JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 0022af6..ac861d8 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -551,8 +551,7 @@ public class AlignmentSorter
    * @return DOCUMENT ME!
    */
   private static List<SequenceI> _sortByTree(SequenceNode node,
-          List<SequenceI> tmp,
-          List<SequenceI> seqset)
+          List<SequenceI> tmp, List<SequenceI> seqset)
   {
     if (node == null)
     {
@@ -719,9 +718,9 @@ public class AlignmentSorter
   public static void sortByFeature(String featureLabel, String groupLabel,
           int start, int stop, AlignmentI alignment, String method)
   {
-    sortByFeature(featureLabel == null ? null : new String[]
-    { featureLabel }, groupLabel == null ? null : new String[]
-    { groupLabel }, start, stop, alignment, method);
+    sortByFeature(featureLabel == null ? null
+            : new String[] { featureLabel }, groupLabel == null ? null
+            : new String[] { groupLabel }, start, stop, alignment, method);
   }
 
   private static boolean containsIgnoreCase(final String lab,
@@ -752,7 +751,9 @@ public class AlignmentSorter
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
             && method != FEATURE_DENSITY)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_sortbyfeature"));
     }
     boolean ignoreScore = method != FEATURE_SCORE;
     StringBuffer scoreLabel = new StringBuffer();
@@ -928,7 +929,8 @@ public class AlignmentSorter
     {
       if (method == FEATURE_LABEL)
       {
-        throw new Error(MessageManager.getString("error.not_yet_implemented"));
+        throw new Error(
+                MessageManager.getString("error.not_yet_implemented"));
       }
     }
     if (lastSortByFeatureScore == null