Extending Jalview with Groovy - Feature Counter Example

- Extending Jalview with Groovy - A customisable - feature counter

The groovy script below shows how to - add a new calculation track to a Jalview alignment window. -

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.

-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)
- * Copyright (C) 2016 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.FeatureCounterI;
-import jalview.workers.AlignmentAnnotationFactory;
-
-/*
- * Example script that registers two alignment annotation calculators
- * - one that counts residues in a column with Pfam annotation
- * - one that counts only charged residues with Pfam annotation
- *
- * To try:
- * 1. load uniref50.fa from the examples folder
- * 2. load features onto it from from examples/exampleFeatures.txt
- * 3. Open this script in the Groovy console.
- * 4. Either execute this script from the console, or via Calculate->Run Groovy Script
- 
- * To explore further, try changing this script to count other kinds of occurrences of 
- * residue and sequence features at columns in an alignment.
- */
-
-/*
- * A closure that returns true for any Charged residue
- */
-def isCharged = { residue ->
-    switch(residue) {
-        case ['D', 'd', 'E', 'e', 'H', 'h', 'K', 'k', 'R', 'r']:
-            return true
-    }
-    false
-} 
-
-/*
- * A closure that returns 1 if sequence features include type 'Pfam', else 0
- * Argument should be a list of SequenceFeature 
- */
-def hasPfam = { features -> 
-    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
-         */
-        if ("Pfam".equals(sf.type))
-        {
-            return true
-        }
-    }
-    false
-}
-
-/*
- * Closure that computes an annotation based on 
- * presence of particular residues and features
- * Parameters are
- * - the name (label) for the alignment annotation
- * - the description (tooltip) for the annotation
- * - a closure (groovy function) that tests whether to include a residue
- * - a closure that tests whether to increment count based on sequence features  
- */
-def getColumnCounter = { name, desc, acceptResidue, acceptFeatures ->
-    [
-     getName: { name }, 
-     getDescription: { desc },
-     getMinColour: { [0, 255, 255] }, // cyan
-     getMaxColour: { [0, 0, 255] }, // blue
-     count: 
-         { res, feats -> 
-            def c = 0
-            if (acceptResidue.call(res))
-            {
-                if (acceptFeatures.call(feats))
-                {
-                    c++
-                }
-            }
-            c
-         }
-     ] as FeatureCounterI
-}
-
-/*
- * Define an annotation row that counts any residue with Pfam domain annotation
- */
-def pfamAnnotation = getColumnCounter("Pfam", "Count of residues with Pfam domain annotation", {true}, hasPfam)
-
-/*
- * Define an annotation row that counts charged residues with Pfam domain annotation
- */
-def chargedPfamAnnotation = getColumnCounter("Pfam charged", "Count of charged residues with Pfam domain annotation", isCharged, hasPfam)
-
-/*
- * Register the annotations
- */
-AlignmentAnnotationFactory.newCalculator(pfamAnnotation) 
-AlignmentAnnotationFactory.newCalculator(chargedPfamAnnotation)
-

+ Extending Jalview with Groovy - A customisable + feature counter

The groovy script below shows how to + add a new calculation track to a Jalview alignment window. +

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.

/*
+ * 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) 
+