X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=b8100506a6f64a5fc8127b986a63c271c356c14f;hb=ac599db2d506591153433ffbf1e6ea2ef4be4943;hp=2fad332458ff5f63f5a3f7d4bdc3b28a180e6006;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 2fad332..b810050 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -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();
@@ -820,7 +821,7 @@ public class AlignmentSorter
         else
         {
           // or, also take a look at the scores if necessary.
-          if (!ignoreScore && sf[f].getScore() != Float.NaN)
+          if (!ignoreScore && !Float.isNaN(sf[f].getScore()))
           {
             if (seqScores[i] == 0)
             {
@@ -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