X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2fb6ce13a229e27ffc74236e97f9b64c719d87b2;hb=2e57729baa0bc97fc03ab1fb8eb4dbc1a12f3d9a;hp=15ea2fcb94cb6b70db80f9929b493d1561a12c5a;hpb=427421de47dacacac55ac29deca78e2f0a1c5408;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 15ea2fc..2fb6ce1 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
@@ -148,7 +150,7 @@ public class AlignSeq
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
-    seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
+    seqInit(s1, string1.toUpperCase(Locale.ROOT), s2, string2.toUpperCase(Locale.ROOT), type);
   }
 
   /**
@@ -561,7 +563,7 @@ public class AlignSeq
         }
       }
 
-      output.append(NEWLINE);// .append(NEWLINE);
+      output.append(NEWLINE).append(NEWLINE);
     }
 
     pid = pid / (aseq1.length - count) * 100;