/* * #%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.BinaryColorScale; import org.gitools.utils.cutoffcmp.CutoffCmp; import org.gitools.utils.formatter.ITextFormatter; import org.gitools.utils.xml.adapter.ColorXmlAdapter; import org.gitools.utils.xml.adapter.CutoffCmpXmlAdapter; import javax.xml.bind.annotation.*; import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; import java.awt.*; import java.util.ArrayList; import java.util.List; @XmlAccessorType(XmlAccessType.NONE) @XmlRootElement(name = "binary") public class BinaryDecorator extends Decorator<BinaryColorScale> { public static final String PROPERTY_COMPARATOR = "comparator"; public static final String PROPERTY_CUTOFF = "cutoff"; public static final String PROPERTY_COLOR = "color"; public static final String PROPERTY_NON_SIGNIFICANT_COLOR = "nonSignificantColor"; public static final String PROPERTY_EMPTY_COLOR = "emptyColor"; @XmlTransient private BinaryColorScale scale; @XmlTransient private NonEventToNullFunction<BinaryColorScale> binaryEvents; public BinaryDecorator() { super(); this.scale = new BinaryColorScale(); } public BinaryColorScale getScale() { return scale; } public void setScale(BinaryColorScale scale) { this.scale = scale; } @XmlElement(name = "comparator") @XmlJavaTypeAdapter(CutoffCmpXmlAdapter.class) public CutoffCmp getComparator() { return CutoffCmp.getFromName(getScale().getComparator()); } public void setComparator(CutoffCmp cutoffCmp) { CutoffCmp old = getComparator(); getScale().setComparator(cutoffCmp.getShortName()); firePropertyChange(PROPERTY_COMPARATOR, old, cutoffCmp); } @XmlElement(name = "cutoff") public double getCutoff() { return getScale().getCutoff(); } public void setCutoff(double cutoff) { double old = getScale().getCutoff(); getScale().setCutoff(cutoff); firePropertyChange(PROPERTY_CUTOFF, old, cutoff); } @XmlElement(name = "true-color") @XmlJavaTypeAdapter(ColorXmlAdapter.class) public Color getColor() { return getScale().getMaxColor(); } public void setColor(Color color) { Color old = getScale().getMaxColor(); getScale().setMaxColor(color); firePropertyChange(PROPERTY_COLOR, old, color); } @XmlElement(name = "false-color") @XmlJavaTypeAdapter(ColorXmlAdapter.class) public Color getNonSignificantColor() { return getScale().getMinColor(); } public void setNonSignificantColor(Color color) { Color old = getScale().getMinColor(); this.getScale().setMinColor(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 c = getScale().valueColor(v); decoration.setBgColor(c); if (isShowValue()) { decoration.setValue(textFormatter.format(value)); } } @Override public NonEventToNullFunction getDefaultEventFunction() { if (binaryEvents == null) { binaryEvents = new NonEventToNullFunction<BinaryColorScale>(scale, "Binary events") { @Override public Double apply(Double value, IMatrixPosition position) { this.position = position; boolean satisfies = value != null && CutoffCmp.getFromName(getColorScale().getComparator()).compare(value, getColorScale().getCutoff()); return satisfies ? 1.0 : null; } @Override public String getDescription() { return ("All 'true' values are events: " + getColorScale().getComparator() + " " + getColorScale().getCutoff()); } }; } return binaryEvents; } @Override public List<NonEventToNullFunction> getEventFunctionAlternatives() { List<NonEventToNullFunction> list = new ArrayList<>(); list.add(binaryEvents); return list; } }