From 0d6fdcd9c4597475c09fd96da43ddcadccf78fa1 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 5 Aug 2012 18:28:03 +0100
Subject: [PATCH] JAL-1131 ensure new dataset sequence is created if seuqence
 replacement results in different non-gap characters

---
 src/jalview/commands/EditCommand.java |   37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 9321524..9413ba8 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -452,6 +452,8 @@ public class EditCommand implements CommandI
     command.number = start + command.string[0].length;
     for (int i = 0; i < command.seqs.length; i++)
     {
+      boolean newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
+
       /**
        * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
        * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
@@ -466,9 +468,44 @@ public class EditCommand implements CommandI
       oldstring = command.seqs[i].getSequenceAsString();
       tmp = new StringBuffer(oldstring.substring(0, start));
       tmp.append(command.string[i]);
+      String nogaprep = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(
+                      command.string[i]));
+      int ipos = command.seqs[i].findPosition(start)
+              - command.seqs[i].getStart();
       tmp.append(oldstring.substring(end));
       command.seqs[i].setSequence(tmp.toString());
       command.string[i] = oldstring.substring(start, end).toCharArray();
+      String nogapold = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(
+                      command.string[i]));
+      if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+      {
+        if (newDSWasNeeded)
+        {
+          SequenceI oldds = command.seqs[i].getDatasetSequence();
+          command.seqs[i].setDatasetSequence(command.oldds[i]);
+          command.oldds[i] = oldds;
+        }
+        else
+        {
+          if (command.oldds == null)
+          {
+            command.oldds = new SequenceI[command.seqs.length];
+          }
+          command.oldds[i] = command.seqs[i].getDatasetSequence();
+          SequenceI newds = new Sequence(
+                  command.seqs[i].getDatasetSequence());
+          String fullseq, osp = newds.getSequenceAsString();
+          fullseq = osp.substring(0, ipos) + nogaprep
+                  + osp.substring(ipos + nogaprep.length());
+          newds.setSequence(fullseq.toUpperCase());
+          // TODO: ensure newly created dataset sequence is added to the set of
+          // dataset sequences associated with the alignment.
+          command.seqs[i].setDatasetSequence(newds);
+
+        }
+      }
       tmp = null;
       oldstring = null;
     }
-- 
1.7.10.2