diff --git a/uk/ac/sanger/artemis/j2ssh/SshFileManager.java b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..bd20d0f7a96f08947ebdcbc68876af421fc0aad0
--- /dev/null
+++ b/uk/ac/sanger/artemis/j2ssh/SshFileManager.java
@@ -0,0 +1,431 @@
+/* ExternalProgram.java
+ *
+ * created: Aug 2005
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2005 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ **/
+
+package uk.ac.sanger.artemis.j2ssh;
+
+
+import javax.swing.JOptionPane;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.JPasswordField;
+import javax.swing.SwingConstants;
+
+import java.awt.GridLayout;
+import java.io.File;
+import java.io.FileReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.BufferedReader;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+
+import java.util.Vector;
+import java.util.Properties;
+import java.util.logging.FileHandler;
+import java.util.logging.Handler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import java.util.logging.SimpleFormatter;
+
+import com.sshtools.j2ssh.SshClient;
+import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
+import com.sshtools.j2ssh.authentication.PasswordAuthenticationClient;
+import com.sshtools.j2ssh.session.SessionChannelClient;
+import com.sshtools.j2ssh.sftp.FileAttributes;
+import com.sshtools.j2ssh.sftp.SftpFile;
+import com.sshtools.j2ssh.sftp.SftpFileOutputStream;
+import com.sshtools.j2ssh.SftpClient;
+import com.sshtools.j2ssh.configuration.ConfigurationLoader;
+
+
+/**
+*
+* Client to use ssh connection to server to run blast/fasta
+* remotely.
+*
+*/
+public class SshFileManager
+{
+
+ private Vector dir_list;
+ private Vector file_list;
+
+ // defaults
+ private String logfile = null;
+ private String wdir = "/nfs/pathscratch1/scratch";
+
+ // login variables
+ private String hostname = null;
+ private String user = null;
+ private int port = -1;
+ private static JPasswordField pfield = new JPasswordField(16);
+ private static JTextField portfield = new JTextField(16);
+ private static JTextField hostfield = new JTextField(16);
+ private static JTextField ufield = new JTextField(16);
+ private SshClient ssh;
+
+ public SshFileManager()
+ {
+ try
+ {
+ // Setup a logfile
+ if(logfile != null)
+ {
+ Handler fh = new FileHandler(logfile);
+ fh.setFormatter(new SimpleFormatter());
+ Logger.getLogger("com.sshtools").setUseParentHandlers(false);
+ Logger.getLogger("com.sshtools").addHandler(fh);
+ Logger.getLogger("com.sshtools").setLevel(Level.ALL);
+ }
+ else
+ Logger.getLogger("com.sshtools").setLevel(Level.OFF);
+ }
+ catch(IOException ioe){}
+
+ Properties settings = getProperties();
+ try
+ {
+ ssh = login();
+ }
+ catch(IOException ioe){}
+ }
+
+ /**
+ *
+ * Log the user in.
+ *
+ */
+ private SshClient login()
+ throws IOException
+ {
+ SshClient ssh = null;
+ int result = AuthenticationProtocolState.FAILED;
+
+ while(result != AuthenticationProtocolState.COMPLETE)
+ {
+ if(!setLogin())
+ return null;
+
+ // Create a password authentication instance
+ PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
+ user = ufield.getText().trim();
+ pwd.setUsername(user);
+ pwd.setPassword(new String(pfield.getPassword()));
+
+ // Make a client connection
+ ssh = new SshClient();
+ hostname = hostfield.getText().trim();
+ if(portfield.getText().trim().equals(""))
+ port = -1;
+ else
+ port = Integer.parseInt(portfield.getText().trim());
+
+ if(port < 0)
+ ssh.connect(hostname);
+ else
+ ssh.connect(hostname,port);
+
+ // Try the authentication
+ result = ssh.authenticate(pwd);
+ }
+ return ssh;
+ }
+
+ /**
+ *
+ * Set the login information.
+ *
+ */
+ private boolean setLogin()
+ {
+ JPanel promptPanel = new JPanel(new GridLayout(4,2));
+
+ if(hostname != null && hostfield.getText().equals(""))
+ hostfield.setText(hostname);
+
+ if(port >-1 && portfield.getText().equals(""))
+ portfield.setText(Integer.toString(port));
+
+ if(user != null && ufield.getText().equals(""))
+ ufield.setText(user);
+
+ JLabel hostlab = new JLabel(" Hostname:", SwingConstants.LEFT);
+ JLabel portlab = new JLabel(" Port:", SwingConstants.LEFT);
+
+ JLabel ulab = new JLabel(" Username:", SwingConstants.LEFT);
+ JLabel plab = new JLabel(" Password:", SwingConstants.LEFT);
+ //add labels etc
+ promptPanel.add(hostlab);
+ promptPanel.add(hostfield);
+
+ promptPanel.add(portlab);
+ promptPanel.add(portfield);
+
+ promptPanel.add(ulab);
+ promptPanel.add(ufield);
+
+ promptPanel.add(plab);
+ promptPanel.add(pfield);
+
+ Object[] options = { "CANCEL", "LOGIN AND RUN"};
+
+ int select = JOptionPane.showOptionDialog(null, promptPanel,
+ "LOGIN",
+ JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[1]);
+
+ if(select == 0)
+ return false;
+
+ return true;
+ }
+
+
+ /**
+ *
+ * Get the properties from the j2ssh.properties file.
