X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=c3396b6553f753c2bef3c96be9ad957ade806012;hb=0bdaa0deb6ee514912d2ed730e19f618bc44cb69;hp=2850eeb9f0786fa8c0f572678f404d6638655cd4;hpb=ae687fbf5b5d6c34e8ccfbe27afdc0ff0eff747f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 2850eeb..c3396b6 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -258,11 +258,14 @@ public class AlignmentAnnotation
       }
 
       /**
-       * Attach the annotation to seqRef, starting from startRes position.
+       * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
        * @param seqRef
        * @param startRes
+       * @param alreadyMapped
        */
-      public void createSequenceMapping(SequenceI seqRef, int startRes)
+      public void createSequenceMapping(SequenceI seqRef,
+                                        int startRes,
+                                        boolean alreadyMapped)
       {
         if(seqRef == null)
           return;
@@ -270,30 +273,22 @@ public class AlignmentAnnotation
         sequenceMapping = new java.util.Hashtable();
 
         sequenceRef = seqRef;
-
-        if(startRes < sequenceRef.getStart())
-          startRes = sequenceRef.getStart();
-
         int seqPos;
 
-        int fileOffset = 0;
-        if(startRes > sequenceRef.getStart())
-        {
-          fileOffset = startRes - sequenceRef.getStart();
-        }
-
         for(int i = 0; i < annotations.length; i++)
         {
-            seqPos = sequenceRef.findPosition(i + fileOffset);
             if (annotations[i] != null)
             {
-              sequenceMapping.put(new Integer(seqPos),
-                  annotations[i]);
+              if(alreadyMapped)
+                seqPos = seqRef.findPosition(i);
+              else
+                seqPos = i+startRes;
+
+              sequenceMapping.put(new Integer(seqPos), annotations[i]);
             }
          }
 
         adjustForAlignment();
-
       }
 
       public void adjustForAlignment()