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Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
[jalview.git]
/
src
/
jalview
/
analysis
/
AnnotationSorter.java
diff --git
a/src/jalview/analysis/AnnotationSorter.java
b/src/jalview/analysis/AnnotationSorter.java
index
9e35330
..
2f556f1
100644
(file)
--- a/
src/jalview/analysis/AnnotationSorter.java
+++ b/
src/jalview/analysis/AnnotationSorter.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-50,8
+50,8
@@
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
+108,8
@@
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
+170,8
@@
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
+280,8
@@
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)
{