/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * 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.
*
*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
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;
* <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>
*/
{
return showAutocalcAbove ? 1 : -1;
}
- int sequenceOrder = compareSequences(o1, o2);
- return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
+ int computedOrder = compareSequences(o1, o2);
+ if (computedOrder == 0)
+ {
+ computedOrder = compareLabels(o1, o2);
+ }
+ if (computedOrder == 0)
+ {
+ computedOrder = compareDescriptions(o1, o2);
+ }
+ return computedOrder;
}
@Override
* <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>
*/
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
- Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(
+ order);
if (alignmentAnnotations != null)
{
}
String label1 = o1.label;
String label2 = o2.label;
+ return compareString(label1, label2);
+ }
+
+ /**
+ * Non-case-sensitive comparison of annotation descriptions. Returns zero if
+ * either argument is null.
+ *
+ * @param o1
+ * @param o2
+ * @return
+ */
+ private int compareDescriptions(AlignmentAnnotation o1,
+ AlignmentAnnotation o2)
+ {
+ if (o1 == null || o2 == null)
+ {
+ return 0;
+ }
+ String label1 = o1.description;
+ String label2 = o2.description;
+ return compareString(label1, label2);
+ }
+
+ private int compareString(String label1, String label2)
+ {
if (label1 == null && label2 == null)
{
return 0;
{
return 1;
}
- return label1.toUpperCase().compareTo(label2.toUpperCase());
+ return label1.toUpperCase(Locale.ROOT)
+ .compareTo(label2.toUpperCase(Locale.ROOT));
}
/**