X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAnnotationWorker.java;h=b812c655048bd65fad36f940c31a517a840051dd;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=8569039f6323219a2c0d480ea63a0c56706643cf;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/workers/AnnotationWorker.java b/src/jalview/workers/AnnotationWorker.java
index 8569039..b812c65 100644
--- a/src/jalview/workers/AnnotationWorker.java
+++ b/src/jalview/workers/AnnotationWorker.java
@@ -51,7 +51,7 @@ class AnnotationWorker extends AlignCalcWorker
           AnnotationProviderI counter)
   {
     super(viewport, panel);
-    ourAnnots = new ArrayList<AlignmentAnnotation>();
+    ourAnnots = new ArrayList<>();
     this.counter = counter;
     calcMan.registerWorker(this);
   }
@@ -90,7 +90,12 @@ class AnnotationWorker extends AlignCalcWorker
           for (AlignmentAnnotation ann : anns)
           {
             AlignmentAnnotation theAnn = alignment.findOrCreateAnnotation(
-                    ann.label, ann.description, false, null, null);
+                    ann.label, ann.getCalcId(), ann.autoCalculated,
+                    ann.sequenceRef,
+                    ann.groupRef);
+            if (ann.description!=null) {
+              theAnn.description = ann.description;
+            }
             theAnn.showAllColLabels = true;
             theAnn.graph = AlignmentAnnotation.BAR_GRAPH;
             theAnn.scaleColLabel = true;
@@ -121,7 +126,10 @@ class AnnotationWorker extends AlignCalcWorker
     if (ap != null)
     {
       ap.adjustAnnotationHeight();
-      ap.paintAlignment(true);
+      // TODO: only need to update colour and geometry if panel height changes
+      // and view is coloured by annotation, and the annotation is actually
+      // changed!
+      ap.paintAlignment(true, true);
     }
   }