From: jprocter <Jim Procter>
Date: Thu, 21 Apr 2011 13:16:27 +0000 (+0000)
Subject: allow an existing alignment annotation row to be bound to a sequenceGroup as its... 
X-Git-Tag: Release_2_7~219
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9ff5fcbe6681e37c441656e2f704f8d9bab9179c;p=jalview.git

allow an existing alignment annotation row to be bound to a sequenceGroup as its consensus or conservation row (JAL-784)
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 7bb9670..d253560 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -998,6 +998,18 @@ public class SequenceGroup
   private boolean showConsensusHistogram;
 
   /**
+   * set this alignmentAnnotation object as the one used to render consensus annotation
+   * @param aan
+   */
+  public void setConsensus(AlignmentAnnotation aan)
+  {
+    if (consensus==null)
+    {
+      consensus=aan;
+    }
+  }
+  
+  /**
    * 
    * @return automatically calculated consensus row
    */
@@ -1026,6 +1038,17 @@ public class SequenceGroup
   }
 
   /**
+   * set this alignmentAnnotation object as the one used to render consensus annotation
+   * @param aan
+   */
+  public void setConservationRow(AlignmentAnnotation aan)
+  {
+    if (conservation==null)
+    {
+      conservation=aan;
+    }
+  }
+  /**
    * get the conservation annotation row for this group
    * 
    * @return autoCalculated annotation row