help/html/groovy/featureCounter.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  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 />
  29     <br />The groovy script below shows how to add a new calculation
  30     track to a Jalview alignment window.</p><p>As currently written, it will
  31     add two tracks to a protein alignment view which count Pfam features
  32     in each column, and ones where a charge residue also occur.</p><p>To try
  33     it for yourself:</p><ol><li>Copy and paste it into the groovy script
  34     console</li><li>Load the example Feredoxin project (the one that opens
  35     by default when you first launched Jalview)</li><li>Select <strong>Calculations&#8594;Execute
  36       Groovy Script</strong> from the alignment window's menu bar to run the script on
  37     the current view.</li></ol>
  38   <em><a
  39       href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a> - rendered with <a href="http://hilite.me">hilite.me</a></em>
  40   <!-- HTML generated using hilite.me -->
  41   <div
  42     style="background: #ffffff; overflow: auto; width: auto; border: solid gray; border-width: .1em .1em .1em .8em; padding: .2em .6em;">
  43     <pre style="margin: 0; line-height: 125%">
  44 <span style="color: #888888">/*</span>
  45 <span style="color: #888888"> * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)</span>
  46 <span style="color: #888888"> * Copyright (C) 2016 The Jalview Authors</span>
  47 <span style="color: #888888"> * </span>
  48 <span style="color: #888888"> * This file is part of Jalview.</span>
  49 <span style="color: #888888"> * </span>
  50 <span style="color: #888888"> * Jalview is free software: you can redistribute it and/or</span>
  51 <span style="color: #888888"> * modify it under the terms of the GNU General Public License </span>
  52 <span style="color: #888888"> * as published by the Free Software Foundation, either version 3</span>
  53 <span style="color: #888888"> * of the License, or (at your option) any later version.</span>
  54 <span style="color: #888888"> *  </span>
  55 <span style="color: #888888"> * Jalview is distributed in the hope that it will be useful, but </span>
  56 <span style="color: #888888"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
  57 <span style="color: #888888"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
  58 <span style="color: #888888"> * PURPOSE.  See the GNU General Public License for more details.</span>
  59 <span style="color: #888888"> * </span>
  60 <span style="color: #888888"> * You should have received a copy of the GNU General Public License</span>
  61 <span style="color: #888888"> * along with Jalview.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
  62 <span style="color: #888888"> * The Jalview Authors are detailed in the &#39;AUTHORS&#39; file.</span>
  63 <span style="color: #888888"> */</span>
  64
  65 <span style="color: #008800; font-weight: bold">import</span> <span
  66         style="color: #0e84b5; font-weight: bold">jalview.workers.FeatureCounterI</span><span
  67         style="color: #333333">;</span>
  68 <span style="color: #008800; font-weight: bold">import</span> <span
  69         style="color: #0e84b5; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span
  70         style="color: #333333">;</span>
  71
  72 <span style="color: #888888">/*</span>
  73 <span style="color: #888888"> * Example script that registers two alignment annotation calculators</span>
  74 <span style="color: #888888"> * - one that counts residues in a column with Pfam annotation</span>
  75 <span style="color: #888888"> * - one that counts only charged residues with Pfam annotation</span>
  76 <span style="color: #888888"> *</span>
  77 <span style="color: #888888"> * To try:</span>
  78 <span style="color: #888888"> * 1. load uniref50.fa from the examples folder</span>
  79 <span style="color: #888888"> * 2. load features onto it from from examples/exampleFeatures.txt</span>
  80 <span style="color: #888888"> * 3. Open this script in the Groovy console.</span>
  81 <span style="color: #888888"> * 4. Either execute this script from the console, or via Calculate-&gt;Run Groovy Script</span>
  82 <span style="color: #888888"> </span>
  83 <span style="color: #888888"> * To explore further, try changing this script to count other kinds of occurrences of </span>
  84 <span style="color: #888888"> * residue and sequence features at columns in an alignment.</span>
  85 <span style="color: #888888"> */</span>
  86
  87 <span style="color: #888888">/*</span>
  88 <span style="color: #888888"> * A closure that returns true for any Charged residue</span>
  89 <span style="color: #888888"> */</span>
  90 <span style="color: #333399; font-weight: bold">def</span> isCharged <span
  91         style="color: #333333">=</span> <span style="color: #333333">{</span> residue <span
  92         style="color: #333333">-&gt;</span>
  93     <span style="color: #008800; font-weight: bold">switch</span><span
  94         style="color: #333333">(</span>residue<span
  95         style="color: #333333">)</span> <span style="color: #333333">{</span>
  96         <span style="color: #008800; font-weight: bold">case</span> <span
  97         style="color: #333333">[</span><span
  98         style="background-color: #fff0f0">&#39;D&#39;</span><span
