/*
* #%L
* gitools-core
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* 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 3 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, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.heatmap.decorator.impl;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.matrix.IMatrixLayer;
import org.gitools.api.matrix.IMatrixPosition;
import org.gitools.heatmap.decorator.Decoration;
import org.gitools.heatmap.decorator.Decorator;
import org.gitools.utils.colorscale.impl.PValueColorScale;
import org.gitools.utils.formatter.ITextFormatter;
import org.gitools.utils.xml.adapter.ColorXmlAdapter;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import java.awt.*;
import java.util.ArrayList;
import java.util.List;
@XmlAccessorType(XmlAccessType.NONE)
public class PValueDecorator extends Decorator<PValueColorScale> {
public static final String PROPERTY_SIGNIFICANCE = "significanceLevel";
public static final String PROPERTY_MIN_COLOR = "minColor";
public static final String PROPERTY_MAX_COLOR = "maxColor";
public static final String PROPERTY_NON_SIGNIFICANT_COLOR = "nonSignificantColor";
public static final String PROPERTY_EMPTY_COLOR = "emptyColor";
@XmlTransient
private NonEventToNullFunction<PValueColorScale> significantEvents;
private double significanceLevel;
private PValueColorScale scale;
public PValueDecorator() {
super();
scale = new PValueColorScale();
significanceLevel = 0.05;
}
public PValueColorScale getScale() {
return scale;
}
public void setScale(PValueColorScale scale) {
this.scale = scale;
}
@XmlElement(name = "significance")
public final double getSignificanceLevel() {
return significanceLevel;
}
public final void setSignificanceLevel(double significanceLevel) {
double old = this.significanceLevel;
this.significanceLevel = significanceLevel;
getScale().setSignificanceLevel(significanceLevel);
firePropertyChange(PROPERTY_SIGNIFICANCE, old, significanceLevel);
}
@XmlElement(name = "min-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getMinColor() {
return getScale().getMinColor();
}
public void setMinColor(Color color) {
Color old = getScale().getMinColor();
getScale().setMinColor(color);
firePropertyChange(PROPERTY_MIN_COLOR, old, color);
}
@XmlElement(name = "max-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getMaxColor() {
return getScale().getMaxColor();
}
public void setMaxColor(Color color) {
Color old = getScale().getMaxColor();
getScale().setMaxColor(color);
firePropertyChange(PROPERTY_MAX_COLOR, old, color);
}
@XmlElement(name = "non-significant-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getNonSignificantColor() {
return getScale().getNonSignificantColor();
}
public void setNonSignificantColor(Color color) {
Color old = getScale().getNonSignificantColor();
getScale().setNonSignificantColor(color);
firePropertyChange(PROPERTY_NON_SIGNIFICANT_COLOR, old, color);
}
@XmlElement(name = "empty-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getEmptyColor() {
return getScale().getEmptyColor();
}
public void setEmptyColor(Color color) {
Color old = getScale().getEmptyColor();
getScale().setEmptyColor(color);
firePropertyChange(PROPERTY_EMPTY_COLOR, old, color);
}
@Override
public void decorate(Decoration decoration, ITextFormatter textFormatter, IMatrix matrix, IMatrixLayer layer, String... identifiers) {
Object value = matrix.get(layer, identifiers);
double v = toDouble(value);
if (Double.isNaN(v)) {
decoration.setBgColor(getScale().getEmptyColor());
return;
}
final Color color = v <= significanceLevel ? getScale().valueColor(v) : getScale().getNonSignificantColor();
decoration.setBgColor(color);
if (isShowValue()) {
decoration.setValue(textFormatter.format(value));
}
}
@Override
public NonEventToNullFunction getDefaultEventFunction() {
if (significantEvents == null) {
initEventFunctions();
}
return significantEvents;
}
@Override
protected void initEventFunctions() {
super.initEventFunctions();
List<NonEventToNullFunction> list = super.getEventFunctionAlternatives();
for (NonEventToNullFunction f : list) {
if (f.getName().equals(Decorator.OUTSIDE_EVENTS_FUNCTION)) {
list.remove(f);
}
}
significantEvents = new NonEventToNullFunction<PValueColorScale>(scale, "Significant Events") {
@Override
public Double apply(Double value, IMatrixPosition position) {
this.position = position;
return (value == null || value > getColorScale().getSignificanceLevel() ? null : 1 - value);
}
@Override
public String getDescription() {
return "All significant values are events: p smaller than " + getColorScale().getSignificanceLevel();
}
};
}
@Override
public List<NonEventToNullFunction> getEventFunctionAlternatives() {
List<NonEventToNullFunction> list = new ArrayList<>();
list.add(significantEvents);
list.addAll(super.getEventFunctionAlternatives());
return list;
}
}