X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAnnotationSorter.java;h=2f556f111221d495380873ad990e5422303f3b89;hb=6d4a6f2f66e8daa7ef1c1bf5ef91392dc15f425a;hp=0873f89dce2d6deb59b7d71fdd9e22e74ced2a97;hpb=6b106f39c410cbb2b1714b905948d68b91a341dd;p=jalview.git

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 0873f89..2f556f1 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -1,3 +1,23 @@
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
 import jalview.datamodel.AlignmentAnnotation;
@@ -30,8 +50,8 @@ 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;
 
@@ -46,7 +66,8 @@ public class AnnotationSorter
       return description;
     }
 
-    public static SequenceAnnotationOrder forDescription(String d) {
+    public static SequenceAnnotationOrder forDescription(String d)
+    {
       for (SequenceAnnotationOrder order : values())
       {
         if (order.toString().equals(d))
@@ -87,7 +108,8 @@ public class AnnotationSorter
    * <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>
    */
@@ -148,7 +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>
-   * <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>
    */
@@ -257,7 +280,8 @@ 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)
     {
@@ -279,9 +303,11 @@ public class AnnotationSorter
           AlignmentAnnotation[] alignmentAnnotations)
   {
     sequenceIndices.clear();
-    for (AlignmentAnnotation ann : alignmentAnnotations) {
+    for (AlignmentAnnotation ann : alignmentAnnotations)
+    {
       SequenceI seq = ann.sequenceRef;
-      if (seq != null) {
+      if (seq != null)
+      {
         int index = AlignmentUtils.getSequenceIndex(alignment, seq);
         sequenceIndices.put(seq, index);
       }