X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=1f2e78f9ad01b30c7d5e8057aaafba3d093cc890;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=b0cfe20f607838f0506f22cbe3d7ff8d86f7594b;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git
diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index b0cfe20..1f2e78f 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -1,5 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
+import java.util.Locale;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
@@ -30,8 +52,8 @@ public class AnnotationSorter
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;
@@ -88,7 +110,8 @@ public class AnnotationSorter
*
* - annotations with a reference to a sequence in the alignment are sorted
* on sequence ordering
- * - other annotations go 'at the end', with their mutual order unchanged
+ * - other annotations go 'at the end', with their mutual order
+ * unchanged
* - within the same sequence ref, sort by label (non-case-sensitive)
*
*/
@@ -133,8 +156,16 @@ public class AnnotationSorter
{
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
@@ -149,7 +180,8 @@ public class AnnotationSorter
*
* - annotations with a reference to a sequence in the alignment are sorted
* on label (non-case-sensitive)
- * - other annotations go 'at the end', with their mutual order unchanged
+ * - other annotations go 'at the end', with their mutual order
+ * unchanged
* - within the same label, sort by order of the related sequences
*
*/
@@ -258,7 +290,8 @@ public class AnnotationSorter
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
- Comparator super AlignmentAnnotation> comparator = getComparator(order);
+ Comparator super AlignmentAnnotation> comparator = getComparator(
+ order);
if (alignmentAnnotations != null)
{
@@ -333,6 +366,31 @@ public class AnnotationSorter
}
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;
@@ -345,7 +403,8 @@ public class AnnotationSorter
{
return 1;
}
- return label1.toUpperCase().compareTo(label2.toUpperCase());
+ return label1.toUpperCase(Locale.ROOT)
+ .compareTo(label2.toUpperCase(Locale.ROOT));
}
/**