From 768a4920722ec46f7c16e35780391e39a76d02ff Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 4 Jul 2016 15:35:13 +0100
Subject: [PATCH] JAL-2110 use shared dataset when copying alignment for split
 frame

---
 src/jalview/analysis/AlignmentUtils.java |   25 ++++---------------------
 src/jalview/gui/AlignFrame.java          |    2 +-
 2 files changed, 5 insertions(+), 22 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 9150d62..aa7cb18 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2211,32 +2211,15 @@ public class AlignmentUtils
    * 
    * @param seqs
    * @param xrefs
+   * @param dataset
+   *          the alignment dataset shared by the new copy
    * @return
    */
   public static AlignmentI makeCopyAlignment(SequenceI[] seqs,
-          SequenceI[] xrefs)
+          SequenceI[] xrefs, AlignmentI dataset)
   {
     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);
-    }
+    copy.setDataset(dataset);
 
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b310ab9..19b5b8c 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4788,7 +4788,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           else
           {
             copyAlignment = AlignmentUtils.makeCopyAlignment(
-                    sequenceSelection, xrefs.getSequencesArray());
+                    sequenceSelection, xrefs.getSequencesArray(), dataset);
           }
           copyAlignment.setGapCharacter(AlignFrame.this.viewport
                   .getGapCharacter());
-- 
1.7.10.2