From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 31 Aug 2016 14:38:21 +0000 (+0100)
Subject: JAL-2034 fix logic so recalcConservation(true) returns true if conservation updates... 
X-Git-Tag: Release_2_10_0~49^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb5e0ce96aa9936a540b4d99a57cc2e5df3704f0;p=jalview.git

JAL-2034 fix logic so recalcConservation(true) returns true if conservation updates were performed on group
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 22c537a..046f1e6 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -529,6 +529,7 @@ 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,
@@ -536,10 +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)
@@ -561,6 +564,8 @@ 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 +575,14 @@ 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)