/*
* #%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.matrix.MatrixUtils;
import org.gitools.utils.colorscale.ColorConstants;
import org.gitools.utils.colorscale.impl.ZScoreColorScale;
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 ZScoreDecorator extends Decorator<ZScoreColorScale> {
public static final String PROPERTY_SIGNIFICANCE = "significanceLevel";
public static final String PROPERTY_CORRECTED_VALUE = "correctedValueIndex";
public static final String PROPERTY_USE_CORRECTION = "useCorrection";
public static final String PROPERTY_SIG_HALF_AMPLITUD = "sigHalfAmplitude";
public static final String PROPERTY_HALF_AMPLITUD = "halfAmplitude";
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 int correctedValueIndex;
private boolean useCorrection;
private double significanceLevel;
private ZScoreColorScale scale;
@XmlTransient
private NonEventToNullFunction<ZScoreColorScale> significantEvents;
public ZScoreDecorator() {
super();
scale = new ZScoreColorScale();
correctedValueIndex = -1;
useCorrection = false;
significanceLevel = 0.05;
}
public ZScoreDecorator(double significanceLevel, double limits) {
super();
scale = new ZScoreColorScale();
correctedValueIndex = -1;
useCorrection = false;
this.significanceLevel = significanceLevel;
scale.setHalfAmplitude(limits);
setSigHalfAmplitude(significanceLevel);
}
public ZScoreColorScale getScale() {
return scale;
}
public void setScale(ZScoreColorScale scale) {
this.scale = scale;
}
@XmlElement(name = "filter-layer-index")
public int getCorrectedValueIndex() {
return correctedValueIndex;
}
public void setCorrectedValueIndex(int correctionValueIndex) {
int old = this.correctedValueIndex;
this.correctedValueIndex = correctionValueIndex;
firePropertyChange(PROPERTY_CORRECTED_VALUE, old, correctionValueIndex);
}
@XmlElement(name = "use-filter")
public final boolean getUseCorrection() {
return useCorrection;
}
public final void setUseCorrection(boolean useCorrection) {
boolean old = this.useCorrection;
this.useCorrection = useCorrection;
firePropertyChange(PROPERTY_USE_CORRECTION, old, useCorrection);
}
@XmlElement(name = "significance")
public double getSignificanceLevel() {
return significanceLevel;
}
public void setSignificanceLevel(double sigLevel) {
double old = this.significanceLevel;
this.significanceLevel = sigLevel;
setSigHalfAmplitude(calculateSigHalfAmplitudeFromSigLevel(sigLevel));
firePropertyChange(PROPERTY_SIGNIFICANCE, old, sigLevel);
}
private static NormalDistribution NORMAL = new NormalDistribution();
private double calculateSigHalfAmplitudeFromSigLevel(double sigLevel) {
double v = NORMAL.inverseCumulativeProbability(sigLevel / 2);
return Math.abs(v);
}
public final double getSigHalfAmplitude() {
return getScale().getSigHalfAmplitude();
}
public final void setSigHalfAmplitude(double sigHalfAmplitude) {
double old = getScale().getSigHalfAmplitude();
getScale().setSigHalfAmplitude(sigHalfAmplitude);
firePropertyChange(PROPERTY_SIG_HALF_AMPLITUD, old, sigHalfAmplitude);
}
@XmlElement(name = "limit")
public final double getHalfAmplitude() {
return getScale().getHalfAmplitude();
}
public final void setHalfAmplitude(double halfAmplitude) {
double old = getScale().getHalfAmplitude();
getScale().setHalfAmplitude(halfAmplitude);
firePropertyChange(PROPERTY_HALF_AMPLITUD, old, halfAmplitude);
}
@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;
if (useCorrection) {
Object corrValue = correctedValueIndex >= 0 ? matrix.get(matrix.getLayers().get(correctedValueIndex), identifiers) : 0.0;
double cv = MatrixUtils.doubleValue(corrValue);
useScale = cv <= significanceLevel;
}
final Color color = useScale ? getScale().valueColor(v) : ColorConstants.nonSignificantColor;
decoration.setBgColor(color);
if (isShowValue()) {
decoration.setValue(textFormatter.format(value));
}
}
@Override
public NonEventToNullFunction getDefaultEventFunction() {
if (significantEvents == null) {
initEvents();
}
return significantEvents;
}
private void initEvents() {
significantEvents = new NonEventToNullFunction<ZScoreColorScale>(scale, "Significant Events") {
@Override
public Double apply(Double value, IMatrixPosition position) {
this.position = position;
return (value == null || Math.abs(value) <= getColorScale().getSigHalfAmplitude()) ?
null : Math.abs(value);
}
@Override
public String getDescription() {
double limit = getColorScale().getSigHalfAmplitude();
return "All values above and below significance threshold (" +
limit + ", " + -limit + ") are events";
}
};
}
@Override
public List<NonEventToNullFunction> getEventFunctionAlternatives() {
List<NonEventToNullFunction> list = new ArrayList<>();
list.add(significantEvents);
list.addAll(super.getEventFunctionAlternatives());
return list;
}
}