BasePlotGroup.java

/* BasePlotGroup.java
 *
 * created: Tue Dec 15 1998
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1998,1999,2000  Genome Research Limited
 *
 * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/BasePlotGroup.java,v 1.1 2004-06-09 09:46:05 tjc Exp $
 */

package uk.ac.sanger.artemis.components;

import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.plot.*;

import java.awt.*;
import java.awt.event.*;
import java.io.IOException;
import java.io.File;
import java.util.Vector;

import javax.swing.*;

/**
 *  This is a super-component containing several BasePlot components, each of
 *  which can toggled off and on.
 *
 *  @author Kim Rutherford
 *  @version $Id: BasePlotGroup.java,v 1.1 2004-06-09 09:46:05 tjc Exp $
 **/

public class BasePlotGroup extends JPanel
  implements DisplayAdjustmentListener {
  /**
   *  Create a new BasePlotGroup component for the given EntryGroup.
   *  @param selection Used to set and display the current selection in the
   *    BasePlot.
   *  @param goto_event_source The object the we will call gotoBase () on.
   *    This allows the user to double click on a base in a BasePlot and have
   *    the FeatureDisplay follow.
   **/
  public BasePlotGroup (final EntryGroup entry_group,
                        final Component owning_component,
                        final Selection selection,
                        final GotoEventSource goto_event_source) {
    this.owning_component = owning_component;
    this.entry_group = entry_group;
    this.selection = selection;
    this.goto_event_source = goto_event_source;

    final Strand forward_strand =
      entry_group.getBases ().getForwardStrand ();

    final Strand reverse_strand =
      entry_group.getBases ().getReverseStrand ();

    // the following arrays are from failed tests
    final float [] [] test_weights = {
      {1, 0,39,99,11}, // a
      {76,8,15,1,45}, // c
      {2,0,42,0,6}, // g
      {21,91,4,0,38}  // t
    };

    final float [] [] test_weights2 = {
      {11,11,10, 8,11,10,11,11, 7, 8,25, 3,100,  0,27},
      {29,33,30,30,32,34,37,38,39,36,26,75,  0,  0,14},
      {14,12,10,10, 9,11,10, 9, 7, 6,26, 1,  0,100,49},
      {46,44,50,52,48,45,42,43,47,51,23,21,  0,  0,10}
    };

    final float [] [] test_weights3 = {
      {0,0,1,0,0,0},
      {0,0,0,1,0,0},
      {1,0,0,0,1,0},
      {0,1,0,0,0,1},
    };

    final float [] cai_test = {
      0.113F, 1.0F,   0.117F, 1.0F,
      1.0F,   0.693F, 0.036F, 0.005F,
      0.071F, 1.0F,   0.0F,   0.0F,
      1.0F,   0.077F, 0.0F,   1.0F,

      0.006F, 0.003F, 0.039F, 0.003F,
      0.047F, 0.009F, 1.0F,   0.002F,
      0.245F, 1.0F,   1.0F,   0.007F,
      0.137F, 0.002F, 0.002F, 0.002F,

      0.823F, 1.0F,   0.003F, 1.0F,
      0.921F, 1.0F,   0.012F, 0.006F,
      0.053F, 1.0F,   0.135F, 1.0F,
      0.021F, 0.031F, 1.0F,   0.003F,

      1.0F,   0.831F, 0.002F, 0.018F,
      1.0F,   0.316F, 0.015F, 0.001F,
      0.554F, 1.0F,   1.0F,   0.016F,
      1.0F,   0.02F,  0.002F, 0.004F
    };

//    plot_algorithms_temp.add (new CAIWindowAlgorithm (forward_strand, cai_test));
//    plot_algorithms_temp.add (new UserBaseAlgorithm (forward_strand, "test", test_weights));
//    plot_algorithms_temp.add (new UserBaseAlgorithm (forward_strand, "test2", test_weights2));
//    plot_algorithms_temp.add (new UserBaseAlgorithm (forward_strand, "test3", test_weights3));

    setLayout (gridbag);

    c.fill = GridBagConstraints.HORIZONTAL;
    c.anchor = GridBagConstraints.NORTH;
    c.gridwidth = GridBagConstraints.REMAINDER;
    c.gridheight = 1;
    c.weightx = 1;
    c.weighty = 0;

    c.insets = new Insets (0,0,5,0);

    addAlgorithm (new GCWindowAlgorithm (forward_strand));
    addAlgorithm (new GCSDWindowAlgorithm (forward_strand));
    addAlgorithm (new AGWindowAlgorithm (forward_strand));
    addAlgorithm (new GCFrameAlgorithm (forward_strand));
    addAlgorithm (new GCFrameAlgorithm (reverse_strand));
    addAlgorithm (new Codon12CorrelationAlgorithm(forward_strand));
    addAlgorithm (new Codon12CorrelationAlgorithm(reverse_strand));
    addAlgorithm (new GCDeviationAlgorithm (forward_strand));
    addAlgorithm (new ATDeviationAlgorithm (forward_strand));
    addAlgorithm (new KarlinSigAlgorithm (forward_strand));
  }

