http://wiki.jsch.org

Here's a minimalistic example of Public Key Authentcation. It is adapted from JSCH examples, but I have stripped out the GUI etc.

import com.jcraft.jsch.*;

public class UserAuthPubKey{
 public static void main(String[] arg){

 String pubkeyfile="/home/cr/users/anand/.ssh/id_dsa";
 String passphrase="";
 String host="gs00", user="root";

 try{
 JSch jsch=new JSch();
 jsch.addIdentity(pubkeyfile);
// jsch.addIdentity(pubkeyfile, passphrase);
 jsch.setKnownHosts("/home/cr/users/anand/.ssh/known_hosts");

 Session session=jsch.getSession(user, host, 22);
 session.connect();

 Channel channel=session.openChannel("shell");

 channel.setInputStream(System.in);
 channel.setOutputStream(System.out);

 channel.connect();
 }
 catch(Exception e){
 System.out.println(e); e.printStackTrace();
 }
 } //end of main 
} //end of class

A quick and dirty example of using JSCH library to transfer files to/from a server.

import com.jcraft.jsch.*;
import java.io.*;
import java.io.IOException;

/**
*
* @author anand
*/
public class sftpex {
 public static void main(String[] args) {
 // TODO code application logic here

 String username = "testuser";
 String host = "testserver.example.com";
 String pass = "testpass";
 String khfile = "/home/testuser/.ssh/known_hosts";
 String identityfile = "/home/testuser/.ssh/id_rsa";

 JSch jsch = null;
 Session session = null;
 Channel channel = null;
 ChannelSftp c = null;
 try {
 jsch = new JSch();
 session = jsch.getSession(username, host, 22);
 session.setPassword(pass);
 jsch.setKnownHosts(khfile);
 jsch.addIdentity(identityfile);
 session.connect();

 channel = session.openChannel("sftp");
 channel.connect();
 c = (ChannelSftp) channel;

 } catch (Exception e) { e.printStackTrace(); }

 try {
 System.out.println("Starting File Upload:");
 String fsrc = "/tmp/abc.txt", fdest = "/tmp/cde.txt";
 c.put(fsrc, fdest);
 
 c.get(fdest, "/tmp/testfile.bin");
 } catch (Exception e) { e.printStackTrace(); }
 
 c.disconnect();
 session.disconnect();

 }
}