diff --git a/uk/ac/sanger/artemis/ExternalProgram.java b/uk/ac/sanger/artemis/ExternalProgram.java
index eb9c4802c8871d316517e6ae372455444fca5012..d46859ea70bcac1b0fe1eefd7635156fb33b2a00 100644
--- a/uk/ac/sanger/artemis/ExternalProgram.java
+++ b/uk/ac/sanger/artemis/ExternalProgram.java
@@ -128,119 +128,89 @@ 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
+ try
+ {
+ if( System.getProperty("j2ssh") != null &&
+ !System.getProperty("j2ssh").equals("false") &&
+ (getRealName().indexOf("blast") > -1 || getRealName().startsWith("fast")))
{
- 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());
- logger4j.debug("GET READY TO CALL SSH CLIENT "+getRealName());
+ final Feature this_feature = features.elementAt(0);
+ Entry entry = this_feature.getEntry();
+ String[] args;
- final Feature this_feature = features.elementAt(0);
- Entry entry = this_feature.getEntry();
- String [] args;
-
- if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
- instanceof RemoteFileDocument)
- {
- RemoteFileDocument nodeDoc =
- (RemoteFileDocument)(((DocumentEntry)entry.getEMBLEntry()).getDocument());
- RemoteFileNode node = nodeDoc.getRemoteFileNode();
-
- String wdir = node.getRootDir()+"/"+node.getFullName();
- int index = wdir.lastIndexOf("/");
- wdir = wdir.substring(0,index);
-
- 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[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();
- }
-
- logger4j.debug("CALL SSH CLIENT "+getRealName());
-
- uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh =
- new uk.ac.sanger.artemis.j2ssh.SshPSUClient(args);
- ssh.start();
- new ProgressBarFrame(1, getName());
- return null;
+ if (((DocumentEntry) entry.getEMBLEntry()).getDocument() instanceof RemoteFileDocument)
+ {
+ RemoteFileDocument nodeDoc = (RemoteFileDocument) (((DocumentEntry) entry
+ .getEMBLEntry()).getDocument());
+ RemoteFileNode node = nodeDoc.getRemoteFileNode();
+
+ String wdir = node.getRootDir() + "/" + node.getFullName();
+ int index = wdir.lastIndexOf("/");
+ wdir = wdir.substring(0, index);
+
+ 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[8] = "-keep";
}
-
- final String [] arguments;
-
- switch(program_type)
+ else
{
- case DNA_PROGRAM:
- // fall through
- case AA_PROGRAM:
- arguments = new String []
- {
- file_of_filenames.getPath(),
- getProgramOptions()
- };
- break;
- case APPLICATION:
- arguments = new String []
- {
- file_of_filenames.getPath(),
- };
- break;
- default:
- throw new Error("internal error - unknown program type");
+ 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();
}
- final Process process =
- startProgram("run_" + getRealName(), arguments);
-
- //
- //
+ logger4j.debug("CALL SSH CLIENT " + getRealName());
+ uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh = new uk.ac.sanger.artemis.j2ssh.SshPSUClient(
+ args);
+ ssh.start();
new ProgressBarFrame(1, getName());
- return new ProcessMonitor(process, getName(), logger);
- }
- catch(SecurityException e)
+ return null;
+ }
+
+ final String[] arguments;
+ switch (program_type)
{
- // re-throw as an ExternalProgramException
- throw new ExternalProgramException("SecurityException while running " +
- getName() + ": " +
- e.getMessage());
+ case DNA_PROGRAM:
+ // fall through
+ case AA_PROGRAM:
+ arguments = new String[]
+ { file_of_filenames.getPath(), getProgramOptions() };
+ break;
+ case APPLICATION:
+ arguments = new String[]
+ { file_of_filenames.getPath(), };
+ break;
+ default:
+ throw new Error("internal error - unknown program type");
}
-// }
+
+ final Process process = startProgram("run_" + getRealName(), arguments);
+
+ //
+ new ProgressBarFrame(1, getName());
+ return new ProcessMonitor(process, getName(), logger);
+ }
+ catch (SecurityException e)
+ {
+ // re-throw as an ExternalProgramException
+ 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);