+ *
+ */
+ private Properties getProperties()
+ {
+ Properties settings = new Properties();
+ ClassLoader cl = this.getClass().getClassLoader();
+ // try out of the classpath
+ try
+ {
+ settings.load(cl.getResourceAsStream("j2ssh.properties"));
+ }
+ catch (Exception e)
+ {
+ }
+
+ if(hostname == null && settings.getProperty("host") != null)
+ hostname = settings.getProperty("host");
+ if(port < 0 && settings.getProperty("port") != null)
+ port = Integer.parseInt(settings.getProperty("port"));
+ if(user == null)
+ user = System.getProperty("user.name");
+
+ return settings;
+ }
+
+ public boolean remoteList(String remoteRootDir)
+ throws IOException
+ {
+ SftpClient sftp = ssh.openSftpClient();
+
+ try
+ {
+ sftp.cd(remoteRootDir);
+ }
+ catch(java.io.FileNotFoundException fnf)
+ {
+ }
+
+ Object list[] = sftp.ls().toArray();
+
+ dir_list = new Vector();
+ file_list = new Vector();
+
+ for(int i=0; i < list.length; i++)
+ {
+ SftpFile sfile = (SftpFile)list[i];
+ if(sfile.isDirectory())
+ dir_list.add(sfile.getFilename());
+
+ file_list.add(sfile.getFilename());
+ }
+
+ sftp.quit();
+ return true;
+ }
+
+ public boolean delete(String filename)
+ {
+ try
+ {
+ SftpClient sftp = ssh.openSftpClient();
+ sftp.rm(filename);
+ sftp.quit();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ return false;
+ }
+
+ return true;
+ }
+
+ public boolean mkdir(String dir)
+ {
+ try
+ {
+ SftpClient sftp = ssh.openSftpClient();
+ sftp.mkdir(dir);
+ sftp.quit();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ return false;
+ }
+
+ return true;
+ }
+
+ public String pwd()
+ {
+ String pwd = null;
+ try
+ {
+ SftpClient sftp = ssh.openSftpClient();
+ pwd = sftp.pwd();
+ sftp.quit();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ }
+
+ return pwd;
+ }
+
+ public boolean rename(String old_file, String new_file)
+ {
+ try
+ {
+ SftpClient sftp = ssh.openSftpClient();
+ sftp.rename(old_file,new_file);
+ sftp.quit();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ return false;
+ }
+
+ return true;
+ }
+
+
+ /**
+ *
+ * @param dir name of directory to write the file to
+ * @param local_file file to copy to the server
+ *
+ */
+ public boolean put(String dir, File local_file)
+ {
+ SftpClient sftp = null;
+
+ try
+ {
+ sftp = ssh.openSftpClient();
+ FileAttributes attr = sftp.stat(dir+"/"+local_file.getName());
+
+ if(attr.isDirectory())
+ {
+ JOptionPane.showMessageDialog(null,
+ "Cannot overwrite the directory\n"+
+ dir+"/"+local_file.getName(),"Cannot Overwrite",
+ JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ else
+ {
+ int n = JOptionPane.showConfirmDialog(null,
+ "Overwrite\n"+
+ dir+"/"+local_file.getName() + "\n?",
+ "Confirm the sequence entry",
+ JOptionPane.YES_NO_OPTION);
+ if(n == JOptionPane.NO_OPTION)
+ return false;
+ }
+ }
+ catch(IOException ioe)
+ {
+ // remote file doesn't exist
+ }
+
+ if(sftp == null)
+ return false;
+
+ try
+ {
+ sftp.put(local_file.getCanonicalPath(),
+ dir+"/"+local_file.getName());
+ sftp.quit();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ return false;
+ }
+
+ return true;
+ }
+
+
+
+ /**
+ *
+ * Return the file contents as a byte array
+ *
+ */
+ public byte[] getFileContents(String file)
+ {
+ try
+ {
+ SftpClient sftp = ssh.openSftpClient();
+
+ ByteArrayOutputStream os = new ByteArrayOutputStream();
+ sftp.get(file, os);
+ sftp.quit();
+ return os.toByteArray();
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ return null;
+ }
+ }
+
+
+ public Vector getFileList()
+ {
+ return file_list;
+ }
+
+ public Vector getDirList()
+ {
+ return dir_list;
+ }
+
+}