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-<head>
-<title>Extending Jalview with Groovy - Feature Counter Example</title>
-</head>
-<body>
- <p>
- <strong>Extending Jalview with Groovy - A customisable
- feature counter</strong><br /> <br />The groovy script below shows how to
- add a new calculation track to a Jalview alignment window.
- </p>
- <p>As currently written, it will add two tracks to a protein
- alignment view which count Pfam features in each column, and ones
- where a charge residue also occur.</p>
- <p>To try it for yourself:</p>
- <ol>
- <li>Copy and paste it into the groovy script console</li>
- <li>Load the example Feredoxin project (the one that opens by
- default when you first launched Jalview)</li>
- <li>Select <strong>Calculations→Execute Groovy
- Script</strong> from the alignment window's menu bar to run the script on
- the current view.
- </li>
- </ol>
- <em><a
- 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>
- <!-- HTML generated using hilite.me -->
- <div
- style="background: #ffffff; overflow: auto; width: auto; border: solid gray; border-width: .1em .1em .1em .8em; padding: .2em .6em;">
- <pre style="margin: 0; line-height: 125%">
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)</span>
-<span style="color: #888888"> * Copyright (C) 2016 The Jalview Authors</span>
-<span style="color: #888888"> * </span>
-<span style="color: #888888"> * This file is part of Jalview.</span>
-<span style="color: #888888"> * </span>
-<span style="color: #888888"> * Jalview is free software: you can redistribute it and/or</span>
-<span style="color: #888888"> * modify it under the terms of the GNU General Public License </span>
-<span style="color: #888888"> * as published by the Free Software Foundation, either version 3</span>
-<span style="color: #888888"> * of the License, or (at your option) any later version.</span>
-<span style="color: #888888"> * </span>
-<span style="color: #888888"> * Jalview is distributed in the hope that it will be useful, but </span>
-<span style="color: #888888"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
-<span style="color: #888888"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
-<span style="color: #888888"> * PURPOSE. See the GNU General Public License for more details.</span>
-<span style="color: #888888"> * </span>
-<span style="color: #888888"> * You should have received a copy of the GNU General Public License</span>
-<span style="color: #888888"> * along with Jalview. If not, see <http://www.gnu.org/licenses/>.</span>
-<span style="color: #888888"> * The Jalview Authors are detailed in the 'AUTHORS' file.</span>
-<span style="color: #888888"> */</span>
-
-<span style="color: #008800; font-weight: bold">import</span> <span
- style="color: #0e84b5; font-weight: bold">jalview.workers.FeatureCounterI</span><span
- style="color: #333333">;</span>
-<span style="color: #008800; font-weight: bold">import</span> <span
- style="color: #0e84b5; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span
- style="color: #333333">;</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * Example script that registers two alignment annotation calculators</span>
-<span style="color: #888888"> * - one that counts residues in a column with Pfam annotation</span>
-<span style="color: #888888"> * - one that counts only charged residues with Pfam annotation</span>
-<span style="color: #888888"> *</span>
-<span style="color: #888888"> * To try:</span>
-<span style="color: #888888"> * 1. load uniref50.fa from the examples folder</span>
-<span style="color: #888888"> * 2. load features onto it from from examples/exampleFeatures.txt</span>
-<span style="color: #888888"> * 3. Open this script in the Groovy console.</span>
-<span style="color: #888888"> * 4. Either execute this script from the console, or via Calculate->Run Groovy Script</span>
-<span style="color: #888888"> </span>
-<span style="color: #888888"> * To explore further, try changing this script to count other kinds of occurrences of </span>
-<span style="color: #888888"> * residue and sequence features at columns in an alignment.</span>
-<span style="color: #888888"> */</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * A closure that returns true for any Charged residue</span>
-<span style="color: #888888"> */</span>
-<span style="color: #333399; font-weight: bold">def</span> isCharged <span
- style="color: #333333">=</span> <span style="color: #333333">{</span> residue <span
