JAL-1065 per sequence and per-alignment scores added to annotation

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 0da4628..cf33671 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -490,6 +490,7 @@ public class TCoffeeScoreFile extends AlignFile {
              aa.annotations=annotations;
              aa.visible=false;
              aa.belowAlignment=false;
+             aa.setScore(header.getScoreFor(id.getKey()));
               aa.createSequenceMapping(s, s.getStart(),true);
               s.addAlignmentAnnotation(aa);
               aa.adjustForAlignment();
@@ -500,11 +501,13 @@ public class TCoffeeScoreFile extends AlignFile {
              aa.annotations=annotations;
               aa.belowAlignment=true;
              aa.visible=true;
+             aa.setScore(header.getScoreAvg());
            }
            aa.showAllColLabels=true;
            aa.validateRangeAndDisplay();
            added=true;
          }
+         
          return added;
        }