todo for JAL-1106

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

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index bbd2a23..1063f8b 100644 (file)
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -53,11 +53,16 @@ public class TCoffeeColourScheme extends ResidueColourScheme {
           ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
           // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
           seqMap = new IdentityHashMap<SequenceI, Color[]>();
-          for (AlignmentAnnotation al:alignment.getAlignmentAnnotation())
+          int w=0;
+          for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
           {
-            if (al.sequenceRef!=null && !al.belowAlignment && al.label!=null && (al.label==TCoffeeScoreFile.TCOFFEE_SCORE || al.label.equals(TCoffeeScoreFile.TCOFFEE_SCORE)))
+            if (al.sequenceRef!=null && !al.belowAlignment)
             {
               annots.add(al);
+              if (w<al.annotations.length)
+              {
+                w=al.annotations.length;
+              }
               Color[] scores=new Color[al.annotations.length];
               int i=0;
               for (Annotation an:al.annotations)
@@ -67,12 +72,17 @@ 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;
          }