help/help/html/groovy/featuresCounter.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   <strong>Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.</strong><br/><br/>
  45   <em><a
  46     href="http://www.jalview.org/examples/groovy/featuresCounter.groovy">http://www.jalview.org/examples/groovy/featuresCounter.groovy</a>
  47     - rendered with <a href="http://hilite.me">hilite.me</a></em>
  48   <!-- HTML generated using hilite.me --><div style="background: #f8f8f8; 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: #408080; font-style: italic">/*</span>
  49 <span style="color: #408080; font-style: italic"> * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)</span>
  50 <span style="color: #408080; font-style: italic"> * Copyright (C) $$Year-Rel$$ The Jalview Authors</span>
  51 <span style="color: #408080; font-style: italic"> * </span>
  52 <span style="color: #408080; font-style: italic"> * This file is part of Jalview.</span>
  53 <span style="color: #408080; font-style: italic"> * </span>
  54 <span style="color: #408080; font-style: italic"> * Jalview is free software: you can redistribute it and/or</span>
  55 <span style="color: #408080; font-style: italic"> * modify it under the terms of the GNU General Public License </span>
  56 <span style="color: #408080; font-style: italic"> * as published by the Free Software Foundation, either version 3</span>
  57 <span style="color: #408080; font-style: italic"> * of the License, or (at your option) any later version.</span>
  58 <span style="color: #408080; font-style: italic"> *  </span>
  59 <span style="color: #408080; font-style: italic"> * Jalview is distributed in the hope that it will be useful, but </span>
  60 <span style="color: #408080; font-style: italic"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
  61 <span style="color: #408080; font-style: italic"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
  62 <span style="color: #408080; font-style: italic"> * PURPOSE.  See the GNU General Public License for more details.</span>
  63 <span style="color: #408080; font-style: italic"> * </span>
  64 <span style="color: #408080; font-style: italic"> * You should have received a copy of the GNU General Public License</span>
  65 <span style="color: #408080; font-style: italic"> * along with Jalview.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
  66 <span style="color: #408080; font-style: italic"> * The Jalview Authors are detailed in the &#39;AUTHORS&#39; file.</span>
  67 <span style="color: #408080; font-style: italic"> */</span>
  68
  69 <span style="color: #008000; font-weight: bold">import</span> <span style="color: #0000FF; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span style="color: #666666">;</span>
  70 <span style="color: #008000; font-weight: bold">import</span> <span style="color: #0000FF; font-weight: bold">jalview.workers.FeatureSetCounterI</span><span style="color: #666666">;</span>
  71
  72 <span style="color: #408080; font-style: italic">/*</span>
  73 <span style="color: #408080; font-style: italic"> * Example script to compute two alignment annotations</span>
  74 <span style="color: #408080; font-style: italic"> * - count of Phosphorylation features</span>
  75 <span style="color: #408080; font-style: italic"> * - count of Turn features</span>
  76 <span style="color: #408080; font-style: italic"> * To try this, first load example file uniref50.fa and load on features file</span>
  77 <span style="color: #408080; font-style: italic"> * exampleFeatures.txt, before running this script</span>
  78 <span style="color: #408080; font-style: italic"> *</span>
  79 <span style="color: #408080; font-style: italic"> * The script only needs to be run once - it will be registered by Jalview</span>
  80 <span style="color: #408080; font-style: italic"> * and recalculated automatically when the alignment changes.</span>
  81 <span style="color: #408080; font-style: italic"> * </span>
  82 <span style="color: #408080; font-style: italic"> * Note: The feature api provided by 2.10.2 is not compatible with scripts</span>
  83 <span style="color: #408080; font-style: italic"> * that worked with earlier Jalview versions. Apologies for the inconvenience.</span>
  84 <span style="color: #408080; font-style: italic"> */</span>
  85
  86 <span style="color: #B00040">def</span> annotator <span style="color: #666666">=</span>
  87     <span style="color: #666666">[</span>
  88      <span style="color: #A0A000">getNames:</span> <span style="color: #666666">{</span> <span style="color: #666666">[</span><span style="color: #BA2121">&#39;Phosphorylation&#39;</span><span style="color: #666666">,</span> <span style="color: #BA2121">&#39;Turn&#39;</span><span style="color: #666666">]</span> <span style="color: #008000; font-weight: bold">as</span> String<span style="color: #666666">[]</span> <span style="color: #666666">},</span>
