From 88d5ff9b60bc7c99a427c2d6fc9d04823e185d68 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 25 Mar 2016 14:52:04 +0000
Subject: [PATCH] =?utf8?q?JAL-2034=20make=20colour=20scheme=20update=20optio?=
 =?utf8?q?nal=20when=20group=20conservation=20is=20calculated,=20and=20pass=20?=
 =?utf8?q?back=20a=20=E2=80=98change=E2=80=99=20flag?=
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---
 src/jalview/datamodel/SequenceGroup.java |   33 +++++++++++++++++++++++++-----
 1 file changed, 28 insertions(+), 5 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c9afec7..ee4d7c2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -504,14 +504,31 @@ 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
     try
     {
       Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
@@ -545,16 +562,22 @@ public class SequenceGroup implements AnnotatedCollectionI
           }
         }
       }
-      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 false;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-
+    return false;
   }
 
   private void _updateConservationRow(Conservation c)
-- 
1.7.10.2