  /**
   *  Implementation of the DisplayAdjustmentListener interface.  Invoked when
   *  a component (FeatureDisplay) scrolls or changes the scale.  Sends the
   *  event to all the BasePlot components in this BasePlotGroup.
   **/
  public void displayAdjustmentValueChanged (DisplayAdjustmentEvent event) {
    final Component [] children = getComponents ();

    for (int i = 0 ; i < children.length ; ++i) {
      if (children[i] instanceof BasePlot) {
        ((BasePlot)children[i]).displayAdjustmentValueChanged (event);
      }
    }
  }

  /**
   *  Add a new BasePlot component for the given algorithm.
   *  @return The new BasePlot
   **/
  public BasePlot addAlgorithm (final BaseAlgorithm algorithm) {
    plot_value_producers.addElement (algorithm);

    return makePlot (algorithm, gridbag, c);
  }

  /**
   *  Return the first CodonUsageAlgorithm or null if there isn't one in the
   *  group.
   **/
  public CodonUsageAlgorithm getCodonUsageAlgorithm () {
    for (int i = 0 ; i < plot_value_producers.size () ; ++i) {
      final BaseAlgorithm this_algorithm =
        (BaseAlgorithm) plot_value_producers.elementAt (i);

      if (this_algorithm instanceof CodonUsageAlgorithm) {
        return (CodonUsageAlgorithm) this_algorithm;
      }
    }

    return null;
  }

  /**
   *  Return an array containing the Algorithm objects of the BasePlot
   *  components in this BasePlotGroup.
   **/
  public BaseAlgorithm [] getPlotAlgorithms () {
    final BaseAlgorithm [] return_array =
      new BaseAlgorithm [plot_value_producers.size ()];

    for (int i = 0 ; i < plot_value_producers.size () ; ++i) {
      final BaseAlgorithm this_algorithm =
        (BaseAlgorithm) plot_value_producers.elementAt (i);
      return_array[i] = this_algorithm;
    }

    return return_array;
  }

  /**
   *  Return true if and only if the BasePlot for the given Algorithm is
   *  visible.
   **/
  public boolean basePlotIsVisible (final Algorithm algorithm) {
    final Component base_plot = findPlotByAlgorithm (algorithm);

    return base_plot.isVisible ();
  }

  /**
   *  Given an Algorithm, find and set the visibility of the corresponding
   *  BasePlot component.
   **/
  public void setVisibleByAlgorithm (final Algorithm algorithm,
                                     final boolean visible) {
    final JComponent base_plot = findPlotByAlgorithm (algorithm);

    base_plot.setVisible (visible);
    if (getParent () != null) {
      // XXX change to revalidate().
      getParent ().validate ();
    }
  }

  /**
   *  Find the BasePlot component in this BasePlotGroup object that is
   *  plotting the given Algorithm or null if no such BasePlot object exists.
   **/
  private JComponent findPlotByAlgorithm (final Algorithm algorithm) {
    final Component [] children = getComponents ();

    for (int i = 0 ; i < children.length ; ++i) {
      if (children[i] instanceof BasePlot) {
        final Algorithm component_algorithm =
          ((BasePlot)children[i]).getAlgorithm ();
        if (component_algorithm == algorithm) {
          return (JComponent)children[i];
        }
      }
    }

    return null;
  }

  /**
   *  Create a Plot component for the given Algorithm and then make a button
   *  for it so that it can be shown and hidden.  Note that button making is
   *  currently disabled
   *  @param algorithm The Algorithm to create a Plot of.
   *  @param gridbag The GridBagLayout to use to lay out the Plot components.
   *  @param constraints The GridBagConstraints object to use to lay out the
   *    Plot components.
   *  @return The new BasePlot
   **/
  private BasePlot makePlot (BaseAlgorithm algorithm,
                             GridBagLayout gridbag,
                             GridBagConstraints constraints) {

    final BasePlot new_base_plot =
      new BasePlot (algorithm, getSelection (), getGotoEventSource ());

    gridbag.setConstraints (new_base_plot, constraints);
    add (new_base_plot);
    new_base_plot.setVisible (false);

    getSelection ().addSelectionChangeListener (new_base_plot);

    if (getParent () != null) {
      // XXX change to revalidate().
      getParent ().validate ();
    }

    return new_base_plot;
  }

  /**
   *  Return the Selection object that was passed to the constructor.
   **/
  private Selection getSelection () {
    return selection;
  }

  /**
   *  Return the EntryGroup object that was passed to the constructor.
   **/
  private EntryGroup getEntryGroup () {
    return entry_group;
  }

  /**
   *  Return the GotoEventSource object that was passed to the constructor.
   **/
  private GotoEventSource getGotoEventSource () {
    return goto_event_source;
  }

  /**
   *  The EntryGroup that contains the sequence that this JComponent is
   *  displaying.
   **/
  private final EntryGroup entry_group;

  /**
   *  This array contains the Algorithm objects of the BasePlot components in
   *  this BasePlotGroup, as set by the constructor.
   **/
  private final Vector plot_value_producers = new Vector ();

  /**
   *  The layout object used by this component.
   **/
  private final GridBagLayout gridbag = new GridBagLayout();

  /**
   *  The constraints object used by this component.
   **/
  private final GridBagConstraints c = new GridBagConstraints();

  /**
   *  The Selection that was passed to the constructor.
   **/
  private Selection selection;

  /**
   *  The GotoEventSource that was passed to the constructor.
   **/
  private GotoEventSource goto_event_source;

  /**
   *  This is a reference to the parent Container of this BasePlot object.
   **/
  private Component owning_component;
}