JAL-1013 - toy menu to switch between nucleotide and blosum 62 modes of calculation...

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 42559c6..707eee8 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -652,6 +652,11 @@ public class Alignment implements AlignmentI
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+  
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -683,7 +688,9 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      unhookAnnotation(aa);
+      if (unhook) {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }