package jalview.io;

import jalview.gui.AlignFrame;
import jalview.gui.Jalview2XML;
import javax.swing.JOptionPane;
import jalview.datamodel.Alignment;
import jalview.gui.Desktop;
import jalview.datamodel.SequenceI;
import jalview.gui.Preferences;

public class FileLoader
{
  public void LoadFile(String file, String protocol, String format)
  {
    LoadingThread loader = new LoadingThread(file, protocol, format);
    loader.start();
  }

  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
                                                  String format)
  {
    LoadingThread loader = new LoadingThread(file, protocol, format);
    loader.start();
    while (loader.isAlive())
    {
      try
      {
        Thread.sleep(50);
      }
      catch (Exception ex)
      {}
    }

    return loader.af;
  }


  class LoadingThread
    extends Thread
{
  String file;
  String protocol;
  String format;
  AlignFrame af;

  public LoadingThread(String file, String protocol, String format)
  {
    this.file = file;
    this.protocol = protocol;
    this.format = format;
  }

  public void run()
  {
    SequenceI[] sequences = null;

    if (format.equalsIgnoreCase("Jalview"))
    {
      af = Jalview2XML.LoadJalviewAlign(file);
    }
    else
    {
      if (FormatAdapter.formats.contains(format))
      {
        sequences = FormatAdapter.readFile(file, protocol, format);
      }

      if ( (sequences != null) && (sequences.length > 0))
      {
        af = new AlignFrame(new Alignment(sequences));
        af.currentFileFormat = format;
        af.statusBar.setText("Successfully loaded file " + file);

        Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
                           AlignFrame.NEW_WINDOW_HEIGHT);


        try
        {
          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
        }
        catch (Exception ex)
        {
        }
      }
      else
      {
        JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                              "Couldn't open file.\n" +
                                              "Formats currently supported are\n" +
                                              "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
                                              , "Error loading file",
                                              JOptionPane.WARNING_MESSAGE);
      }
    }
  }
}

}