javadoc

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

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 47aebd1..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.
@@ -72,12 +77,17 @@ public class TCoffeeColourScheme extends ResidueColourScheme {
               seqMap.put(al.sequenceRef, scores);
             }
           }
+    // TODO: compute average colour for each symbol type in each column - gives
+    // a second order colourscheme for colouring a sequence logo derived from
+    // the alignment (colour reflects quality of alignment for each residue
+    // class)
        }
        @Override
        public Color findColour(char c, int j, SequenceI seq) {
           Color[] cols;
 
          if( seqMap==null || (cols=seqMap.get(seq))==null) {
+//      see above TODO about computing a colour for each residue in each column:           cc = _rcols[i][indexFor[c]];
            return Color.white;
          }