X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=081f446f0dcbd13ca7676ec949be1a16d27ff918;hb=be1666f6c9be6b18051b233abdde85962ac0c89a;hp=fba023f973bbb6474e598c03f4d3f5215665d483;hpb=1861ba00ddfe2274a788ad03f82c44b6523ad8b7;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index fba023f..081f446 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2114,6 +2114,26 @@ public class AlignmentUtils
   {
     AlignmentI copy = new Alignment(new Alignment(seqs));
 
+    /*
+     * add mappings between sequences to the new alignment
+     */
+    AlignedCodonFrame mappings = new AlignedCodonFrame();
+    copy.addCodonFrame(mappings);
+    for (int i = 0; i < copy.getHeight(); i++)
+    {
+      SequenceI from = seqs[i];
+      SequenceI to = copy.getSequenceAt(i);
+      if (to.getDatasetSequence() != null)
+      {
+        to = to.getDatasetSequence();
+      }
+      int start = from.getStart();
+      int end = from.getEnd();
+      MapList map = new MapList(new int[] { start, end }, new int[] {
+          start, end }, 1, 1);
+      mappings.addMap(to, from, map);
+    }
+
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {