From 72fafa02724acf81264142acb90d1c1428b21638 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 13 Nov 2017 09:08:36 +0000
Subject: [PATCH] JAL-2541 add new dataset sequence to alignment dataset

---
 src/jalview/commands/EditCommand.java |   23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 334f30d..d603a0d 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -536,8 +536,21 @@ public class EditCommand implements CommandI
         boolean cutIsInternal = cutPositions != null
                 && sequence.getStart() != cutPositions
                 .getBegin() && sequence.getEnd() != cutPositions.getEnd();
+
+        /*
+         * perform the cut; if this results in a new dataset sequence, add
+         * that to the alignment dataset
+         */
+        SequenceI ds = sequence.getDatasetSequence();
         sequence.deleteChars(command.position, command.position
                 + command.number);
+        SequenceI newDs = sequence.getDatasetSequence();
+        if (newDs != ds && command.al != null
+                && command.al.getDataset() != null
+                && !command.al.getDataset().getSequences().contains(newDs))
+        {
+          command.al.getDataset().addSequence(newDs);
+        }
 
         if (command.oldds != null && command.oldds[i] != null)
         {
@@ -556,12 +569,13 @@ public class EditCommand implements CommandI
           {
             command.oldds = new SequenceI[command.seqs.length];
           }
-          command.oldds[i] = oldds;
+          command.oldds[i] = oldds;// todo not if !cutIsInternal?
 
           // do we need to edit sequence features for new sequence ?
           if (oldds != sequence.getDatasetSequence()
                   || (cutIsInternal
                           && sequence.getFeatures().hasFeatures()))
+          // todo or just test cutIsInternal && cutPositions != null ?
           {
             if (cutPositions != null)
             {
@@ -1529,7 +1543,7 @@ public class EditCommand implements CommandI
    * <li>features right of the cut are shifted left</li>
    * <li>features internal to the cut region are deleted</li>
    * <li>features that overlap or span the cut are shortened</li>
-   * <li>the originals of any deleted or shorted features are saved, to re-add
+   * <li>the originals of any deleted or shortened features are saved, to re-add
    * on Undo</li>
    * <li>any added (shortened) features are saved, to delete on Undo</li>
    * </ul>
@@ -1543,8 +1557,9 @@ public class EditCommand implements CommandI
   protected static void cutFeatures(Edit command, SequenceI seq,
           int fromPosition, int toPosition, boolean cutIsInternal)
   {
-    /* if the cut is at start or end of sequence
-     * then we don't modify the seuqence feature store
+    /* 
+     * if the cut is at start or end of sequence
+     * then we don't modify the sequence feature store
      */
     if (!cutIsInternal)
     {
-- 
1.7.10.2