/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 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.gui;

import jalview.analysis.*;

import jalview.datamodel.*;

import jalview.jbgui.*;

import java.awt.*;
import java.awt.event.*;

import java.util.*;
import javax.swing.*;
import java.awt.print.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class PCAPanel extends GPCAPanel implements Runnable
{
    PCA pca;
    int top;
    RotatableCanvas rc;
    AlignViewport av;
    SequenceI [] seqs;

    /**
     * Creates a new PCAPanel object.
     *
     * @param av DOCUMENT ME!
     * @param s DOCUMENT ME!
     */
    public PCAPanel(AlignViewport av)
    {
        this.av = av;

        boolean sameLength = true;

        if ((av.getSelectionGroup() != null) &&
                (av.getSelectionGroup().getSize(false) > 3))
        {
            seqs = new Sequence[av.getSelectionGroup().getSize(false)];
            int length = av.getSelectionGroup().getSequenceAt(0).getLength();
            for (int i = 0; i < av.getSelectionGroup().getSize(false); i++)
            {
                seqs[i] = av.getSelectionGroup().getSequenceAt(i);
                if(seqs[i].getLength()!=length)
                {
                  sameLength = false;
                  break;
                }
            }
        }
        else
        {
            seqs = new Sequence[av.getAlignment().getHeight()];
            int length = av.alignment.getSequenceAt(0).getLength();

            for (int i = 0; i < av.getAlignment().getHeight(); i++)
            {
                seqs[i] = av.getAlignment().getSequenceAt(i);
                if(seqs[i].getLength()!=length)
               {
                 sameLength = false;
                 break;
               }

            }
        }

        if (!sameLength)
        {
          JOptionPane.showMessageDialog(Desktop.desktop,
                                        "The sequences must be aligned before calculating PCA.\n" +
                                        "Try using the Pad function in the edit menu,\n" +
                                        "or one of the multiple sequence alignment web services.",
                                        "Sequences not aligned",
                                        JOptionPane.WARNING_MESSAGE);

          return;
        }


        Desktop.addInternalFrame(this, "Principal component analysis",
                               400, 400);


        rc = new RotatableCanvas(av);
        this.getContentPane().add(rc, BorderLayout.CENTER);
        Thread worker = new Thread(this);
        worker.start();
    }

    public void bgcolour_actionPerformed(ActionEvent e)
    {
      Color col = JColorChooser.showDialog(this, "Select Background Colour",
                rc.bgColour);

      if(col!=null)
        rc.bgColour = col;
      rc.repaint();
    }




    /**
     * DOCUMENT ME!
     */
    public void run()
    {
      try{
        pca = new PCA(seqs);
        pca.run();

        // Now find the component coordinates
        int ii = 0;

        while ( (ii < seqs.length) && (seqs[ii] != null))
        {
          ii++;
        }

        double[][] comps = new double[ii][ii];

        for (int i = 0; i < ii; i++)
        {
          if (pca.getEigenvalue(i) > 1e-4)
          {
            comps[i] = pca.component(i);
          }
        }

        //////////////////
        xCombobox.setSelectedIndex(0);
        yCombobox.setSelectedIndex(1);
        zCombobox.setSelectedIndex(2);

        top = pca.getM().rows - 1;

        Vector points = new Vector();
        float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);

        for (int i = 0; i < pca.getM().rows; i++)
        {
          SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
          points.addElement(sp);
        }

        rc.setPoints(points, pca.getM().rows);
        rc.repaint();
        seqs = null;
      }
     catch(OutOfMemoryError er)
      { JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                              "Out of memory calculating PCA!!"
                                              +
                                              "\nSee help files for increasing Java Virtual Machine memory."
                                              , "Out of memory",
                                              JOptionPane.WARNING_MESSAGE);
        System.out.println("PCAPanel: "+er);
        System.gc();

      }

    }

    /**
     * DOCUMENT ME!
     */
    void doDimensionChange()
    {
        if (top == 0)
        {
            return;
        }

        int dim1 = top - xCombobox.getSelectedIndex();
        int dim2 = top - yCombobox.getSelectedIndex();
        int dim3 = top - zCombobox.getSelectedIndex();

        float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);

        for (int i = 0; i < pca.getM().rows; i++)
        {
            ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
        }

        rc.img = null;
        rc.rotmat.setIdentity();
        rc.initAxes();
        rc.paint(rc.getGraphics());
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void xCombobox_actionPerformed(ActionEvent e)
    {
        doDimensionChange();
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void yCombobox_actionPerformed(ActionEvent e)
    {
        doDimensionChange();
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    protected void zCombobox_actionPerformed(ActionEvent e)
    {
        doDimensionChange();
    }


    public void outputValues_actionPerformed(ActionEvent e)
    {
      CutAndPasteTransfer cap = new CutAndPasteTransfer();
      Desktop.addInternalFrame(cap, "PCA details", 500,
                500);

      cap.setText(pca.getDetails());
     }

    public void showLabels_actionPerformed(ActionEvent e)
    {
      rc.showLabels(showLabels.getState());
    }

    public void print_actionPerformed(ActionEvent e)
    {
      PCAPrinter printer = new PCAPrinter();
      printer.start();
    }


    class PCAPrinter extends Thread implements Printable
    {
      public void run()
      {
        PrinterJob printJob = PrinterJob.getPrinterJob();
        PageFormat pf = printJob.pageDialog(printJob.defaultPage());

        printJob.setPrintable(this, pf);

        if (printJob.printDialog())
        {
          try
          {
            printJob.print();
          }
          catch (Exception PrintException)
          {
            PrintException.printStackTrace();
          }
        }
      }

      public int print(Graphics pg, PageFormat pf, int pi)
          throws PrinterException
      {
        pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());

        rc.drawBackground(pg, rc.bgColour);
        rc.drawScene(pg);
        if (rc.drawAxes == true)
        {
          rc.drawAxes(pg);
        }

        if (pi == 0)
          return Printable.PAGE_EXISTS;
        else
          return Printable.NO_SUCH_PAGE;
      }
    }



    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void eps_actionPerformed(ActionEvent e)
    {
      makePCAImage(jalview.util.ImageMaker.EPS);
    }

    /**
     * DOCUMENT ME!
     *
     * @param e DOCUMENT ME!
     */
    public void png_actionPerformed(ActionEvent e)
    {
       makePCAImage(jalview.util.ImageMaker.PNG);
    }

    void makePCAImage(int type)
    {
      int width = rc.getWidth();
      int height = rc.getHeight();

      jalview.util.ImageMaker im;

      if(type == jalview.util.ImageMaker.PNG)
        im = new jalview.util.ImageMaker(this,
                                         jalview.util.ImageMaker.PNG,
                                         "Make PNG image from PCA",
                                         width, height,
                                         null, null);
        else
          im = new jalview.util.ImageMaker(this,
                                 jalview.util.ImageMaker.EPS,
                                 "Make EPS file from PCA",
                                 width, height,
                                 null, this.getTitle());

      if(im.getGraphics()!=null)
       {
         rc.drawBackground(im.getGraphics(), Color.black);
         rc.drawScene(im.getGraphics());
         if (rc.drawAxes == true)
         {
           rc.drawAxes(im.getGraphics());
         }
         im.writeImage();
       }
    }
  }