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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
commands
/
EditCommand.java
diff --git
a/src/jalview/commands/EditCommand.java
b/src/jalview/commands/EditCommand.java
index
4b21137
..
21ff841
100644
(file)
--- a/
src/jalview/commands/EditCommand.java
+++ b/
src/jalview/commands/EditCommand.java
@@
-1220,10
+1220,15
@@
public class EditCommand implements CommandI
for (SequenceI seq : e.getSequences())
{
SequenceI ds = seq.getDatasetSequence();
for (SequenceI seq : e.getSequences())
{
SequenceI ds = seq.getDatasetSequence();
- SequenceI preEdit = result.get(ds);
- if (preEdit == null)
+ // SequenceI preEdit = result.get(ds);
+ if (!result.containsKey(ds))
{
{
- preEdit = new Sequence("", seq.getSequenceAsString());
+ /*
+ * copy sequence including start/end (but don't use copy constructor
+ * as we don't need annotations)
+ */
+ SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
+ seq.getStart(), seq.getEnd());
preEdit.setDatasetSequence(ds);
result.put(ds, preEdit);
}
preEdit.setDatasetSequence(ds);
result.put(ds, preEdit);
}
@@
-1236,10
+1241,10
@@
public class EditCommand implements CommandI
* Work backwards through the edit list, deriving the sequences before each
* was applied. The final result is the sequence set before any edits.
*/
* Work backwards through the edit list, deriving the sequences before each
* was applied. The final result is the sequence set before any edits.
*/
- Iterator<Edit> edits = new ReverseListIterator<Edit>(getEdits());
- while (edits.hasNext())
+ Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
+ while (editList.hasNext())
{
{
- Edit oldEdit = edits.next();
+ Edit oldEdit = editList.next();
Action action = oldEdit.getAction();
int position = oldEdit.getPosition();
int number = oldEdit.getNumber();
Action action = oldEdit.getAction();
int position = oldEdit.getPosition();
int number = oldEdit.getNumber();
@@
-1250,7
+1255,8
@@
public class EditCommand implements CommandI
SequenceI preEdit = result.get(ds);
if (preEdit == null)
{
SequenceI preEdit = result.get(ds);
if (preEdit == null)
{
- preEdit = new Sequence("", seq.getSequenceAsString());
+ preEdit = new Sequence("", seq.getSequenceAsString(),
+ seq.getStart(), seq.getEnd());
preEdit.setDatasetSequence(ds);
result.put(ds, preEdit);
}
preEdit.setDatasetSequence(ds);
result.put(ds, preEdit);
}