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/* 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 1.5 2004-11-24 09:38:20 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 1.5 2004-11-24 09:38:20 tjc Exp $
/**
* 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 =
// 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
};
{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}
};
{0,0,1,0,0,0},
{0,0,0,1,0,0},
{1,0,0,0,1,0},
{0,1,0,0,0,1},
};
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));
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));
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//CumulativeATSkewAlgorithm
addAlgorithm(new CumulativeATSkewAlgorithm(forward_strand));
addAlgorithm(new CumulativeGCSkewAlgorithm(forward_strand));
//Positional Asymmetry
addAlgorithm(new PositionalAsymmetryAlgorithm(forward_strand));
//Informational Entropy
addAlgorithm(new EntropyAlgorithm(forward_strand));
//Scaled Chi
addAlgorithm(new ScaledChiAlgorithm(forward_strand));
addAlgorithm(new ScaledChiAlgorithm(reverse_strand));
// addAlgorithm(new ScaledChiRevAlgorithm(reverse_strand));
//Corrected Scaled Chi Square
addAlgorithm(new CSCSAlgorithm(forward_strand));
addAlgorithm(new CSCSAlgorithm(reverse_strand));
// addAlgorithm(new CSCSRevAlgorithm(reverse_strand));
//Mutational Response Index
addAlgorithm(new MRIAlgorithm(forward_strand));
addAlgorithm(new MRIAlgorithm(reverse_strand));
// addAlgorithm(new MRIRevAlgorithm(reverse_strand));
//Effective Codon Number
addAlgorithm(new NcAlgorithm(forward_strand));
addAlgorithm(new NcAlgorithm(reverse_strand));
// addAlgorithm(new NcRevAlgorithm(reverse_strand));
//Intrinsic Codon Deviation Index
addAlgorithm(new ICDIAlgorithm(forward_strand));
addAlgorithm(new ICDIAlgorithm(reverse_strand));
// addAlgorithm(new ICDIRevAlgorithm(reverse_strand));
/**
*
* Routine for printing graphs in artemis
*
*/
protected void printComponent(Graphics g)
{
final Component[] children = getComponents();
for(int i = 0 ; i<children.length ; ++i)
if(children[i] instanceof BasePlot)
{
BasePlot bp = (BasePlot)children[i];
if(!bp.isVisible())
continue;
/**
*
* Return the number of visible BasePlot objects
*
*/
protected int getNumberBasePlots()
{
final Component[] children = getComponents();
int num = 0;
for(int i = 0 ; i<children.length ; ++i)
if(children[i] instanceof BasePlot)
{
BasePlot bp = (BasePlot)children[i];
if(bp.isVisible())
num++;
}
return num;
}
/**
* 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 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)
{
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);
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)
{
((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)
{
new BasePlot(algorithm, getSelection(), getGotoEventSource());
gridbag.setConstraints(new_base_plot, constraints);
add(new_base_plot);
new_base_plot.setVisible(false);
if (getParent () != null) {
// XXX change to revalidate().
getParent ().validate ();
}
return new_base_plot;
}
/**
* Return the Selection object that was passed to the constructor.
**/
return selection;
}
/**
* Return the EntryGroup object that was passed to the constructor.
**/
return entry_group;
}
/**
* Return the GotoEventSource object that was passed to the constructor.
**/
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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;
}