Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / examples / groovy / featuresCounter.groovy

diff --git a/examples/groovy/featuresCounter.groovy b/examples/groovy/featuresCounter.groovy
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+/*
+ * 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.
+ */
+
+import jalview.workers.AlignmentAnnotationFactory;
+import jalview.workers.FeatureSetCounterI;
+
+/*
+ * Example script to compute two alignment annotations
+ * - count of Phosphorylation features
+ * - count of Turn features
+ * To try this, first load example file uniref50.fa and load on features file
+ * exampleFeatures.txt, before running this script
+ *
+ * The script only needs to be run once - it will be registered by Jalview
+ * and recalculated automatically when the alignment changes.
+ * 
+ * Note: The feature api provided by 2.10.2 is not compatible with scripts
+ * that worked with earlier Jalview versions. Apologies for the inconvenience.
+ */
+ 
+def annotator = 
+    [
+     getNames: { ['Phosphorylation', 'Turn'] as String[] }, 
+     getDescriptions:  { ['Count of Phosphorylation features', 'Count of Turn features'] as String[] },
+     getMinColour: { [0, 255, 255] as int[] }, // cyan
+     getMaxColour: { [0, 0, 255] as int[] }, // blue
+     count: 
+         { res, feats -> 
+                int phos
+                int turn
+                for (sf in feats)
+                {
+                         /*
+                          * Here we inspect the type of the sequence feature.
+                          * You can also test sf.description, sf.score, sf.featureGroup,
+                          * sf.strand, sf.phase, sf.begin, sf.end
+                          * or sf.getValue(attributeName) for GFF 'column 9' properties
+                          */
+                          if (sf.type.contains('TURN'))
+                   {
+                      turn++
+                   }
+                   if (sf.type.contains('PHOSPHORYLATION'))
+                   {
+                      phos++
+                   }
+                }
+                [phos, turn] as int[]
+         }
+     ] as FeatureSetCounterI
+    
+/*
+ * Register the annotation calculator with Jalview
+ */
+AlignmentAnnotationFactory.newCalculator(annotator)