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

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index f965c4e..dadb532 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.vcf;
 
+import java.util.Locale;
+
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -431,7 +433,7 @@ public class VCFLoader
               + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
       reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
     }
-    reference = reference.toLowerCase();
+    reference = reference.toLowerCase(Locale.ROOT);
 
     /*
      * for a non-human species, or other assembly identifier,
@@ -446,7 +448,7 @@ public class VCFLoader
       String[] tokens = token.split("=");
       if (tokens.length == 2)
       {
-        if (reference.contains(tokens[0].trim().toLowerCase()))
+        if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
         {
           vcfAssembly = tokens[1].trim();
           break;
@@ -463,7 +465,7 @@ public class VCFLoader
         String[] tokens = token.split("=");
         if (tokens.length == 2)
         {
-          if (reference.contains(tokens[0].trim().toLowerCase()))
+          if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
           {
             vcfSpecies = tokens[1].trim();
             break;
@@ -568,7 +570,7 @@ public class VCFLoader
   {
     for (Pattern p : filters)
     {
-      if (p.matcher(id.toUpperCase()).matches())
+      if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
       {
         return true;
       }
@@ -662,7 +664,7 @@ public class VCFLoader
     {
       try
       {
-      patterns.add(Pattern.compile(token.toUpperCase()));
+      patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
       } catch (PatternSyntaxException e)
       {
         System.err.println("Invalid pattern ignored: " + token);
@@ -1033,7 +1035,7 @@ public class VCFLoader
      */
     String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
             altAlleleIndex, csqAlleleFieldIndex,
-            csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+            csqAlleleNumberFieldIndex, seq.getName().toLowerCase(Locale.ROOT),
             csqFeatureFieldIndex);
 
     /*
@@ -1226,7 +1228,7 @@ public class VCFLoader
       {
         String featureIdentifier = csqFields[featureFieldIndex];
         if (featureIdentifier.length() > 4
-                && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+                && seqName.indexOf(featureIdentifier.toLowerCase(Locale.ROOT)) > -1)
         {
           /*
            * feature (transcript) matched - now check for allele match