JAL-384 - groovy scripts for conserved/unconserved colourscheme requests

diff --git a/examples/groovy/colourConserved.groovy b/examples/groovy/colourConserved.groovy
new file mode 100644 (file)
index 0000000..4a15922
--- /dev/null
+++ b/examples/groovy/colourConserved.groovy
@@ -0,0 +1,88 @@
+/*
+ * 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 java.awt.Color
+import jalview.schemes.ColourSchemeI
+import jalview.schemes.ColourSchemes
+import jalview.datamodel.AnnotatedCollectionI
+import jalview.datamodel.SequenceI
+import jalview.datamodel.SequenceCollectionI
+import jalview.util.Comparison
+
+/*
+ * Closure that defines a colour scheme where fully conserved residues are red,
+ * partly conserved (match consensus but < 100% consensus) are yellow,
+ * unconserved and gaps are white
+ */
+def conserved
+conserved = { ->
+  [
+    /*
+     * name shown in the colour menu
+     */
+    getSchemeName: { -> 'Conserved' },
+    
+    /*
+     * to make a new instance for each alignment view
+     */
+    getInstance: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> conserved() },
+    
+    /*
+     * method only needed if colour scheme has to recalculate
+     * values when an alignment is modified
+     */
+    alignmentChanged: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> },
+    
+    /*
+     * determine colour for a residue at an aligned position of a
+     * sequence, given consensus residue(s) for the column and the
+     * consensus percentage identity score for the column
+     */
+    findColour: { char res, int col, SequenceI seq, String consensus, float pid -> 
+        if ('a' <= res && res <= 'z')
+        {
+            res -= ('a' - 'A');
+        }
+        if (Comparison.isGap(res) || !consensus.contains(String.valueOf(res)))
+        {
+            Color.white
+        } else if (pid < 100)
+        {
+            Color.yellow
+        } else
+        {
+            Color.red
+        }
+    },
+    
+    /*
+     * true means applicable to nucleotide or peptide data
+     */
+    isApplicableTo: {AnnotatedCollectionI coll -> true},
+    
+    /*
+     * simple colour schemes are those that depend on the residue
+     * only (these are also available to colour structure viewers)
+     */
+    isSimple: { false }
+ ] as ColourSchemeI
+}
+
+ColourSchemes.instance.registerColourScheme(conserved())

diff --git a/examples/groovy/colourUnconserved.groovy b/examples/groovy/colourUnconserved.groovy
new file mode 100644 (file)
index 0000000..68730f3
--- /dev/null
+++ b/examples/groovy/colourUnconserved.groovy
@@ -0,0 +1,84 @@
+/*
+ * 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 java.awt.Color
+import jalview.schemes.ColourSchemeI
+import jalview.schemes.ColourSchemes
+import jalview.datamodel.AnnotatedCollectionI
+import jalview.datamodel.SequenceI
+import jalview.datamodel.SequenceCollectionI
+import jalview.util.Comparison
+
+/*
+ * Closure that defines a colour scheme where non-consensus residues are pink,
+ * other residues (and gaps) are white
+ */
+def unconserved
+unconserved = { ->
+  [
+    /*
+     * name shown in the colour menu
+     */
+    getSchemeName: { -> 'Unconserved' },
+    
+    /*
+     * to make a new instance for each alignment view
+     */
+    getInstance: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> unconserved() },
+    
+    /*
+     * method only needed if colour scheme has to recalculate
+     * values when an alignment is modified
+     */
+    alignmentChanged: { AnnotatedCollectionI coll, Map<SequenceI, SequenceCollectionI> map -> },
+    
+    /*
+     * determine colour for a residue at an aligned position of a
+     * sequence, given consensus residue(s) for the column and the
+     * consensus percentage identity score for the column
+     */
+    findColour: { char res, int col, SequenceI seq, String consensus, float pid -> 
+        if ('a' <= res && res <= 'z')
+        {
+            res -= ('a' - 'A');
+        }
+        if (Comparison.isGap(res) || consensus.contains(String.valueOf(res)))
+        {
+            Color.white
+        } else 
+        {
+            Color.pink
+        }
+    },
+    
+    /*
+     * true means applicable to nucleotide or peptide data
+     */
+    isApplicableTo: {AnnotatedCollectionI coll -> true},
+    
+    /*
+     * simple colour schemes are those that depend on the residue
+     * only (these are also available to colour structure viewers)
+     */
+    isSimple: { false }
+ ] as ColourSchemeI
+}
+
+ColourSchemes.instance.registerColourScheme(unconserved())