From 516ce4f35f75fe4775f3299742b2f453ae7d21fe Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 23 May 2012 20:03:14 +0100
Subject: [PATCH] JAL-1066,JAL-1068,JAL-961 - use alignment annotation query
 api to get t-coffee annotation

---
 src/jalview/schemes/TCoffeeColourScheme.java |    9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index bbd2a23..47aebd1 100644
--- 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)
-- 
1.7.10.2