X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=046f1e6cda95f029b3156180e2e2bb94ab037006;hb=3f12f4932226512316ec113e600695150431fd0a;hp=0e8fa170cda9091a4bf5ea8723a5dddac0665386;hpb=23c12388658b08e4bbda2ebfdad286d881689366;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 0e8fa17..046f1e6 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -504,14 +504,32 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * calculate residue conservation for group - but only if necessary.
+   * calculate residue conservation and colourschemes for group - but only if
+   * necessary. returns true if the calculation resulted in a visible change to
+   * group
    */
-  public void recalcConservation()
+  public boolean recalcConservation()
+  {
+    return recalcConservation(false);
+  }
+
+  /**
+   * calculate residue conservation for group - but only if necessary. returns
+   * true if the calculation resulted in a visible change to group
+   * 
+   * @param defer
+   *          when set, colourschemes for this group are not refreshed after
+   *          recalculation
+   */
+  public boolean recalcConservation(boolean defer)
   {
     if (cs == null && consensus == null && conservation == null)
     {
-      return;
+      return false;
     }
+    // TODO: try harder to detect changes in state in order to minimise
+    // recalculation effort
+    boolean upd = false;
     try
     {
       Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@ -519,10 +537,12 @@ 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)
@@ -544,17 +564,25 @@ public class SequenceGroup implements AnnotatedCollectionI
             cs.setConservation(c);
           }
         }
+        // eager update - will cause a refresh of overview regardless
+        upd = true;
       }
-      if (cs != null)
+      if (cs != null && !defer)
       {
+        // TODO: JAL-2034 should cs.alignmentChanged modify return state
         cs.alignmentChanged(context != null ? context : this, null);
+        return true;
+      }
+      else
+      {
+        return upd;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-
+    return upd;
   }
 
   private void _updateConservationRow(Conservation c)
@@ -894,6 +922,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * @return the representative sequence for this group
    */
+  @Override
   public SequenceI getSeqrep()
   {
     return seqrep;
@@ -906,6 +935,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    * @param seqrep
    *          the seqrep to set (null means no sequence representative)
    */
+  @Override
   public void setSeqrep(SequenceI seqrep)
   {
     this.seqrep = seqrep;
@@ -915,6 +945,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @return true if group has a sequence representative
    */
+  @Override
   public boolean hasSeqrep()
   {
     return seqrep != null;
@@ -1036,7 +1067,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * 
-   * @return automatically calculated consensus row
+   * @return automatically calculated consensus row note: the row is a stub if a
+   *         consensus calculation has not yet been performed on the group
    */
   public AlignmentAnnotation getConsensus()
   {