Merge branch 'benreview/JAL-3691_for_2_11_2_getdownrebuilds' into develop

diff --git a/getdown/lib/FJVL_VERSION b/getdown/lib/FJVL_VERSION
index 2cac91c..4a5376d 100644 (file)
--- a/getdown/lib/FJVL_VERSION
+++ b/getdown/lib/FJVL_VERSION
@@ -1 +1 @@
-1.8.3-1.2.11_FJVL
+1.8.3-1.2.12_FJVL

diff --git a/getdown/lib/JVL_VERSION b/getdown/lib/JVL_VERSION
index 99f8359..ed249ad 100644 (file)
--- a/getdown/lib/JVL_VERSION
+++ b/getdown/lib/JVL_VERSION
@@ -1 +1 @@
-1.8.3-1.2.11_JVL
+1.8.3-1.2.12_JVL

diff --git a/getdown/lib/getdown-core.jar b/getdown/lib/getdown-core.jar
index a11a269..2e695eb 100644 (file)
Binary files a/getdown/lib/getdown-core.jar and b/getdown/lib/getdown-core.jar differ

diff --git a/getdown/lib/getdown-launcher-local.jar b/getdown/lib/getdown-launcher-local.jar
index 4ac9d5d..fd89e15 100644 (file)
Binary files a/getdown/lib/getdown-launcher-local.jar and b/getdown/lib/getdown-launcher-local.jar differ

diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index 999c3fa..38c3a19 100644 (file)
Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ

diff --git a/getdown/src/getdown/ant/pom.xml b/getdown/src/getdown/ant/pom.xml
index e67984c..881c952 100644 (file)
--- a/getdown/src/getdown/ant/pom.xml
+++ b/getdown/src/getdown/ant/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.11_FJVL</version>
+    <version>1.8.3-1.2.12_FJVL</version>
   </parent>
 
   <artifactId>getdown-ant</artifactId>

diff --git a/getdown/src/getdown/core/pom.xml b/getdown/src/getdown/core/pom.xml
index f909444..3e52eca 100644 (file)
--- a/getdown/src/getdown/core/pom.xml
+++ b/getdown/src/getdown/core/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.11_FJVL</version>
+    <version>1.8.3-1.2.12_FJVL</version>
   </parent>
 
   <artifactId>getdown-core</artifactId>

diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
index 9deb5bc..8048728 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
@@ -1248,7 +1248,7 @@ public class Application
           if (j > -1) {
             ext = filename.substring(j+1);
           }
-          if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
+          if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase(Locale.ROOT))) {
             // this file extension should have been dealt with in Getdown class
           } else {
             _appargs.add(0, "-open");
@@ -1997,7 +1997,7 @@ public class Application
         String locatorFilename = filenames.length >= 1 ? filenames[0] : null;
         if (
                 !StringUtil.isBlank(locatorFilename)
-                && locatorFilename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)
+                && locatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
                 ) {
           setLocatorFile(locatorFilename);
           // remove the locator filename from the filenames array
@@ -2011,7 +2011,7 @@ public class Application
           // skip any other locator files in a multiple file list
           if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) {
             setJalviewUri(filename);
-          } else if (! filename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+          } else if (! filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
             addStartupFile(filename);
           }
         }

diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java
index 57b8d84..77997d2 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/EnvConfig.java
@@ -147,7 +147,7 @@ public final class EnvConfig {
         String argvLocatorFilename = argv.length > 2 ? argv[2] : null;
         if (
                 !StringUtil.isBlank(argvLocatorFilename)
-                && argvLocatorFilename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)
+                && argvLocatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
                 ) {
           notes.add(Note.info("locatorFilename in args: '"+argv[2]+"'"));
           Application.setLocatorFile(argvLocatorFilename);

diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java
index ae493bb..31a69c3 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java
@@ -139,7 +139,7 @@ public class LaunchUtil
                MessageDigest md = MessageDigest.getInstance(algo);
                md.update(Files.readAllBytes(Paths.get(file.getAbsolutePath())));
                byte[] digest = md.digest();
-               checksum = DatatypeConverter.printHexBinary(digest).toUpperCase();
+               checksum = DatatypeConverter.printHexBinary(digest).toUpperCase(Locale.ROOT);
        } catch (Exception e) {
                System.out.println("Couldn't create "+algo+" digest of "+file.getPath());
        }

diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java b/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java
index d6d440a..75106cc 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java
+++ b/getdown/src/getdown/core/src/main/java/jalview/bin/HiDPISetting.java
@@ -1,6 +1,8 @@
 package jalview.bin;
 
 import java.awt.HeadlessException;
+import java.util.Locale;
+
 
 public class HiDPISetting
 {
@@ -43,7 +45,7 @@ public class HiDPISetting
   static
   {
     String system = System.getProperty("os.name") == null ? null
-            : System.getProperty("os.name").toLowerCase();
+            : System.getProperty("os.name").toLowerCase(Locale.ROOT);
     if (system != null)
     {
       isLinux = system.indexOf("linux") > -1;

diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
index 55e304d..f5f0196 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
+++ b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
@@ -33,6 +33,7 @@ package jalview.bin;
  * @author bsoares
  *
  */
+import java.util.Locale;
 
 public class MemorySetting
 {
@@ -58,10 +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/getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java b/getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java
index d758395..afb9c89 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java
+++ b/getdown/src/getdown/core/src/main/java/jalview/util/StringUtils.java
@@ -24,6 +24,7 @@ import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 import java.util.regex.Pattern;
 
 public class StringUtils
@@ -409,9 +410,9 @@ public class StringUtils
     }
     if (s.length() <= 1)
     {
-      return s.toUpperCase();
+      return s.toUpperCase(Locale.ROOT);
     }
-    return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
+    return s.substring(0, 1).toUpperCase(Locale.ROOT) + s.substring(1).toLowerCase(Locale.ROOT);
   }
 
   /**
@@ -427,7 +428,7 @@ public class StringUtils
     {
       return null;
     }
-    String tmp2up = text.toUpperCase();
+    String tmp2up = text.toUpperCase(Locale.ROOT);
     int startTag = tmp2up.indexOf("<HTML>");
     if (startTag > -1)
     {
@@ -572,9 +573,9 @@ 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/getdown/src/getdown/launcher/pom.xml b/getdown/src/getdown/launcher/pom.xml
index 5284412..df0ebbe 100644 (file)
--- a/getdown/src/getdown/launcher/pom.xml
+++ b/getdown/src/getdown/launcher/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.11_FJVL</version>
+    <version>1.8.3-1.2.12_FJVL</version>
   </parent>
 
   <artifactId>getdown-launcher</artifactId>

diff --git a/getdown/src/getdown/mvn_cmd b/getdown/src/getdown/mvn_cmd
index 4ffb086..4a9d2ea 100755 (executable)
--- a/getdown/src/getdown/mvn_cmd
+++ b/getdown/src/getdown/mvn_cmd
@@ -3,7 +3,7 @@
 if [ x$JVLVERSION != x ]; then
   export VERSION=$JVLVERSION
 else
-  export VERSION=1.8.3-1.2.11_JVL
+  export VERSION=1.8.3-1.2.12_JVL
 fi
 
 if [ x${VERSION%_JVL} = x$VERSION ]; then

diff --git a/getdown/src/getdown/pom.xml b/getdown/src/getdown/pom.xml
index 61b1440..87b361e 100644 (file)
--- a/getdown/src/getdown/pom.xml
+++ b/getdown/src/getdown/pom.xml
@@ -10,7 +10,7 @@
   <groupId>com.threerings.getdown</groupId>
   <artifactId>getdown</artifactId>
   <packaging>pom</packaging>
-  <version>1.8.3-1.2.11_FJVL</version>
+  <version>1.8.3-1.2.12_FJVL</version>
 
   <name>getdown</name>
   <description>An application installer and updater.</description>

diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
index a11a269..2e695eb 100644 (file)
Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ

diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
index a11a269..2e695eb 100644 (file)
Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ

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 {