git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3438 spotless for 2.11.2.0
[jalview.git]
/
src
/
jalview
/
analysis
/
AnnotationSorter.java
diff --git
a/src/jalview/analysis/AnnotationSorter.java
b/src/jalview/analysis/AnnotationSorter.java
index
711e8c9
..
92ed9be
100644
(file)
--- a/
src/jalview/analysis/AnnotationSorter.java
+++ b/
src/jalview/analysis/AnnotationSorter.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
@@
-50,8
+52,8
@@
public class AnnotationSorter
public enum SequenceAnnotationOrder
{
// Text descriptions surface in the Preferences Sort by... options
public enum SequenceAnnotationOrder
{
// Text descriptions surface in the Preferences Sort by... options
- SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
- "No sort");
+ SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
+ NONE("No sort");
private String description;
private String description;
@@
-108,7
+110,8
@@
public class AnnotationSorter
* <ul>
* <li>annotations with a reference to a sequence in the alignment are sorted
* on sequence ordering</li>
* <ul>
* <li>annotations with a reference to a sequence in the alignment are sorted
* on sequence ordering</li>
- * <li>other annotations go 'at the end', with their mutual order unchanged</li>
+ * <li>other annotations go 'at the end', with their mutual order
+ * unchanged</li>
* <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
* </ul>
*/
* <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
* </ul>
*/
@@
-169,7
+172,8
@@
public class AnnotationSorter
* <ul>
* <li>annotations with a reference to a sequence in the alignment are sorted
* on label (non-case-sensitive)</li>
* <ul>
* <li>annotations with a reference to a sequence in the alignment are sorted
* on label (non-case-sensitive)</li>
- * <li>other annotations go 'at the end', with their mutual order unchanged</li>
+ * <li>other annotations go 'at the end', with their mutual order
+ * unchanged</li>
* <li>within the same label, sort by order of the related sequences</li>
* </ul>
*/
* <li>within the same label, sort by order of the related sequences</li>
* </ul>
*/
@@
-278,7
+282,8
@@
public class AnnotationSorter
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
- Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(
+ order);
if (alignmentAnnotations != null)
{
if (alignmentAnnotations != null)
{
@@
-365,7
+370,8
@@
public class AnnotationSorter
{
return 1;
}
{
return 1;
}
- return label1.toUpperCase().compareTo(label2.toUpperCase());
+ return label1.toUpperCase(Locale.ROOT)
+ .compareTo(label2.toUpperCase(Locale.ROOT));
}
/**
}
/**