tidy

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13780 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/ExternalProgram.java

@@ -128,48 +128,22 @@ public class ExternalProgram
     // sequence_file_names will be set by prepareRun()
     final File file_of_filenames = prepareRun(features, sequence_file_names);
 
-//  final Integer job_control_id =
-//    Options.getOptions().getIntegerProperty("jcon_" + getName() +
-//                                              "_program_id");
-
-//  final Integer min_jc_jobs =
-//    Options.getOptions().getIntegerProperty("jcon_min_jobs");
-
-//  String jcon_template =
-//    Options.getOptions().getProperty("jcon_" + getName() + "_template");
-
-//  final String jcon_batch_queue =
-//    Options.getOptions().getProperty("jcon_batch_queue");
-
-//  if(job_control_id != null &&
-//     min_jc_jobs != null &&
-//     jcon_template != null &&
-//     jcon_batch_queue != null &&
-//     features.size() >= min_jc_jobs.intValue()) 
-//  {
-//    return ExternalProgramUtils.runJConProgram(this, features, 
-//                			         sequence_file_names, logger);
-//  }
-//  else 
-//  {
     try
     {
       if( System.getProperty("j2ssh") != null && 
          !System.getProperty("j2ssh").equals("false") && 
           (getRealName().indexOf("blast") > -1 || getRealName().startsWith("fast")))
       {
-
         logger4j.debug("GET READY TO CALL SSH CLIENT " + getRealName());
 
         final Feature this_feature = features.elementAt(0);
         Entry entry = this_feature.getEntry();
         String[] args;
 
-          if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
-                            instanceof RemoteFileDocument)
+        if (((DocumentEntry) entry.getEMBLEntry()).getDocument() instanceof RemoteFileDocument)
         {
-            RemoteFileDocument nodeDoc =
-               (RemoteFileDocument)(((DocumentEntry)entry.getEMBLEntry()).getDocument());
+          RemoteFileDocument nodeDoc = (RemoteFileDocument) (((DocumentEntry) entry
+              .getEMBLEntry()).getDocument());
           RemoteFileNode node = nodeDoc.getRemoteFileNode();
 
           String wdir = node.getRootDir() + "/" + node.getFullName();
@@ -178,57 +152,55 @@ public class ExternalProgram
 
           args = new String[9];
 
-            args[0] = "-f";    args[1] = file_of_filenames.getPath();
-            args[2] = "-cmd";  args[3] = getRealName();
-            args[4] = "-wdir"; args[5] = wdir; 
-            args[6] = "-d";    args[7] = getProgramOptions();
+          args[0] = "-f";
+          args[1] = file_of_filenames.getPath();
+          args[2] = "-cmd";
+          args[3] = getRealName();
+          args[4] = "-wdir";
+          args[5] = wdir;
+          args[6] = "-d";
+          args[7] = getProgramOptions();
           args[8] = "-keep";
         }
         else
         {
           args = new String[6];
 
-            args[0] = "-f";    args[1] = file_of_filenames.getPath();
-            args[2] = "-cmd";  args[3] = getRealName();
-            args[4] = "-d";    args[5] = getProgramOptions();
+          args[0] = "-f";
+          args[1] = file_of_filenames.getPath();
+          args[2] = "-cmd";
+          args[3] = getRealName();
+          args[4] = "-d";
+          args[5] = getProgramOptions();
         }
 
         logger4j.debug("CALL SSH CLIENT " + getRealName());
-
-          uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
-                new uk.ac.sanger.artemis.j2ssh.SshPSUClient(args);
+        uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh = new uk.ac.sanger.artemis.j2ssh.SshPSUClient(
+            args);
         ssh.start();
         new ProgressBarFrame(1, getName());
         return null;
       }
 
       final String[] arguments;
-
       switch (program_type)
       {
       case DNA_PROGRAM:
         // fall through
       case AA_PROGRAM:
         arguments = new String[]
-            {
-              file_of_filenames.getPath(),
-              getProgramOptions()
-            };
+        { file_of_filenames.getPath(), getProgramOptions() };
         break;
       case APPLICATION:
         arguments = new String[]
-            {
-              file_of_filenames.getPath(),
-            };
+        { file_of_filenames.getPath(), };
         break;
       default:
         throw new Error("internal error - unknown program type");
       }
 
-        final Process process =
-          startProgram("run_" + getRealName(), arguments);
+      final Process process = startProgram("run_" + getRealName(), arguments);
 
-        //
       //
       new ProgressBarFrame(1, getName());
       return new ProcessMonitor(process, getName(), logger);
@@ -236,11 +208,9 @@ public class ExternalProgram
     catch (SecurityException e)
     {
       // re-throw as an ExternalProgramException
-        throw new ExternalProgramException("SecurityException while running " +
-                                            getName() + ": " +
-                                            e.getMessage());
+      throw new ExternalProgramException("SecurityException while running "
+          + getName() + ": " + e.getMessage());
     }
-//  }
   }
   
 
@@ -298,7 +268,7 @@ public class ExternalProgram
     File first_directory = null;
 
     // stores the number of features in each directory
-    final Hashtable feature_count_hash = new Hashtable();
+    final Hashtable<File, Long> feature_count_hash = new Hashtable<File, Long>();
 
     for(int i = 0 ; i < features.size() ; ++i) 
     {
@@ -341,12 +311,12 @@ public class ExternalProgram
       node = nodeDoc.getRemoteFileNode();
     }  
     
-    final java.util.Hashtable file_number_hash = new java.util.Hashtable();
+    final Hashtable<File, Long> file_number_hash = new Hashtable<File, Long>();
 
-    for(final Enumeration e = feature_count_hash.keys() ;
+    for(final Enumeration<File> e = feature_count_hash.keys() ;
          e.hasMoreElements() ;) 
     {
-      final File directory =(File) e.nextElement();
+      final File directory = e.nextElement();
 
       final long old_file_number = getFileNumber(directory, node);