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JAL-3140 update for change to SequenceI api
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 1 Mar 2019 09:59:24 +0000
(09:59 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 1 Mar 2019 09:59:24 +0000
(09:59 +0000)
src/jalview/commands/EditCommand.java
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diff --git
a/src/jalview/commands/EditCommand.java
b/src/jalview/commands/EditCommand.java
index
1a227c5
..
f80bd4a
100644
(file)
--- a/
src/jalview/commands/EditCommand.java
+++ b/
src/jalview/commands/EditCommand.java
@@
-24,6
+24,7
@@
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.Range;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.Range;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
@@
-526,8
+527,8
@@
public class EditCommand implements CommandI
command.string[i] = sequence.getSequence(command.position,
command.position + command.number);
SequenceI oldds = sequence.getDatasetSequence();
command.string[i] = sequence.getSequence(command.position,
command.position + command.number);
SequenceI oldds = sequence.getDatasetSequence();
- Range cutPositions = sequence.findPositions(command.position + 1,
- command.position + command.number);
+ ContiguousI cutPositions = sequence.findPositions(
+ command.position + 1, command.position + command.number);
boolean cutIsInternal = cutPositions != null
&& sequence.getStart() != cutPositions
.getBegin() && sequence.getEnd() != cutPositions.getEnd();
boolean cutIsInternal = cutPositions != null
&& sequence.getStart() != cutPositions
.getBegin() && sequence.getEnd() != cutPositions.getEnd();
@@
-763,9
+764,9
@@
public class EditCommand implements CommandI
* EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
*
*/
* EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
*
*/
-
- Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
- Range afterEditedPositions = command.seqs[i]
+ ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1,
+ start);
+ ContiguousI afterEditedPositions = command.seqs[i]
.findPositions(end + 1, command.seqs[i].getLength());
oldstring = command.seqs[i].getSequenceAsString();
.findPositions(end + 1, command.seqs[i].getLength());
oldstring = command.seqs[i].getSequenceAsString();