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

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

diff --git a/examples/groovy/visibleFeaturesCounter.groovy b/examples/groovy/visibleFeaturesCounter.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.bin.Jalview
+import jalview.workers.FeatureSetCounterI
+import jalview.workers.AlignmentAnnotationFactory
+
+/*
+ * Demonstration of FeatureSetCounterI
+ * compute annotation tracks counting number of displayed 
+ * features of each type in each column
+ */
+
+/*
+ * discover features on the current view
+ */
+ 
+def featuresDisp=Jalview.currentAlignFrame.currentView.featuresDisplayed
+if (featuresDisp == null) {
+    print 'Need at least one feature visible on alignment'
+}
+def visibleFeatures=featuresDisp.visibleFeatures.toList()
+assert 'java.util.ArrayList' == visibleFeatures.class.name
+
+/*
+ * A closure that returns an array of features present 
+ * for each feature type in visibleFeatures
+ * Argument 'features' will be a list of SequenceFeature 
+ */
+def getCounts = 
+    { features -> 
+        int[] obs = new int[visibleFeatures.size]
+        for (sf in features)
+        {
+            /*
+             * 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
+             */
+            int pos = 0
+            for (type in visibleFeatures) 
+            {
+              if (type.equals(sf.type)) 
+              {
+                  obs[pos]++
+              }
+              pos++
+            }
+        }
+        obs
+}
+  
+/*
+ * Define something that counts each visible feature type
+ */
+def columnSetCounter =
+    [
+     getNames: { visibleFeatures as String[] }, 
+     getDescriptions:  { visibleFeatures as String[] },
+     getMinColour: { [0, 255, 255] as int[] }, // cyan
+     getMaxColour: { [0, 0, 255] as int[] }, // blue
+     count: 
+         { res, feats -> 
+             getCounts.call(feats) 
+         }
+     ] as FeatureSetCounterI
+
+/*
+ * and register the counter
+ */
+AlignmentAnnotationFactory.newCalculator(columnSetCounter)