JAL-3933 remove obsolete Castor logging configuration

[jalview.git] / src / jalview / io / packed / ParsePackedSet.java

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 138fef7..91575bf 100644 (file)
--- 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
 {
@@ -157,7 +158,8 @@ public class ParsePackedSet
         {
           jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
           context.updateSetModified(ff.parse(context.getLastAlignment(),
-                  context.featureColours, false, context.relaxedIdMatching));
+                  context.featureColours, false,
+                  context.relaxedIdMatching));
         } catch (Exception e)
         {
           errmsg = ("Failed to parse the Features file associated with the alignment.");
@@ -232,8 +234,8 @@ public class ParsePackedSet
     {
       String type = args[i++];
       final String file = args[i++];
-      final JvDataType jtype = DataProvider.JvDataType.valueOf(type
-              .toUpperCase());
+      final JvDataType jtype = DataProvider.JvDataType
+              .valueOf(type.toUpperCase(Locale.ROOT));
       if (jtype != null)
       {
         final FileParse fp;
@@ -252,7 +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)
@@ -271,8 +273,8 @@ public class ParsePackedSet
     ParsePackedSet pps;
     try
     {
-      newdm = (pps = new ParsePackedSet()).getAlignment(
-              context = new JalviewDataset(), dp);
+      newdm = (pps = new ParsePackedSet())
+              .getAlignment(context = new JalviewDataset(), dp);
     } catch (Exception e)
     {
       System.out.println("Test failed for these arguments.\n");
@@ -296,8 +298,8 @@ public class ParsePackedSet
     {
       if (context.getLastAlignmentSet().isModified())
       {
-        System.err
-                .println("Initial alignment set was modified and any associated views should be updated.");
+        System.err.println(
+                "Initial alignment set was modified and any associated views should be updated.");
       }
     }
   }