- style="color: #333333">-></span>
- <span style="color: #008800; font-weight: bold">switch</span><span
- style="color: #333333">(</span>residue<span
- style="color: #333333">)</span> <span style="color: #333333">{</span>
- <span style="color: #008800; font-weight: bold">case</span> <span
- style="color: #333333">[</span><span
- style="background-color: #fff0f0">'D'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'d'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'E'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'e'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'H'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'h'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'K'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'k'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'R'</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">'r'</span><span
- style="color: #333333">]:</span>
- <span style="color: #008800; font-weight: bold">return</span> <span
- style="color: #008800; font-weight: bold">true</span>
- <span style="color: #333333">}</span>
- <span style="color: #008800; font-weight: bold">false</span>
-<span style="color: #333333">}</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * A closure that returns 1 if sequence features include type 'Pfam', else 0</span>
-<span style="color: #888888"> * Argument should be a list of SequenceFeature </span>
-<span style="color: #888888"> */</span>
-<span style="color: #333399; font-weight: bold">def</span> hasPfam <span
- style="color: #333333">=</span> <span style="color: #333333">{</span> features <span
- style="color: #333333">-></span>
- <span style="color: #008800; font-weight: bold">for</span> <span
- style="color: #333333">(</span>sf <span
- style="color: #008800; font-weight: bold">in</span> features<span
- style="color: #333333">)</span>
- <span style="color: #333333">{</span>
- <span style="color: #888888">/*</span>
-<span style="color: #888888"> * Here we inspect the type of the sequence feature.</span>
-<span style="color: #888888"> * You can also test sf.description, sf.score, sf.featureGroup,</span>
-<span style="color: #888888"> * sf.strand, sf.phase, sf.begin, sf.end</span>
-<span style="color: #888888"> * or sf.getValue(attributeName) for GFF 'column 9' properties</span>
-<span style="color: #888888"> */</span>
- <span style="color: #008800; font-weight: bold">if</span> <span
- style="color: #333333">(</span><span
- style="background-color: #fff0f0">"Pfam"</span><span
- style="color: #333333">.</span><span style="color: #0000CC">equals</span><span
- style="color: #333333">(</span>sf<span style="color: #333333">.</span><span
- style="color: #0000CC">type</span><span style="color: #333333">))</span>
- <span style="color: #333333">{</span>
- <span style="color: #008800; font-weight: bold">return</span> <span
- style="color: #008800; font-weight: bold">true</span>
- <span style="color: #333333">}</span>
- <span style="color: #333333">}</span>
- <span style="color: #008800; font-weight: bold">false</span>
-<span style="color: #333333">}</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * Closure that computes an annotation based on </span>
-<span style="color: #888888"> * presence of particular residues and features</span>
-<span style="color: #888888"> * Parameters are</span>
-<span style="color: #888888"> * - the name (label) for the alignment annotation</span>
-<span style="color: #888888"> * - the description (tooltip) for the annotation</span>
-<span style="color: #888888"> * - a closure (groovy function) that tests whether to include a residue</span>
-<span style="color: #888888"> * - a closure that tests whether to increment count based on sequence features </span>
-<span style="color: #888888"> */</span>
-<span style="color: #333399; font-weight: bold">def</span> getColumnCounter <span
- style="color: #333333">=</span> <span style="color: #333333">{</span> name<span
- style="color: #333333">,</span> desc<span style="color: #333333">,</span> acceptResidue<span
- style="color: #333333">,</span> acceptFeatures <span
- style="color: #333333">-></span>
- <span style="color: #333333">[</span>
- <span style="color: #997700; font-weight: bold">getName:</span> <span
- style="color: #333333">{</span> name <span
- style="color: #333333">},</span>
- <span style="color: #997700; font-weight: bold">getDescription:</span> <span
- style="color: #333333">{</span> desc <span
