JAL-4153 avoid use of invokeAndWait, increase wait time and add timeout for the cache...

[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 1635682..3ce774e 100644 (file)
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.packed;
 
+import java.util.Locale;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
 import jalview.io.AppletFormatAdapter;
@@ -52,7 +54,7 @@ public class ParsePackedSet
   public Object[] getAlignment(JalviewDataset context,
           Iterable<DataProvider> files) throws Exception
   {
-    List<Object> rslt = new ArrayList<Object>();
+    List<Object> rslt = new ArrayList<>();
     if (context == null)
     {
       context = new JalviewDataset();
@@ -151,7 +153,7 @@ public class ParsePackedSet
         // if not, create one.
         if (context.featureColours == null)
         {
-          context.featureColours = new HashMap<String, FeatureColourI>();
+          context.featureColours = new HashMap<>();
         }
         try
         {
@@ -223,18 +225,19 @@ public class ParsePackedSet
    * would be created.
    * 
    * @param args
+   * @j2sIgnore
    */
   public static void main(String args[])
   {
     // make data providers from the set of keys/files
     int i = 0;
-    List<DataProvider> dp = new ArrayList<DataProvider>();
+    List<DataProvider> dp = new ArrayList<>();
     while ((i + 1) < args.length)
     {
       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;
@@ -243,7 +246,7 @@ public class ParsePackedSet
           fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
         } catch (Exception e)
         {
-          System.err.println("Couldn't handle datasource of type " + jtype
+          jalview.bin.Console.errPrintln("Couldn't handle datasource of type " + jtype
                   + " using URI " + file);
           e.printStackTrace();
           return;
@@ -252,8 +255,8 @@ public class ParsePackedSet
       }
       else
       {
-        System.out.println("Couldn't parse source type token '"
-                + type.toUpperCase() + "'");
+        jalview.bin.Console.outPrintln("Couldn't parse source type token '"
+                + type.toUpperCase(Locale.ROOT) + "'");
       }
     }
     if (i < args.length)
@@ -266,7 +269,7 @@ public class ParsePackedSet
       System.out.print("\n");
 
     }
-    System.out.println("Now trying to parse set:");
+    jalview.bin.Console.outPrintln("Now trying to parse set:");
     JalviewDataset context;
     Object[] newdm;
     ParsePackedSet pps;
@@ -276,7 +279,7 @@ public class ParsePackedSet
               .getAlignment(context = new JalviewDataset(), dp);
     } catch (Exception e)
     {
-      System.out.println("Test failed for these arguments.\n");
+      jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
       e.printStackTrace(System.out);
       return;
     }
@@ -284,7 +287,7 @@ public class ParsePackedSet
     {
       for (Object o : newdm)
       {
-        System.out.println("Will need to create an " + o.getClass());
+        jalview.bin.Console.outPrintln("Will need to create an " + o.getClass());
       }
 
       // now test uniquify/deuniquify stuff
@@ -297,7 +300,7 @@ public class ParsePackedSet
     {
       if (context.getLastAlignmentSet().isModified())
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Initial alignment set was modified and any associated views should be updated.");
       }
     }