JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...

[jalview.git] / src / jalview / datamodel / MappedFeatures.java

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 87609c6..f145d93 100644 (file)
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -1,5 +1,27 @@
+/*
+ * 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.datamodel;
 
+import java.util.Locale;
+
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -179,12 +201,12 @@ public class MappedFeatures
      * e.g. C,G,T gives variants G and T for base C
      */
     Set<String> variantPeptides = new HashSet<>();
-    String[] alleles = alls.toUpperCase().split(",");
+    String[] alleles = alls.toUpperCase(Locale.ROOT).split(",");
     StringBuilder vars = new StringBuilder();
 
     for (String allele : alleles)
     {
-      allele = allele.trim().toUpperCase();
+      allele = allele.trim().toUpperCase(Locale.ROOT);
       if (allele.length() > 1 || "-".equals(allele))
       {
         continue; // multi-locus variant
@@ -200,7 +222,7 @@ public class MappedFeatures
        */
       final int i = cdsPos == codonPos[0] ? 0
               : (cdsPos == codonPos[1] ? 1 : 2);
-      variantCodon[i] = allele.toUpperCase().charAt(0);
+      variantCodon[i] = allele.toUpperCase(Locale.ROOT).charAt(0);
       if (variantCodon[i] == baseCodon[i])
       {
         continue;