help/html/groovy/featureCounter.html

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  22 <head>
  23 <title>Extending Jalview with Groovy - Feature Counter Example</title>
  24 </head>
  25 <body>
  26   <p>
  27     <strong>Extending Jalview with Groovy - A customisable
  28       feature counter</strong><br /> <br />The groovy script below shows how to
  29     add a new calculation track to a Jalview alignment window.
  30   </p>
  31   <p>As currently written, it will add two tracks to a protein
  32     alignment view which count Pfam features in each column, and ones
  33     where a charge residue also occur.</p>
  34   <p>To try it for yourself:</p>
  35   <ol>
  36     <li>Copy and paste it into the groovy script console</li>
  37     <li>Load the example Feredoxin project (the one that opens by
  38       default when you first launched Jalview)</li>
  39     <li>Select <strong>Calculations&#8594;Execute Groovy
  40         Script</strong> from the alignment window's menu bar to run the script on
  41       the current view.
  42     </li>
  43   </ol>
  44   <em><a
  45     href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a>
  46     - rendered with <a href="http://hilite.me">hilite.me</a></em>
  47   <!-- HTML generated using hilite.me -->
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  49     style="background: #ffffff; overflow: auto; width: auto; border: solid gray; border-width: .1em .1em .1em .8em; padding: .2em .6em;">
  50     <pre style="margin: 0; line-height: 125%">
  51 <span style="color: #888888">/*</span>
  52 <span style="color: #888888"> * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)</span>
  53 <span style="color: #888888"> * Copyright (C) 2016 The Jalview Authors</span>
  54 <span style="color: #888888"> * </span>
  55 <span style="color: #888888"> * This file is part of Jalview.</span>
  56 <span style="color: #888888"> * </span>
  57 <span style="color: #888888"> * Jalview is free software: you can redistribute it and/or</span>
  58 <span style="color: #888888"> * modify it under the terms of the GNU General Public License </span>
  59 <span style="color: #888888"> * as published by the Free Software Foundation, either version 3</span>
  60 <span style="color: #888888"> * of the License, or (at your option) any later version.</span>
  61 <span style="color: #888888"> *  </span>
  62 <span style="color: #888888"> * Jalview is distributed in the hope that it will be useful, but </span>
  63 <span style="color: #888888"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
  64 <span style="color: #888888"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
  65 <span style="color: #888888"> * PURPOSE.  See the GNU General Public License for more details.</span>
  66 <span style="color: #888888"> * </span>
  67 <span style="color: #888888"> * You should have received a copy of the GNU General Public License</span>
  68 <span style="color: #888888"> * along with Jalview.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
  69 <span style="color: #888888"> * The Jalview Authors are detailed in the &#39;AUTHORS&#39; file.</span>
  70 <span style="color: #888888"> */</span>
  71
  72 <span style="color: #008800; font-weight: bold">import</span> <span
  73         style="color: #0e84b5; font-weight: bold">jalview.workers.FeatureCounterI</span><span
  74         style="color: #333333">;</span>
  75 <span style="color: #008800; font-weight: bold">import</span> <span
  76         style="color: #0e84b5; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span
  77         style="color: #333333">;</span>
  78
  79 <span style="color: #888888">/*</span>
  80 <span style="color: #888888"> * Example script that registers two alignment annotation calculators</span>
  81 <span style="color: #888888"> * - one that counts residues in a column with Pfam annotation</span>
  82 <span style="color: #888888"> * - one that counts only charged residues with Pfam annotation</span>
  83 <span style="color: #888888"> *</span>
  84 <span style="color: #888888"> * To try:</span>
  85 <span style="color: #888888"> * 1. load uniref50.fa from the examples folder</span>
  86 <span style="color: #888888"> * 2. load features onto it from from examples/exampleFeatures.txt</span>
  87 <span style="color: #888888"> * 3. Open this script in the Groovy console.</span>
  88 <span style="color: #888888"> * 4. Either execute this script from the console, or via Calculate-&gt;Run Groovy Script</span>
  89 <span style="color: #888888"> </span>
  90 <span style="color: #888888"> * To explore further, try changing this script to count other kinds of occurrences of </span>
  91 <span style="color: #888888"> * residue and sequence features at columns in an alignment.</span>
  92 <span style="color: #888888"> */</span>
  93
  94 <span style="color: #888888">/*</span>
  95 <span style="color: #888888"> * A closure that returns true for any Charged residue</span>
  96 <span style="color: #888888"> */</span>
  97 <span style="color: #333399; font-weight: bold">def</span> isCharged <span
  98         style="color: #333333">=</span> <span style="color: #333333">{</span> residue <span
  99         style="color: #333333">-&gt;</span>
 100     <span style="color: #008800; font-weight: bold">switch</span><span
 101         style="color: #333333">(</span>residue<span
 102         style="color: #333333">)</span> <span style="color: #333333">{</span>