  99         style="color: #333333">,</span> <span
 100         style="background-color: #fff0f0">&#39;d&#39;</span><span
 101         style="color: #333333">,</span> <span
 102         style="background-color: #fff0f0">&#39;E&#39;</span><span
 103         style="color: #333333">,</span> <span
 104         style="background-color: #fff0f0">&#39;e&#39;</span><span
 105         style="color: #333333">,</span> <span
 106         style="background-color: #fff0f0">&#39;H&#39;</span><span
 107         style="color: #333333">,</span> <span
 108         style="background-color: #fff0f0">&#39;h&#39;</span><span
 109         style="color: #333333">,</span> <span
 110         style="background-color: #fff0f0">&#39;K&#39;</span><span
 111         style="color: #333333">,</span> <span
 112         style="background-color: #fff0f0">&#39;k&#39;</span><span
 113         style="color: #333333">,</span> <span
 114         style="background-color: #fff0f0">&#39;R&#39;</span><span
 115         style="color: #333333">,</span> <span
 116         style="background-color: #fff0f0">&#39;r&#39;</span><span
 117         style="color: #333333">]:</span>
 118             <span style="color: #008800; font-weight: bold">return</span> <span
 119         style="color: #008800; font-weight: bold">true</span>
 120     <span style="color: #333333">}</span>
 121     <span style="color: #008800; font-weight: bold">false</span>
 122 <span style="color: #333333">}</span>
 123
 124 <span style="color: #888888">/*</span>
 125 <span style="color: #888888"> * A closure that returns 1 if sequence features include type &#39;Pfam&#39;, else 0</span>
 126 <span style="color: #888888"> * Argument should be a list of SequenceFeature </span>
 127 <span style="color: #888888"> */</span>
 128 <span style="color: #333399; font-weight: bold">def</span> hasPfam <span
 129         style="color: #333333">=</span> <span style="color: #333333">{</span> features <span
 130         style="color: #333333">-&gt;</span>
 131     <span style="color: #008800; font-weight: bold">for</span> <span
 132         style="color: #333333">(</span>sf <span
 133         style="color: #008800; font-weight: bold">in</span> features<span
 134         style="color: #333333">)</span>
 135     <span style="color: #333333">{</span>
 136         <span style="color: #888888">/*</span>
 137 <span style="color: #888888">         * Here we inspect the type of the sequence feature.</span>
 138 <span style="color: #888888">         * You can also test sf.description, sf.score, sf.featureGroup,</span>
 139 <span style="color: #888888">         * sf.strand, sf.phase, sf.begin, sf.end</span>
 140 <span style="color: #888888">         * or sf.getValue(attributeName) for GFF &#39;column 9&#39; properties</span>
 141 <span style="color: #888888">         */</span>
 142         <span style="color: #008800; font-weight: bold">if</span> <span
 143         style="color: #333333">(</span><span
 144         style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
 145         style="color: #333333">.</span><span style="color: #0000CC">equals</span><span
 146         style="color: #333333">(</span>sf<span style="color: #333333">.</span><span
 147         style="color: #0000CC">type</span><span style="color: #333333">))</span>
 148         <span style="color: #333333">{</span>
 149             <span style="color: #008800; font-weight: bold">return</span> <span
 150         style="color: #008800; font-weight: bold">true</span>
 151         <span style="color: #333333">}</span>
 152     <span style="color: #333333">}</span>
 153     <span style="color: #008800; font-weight: bold">false</span>
 154 <span style="color: #333333">}</span>
 155
 156 <span style="color: #888888">/*</span>
 157 <span style="color: #888888"> * Closure that computes an annotation based on </span>
 158 <span style="color: #888888"> * presence of particular residues and features</span>
 159 <span style="color: #888888"> * Parameters are</span>
 160 <span style="color: #888888"> * - the name (label) for the alignment annotation</span>
 161 <span style="color: #888888"> * - the description (tooltip) for the annotation</span>
 162 <span style="color: #888888"> * - a closure (groovy function) that tests whether to include a residue</span>
 163 <span style="color: #888888"> * - a closure that tests whether to increment count based on sequence features  </span>
 164 <span style="color: #888888"> */</span>
 165 <span style="color: #333399; font-weight: bold">def</span> getColumnCounter <span
 166         style="color: #333333">=</span> <span style="color: #333333">{</span> name<span
 167         style="color: #333333">,</span> desc<span style="color: #333333">,</span> acceptResidue<span
 168         style="color: #333333">,</span> acceptFeatures <span
 169         style="color: #333333">-&gt;</span>
 170     <span style="color: #333333">[</span>
 171      <span style="color: #997700; font-weight: bold">getName:</span> <span
 172         style="color: #333333">{</span> name <span
 173         style="color: #333333">},</span>
 174      <span style="color: #997700; font-weight: bold">getDescription:</span> <span
 175         style="color: #333333">{</span> desc <span
 176         style="color: #333333">},</span>
