coordinates </td></tr>
 247   </table>
 248   </dd>
 249 </dl>
 250 <dl class="return"><dt><b>Returns:</b></dt><dd>length of sequence on success, 0 otherwise </dd></dl>
 251
 252 </div>
 253 </div>
 254 <hr/><h2>Variable Documentation</h2>
 255 <a class="anchor" id="a5964c4581431b098b80027d6e14dcdd4"></a><!-- doxytag: member="plot_layouts.h::rna_plot_type" ref="a5964c4581431b098b80027d6e14dcdd4" args="" -->
 256 <div class="memitem">
 257 <div class="memproto">
 258       <table class="memname">
 259         <tr>
 260           <td class="memname">int <a class="el" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4">rna_plot_type</a></td>
 261         </tr>
 262       </table>
 263 </div>
 264 <div class="memdoc">
 265
 266 <p>Switch for changing the secondary structure layout algorithm. </p>
 267 <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 &amp; Heinrich (1988).</p>
 268 <dl class="note"><dt><b>Note:</b></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>
 269 <dl class="see"><dt><b>See also:</b></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>
 270
 271 </div>
 272 </div>
 273 </div>
 274 <hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
 275 <a href="http://www.doxygen.org/index.html">
 276 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 277 </body>
 278 </html>