- style="color: #333333">},</span>
- <span style="color: #997700; font-weight: bold">getMinColour:</span> <span
- style="color: #333333">{</span> <span style="color: #333333">[</span><span
- style="color: #0000DD; font-weight: bold">0</span><span
- style="color: #333333">,</span> <span
- style="color: #0000DD; font-weight: bold">255</span><span
- style="color: #333333">,</span> <span
- style="color: #0000DD; font-weight: bold">255</span><span
- style="color: #333333">]</span> <span style="color: #333333">},</span> <span
- style="color: #888888">// cyan</span>
- <span style="color: #997700; font-weight: bold">getMaxColour:</span> <span
- style="color: #333333">{</span> <span style="color: #333333">[</span><span
- style="color: #0000DD; font-weight: bold">0</span><span
- style="color: #333333">,</span> <span
- style="color: #0000DD; font-weight: bold">0</span><span
- style="color: #333333">,</span> <span
- style="color: #0000DD; font-weight: bold">255</span><span
- style="color: #333333">]</span> <span style="color: #333333">},</span> <span
- style="color: #888888">// blue</span>
- <span style="color: #997700; font-weight: bold">count:</span>
- <span style="color: #333333">{</span> res<span
- style="color: #333333">,</span> feats <span
- style="color: #333333">-></span>
- <span style="color: #333399; font-weight: bold">def</span> c <span
- style="color: #333333">=</span> <span
- style="color: #0000DD; font-weight: bold">0</span>
- <span style="color: #008800; font-weight: bold">if</span> <span
- style="color: #333333">(</span>acceptResidue<span
- style="color: #333333">.</span><span style="color: #0000CC">call</span><span
- style="color: #333333">(</span>res<span style="color: #333333">))</span>
- <span style="color: #333333">{</span>
- <span style="color: #008800; font-weight: bold">if</span> <span
- style="color: #333333">(</span>acceptFeatures<span
- style="color: #333333">.</span><span style="color: #0000CC">call</span><span
- style="color: #333333">(</span>feats<span style="color: #333333">))</span>
- <span style="color: #333333">{</span>
- c<span style="color: #333333">++</span>
- <span style="color: #333333">}</span>
- <span style="color: #333333">}</span>
- c
- <span style="color: #333333">}</span>
- <span style="color: #333333">]</span> <span
- style="color: #008800; font-weight: bold">as</span> FeatureCounterI
-<span style="color: #333333">}</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * Define an annotation row that counts any residue with Pfam domain annotation</span>
-<span style="color: #888888"> */</span>
-<span style="color: #333399; font-weight: bold">def</span> pfamAnnotation <span
- style="color: #333333">=</span> getColumnCounter<span
- style="color: #333333">(</span><span
- style="background-color: #fff0f0">"Pfam"</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">"Count of residues with Pfam domain annotation"</span><span
- style="color: #333333">,</span> <span style="color: #333333">{</span><span
- style="color: #008800; font-weight: bold">true</span><span
- style="color: #333333">},</span> hasPfam<span
- style="color: #333333">)</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * Define an annotation row that counts charged residues with Pfam domain annotation</span>
-<span style="color: #888888"> */</span>
-<span style="color: #333399; font-weight: bold">def</span> chargedPfamAnnotation <span
- style="color: #333333">=</span> getColumnCounter<span
- style="color: #333333">(</span><span
- style="background-color: #fff0f0">"Pfam charged"</span><span
- style="color: #333333">,</span> <span
- style="background-color: #fff0f0">"Count of charged residues with Pfam domain annotation"</span><span
- style="color: #333333">,</span> isCharged<span
- style="color: #333333">,</span> hasPfam<span
- style="color: #333333">)</span>
-
-<span style="color: #888888">/*</span>
-<span style="color: #888888"> * Register the annotations</span>
-<span style="color: #888888"> */</span>
-AlignmentAnnotationFactory<span style="color: #333333">.</span><span
- style="color: #0000CC">newCalculator</span><span
- style="color: #333333">(</span>pfamAnnotation<span
- style="color: #333333">)</span>
-AlignmentAnnotationFactory<span style="color: #333333">.</span><span
- style="color: #0000CC">newCalculator</span><span
- style="color: #333333">(</span>chargedPfamAnnotation<span
- style="color: #333333">)</span>
-</pre>
- </div>
-</body>
-</html>
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