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JAL-2189 JAL-1812 JAL-2068 new groovy docs (new files add to commit c8c1f2a)
authorJim Procter <jprocter@issues.jalview.org>
Thu, 22 Sep 2016 14:04:06 +0000 (15:04 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Thu, 22 Sep 2016 14:04:06 +0000 (15:04 +0100)
help/html/groovy/featureCounter.html [new file with mode: 0644] patch | blob

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+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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&#8594;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 &lt;http://www.gnu.org/licenses/&gt;.</span>
+<span style="color: #888888"> * The Jalview Authors are detailed in the &#39;AUTHORS&#39; 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-&gt;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">-&gt;</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">&#39;D&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;d&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;E&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;e&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;H&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;h&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;K&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;k&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;R&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;r&#39;</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 &#39;Pfam&#39;, 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">-&gt;</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 &#39;column 9&#39; 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">&quot;Pfam&quot;</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">-&gt;</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">-&gt;</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">&quot;Pfam&quot;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&quot;Count of residues with Pfam domain annotation&quot;</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">&quot;Pfam charged&quot;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&quot;Count of charged residues with Pfam domain annotation&quot;</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>