JAL-3066 JAL-3070 pull up non-jabaws specific service descriptor components for annot...

[jalview.git] / src / jalview / workers / InformationThread.java

diff --git a/src/jalview/workers/InformationThread.java b/src/jalview/workers/InformationThread.java
index d719189..85cd92f 100644 (file)
--- a/src/jalview/workers/InformationThread.java
+++ b/src/jalview/workers/InformationThread.java
@@ -178,7 +178,7 @@ public class InformationThread extends AlignCalcWorker
    */
   protected AlignmentAnnotation getGapAnnotation()
   {
-    return alignViewport.getOccupancyAnnotation();
+               return alignViewport.getAlignmentGapAnnotation();
   }
 
   /**
@@ -212,10 +212,13 @@ public class InformationThread extends AlignCalcWorker
     for (SequenceGroup group : alignment.getGroups())
     {
       hmmSeqs = group.getHmmSequences();
-      ProfilesI profiles = group.getHmmProfiles();
-      float m = updateInformationAnnotation(hmmSeqs.get(0), profiles, group,
-              infos);
-      maxInformation = Math.max(maxInformation, m);
+      if (!hmmSeqs.isEmpty())
+      {
+        ProfilesI profiles = group.getHmmProfiles();
+        float m = updateInformationAnnotation(hmmSeqs.get(0), profiles,
+                group, infos);
+        maxInformation = Math.max(maxInformation, m);
+      }
     }
 
     /*