total annotation score is a double for maximum precision.

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index bae5863..47d56b7 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -39,7 +39,7 @@ public class SequenceGroup
   Vector aaFrequency;
   boolean displayBoxes = true;
   boolean displayText = true;
-  boolean colourText = true;
+  boolean colourText = false;
   private Vector sequences = new Vector();
   int width = -1;
 
@@ -98,10 +98,7 @@ public class SequenceGroup
     {
       SequenceI seq = inorder[i];
 
-      seqs[i] = new Sequence(seq.getName(),
-                             seq.getSequence(startRes, endRes + 1),
-                             seq.findPosition(startRes),
-                             findEndRes(seq));
+      seqs[i] = seq.getSubSequence(startRes, endRes+1);
 
       seqs[i].setDescription(seq.getDescription());
       seqs[i].setDBRef(seq.getDBRef());
@@ -115,7 +112,11 @@ public class SequenceGroup
       {
         for (int a = 0; a < seq.getAnnotation().length; a++)
         {
-          seqs[i].addAlignmentAnnotation(new AlignmentAnnotation(seq.getAnnotation()[a]));
+          AlignmentAnnotation newannot = new AlignmentAnnotation(seq.getAnnotation()[a]);
+          newannot.restrict(startRes, endRes);
+          newannot.setSequenceRef(seqs[i]);
+          newannot.adjustForAlignment();
+          seqs[i].addAlignmentAnnotation(newannot);
         }
       }
     }