/**
 * 
 */
package jalview.gui;

import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.Vector;
import java.util.jar.JarOutputStream;

import javax.swing.JInternalFrame;

import jalview.bin.Cache;

import org.vamsas.client.UserHandle;
import org.vamsas.client.simpleclient.FileWatcher;
import org.vamsas.client.simpleclient.VamsasArchive;
import org.vamsas.client.simpleclient.VamsasFile;
import org.vamsas.objects.core.VamsasDocument;
import org.vamsas.test.simpleclient.ArchiveClient;

/**
 * @author jimp
 *
 */
public class VamsasClient extends ArchiveClient {
	Desktop us;
	// Cache.preferences for vamsas client session arena
	// preferences for check for default session at startup.
	// user and organisation stuff.
	public VamsasClient(Desktop jdesktop,
			String sessionPath) {
		super("Jalview User", "Dundee", // new org.vamsas.client.ClientHandle("jalview","2.7"),
				sessionPath);
		us=jdesktop;
	}
	public void initial_update() {
		Cache.log.info("Jalview loading the Vamsas Session.");
		// load in the vamsas archive for the first time
		
		// VamsasArchive doc = new VamsasArchive();
	}
	public void get_update(VamsasArchive doc) {
		Cache.log.info("Jalview updating from Vamsas Session.");
	}
	public void push_update() {
		// collect all uncached alignments and put them into the vamsas dataset.
		// store them.
		Cache.log.info("Jalview updating the Vamsas Session.");
	}
	public void end_session() {
		// stop any update/watcher thread.
		Cache.log.info("Jalview disconnecting from the Vamsas Session.");
	}
	public void updateVamsasDocument(VamsasDocument doc) {
		// wander through frames 
		JInternalFrame[] frames = Desktop.desktop.getAllFrames();

        if (frames == null)
        {
            return;
        }

        try
        {	
        	Vector shortNames = new Vector();
        	
        	//REVERSE ORDER
            for (int i = frames.length - 1; i > -1; i--)
            {
                if (frames[i] instanceof AlignFrame)
                {
                	AlignFrame af = (AlignFrame) frames[i];
                	// check if this frame has an associated alignment object ?
                	// update alignment and root from frame.
                	
                	
                    String shortName = af.getTitle();

                    if (shortName.indexOf(File.separatorChar) > -1)
                    {
                        shortName = shortName.substring(shortName.lastIndexOf(
                                    File.separatorChar) + 1);
                    }

                    int count = 1;

                    while (shortNames.contains(shortName))
                    {
                        if (shortName.endsWith("_" + (count - 1)))
                        {
                            shortName = shortName.substring(0,
                                    shortName.lastIndexOf("_"));
                        }

                        shortName = shortName.concat("_" + count);
                        count++;
                    }

                    shortNames.addElement(shortName);

                    if (!shortName.endsWith(".xml"))
                    {
                        shortName = shortName + ".xml";
                    }

                }
            }
        }
        catch (Exception e) {
        	Cache.log.error("Vamsas Document store exception",e);
        }
	}
	protected class VamsasClientWatcher extends Thread implements Runnable {
		/* (non-Javadoc)
		 * @see java.lang.Thread#run()
		 */
		VamsasClient client=null;
		VamsasClientWatcher(VamsasClient client) {
			this.client = client;
		}
		public void run() {
			VamsasArchive docio = client.watch(0);
			client.get_update(docio);
		}
		
	}
	/**
	 * @param args
	 */
	public static void main(String[] args) {
		// TODO Auto-generated method stub

	}

}