 103         <span style="color: #008800; font-weight: bold">case</span> <span
 104         style="color: #333333">[</span><span
 105         style="background-color: #fff0f0">&#39;D&#39;</span><span
 106         style="color: #333333">,</span> <span
 107         style="background-color: #fff0f0">&#39;d&#39;</span><span
 108         style="color: #333333">,</span> <span
 109         style="background-color: #fff0f0">&#39;E&#39;</span><span
 110         style="color: #333333">,</span> <span
 111         style="background-color: #fff0f0">&#39;e&#39;</span><span
 112         style="color: #333333">,</span> <span
 113         style="background-color: #fff0f0">&#39;H&#39;</span><span
 114         style="color: #333333">,</span> <span
 115         style="background-color: #fff0f0">&#39;h&#39;</span><span
 116         style="color: #333333">,</span> <span
 117         style="background-color: #fff0f0">&#39;K&#39;</span><span
 118         style="color: #333333">,</span> <span
 119         style="background-color: #fff0f0">&#39;k&#39;</span><span
 120         style="color: #333333">,</span> <span
 121         style="background-color: #fff0f0">&#39;R&#39;</span><span
 122         style="color: #333333">,</span> <span
 123         style="background-color: #fff0f0">&#39;r&#39;</span><span
 124         style="color: #333333">]:</span>
 125             <span style="color: #008800; font-weight: bold">return</span> <span
 126         style="color: #008800; font-weight: bold">true</span>
 127     <span style="color: #333333">}</span>
 128     <span style="color: #008800; font-weight: bold">false</span>
 129 <span style="color: #333333">}</span>
 130
 131 <span style="color: #888888">/*</span>
 132 <span style="color: #888888"> * A closure that returns 1 if sequence features include type &#39;Pfam&#39;, else 0</span>
 133 <span style="color: #888888"> * Argument should be a list of SequenceFeature </span>
 134 <span style="color: #888888"> */</span>
 135 <span style="color: #333399; font-weight: bold">def</span> hasPfam <span
 136         style="color: #333333">=</span> <span style="color: #333333">{</span> features <span
 137         style="color: #333333">-&gt;</span>
 138     <span style="color: #008800; font-weight: bold">for</span> <span
 139         style="color: #333333">(</span>sf <span
 140         style="color: #008800; font-weight: bold">in</span> features<span
 141         style="color: #333333">)</span>
 142     <span style="color: #333333">{</span>
 143         <span style="color: #888888">/*</span>
 144 <span style="color: #888888">         * Here we inspect the type of the sequence feature.</span>
 145 <span style="color: #888888">         * You can also test sf.description, sf.score, sf.featureGroup,</span>
 146 <span style="color: #888888">         * sf.strand, sf.phase, sf.begin, sf.end</span>
 147 <span style="color: #888888">         * or sf.getValue(attributeName) for GFF &#39;column 9&#39; properties</span>
 148 <span style="color: #888888">         */</span>
 149         <span style="color: #008800; font-weight: bold">if</span> <span
 150         style="color: #333333">(</span><span
 151         style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
 152         style="color: #333333">.</span><span style="color: #0000CC">equals</span><span
 153         style="color: #333333">(</span>sf<span style="color: #333333">.</span><span
 154         style="color: #0000CC">type</span><span style="color: #333333">))</span>
 155         <span style="color: #333333">{</span>
 156             <span style="color: #008800; font-weight: bold">return</span> <span
 157         style="color: #008800; font-weight: bold">true</span>
 158         <span style="color: #333333">}</span>
 159     <span style="color: #333333">}</span>
 160     <span style="color: #008800; font-weight: bold">false</span>
 161 <span style="color: #333333">}</span>
 162
 163 <span style="color: #888888">/*</span>
 164 <span style="color: #888888"> * Closure that computes an annotation based on </span>
 165 <span style="color: #888888"> * presence of particular residues and features</span>
 166 <span style="color: #888888"> * Parameters are</span>
 167 <span style="color: #888888"> * - the name (label) for the alignment annotation</span>
 168 <span style="color: #888888"> * - the description (tooltip) for the annotation</span>
 169 <span style="color: #888888"> * - a closure (groovy function) that tests whether to include a residue</span>
 170 <span style="color: #888888"> * - a closure that tests whether to increment count based on sequence features  </span>
 171 <span style="color: #888888"> */</span>
 172 <span style="color: #333399; font-weight: bold">def</span> getColumnCounter <span
 173         style="color: #333333">=</span> <span style="color: #333333">{</span> name<span
 174         style="color: #333333">,</span> desc<span style="color: #333333">,</span> acceptResidue<span
 175         style="color: #333333">,</span> acceptFeatures <span
 176         style="color: #333333">-&gt;</span>
 177     <span style="color: #333333">[</span>
 178      <span style="color: #997700; font-weight: bold">getName:</span> <span
 179         style="color: #333333">{</span> name <span
 180         style="color: #333333">},</span>
 181      <span style="color: #997700; font-weight: bold">getDescription:</span> <span
 182         style="color: #333333">{</span> desc <span
