/*
 * 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.appletgui;

import java.util.*;

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

import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.jbappletgui.*;

public class PCAPanel
    extends GPCAPanel implements Runnable
{
  PCA pca;
  int top;
  RotatableCanvas rc;
  AlignViewport av;
  SequenceI [] seqs;


  public PCAPanel(AlignViewport av)
  {

    this.av = av;
    if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() > 3)
    {
      seqs = new Sequence[av.getSelectionGroup().getSize()];
      for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
      {
        seqs[i] = av.getSelectionGroup().getSequenceAt(i);
      }
    }
    else
    {
      seqs = new Sequence[av.getAlignment().getHeight()];
      for (int i = 0; i < av.getAlignment().getHeight(); i++)
      {
        seqs[i] = av.getAlignment().getSequenceAt(i);
      }
    }
    rc = new RotatableCanvas(av);
    add(rc, BorderLayout.CENTER);
    Thread worker = new Thread(this);
    worker.start();
  }

  /**
   * DOCUMENT ME!
   */
  public void run()
  {
              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.select(0);
              yCombobox.select(1);
              zCombobox.select(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;
  }

  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());
  }

  protected void xCombobox_actionPerformed(ActionEvent e)
  {
    doDimensionChange();
  }

  protected void yCombobox_actionPerformed(ActionEvent e)
  {
    doDimensionChange();
  }

  protected void zCombobox_actionPerformed(ActionEvent e)
  {
    doDimensionChange();
  }

}