diff --git a/uk/ac/sanger/artemis/components/ActMain.java b/uk/ac/sanger/artemis/components/ActMain.java
index 18beef5f7964ed01db9b89fcd3672bde420a0702..dd1d8ced0efa68a1495fd07f61c3babcea99bc22 100644
--- a/uk/ac/sanger/artemis/components/ActMain.java
+++ b/uk/ac/sanger/artemis/components/ActMain.java
@@ -20,13 +20,14 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ActMain.java,v 1.6 2005-02-21 11:25:43 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ActMain.java,v 1.7 2005-08-17 08:43:05 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.components.filetree.FileManager;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.EntryInformation;
@@ -40,7 +41,7 @@ import javax.swing.JFrame;
* The main window for the Artemis Comparison Tool.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ActMain.java,v 1.6 2005-02-21 11:25:43 tjc Exp $
+ * @version $Id: ActMain.java,v 1.7 2005-08-17 08:43:05 tjc Exp $
**/
public class ActMain extends Splash
diff --git a/uk/ac/sanger/artemis/components/ArtemisMain.java b/uk/ac/sanger/artemis/components/ArtemisMain.java
index 95acf23b804b49b770d7713c71551952665cae22..2c1671d07709f0e746cc521e6e65b81387e348c1 100644
--- a/uk/ac/sanger/artemis/components/ArtemisMain.java
+++ b/uk/ac/sanger/artemis/components/ArtemisMain.java
@@ -20,11 +20,12 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.16 2005-07-20 09:29:56 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.17 2005-08-17 08:43:05 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
+import uk.ac.sanger.artemis.components.filetree.FileManager;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.sequence.Bases;
@@ -45,7 +46,7 @@ import java.io.*;
* The main window for the Artemis sequence editor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ArtemisMain.java,v 1.16 2005-07-20 09:29:56 tjc Exp $
+ * @version $Id: ArtemisMain.java,v 1.17 2005-08-17 08:43:05 tjc Exp $
**/
public class ArtemisMain extends Splash
diff --git a/uk/ac/sanger/artemis/components/EntryEdit.java b/uk/ac/sanger/artemis/components/EntryEdit.java
index f2a760e2558a322e0db6d9107d04edbf5d92b26d..f2a5725047cfe45fa5462d4d54b2c089f7302c57 100644
--- a/uk/ac/sanger/artemis/components/EntryEdit.java
+++ b/uk/ac/sanger/artemis/components/EntryEdit.java
@@ -20,13 +20,15 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryEdit.java,v 1.19 2005-08-11 16:12:43 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryEdit.java,v 1.20 2005-08-17 08:43:05 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.chado.*;
+import uk.ac.sanger.artemis.components.filetree.FileManager;
+import uk.ac.sanger.artemis.components.filetree.FileNode;
import uk.ac.sanger.artemis.sequence.Marker;
import uk.ac.sanger.artemis.sequence.Bases;
@@ -56,7 +58,7 @@ import javax.swing.border.BevelBorder;
* Each object of this class is used to edit an EntryGroup object.
*
* @author Kim Rutherford
- * @version $Id: EntryEdit.java,v 1.19 2005-08-11 16:12:43 tjc Exp $
+ * @version $Id: EntryEdit.java,v 1.20 2005-08-17 08:43:05 tjc Exp $
*
*/
public class EntryEdit extends JFrame
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index c6e800dadc5dfa2032efcafbb84526ed1ca85fcc..fc1ad94e3ab148f2e44fdac29ed0ef75fbe9ef89 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -20,13 +20,14 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/MultiComparator.java,v 1.12 2005-04-15 09:53:08 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/MultiComparator.java,v 1.13 2005-08-17 08:43:05 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
-
+import uk.ac.sanger.artemis.components.filetree.FileManager;
+import uk.ac.sanger.artemis.components.filetree.FileNode;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
@@ -57,7 +58,7 @@ import javax.swing.border.BevelBorder;
* to keep them synchronized.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: MultiComparator.java,v 1.12 2005-04-15 09:53:08 tjc Exp $
+ * @version $Id: MultiComparator.java,v 1.13 2005-08-17 08:43:05 tjc Exp $
**/
public class MultiComparator extends JFrame
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index 70c015d858437a25caf64a87b287036cee63cce6..d012a38e33ea4c97ddf8887938288a9a88179bd6 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -69,6 +69,9 @@ import com.sshtools.j2ssh.configuration.ConfigurationLoader;
public class SshPSUClient extends Thread
{
+ private Vector dir_list;
+ private Vector file_list;
+
// defaults
private String listfilepath = null;
private String cmd = null;
@@ -343,22 +346,27 @@ public class SshPSUClient extends Thread
else
db = "%uniprot";
}
- if(cmd.equals("blastp") && settings.getProperty("blastp") != null)
- cmd = settings.getProperty("blastp");
- else if(cmd.equals("blastn") && settings.getProperty("blastn") != null)
- cmd = settings.getProperty("blastn");
- else if(cmd.equals("blastx") && settings.getProperty("blastx") != null)
- cmd = settings.getProperty("blastx");
- else if(cmd.equals("tblastx") && settings.getProperty("tblastx") != null)
- cmd = settings.getProperty("tblastx");
- else if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
- cmd = settings.getProperty("fasta");
- else if(cmd.equals("fastx") && settings.getProperty("fastx") != null)
- cmd = settings.getProperty("fastx");
+
+ if(cmd != null)
+ {
+ if(cmd.equals("blastp") && settings.getProperty("blastp") != null)
+ cmd = settings.getProperty("blastp");
+ else if(cmd.equals("blastn") && settings.getProperty("blastn") != null)
+ cmd = settings.getProperty("blastn");
+ else if(cmd.equals("blastx") && settings.getProperty("blastx") != null)
+ cmd = settings.getProperty("blastx");
+ else if(cmd.equals("tblastx") && settings.getProperty("tblastx") != null)
+ cmd = settings.getProperty("tblastx");
+ else if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
+ cmd = settings.getProperty("fasta");
+ else if(cmd.equals("fastx") && settings.getProperty("fastx") != null)
+ cmd = settings.getProperty("fastx");
+ }
return settings;
}
+
/**
*
* Run fasta or blast on the server ssh'ed into