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Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate
[jalview.git]
/
src
/
jalview
/
commands
/
EditCommand.java
diff --git
a/src/jalview/commands/EditCommand.java
b/src/jalview/commands/EditCommand.java
index
d0790c8
..
30595bc
100644
(file)
--- a/
src/jalview/commands/EditCommand.java
+++ b/
src/jalview/commands/EditCommand.java
@@
-20,6
+20,8
@@
*/
package jalview.commands;
*/
package jalview.commands;
+import java.util.Locale;
+
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-789,7
+791,7
@@
public class EditCommand implements CommandI
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
- if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+ if (!nogaprep.toLowerCase(Locale.ROOT).equals(nogapold.toLowerCase(Locale.ROOT)))
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
@@
-838,7
+840,7
@@
public class EditCommand implements CommandI
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
- newds.setSequence(fullseq.toUpperCase());
+ newds.setSequence(fullseq.toUpperCase(Locale.ROOT));
if (command.oldds == null)
{
if (command.oldds == null)
{
@@
-891,7
+893,7
@@
public class EditCommand implements CommandI
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
- command.seqs[i].getSequenceAsString().toUpperCase());
+ command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT));
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)