/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/

package jalview.io;

import jalview.gui.AlignFrame;
import jalview.gui.Jalview2XML;
import javax.swing.JOptionPane;

import jalview.gui.*;
import jalview.datamodel.*;
import java.util.Vector;
import java.util.StringTokenizer;
import javax.swing.SwingUtilities;

public class FileLoader implements Runnable
{
  String file;
  String protocol;
  String format;
  AlignViewport viewport;
  AlignFrame alignFrame;

  public void LoadFile(AlignViewport viewport, String file, String protocol, String format)
  {
    this.viewport = viewport;
    LoadFile(file, protocol, format);
  }



  public void LoadFile(String file, String protocol, String format)
  {
    this.file = file;
    this.protocol = protocol;
    this.format = format;

    final Thread loader = new Thread(this);

    SwingUtilities.invokeLater(new Runnable()
    {
      public void run()
      {
        loader.start();
      }
    });
  }


  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
                                                  String format)
  {
    this.file = file;
    this.protocol = protocol;
    this.format = format;

    Thread loader = new Thread(this);
    loader.start();

    while (loader.isAlive())
    {
      try
      {
        Thread.sleep(500);
      }
      catch (Exception ex)
      {}
    }

    return alignFrame;
  }



  public void updateRecentlyOpened()
  {
    Vector recent = new Vector();

    String type = protocol.equals(FormatAdapter.FILE)
        ? "RECENT_FILE" : "RECENT_URL";

    String historyItems = jalview.bin.Cache.getProperty(type);

    StringTokenizer st;

    if (historyItems != null)
    {
      st = new StringTokenizer(historyItems, "\t");

      while (st.hasMoreTokens())
      {
        recent.addElement(st.nextElement().toString().trim());
      }
    }

    if (recent.contains(file))
    {
      recent.remove(file);
    }

    StringBuffer newHistory = new StringBuffer(file);
    for (int i = 0; i < recent.size() && i < 10; i++)
    {
      newHistory.append("\t");
      newHistory.append(recent.elementAt(i));
    }

    jalview.bin.Cache.setProperty(type, newHistory.toString());

    if(type.equals(FormatAdapter.FILE))
      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
  }

    public void run()
    {
      try{
        if (Desktop.instance != null)
          Desktop.instance.startLoading(file);

        SequenceI[] sequences = null;

        if (format.equalsIgnoreCase("Jalview"))
        {
          alignFrame = new Jalview2XML().LoadJalviewAlign(file);
        }
        else
        {
          String error = AppletFormatAdapter.SUPPORTED_FORMATS;

          if (FormatAdapter.isValidFormat(format))
          {
            try
            {
              sequences = new FormatAdapter().readFile(file, protocol, format);
            }
            catch (java.io.IOException ex)
            {
              error = ex.getMessage();
            }
          }

          if ( (sequences != null) && (sequences.length > 0))
          {
            if (viewport != null)
            {
              for (int i = 0; i < sequences.length; i++)
              {
                viewport.getAlignment().addSequence(sequences[i]);
              }
              viewport.firePropertyChange("alignment", null,
                                          viewport.getAlignment().getSequences());

            }
            else
            {
              Alignment al = new Alignment(sequences);

              alignFrame = new AlignFrame(al,
                                           AlignFrame.DEFAULT_WIDTH,
                                           AlignFrame.DEFAULT_HEIGHT);
              alignFrame.currentFileFormat = format;
              alignFrame.statusBar.setText("Successfully loaded file " + file);

              Desktop.addInternalFrame(alignFrame, file,
                                       AlignFrame.DEFAULT_WIDTH,
                                       AlignFrame.DEFAULT_HEIGHT);

              try
              {
               alignFrame.setMaximum(jalview.bin.Cache.getDefault(
                   "SHOW_FULLSCREEN", false));
              }
              catch (java.beans.PropertyVetoException ex)
              {
              }
            }
          }
          else
          {
            if (Desktop.instance != null)
              Desktop.instance.stopLoading();

            final String errorMessage = "Couldn't load file " + file + "\n" +
                error;

            javax.swing.SwingUtilities.invokeLater(new Runnable()
            {
              public void run()
              {
                JOptionPane.showInternalMessageDialog(Desktop.desktop,
                    errorMessage,
                    "Error loading file",
                    JOptionPane.WARNING_MESSAGE);
              }
            });
          }
        }

        if (alignFrame != null)
        {
         alignFrame.fileName = file;
         alignFrame.currentFileFormat = format;
         updateRecentlyOpened();
        }
      }
      catch (OutOfMemoryError er)
      {

        er.printStackTrace();
        alignFrame = null;

        javax.swing.SwingUtilities.invokeLater(new Runnable()
        {
          public void run()
          {
            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
                "Out of memory loading file "+file+"!!"
                +
                "\nSee help files for increasing Java Virtual Machine memory."
                , "Out of memory",
                javax.swing.JOptionPane.WARNING_MESSAGE);
          }
        });
      }

     System.gc();
     if (Desktop.instance != null)
        Desktop.instance.stopLoading();

    }

}