X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=2545ec1355a8d852ea3201da6ddc9048fd9addf8;hb=7e4c4ad887a30dc26496087b0150f4ac2fe355ec;hp=e9af7f457ee0d674b3bb3646b0ceaf730860852c;hpb=627834dc46a79d74dec14c3d7a64a529f2337f6f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e9af7f4..2545ec1 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -642,6 +642,27 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
+
+    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)
+    {
+      aa.refSequence = seqRef;
+      if(seqRef!=null && index!=0)
+      {
+        int aSize = aa.annotations.length;
+        int newIndex;
+        Annotation [] temp = new Annotation[seqRef.getLength()];
+        for(int a=0; a<aSize; a++)
+        {
+          newIndex = seqRef.findIndex(a + index)-1;
+          temp[newIndex] = aa.annotations[a];
+        }
+
+        aa.annotations = temp;
+      }
+
+      addAnnotation(aa);
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -658,18 +679,19 @@ public class Alignment implements AlignmentI
 
 
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-        int i = 0;
+
+        temp[0] = aa;
+
+        int i = 1;
 
         if (aSize > 1)
         {
-            for (i = 0; i < (aSize - 1); i++)
+            for (i = 1; i < (aSize); i++)
             {
-                temp[i] = annotations[i];
+                temp[i] = annotations[i-1];
             }
         }
 
-        temp[i] = aa;
-
         annotations = temp;
     }