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Commit 3735d61b authored by tjc's avatar tjc
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ssh file manager

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3418 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 65e84cd9
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......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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
......
......@@ -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;
......@@ -343,6 +346,9 @@ public class SshPSUClient extends Thread
else
db = "%uniprot";
}
if(cmd != null)
{
if(cmd.equals("blastp") && settings.getProperty("blastp") != null)
cmd = settings.getProperty("blastp");
else if(cmd.equals("blastn") && settings.getProperty("blastn") != null)
......@@ -355,10 +361,12 @@ public class SshPSUClient extends Thread
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
......
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