X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=6cc9dd344addced46f9e8f5a06f7184ce47a86a7;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=bd87ee87df1b8c446401f322f058064ef5b584d0;hpb=fab0afc9e1e7a5ca460f0cbd48545536f989a435;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index bd87ee8..6cc9dd3 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
@@ -312,7 +314,7 @@ public class Conservation
   protected static void recordConservation(Map<String, Integer> resultMap,
           String res)
   {
-    res = res.toUpperCase();
+    res = res.toUpperCase(Locale.ROOT);
     for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
             .entrySet())
     {
@@ -698,7 +700,7 @@ public class Conservation
 
       max = Math.max(max, bigtot);
 
-      quality.addElement(new Double(bigtot));
+      quality.addElement(Double.valueOf(bigtot));
     }
 
     double newmax = -Double.MAX_VALUE;
@@ -710,7 +712,7 @@ public class Conservation
       tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
 
       // System.out.println(tmp+ " " + j);
-      quality.setElementAt(new Double(tmp), j);
+      quality.setElementAt(Double.valueOf(tmp), j);
 
       if (tmp > newmax)
       {