/*
* #%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.apache.commons.math3.distribution.NormalDistribution;
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.ColorConstants;
import org.gitools.utils.colorscale.impl.PValueLogSumScale;
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 PValueLogSumDecorator extends Decorator<PValueLogSumScale> {
public static final String PROPERTY_SIGNIFICANCE = "significanceLevel";
public static final String PROPERTY_SIGNIFICANCE_TRANSLATION = "significanceLimit";
public static final String PROPERTY_LIMIT = "limit";
public static final String PROPERTY_LEFT_MIN_COLOR = "leftMinColor";
public static final String PROPERTY_LEFT_MAX_COLOR = "leftMaxColor";
public static final String PROPERTY_RIGHT_MIN_COLOR = "rightMinColor";
public static final String PROPERTY_RIGHT_MAX_COLOR = "rightMaxColor";
public static final String PROPERTY_NON_SIGNIFICANT_COLOR = "nonSignificantColor";
public static final String PROPERTY_EMPTY_COLOR = "emptyColor";
private double significanceLevel;
private PValueLogSumScale scale;
@XmlTransient
NonEventToNullFunction<PValueLogSumScale> significantEvents;
public PValueLogSumDecorator() {
super();
scale = new PValueLogSumScale();
significanceLevel = 0.05;
}
public PValueLogSumDecorator(double significanceLevel, double limits) {
super();
scale = new PValueLogSumScale();
this.significanceLevel = significanceLevel;
scale.setLimit(limits);
setSignificanceLimit(significanceLevel);
}
public PValueLogSumScale getScale() {
return scale;
}
public void setScale(PValueLogSumScale scale) {
this.scale = scale;
}
@XmlElement(name = "significance")
public double getSignificanceLevel() {
return significanceLevel;
}
public void setSignificanceLevel(double sigLevel) {
double old = this.significanceLevel;
this.significanceLevel = sigLevel;
setSignificanceLimit(translateSignificance(sigLevel));
firePropertyChange(PROPERTY_SIGNIFICANCE, old, sigLevel);
}
private static NormalDistribution NORMAL = new NormalDistribution();
private double translateSignificance(double sigLevel) {
double v = Math.log10(1 - sigLevel) - Math.log10(sigLevel);
return Math.abs(v);
}
public final double getSignificanceLimit() {
return getScale().getSignificanceLimit();
}
final void setSignificanceLimit(double significanceLimit) {
double old = getScale().getSignificanceLimit();
getScale().setSignificanceLimit(significanceLimit);
firePropertyChange(PROPERTY_SIGNIFICANCE_TRANSLATION, old, significanceLimit);
}
@XmlElement(name = "limit")
public final double getLimit() {
return getScale().getLimit();
}
public final void setLimit(double limit) {
double old = getScale().getLimit();
getScale().setLimit(limit);
firePropertyChange(PROPERTY_LIMIT, old, limit);
}
@XmlElement(name = "left-min-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getLeftMinColor() {
return getScale().getLeftMinColor();
}
public void setLeftMinColor(Color color) {
Color old = getScale().getLeftMinColor();
getScale().setLeftMinColor(color);
firePropertyChange(PROPERTY_LEFT_MIN_COLOR, old, color);
}
@XmlElement(name = "left-max-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getLeftMaxColor() {
return getScale().getLeftMaxColor();
}
public void setLeftMaxColor(Color color) {
Color old = getScale().getLeftMaxColor();
getScale().setLeftMaxColor(color);
firePropertyChange(PROPERTY_LEFT_MAX_COLOR, old, color);
}
@XmlElement(name = "right-min-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getRightMinColor() {
return getScale().getRightMinColor();
}
public void setRightMinColor(Color color) {
Color old = getScale().getRightMinColor();
getScale().setRightMinColor(color);
firePropertyChange(PROPERTY_RIGHT_MIN_COLOR, old, color);
}
@XmlElement(name = "right-max-color")
@XmlJavaTypeAdapter(ColorXmlAdapter.class)
public Color getRightMaxColor() {
return getScale().getRightMaxColor();
}
public void setRightMaxColor(Color color) {
Color old = getScale().getRightMaxColor();
getScale().setRightMaxColor(color);
firePropertyChange(PROPERTY_RIGHT_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;
}
boolean useScale = true;
final Color color = useScale ? getScale().valueColor(v) : ColorConstants.nonSignificantColor;
decoration.setBgColor(color);
if (isShowValue()) {
decoration.setValue(textFormatter.format(value));
}
}
@Override
public List<NonEventToNullFunction> getEventFunctionAlternatives() {
List<NonEventToNullFunction> list = new ArrayList<>();
list.add(getDefaultEventFunction());
list.addAll(super.getEventFunctionAlternatives());
return list;
}
@Override
public NonEventToNullFunction getDefaultEventFunction() {
if (significantEvents == null) {
initEvents();
}
return significantEvents;
}
private void initEvents() {
significantEvents =
new NonEventToNullFunction<PValueLogSumScale>(scale, "Significant Events") {
@Override
public Double apply(Double value, IMatrixPosition position) {
this.position = position;
return (value == null || Math.abs(value) <= getColorScale().getSignificanceLimit()) ?
null : Math.abs(value);
}
@Override
public String getDescription() {
double limit = getColorScale().getSignificanceLimit();
return "All values above and below significance threshold (" +
limit + ", " + -limit + ") are events";
}
};
}
}