  89      <span style="color: #A0A000">getDescriptions:</span>  <span style="color: #666666">{</span> <span style="color: #666666">[</span><span style="color: #BA2121">&#39;Count of Phosphorylation features&#39;</span><span style="color: #666666">,</span> <span style="color: #BA2121">&#39;Count of Turn features&#39;</span><span style="color: #666666">]</span> <span style="color: #008000; font-weight: bold">as</span> String<span style="color: #666666">[]</span> <span style="color: #666666">},</span>
  90      <span style="color: #A0A000">getMinColour:</span> <span style="color: #666666">{</span> <span style="color: #666666">[0,</span> <span style="color: #666666">255,</span> <span style="color: #666666">255]</span> <span style="color: #008000; font-weight: bold">as</span> <span style="color: #B00040">int</span><span style="color: #666666">[]</span> <span style="color: #666666">},</span> <span style="color: #408080; font-style: italic">// cyan</span>
  91      <span style="color: #A0A000">getMaxColour:</span> <span style="color: #666666">{</span> <span style="color: #666666">[0,</span> <span style="color: #666666">0,</span> <span style="color: #666666">255]</span> <span style="color: #008000; font-weight: bold">as</span> <span style="color: #B00040">int</span><span style="color: #666666">[]</span> <span style="color: #666666">},</span> <span style="color: #408080; font-style: italic">// blue</span>
  92      <span style="color: #A0A000">count:</span>
  93          <span style="color: #666666">{</span> res<span style="color: #666666">,</span> feats <span style="color: #666666">-&gt;</span>
  94                 <span style="color: #B00040">int</span> phos
  95                 <span style="color: #B00040">int</span> turn
  96                 <span style="color: #0000FF">for</span> <span style="color: #666666">(</span>sf <span style="color: #008000; font-weight: bold">in</span> feats<span style="color: #666666">)</span>
  97                 <span style="color: #666666">{</span>
  98                           <span style="color: #408080; font-style: italic">/*</span>
  99 <span style="color: #408080; font-style: italic">                          * Here we inspect the type of the sequence feature.</span>
 100 <span style="color: #408080; font-style: italic">                          * You can also test sf.description, sf.score, sf.featureGroup,</span>
 101 <span style="color: #408080; font-style: italic">                          * sf.strand, sf.phase, sf.begin, sf.end</span>
 102 <span style="color: #408080; font-style: italic">                          * or sf.getValue(attributeName) for GFF &#39;column 9&#39; properties</span>
 103 <span style="color: #408080; font-style: italic">                          */</span>
 104                            <span style="color: #008000; font-weight: bold">if</span> <span style="color: #666666">(</span>sf<span style="color: #666666">.</span><span style="color: #7D9029">type</span><span style="color: #666666">.</span><span style="color: #7D9029">contains</span><span style="color: #666666">(</span><span style="color: #BA2121">&#39;TURN&#39;</span><span style="color: #666666">))</span>
 105                    <span style="color: #666666">{</span>
 106                       turn<span style="color: #666666">++</span>
 107                    <span style="color: #666666">}</span>
 108                    <span style="color: #008000; font-weight: bold">if</span> <span style="color: #666666">(</span>sf<span style="color: #666666">.</span><span style="color: #7D9029">type</span><span style="color: #666666">.</span><span style="color: #7D9029">contains</span><span style="color: #666666">(</span><span style="color: #BA2121">&#39;PHOSPHORYLATION&#39;</span><span style="color: #666666">))</span>
 109                    <span style="color: #666666">{</span>
 110                       phos<span style="color: #666666">++</span>
 111                    <span style="color: #666666">}</span>
 112                 <span style="color: #666666">}</span>
 113                 <span style="color: #666666">[</span>phos<span style="color: #666666">,</span> turn<span style="color: #666666">]</span> <span style="color: #008000; font-weight: bold">as</span> <span style="color: #B00040">int</span><span style="color: #666666">[]</span>
 114          <span style="color: #666666">}</span>
 115      <span style="color: #666666">]</span> <span style="color: #008000; font-weight: bold">as</span> FeatureSetCounterI
 116
 117 <span style="color: #408080; font-style: italic">/*</span>
 118 <span style="color: #408080; font-style: italic"> * Register the annotation calculator with Jalview</span>
 119 <span style="color: #408080; font-style: italic"> */</span>
 120 AlignmentAnnotationFactory<span style="color: #666666">.</span><span style="color: #7D9029">newCalculator</span><span style="color: #666666">(</span>annotator<span style="color: #666666">)</span>
 121 </pre></div>
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