JAL-3691 patch toUpper/toLower to use Locale.ROOT for 2.11.2 src

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
index 6b5e36c..ad5e350 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
@@ -36,6 +36,7 @@ import java.awt.Color;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import org.slf4j.Logger;
@@ -327,11 +328,11 @@ public abstract class ChimUtils
     String resType = "";
     if (split.length == 2)
     {
-      resType = split[0].trim().toUpperCase();
+      resType = split[0].trim().toUpperCase(Locale.ROOT);
     }
     else if (split.length == 3)
     {
-      resType = split[1].trim().toUpperCase();
+      resType = split[1].trim().toUpperCase(Locale.ROOT);
     }
     if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
     {

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index 0a248cf..46ed164 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -39,6 +39,7 @@ import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
@@ -978,16 +979,16 @@ public class StructureManager
     if (os.startsWith("Linux"))
     {
       // ChimeraX .deb and .rpm packages put symbolic link from /usr/bin/chimerax
-      pathList.add(String.format("/usr/bin/%s", chimeraExe.toLowerCase()));
+      pathList.add(String.format("/usr/bin/%s", chimeraExe.toLowerCase(Locale.ROOT)));
       pathList.add(String.format("/usr/bin/%s", chimeraExe));
 
       pathList.add(
-              String.format("/usr/local/bin/%s", chimeraExe.toLowerCase()));
+              String.format("/usr/local/bin/%s", chimeraExe.toLowerCase(Locale.ROOT)));
       pathList.add(String.format("/usr/local/bin/%s", chimeraExe));
 
       // these paths also used by .deb and .rpm
       pathList.add(String.format("/usr/lib/ucsf-%s/bin/%s",
-              chimera.toLowerCase(), chimeraExe));
+              chimera.toLowerCase(Locale.ROOT), chimeraExe));
       pathList.add(String.format("/usr/libexec/UCSF-%s/bin/%s", chimera,
               chimeraExe));
 
@@ -995,15 +996,15 @@ public class StructureManager
 
       // user home paths
       pathList.add(String.format("%s/bin/%s",
-              System.getProperty("user.home"), chimeraExe.toLowerCase()));
+              System.getProperty("user.home"), chimeraExe.toLowerCase(Locale.ROOT)));
       pathList.add(String.format("%s/bin/%s",
               System.getProperty("user.home"), chimeraExe));
       pathList.add(String.format("%s/opt/bin/%s",
-              System.getProperty("user.home"), chimeraExe.toLowerCase()));
+              System.getProperty("user.home"), chimeraExe.toLowerCase(Locale.ROOT)));
       pathList.add(String.format("%s/opt/bin/%s",
               System.getProperty("user.home"), chimeraExe));
       pathList.add(String.format("%s/local/bin/%s",
-              System.getProperty("user.home"), chimeraExe.toLowerCase()));
+              System.getProperty("user.home"), chimeraExe.toLowerCase(Locale.ROOT)));
       pathList.add(String.format("%s/local/bin/%s",
               System.getProperty("user.home"), chimeraExe));
     }

diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java
index 56713b0..bb545cb 100644 (file)
--- a/src/jalview/bin/MemorySetting.java
+++ b/src/jalview/bin/MemorySetting.java
@@ -22,6 +22,8 @@
  */
 package jalview.bin;
 
+import java.util.Locale;
+
 /**
  * Methods to decide on appropriate memory setting for Jalview based on two
  * optionally provided values: jvmmempc - the maximum percentage of total
@@ -57,10 +59,10 @@ public class MemorySetting
           + "_CUSTOMISED_SETTINGS";
 
   public static final String MEMORY_JVMMEMPC = NS + "_"
-          + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase();
+          + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase(Locale.ROOT);
 
   public static final String MEMORY_JVMMEMMAX = NS + "_"
-          + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase();
+          + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase(Locale.ROOT);
 
   protected static boolean logToClassChecked = false;
 

diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java
index 273f6ec..ff1c944 100644 (file)
--- a/src/jalview/util/StringUtils.java
+++ b/src/jalview/util/StringUtils.java
@@ -574,9 +574,9 @@ public class StringUtils
   public static int firstCharPosIgnoreCase(String text, String chars)
   {
     int min = text.length() + 1;
-    for (char c : chars.toLowerCase().toCharArray())
+    for (char c : chars.toLowerCase(Locale.ROOT).toCharArray())
     {
-      int i = text.toLowerCase().indexOf(c);
+      int i = text.toLowerCase(Locale.ROOT).indexOf(c);
       if (0 <= i && i < min)
       {
         min = i;

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 425bc18..97514e9 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -35,6 +35,7 @@ import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
+import java.util.Locale;
 import java.util.Vector;
 
 public class PDBChain
@@ -83,7 +84,7 @@ public class PDBChain
 
   public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
   {
-    this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
+    this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(Locale.ROOT);
     this.id = theId;
     if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
     {

diff --git a/src/org/json/simple/JSONValue.java b/src/org/json/simple/JSONValue.java
index d6b2185..eb11cb2 100644 (file)
--- a/src/org/json/simple/JSONValue.java
+++ b/src/org/json/simple/JSONValue.java
@@ -10,6 +10,7 @@ import java.io.StringReader;
 import java.io.StringWriter;
 import java.io.Writer;
 import java.util.Collection;
+import java.util.Locale;
 // import java.util.List;
 import java.util.Map;
 
@@ -306,7 +307,7 @@ public class JSONValue {
                                        for(int k=0;k<4-ss.length();k++){
                                                sb.append('0');
                                        }
-                                       sb.append(ss.toUpperCase());
+                                       sb.append(ss.toUpperCase(Locale.ROOT));
                                }
                                else{
                                        sb.append(ch);

diff --git a/src/org/stackoverflowusers/file/WindowsShortcut.java b/src/org/stackoverflowusers/file/WindowsShortcut.java
index 671e002..60c814b 100644 (file)
--- a/src/org/stackoverflowusers/file/WindowsShortcut.java
+++ b/src/org/stackoverflowusers/file/WindowsShortcut.java
@@ -6,6 +6,7 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.text.ParseException;
+import java.util.Locale;
 
 /**
  * Represents a Windows shortcut (typically visible to Java only as a '.lnk' file).
@@ -46,7 +47,7 @@ public class WindowsShortcut
         boolean isPotentiallyValid = false;
         try {
             isPotentiallyValid = file.isFile()
-                && file.getName().toLowerCase().endsWith(".lnk")
+                && file.getName().toLowerCase(Locale.ROOT).endsWith(".lnk")
                 && fis.available() >= minimum_length
                 && isMagicPresent(getBytes(fis, 32));
         } finally {