X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;fp=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=bbd2a23c4c4bce57c2a004f31d8f9d8f6b04aabb;hb=6a3f4318037072a77588afb951a5a53835d5da99;hp=740c15ec6388b0b30bbdf82f33a624bf0d40caa8;hpb=1379350f04bc63ca05bd428afb86717c4764755d;p=jalview.git

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 740c15e..bbd2a23 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,8 +1,17 @@
 package jalview.schemes;
 
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 import jalview.io.TCoffeeScoreFile;
 
 import java.awt.Color;
+import java.util.ArrayList;
+import java.util.IdentityHashMap;
+import java.util.TreeMap;
 
 /**
  * Defines the color score for T-Coffee MSA 
@@ -29,38 +38,47 @@ public class TCoffeeColourScheme extends ResidueColourScheme {
 	};
 
 
-	byte[][] scoreMatrix = null;
-
+	IdentityHashMap<SequenceI, Color[]> seqMap;
 	/**
-	 * Initialize the color sheme based on the content of the T-Coffee score file 
+	 * the color scheme needs to look at the alignment to get and cache T-COFFEE scores 
 	 * 
-	 * @param scoreFile
+	 * @param alignment - annotated sequences to be searched
 	 */
-	public TCoffeeColourScheme(TCoffeeScoreFile scoreFile) {
-
-		scoreMatrix = scoreFile != null ? scoreFile.getScoresArray() : null;
-
+	public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
+	  alignmentChanged(alignment);
+	}
+	@Override public void alignmentChanged(AnnotatedCollectionI alignment)
+	{
+          // 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.
+          seqMap = new IdentityHashMap<SequenceI, Color[]>();
+          for (AlignmentAnnotation al:alignment.getAlignmentAnnotation())
+          {
+            if (al.sequenceRef!=null && !al.belowAlignment && al.label!=null && (al.label==TCoffeeScoreFile.TCOFFEE_SCORE || al.label.equals(TCoffeeScoreFile.TCOFFEE_SCORE)))
+            {
+              annots.add(al);
+              Color[] scores=new Color[al.annotations.length];
+              int i=0;
+              for (Annotation an:al.annotations)
+              {
+                scores[i++]=(an!=null) ? an.colour : Color.white;
+              }
+              seqMap.put(al.sequenceRef, scores);
+            }
+          }
 	}
-
 	@Override
-	public Color findColour(char c, int j, int sequenceIndex) {
-
-		if( scoreMatrix == null ) {
-			return Color.white;
-		}
-		
-		if( sequenceIndex<0  || sequenceIndex >= scoreMatrix.length ) {
-			System.out.printf("Sequence index out of range for the T-Coffee color scheme. Index:  %s\n", sequenceIndex);
-			return Color.white;
-		}
+	public Color findColour(char c, int j, SequenceI seq) {
+          Color[] cols;
 
-		byte[] seqScores = scoreMatrix[sequenceIndex]; 
-		if( j < 0 || j>= seqScores.length ) {
-			System.out.printf("Residue index out of range for the T-Coffee color scheme. Sequence %s - residue: %s\n", sequenceIndex, j);
-			return Color.white;
-		}
-		
-		byte val = seqScores[j];
-		return val >= 0 && val < colors.length ? colors[val] : Color.white;
+	  if( seqMap==null || (cols=seqMap.get(seq))==null) {
+	    return Color.white;
+	  }
+	  
+	  if( j < 0 || j>= cols.length ) {
+	    return Color.white;
+	  }
+	  return cols[j];
 	}
 }