JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

[jalview.git] / src / jalview / schemes / TCoffeeColourScheme.java

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 1063f8b..5a49640 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -5,12 +5,14 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.io.TCoffeeScoreFile;
 
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.IdentityHashMap;
+import java.util.Map;
 import java.util.TreeMap;
 
 /**
@@ -45,10 +47,13 @@ public class TCoffeeColourScheme extends ResidueColourScheme {
         * @param alignment - annotated sequences to be searched
         */
        public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
-         alignmentChanged(alignment);
+         alignmentChanged(alignment, null);
        }
-       @Override public void alignmentChanged(AnnotatedCollectionI alignment)
+       @Override 
+       public void alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)
        {
+         // TODO: if sequences have been represented and they have scores, could compute an average sequence score for the representative
+         
           // assume only one set of TCOFFEE scores - but could have more than one potentially.
           ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
           // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.