 177      <span style="color: #997700; font-weight: bold">getMinColour:</span> <span
 178         style="color: #333333">{</span> <span style="color: #333333">[</span><span
 179         style="color: #0000DD; font-weight: bold">0</span><span
 180         style="color: #333333">,</span> <span
 181         style="color: #0000DD; font-weight: bold">255</span><span
 182         style="color: #333333">,</span> <span
 183         style="color: #0000DD; font-weight: bold">255</span><span
 184         style="color: #333333">]</span> <span style="color: #333333">},</span> <span
 185         style="color: #888888">// cyan</span>
 186      <span style="color: #997700; font-weight: bold">getMaxColour:</span> <span
 187         style="color: #333333">{</span> <span style="color: #333333">[</span><span
 188         style="color: #0000DD; font-weight: bold">0</span><span
 189         style="color: #333333">,</span> <span
 190         style="color: #0000DD; font-weight: bold">0</span><span
 191         style="color: #333333">,</span> <span
 192         style="color: #0000DD; font-weight: bold">255</span><span
 193         style="color: #333333">]</span> <span style="color: #333333">},</span> <span
 194         style="color: #888888">// blue</span>
 195      <span style="color: #997700; font-weight: bold">count:</span>
 196          <span style="color: #333333">{</span> res<span
 197         style="color: #333333">,</span> feats <span
 198         style="color: #333333">-&gt;</span>
 199             <span style="color: #333399; font-weight: bold">def</span> c <span
 200         style="color: #333333">=</span> <span
 201         style="color: #0000DD; font-weight: bold">0</span>
 202             <span style="color: #008800; font-weight: bold">if</span> <span
 203         style="color: #333333">(</span>acceptResidue<span
 204         style="color: #333333">.</span><span style="color: #0000CC">call</span><span
 205         style="color: #333333">(</span>res<span style="color: #333333">))</span>
 206             <span style="color: #333333">{</span>
 207                 <span style="color: #008800; font-weight: bold">if</span> <span
 208         style="color: #333333">(</span>acceptFeatures<span
 209         style="color: #333333">.</span><span style="color: #0000CC">call</span><span
 210         style="color: #333333">(</span>feats<span style="color: #333333">))</span>
 211                 <span style="color: #333333">{</span>
 212                     c<span style="color: #333333">++</span>
 213                 <span style="color: #333333">}</span>
 214             <span style="color: #333333">}</span>
 215             c
 216          <span style="color: #333333">}</span>
 217      <span style="color: #333333">]</span> <span
 218         style="color: #008800; font-weight: bold">as</span> FeatureCounterI
 219 <span style="color: #333333">}</span>
 220
 221 <span style="color: #888888">/*</span>
 222 <span style="color: #888888"> * Define an annotation row that counts any residue with Pfam domain annotation</span>
 223 <span style="color: #888888"> */</span>
 224 <span style="color: #333399; font-weight: bold">def</span> pfamAnnotation <span
 225         style="color: #333333">=</span> getColumnCounter<span
 226         style="color: #333333">(</span><span
 227         style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
 228         style="color: #333333">,</span> <span
 229         style="background-color: #fff0f0">&quot;Count of residues with Pfam domain annotation&quot;</span><span
 230         style="color: #333333">,</span> <span style="color: #333333">{</span><span
 231         style="color: #008800; font-weight: bold">true</span><span
 232         style="color: #333333">},</span> hasPfam<span
 233         style="color: #333333">)</span>
 234
 235 <span style="color: #888888">/*</span>
 236 <span style="color: #888888"> * Define an annotation row that counts charged residues with Pfam domain annotation</span>
 237 <span style="color: #888888"> */</span>
 238 <span style="color: #333399; font-weight: bold">def</span> chargedPfamAnnotation <span
 239         style="color: #333333">=</span> getColumnCounter<span
 240         style="color: #333333">(</span><span
 241         style="background-color: #fff0f0">&quot;Pfam charged&quot;</span><span
 242         style="color: #333333">,</span> <span
 243         style="background-color: #fff0f0">&quot;Count of charged residues with Pfam domain annotation&quot;</span><span
 244         style="color: #333333">,</span> isCharged<span
 245         style="color: #333333">,</span> hasPfam<span
 246         style="color: #333333">)</span>
 247
 248 <span style="color: #888888">/*</span>
 249 <span style="color: #888888"> * Register the annotations</span>
 250 <span style="color: #888888"> */</span>
 251 AlignmentAnnotationFactory<span style="color: #333333">.</span><span
 252         style="color: #0000CC">newCalculator</span><span
 253         style="color: #333333">(</span>pfamAnnotation<span
 254         style="color: #333333">)</span>
 255 AlignmentAnnotationFactory<span style="color: #333333">.</span><span
 256         style="color: #0000CC">newCalculator</span><span
 257         style="color: #333333">(</span>chargedPfamAnnotation<span
 258         style="color: #333333">)</span>
 259 </pre>
 260   </div>
 261 </body>
 262 </html>