X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=9a408e31dda4dfdce5d63638009bb6884a8cc3ab;hb=d7361eaa08dc9af7d996851f39b7a2007d1b8832;hp=22c537af3d0844dd42ffea673b212f3bdfc076f0;hpb=ebca5f7880f838a5564dd419274ad6025b456dab;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 22c537a..9a408e3 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -23,7 +23,6 @@ package jalview.datamodel;
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -529,6 +528,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     // TODO: try harder to detect changes in state in order to minimise
     // recalculation effort
+    boolean upd = false;
     try
     {
       Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@ -536,18 +536,19 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (consensus != null)
       {
         _updateConsensusRow(cnsns, sequences.size());
+        upd = true;
       }
       if (cs != null)
       {
         cs.setConsensus(cnsns);
+        upd = true;
       }
 
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName,
-                ResidueProperties.propHash, 3, sequences, startRes,
-                endRes + 1);
+        Conservation c = new Conservation(groupName, 3, sequences,
+                startRes, endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
         if (conservation != null)
@@ -561,6 +562,8 @@ public class SequenceGroup implements AnnotatedCollectionI
             cs.setConservation(c);
           }
         }
+        // eager update - will cause a refresh of overview regardless
+        upd = true;
       }
       if (cs != null && !defer)
       {
@@ -570,14 +573,14 @@ public class SequenceGroup implements AnnotatedCollectionI
       }
       else
       {
-        return false;
+        return upd;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-    return false;
+    return upd;
   }
 
   private void _updateConservationRow(Conservation c)