From 2305d687bac5ed8a76ecb93c54c7b090a928e362 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 10 Aug 2020 15:10:35 +0100
Subject: [PATCH] JAL-3691 toUpperCase(Locale.ROOT) for all standard file
 format operations

---
 src/jalview/io/FeaturesFile.java          |    4 +++-
 src/jalview/io/FileFormats.java           |    7 ++++---
 src/jalview/io/FormatAdapter.java         |    3 ++-
 src/jalview/io/IdentifyFile.java          |    5 +++--
 src/jalview/io/JPredFile.java             |    3 ++-
 src/jalview/io/JnetAnnotationMaker.java   |    4 +++-
 src/jalview/io/MSFfile.java               |    3 ++-
 src/jalview/io/packed/ParsePackedSet.java |    5 +++--
 src/jalview/io/vcf/VCFLoader.java         |    5 +++--
 9 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 92473ec..7e62f6b 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -28,6 +28,7 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.TreeMap;
@@ -346,7 +347,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     String line;
     while ((line = nextLine()) != null)
     {
-      if (line.toUpperCase().startsWith(ENDFILTERS))
+      // TODO: use .trim().equalsIgnoreCase here instead ? 
+      if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
       {
         return;
       }
diff --git a/src/jalview/io/FileFormats.java b/src/jalview/io/FileFormats.java
index aadcdb9..de83e9b 100644
--- a/src/jalview/io/FileFormats.java
+++ b/src/jalview/io/FileFormats.java
@@ -24,6 +24,7 @@ import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 
@@ -102,7 +103,7 @@ public class FileFormats
   protected void registerFileFormat(FileFormatI format,
           boolean isIdentifiable)
   {
-    String name = format.getName().toUpperCase();
+    String name = format.getName().toUpperCase(Locale.ROOT);
     if (formats.containsKey(name))
     {
       System.err.println("Overwriting file format: " + format.getName());
@@ -121,7 +122,7 @@ public class FileFormats
    */
   public void deregisterFileFormat(String name)
   {
-    FileFormatI ff = formats.remove(name.toUpperCase());
+    FileFormatI ff = formats.remove(name.toUpperCase(Locale.ROOT));
     identifiable.remove(ff);
   }
 
@@ -174,7 +175,7 @@ public class FileFormats
    */
   public FileFormatI forName(String format)
   {
-    return format == null ? null : formats.get(format.toUpperCase());
+    return format == null ? null : formats.get(format.toUpperCase(Locale.ROOT));
   }
 
   /**
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 6d3c18a..4d8794f 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
 import java.io.IOException;
+import java.util.Locale;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -161,7 +162,7 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+    return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
             true);
   }
 
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ff959b0..ed1c29f 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import java.io.IOException;
+import java.util.Locale;
 
 /**
  * DOCUMENT ME!
@@ -143,7 +144,7 @@ public class IdentifyFile
             break;
           }
         }
-        data = data.toUpperCase();
+        data = data.toUpperCase(Locale.ROOT);
 
         if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
         {
@@ -284,7 +285,7 @@ public class IdentifyFile
         if ((lessThan > -1)) // possible Markup Language data i.e HTML,
                              // RNAML, XML
         {
-          String upper = data.toUpperCase();
+          String upper = data.toUpperCase(Locale.ROOT);
           if (upper.substring(lessThan).startsWith("<HTML"))
           {
             reply = FileFormat.Html;
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 6732e82..8f93b48 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -33,6 +33,7 @@ import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.Hashtable;
+import java.util.Locale;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -408,7 +409,7 @@ public class JPredFile extends AlignFile
     // check that no stray annotations have been added at the end.
     {
       SequenceI sq = seqs.elementAt(j - 1);
-      if (sq.getName().toUpperCase().startsWith("JPRED"))
+      if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
       {
         annotSeqs.addElement(sq);
         seqs.removeElementAt(--j);
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 6828202..27fc869 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -88,7 +90,7 @@ public class JnetAnnotationMaker
 
     while (i < preds.length)
     {
-      String id = preds[i].getName().toUpperCase();
+      String id = preds[i].getName().toUpperCase(Locale.ROOT);
 
       if (id.startsWith("LUPAS") || id.startsWith("JNET")
               || id.startsWith("JPRED"))
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index df2bed2..db29848 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -29,6 +29,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
 /**
@@ -184,7 +185,7 @@ public class MSFfile extends AlignFile
   public int checkSum(String seq)
   {
     int check = 0;
-    String sequence = seq.toUpperCase();
+    String sequence = seq.toUpperCase(Locale.ROOT);
 
     for (int i = 0; i < sequence.length(); i++)
     {
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 1635682..91575bf 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -34,6 +34,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 
 public class ParsePackedSet
 {
@@ -234,7 +235,7 @@ public class ParsePackedSet
       String type = args[i++];
       final String file = args[i++];
       final JvDataType jtype = DataProvider.JvDataType
-              .valueOf(type.toUpperCase());
+              .valueOf(type.toUpperCase(Locale.ROOT));
       if (jtype != null)
       {
         final FileParse fp;
@@ -253,7 +254,7 @@ public class ParsePackedSet
       else
       {
         System.out.println("Couldn't parse source type token '"
-                + type.toUpperCase() + "'");
+                + type.toUpperCase(Locale.ROOT) + "'");
       }
     }
     if (i < args.length)
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 13d7ae8..d6a530b 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -48,6 +48,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -569,7 +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;
       }
@@ -663,7 +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);
-- 
1.7.10.2