X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=0ab75158ee69368b7c0e9c235c186f1beb5a5eb4;hb=890092d4ca9b8c17a3f356eeb12f49440d5fc51c;hp=0239bb4ba36fd8b68e64ac03eca958406627b311;hpb=15c6c6724878a5445e9f5bc6594719dbe81c1735;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0239bb4..0ab7515 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1203,7 +1203,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           PrintWriter out = new PrintWriter(
                   new FileWriter(backupfiles.getTempFilePath()));
 
+          // TESTING code here
+          boolean TESTING = true;
+          if (TESTING)
+          {
+            out.print("; TESTSTART\n");
+            int count = 20;
+            for (int i = 0; i < count; i++)
+            {
+              // Thread.sleep(1000);
+              out.println("; TEST: " + (count - 1 - i));
+            }
+          }
           out.print(output);
+          if (TESTING)
+          {
+            out.print("; TESTEND\n");
+          }
           out.close();
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
@@ -2092,7 +2108,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2139,7 +2155,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -4491,7 +4507,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              boolean autoAssociate = Cache
+                      .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
               if (!autoAssociate)
               {
                 String msg = MessageManager.formatMessage(