X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fgroovy%2FcolourSchemes.groovy;h=eb40cc627dd9cb8b29277127b3ef47382a38dcee;hb=HEAD;hp=27e179b39235203296e639878cdd0fb2707d0c27;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/examples/groovy/colourSchemes.groovy b/examples/groovy/colourSchemes.groovy
index 27e179b..eb40cc6 100644
--- a/examples/groovy/colourSchemes.groovy
+++ b/examples/groovy/colourSchemes.groovy
@@ -1,54 +1,94 @@
 import java.awt.Color;
-import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.api.AlignViewportI
 
 /*
  * Example script that registers two new alignment colour schemes
  */
 
 /*
- * Class that defines a colour scheme where odd columns are red,
- * even numbered columns are blue, and gaps are yellow  
+ * Closure that defines a colour scheme where consensus residues are pink,
+ * other residues are red in odd columns and blue in even columns, and
+ * gaps are yellow  
  */
-class Stripy extends ResidueColourScheme {
-    Stripy() { }
-    String getSchemeName() { "stripy" }
-    Stripy getInstance(AnnotatedCollectionI coll, Map map) { new Stripy() }
-    Color findColour(char res, int col, SequenceI seq) 
-    {
+def candy
+candy = { ->
+  [
+    /*
+     * name shown in the colour menu
+     */
+    getSchemeName: { -> 'candy' },
+    
+    /*
+     * to make a new instance for each alignment view
+     */
+    getInstance: { view, coll -> candy() },
+    
+    /*
+     * 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 (res == ' ' || res == '-' || res == '.') 
         {
             Color.yellow
-         } else if (col % 2 == 0) 
-         {
+        } else if (consensus.contains(String.valueOf(res)))
+        {
+            Color.pink
+        } else if (col % 2 == 0) 
+        {
             Color.blue
-         } else 
-         {
+        } 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
 }
 
 /*
- * Class that defines a colour scheme graduated 
- * (approximately) by amino acid weight  
+ * A closure that defines a colour scheme graduated 
+ * (approximately) by amino acid weight
+ * here from lightest (G) Blue, to heaviest (W) Red
  */
-class ByWeight extends ResidueColourScheme {
-    int min = 75
-    int max = 204
-    ByWeight() { }
-    boolean isPeptideSpecific() {true}
-    String getSchemeName() { "By Weight" }
-    ByWeight getInstance(AnnotatedCollectionI coll, Map map) { new ByWeight() }
-    Color makeColour(int weight) 
-    {
-      int i = 255 * (weight - min) / (max - min);
-      new Color(i, 0, i);
-    }
-    Color findColour(char res, int col, SequenceI seq) 
-    {
+def makeColour = { weight -> 
+    minWeight = 75 // Glycine
+    maxWeight = 204 // Tryptophan
+    int i = 255 * (weight - minWeight) / (maxWeight - minWeight);
+    new Color(i, 0, 255-i);
+}
+def byWeight
+byWeight = { ->
+  [
+    getSchemeName: { 'By Weight' },
+    // this colour scheme is peptide-specific:
+    isApplicableTo: { coll -> !coll.isNucleotide() },
+    alignmentChanged: { coll, map -> },
+    getInstance: { view, coll -> byWeight() },
+    isSimple: { true },
+    findColour: {res, col, seq, consensus, pid -> 
         switch (res) {
           case ' ':
           case '-':
@@ -109,7 +149,8 @@ class ByWeight extends ResidueColourScheme {
             makeColour(150)
         }
       }
+  ] as ColourSchemeI
 }
 
-ColourSchemes.instance.registerColourScheme(new Stripy())
-ColourSchemes.instance.registerColourScheme(new ByWeight())
+ColourSchemes.instance.registerColourScheme(candy())
+ColourSchemes.instance.registerColourScheme(byWeight())