JAL-3416 Added some mac specific FlatLAF settings. Note this is not the default...

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

diff --git a/src/jalview/analysis/GeneticCodes.java b/src/jalview/analysis/GeneticCodes.java
index 137b7f8..8d69b0b 100644 (file)
--- a/src/jalview/analysis/GeneticCodes.java
+++ b/src/jalview/analysis/GeneticCodes.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.analysis;
 
+import java.util.Locale;
+
 import jalview.bin.Cache;
 
 import java.io.BufferedReader;
@@ -178,13 +200,13 @@ public final class GeneticCodes
       while (line != null)
       {
         line = readLine(dataIn);
-        if (line != null && !"DNA".equals(line.toUpperCase()))
+        if (line != null && !"DNA".equals(line.toUpperCase(Locale.ROOT)))
         {
           String[] tokens = line.split("\\t");
           if (tokens.length == 2)
           {
-          ambiguityCodes.put(tokens[0].toUpperCase(),
-                  tokens[1].toUpperCase());
+          ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
+                  tokens[1].toUpperCase(Locale.ROOT));
           }
           else
           {
@@ -321,13 +343,13 @@ public final class GeneticCodes
       @Override
       public String translateCanonical(String codon)
       {
-        return codons.get(codon.toUpperCase());
+        return codons.get(codon.toUpperCase(Locale.ROOT));
       }
 
       @Override
       public String translate(String codon)
       {
-        String upper = codon.toUpperCase();
+        String upper = codon.toUpperCase(Locale.ROOT);
         String peptide = translateCanonical(upper);
 
         /*