Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDat...

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 9a63eb1..f95ff73 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -182,9 +184,9 @@ public class AlignmentUtils
       // TODO use Character.toLowerCase to avoid creating String objects?
       char[] upstream = new String(ds
               .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
-                      .toLowerCase().toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] downstream = new String(
-              ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase()
+              ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT)
                       .toCharArray();
       char[] coreseq = s.getSequence();
       char[] nseq = new char[offset + upstream.length + downstream.length
@@ -463,7 +465,7 @@ public class AlignmentUtils
     if (cdnaLength != mappedLength && cdnaLength > 2)
     {
       String lastCodon = String.valueOf(cdnaSeqChars,
-              cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
+              cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT);
       for (String stop : ResidueProperties.STOP_CODONS)
       {
         if (lastCodon.equals(stop))
@@ -480,7 +482,7 @@ public class AlignmentUtils
      */
     int startOffset = 0;
     if (cdnaLength != mappedLength && cdnaLength > 2
-            && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
+            && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT)
                     .equals(ResidueProperties.START))
     {
       startOffset += CODON_LENGTH;