 183         style="color: #333333">},</span>
 184      <span style="color: #997700; font-weight: bold">getMinColour:</span> <span
 185         style="color: #333333">{</span> <span style="color: #333333">[</span><span
 186         style="color: #0000DD; font-weight: bold">0</span><span
 187         style="color: #333333">,</span> <span
 188         style="color: #0000DD; font-weight: bold">255</span><span
 189         style="color: #333333">,</span> <span
 190         style="color: #0000DD; font-weight: bold">255</span><span
 191         style="color: #333333">]</span> <span style="color: #333333">},</span> <span
 192         style="color: #888888">// cyan</span>
 193      <span style="color: #997700; font-weight: bold">getMaxColour:</span> <span
 194         style="color: #333333">{</span> <span style="color: #333333">[</span><span
 195         style="color: #0000DD; font-weight: bold">0</span><span
 196         style="color: #333333">,</span> <span
 197         style="color: #0000DD; font-weight: bold">0</span><span
 198         style="color: #333333">,</span> <span
 199         style="color: #0000DD; font-weight: bold">255</span><span
 200         style="color: #333333">]</span> <span style="color: #333333">},</span> <span
 201         style="color: #888888">// blue</span>
 202      <span style="color: #997700; font-weight: bold">count:</span>
 203          <span style="color: #333333">{</span> res<span
 204         style="color: #333333">,</span> feats <span
 205         style="color: #333333">-&gt;</span>
 206             <span style="color: #333399; font-weight: bold">def</span> c <span
 207         style="color: #333333">=</span> <span
 208         style="color: #0000DD; font-weight: bold">0</span>
 209             <span style="color: #008800; font-weight: bold">if</span> <span
 210         style="color: #333333">(</span>acceptResidue<span
 211         style="color: #333333">.</span><span style="color: #0000CC">call</span><span
 212         style="color: #333333">(</span>res<span style="color: #333333">))</span>
 213             <span style="color: #333333">{</span>
 214                 <span style="color: #008800; font-weight: bold">if</span> <span
 215         style="color: #333333">(</span>acceptFeatures<span
 216         style="color: #333333">.</span><span style="color: #0000CC">call</span><span
 217         style="color: #333333">(</span>feats<span style="color: #333333">))</span>
 218                 <span style="color: #333333">{</span>
 219                     c<span style="color: #333333">++</span>
 220                 <span style="color: #333333">}</span>
 221             <span style="color: #333333">}</span>
 222             c
 223          <span style="color: #333333">}</span>
 224      <span style="color: #333333">]</span> <span
 225         style="color: #008800; font-weight: bold">as</span> FeatureCounterI
 226 <span style="color: #333333">}</span>
 227
 228 <span style="color: #888888">/*</span>
 229 <span style="color: #888888"> * Define an annotation row that counts any residue with Pfam domain annotation</span>
 230 <span style="color: #888888"> */</span>
 231 <span style="color: #333399; font-weight: bold">def</span> pfamAnnotation <span
 232         style="color: #333333">=</span> getColumnCounter<span
 233         style="color: #333333">(</span><span
 234         style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
 235         style="color: #333333">,</span> <span
 236         style="background-color: #fff0f0">&quot;Count of residues with Pfam domain annotation&quot;</span><span
 237         style="color: #333333">,</span> <span style="color: #333333">{</span><span
 238         style="color: #008800; font-weight: bold">true</span><span
 239         style="color: #333333">},</span> hasPfam<span
 240         style="color: #333333">)</span>
 241
 242 <span style="color: #888888">/*</span>
 243 <span style="color: #888888"> * Define an annotation row that counts charged residues with Pfam domain annotation</span>
 244 <span style="color: #888888"> */</span>
 245 <span style="color: #333399; font-weight: bold">def</span> chargedPfamAnnotation <span
 246         style="color: #333333">=</span> getColumnCounter<span
 247         style="color: #333333">(</span><span
 248         style="background-color: #fff0f0">&quot;Pfam charged&quot;</span><span
 249         style="color: #333333">,</span> <span
 250         style="background-color: #fff0f0">&quot;Count of charged residues with Pfam domain annotation&quot;</span><span
 251         style="color: #333333">,</span> isCharged<span
 252         style="color: #333333">,</span> hasPfam<span
 253         style="color: #333333">)</span>
 254
 255 <span style="color: #888888">/*</span>
 256 <span style="color: #888888"> * Register the annotations</span>
 257 <span style="color: #888888"> */</span>
 258 AlignmentAnnotationFactory<span style="color: #333333">.</span><span
 259         style="color: #0000CC">newCalculator</span><span
 260         style="color: #333333">(</span>pfamAnnotation<span
 261         style="color: #333333">)</span>
 262 AlignmentAnnotationFactory<span style="color: #333333">.</span><span
 263         style="color: #0000CC">newCalculator</span><span
 264         style="color: #333333">(</span>chargedPfamAnnotation<span
 265         style="color: #333333">)</span>
 266 </pre>
 267   </div>
 268 </body>
 269 </html>