/*
* #%L
* gitools-ui-app
* %%
* 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.ui.app.commands;
import org.gitools.analysis.clustering.ClusteringData;
import org.gitools.analysis.clustering.ClusteringException;
import org.gitools.analysis.clustering.annotations.AnnPatClusteringData;
import org.gitools.analysis.clustering.annotations.AnnPatClusteringMethod;
import org.gitools.api.analysis.Clusters;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.MatrixDimensionKey;
import org.gitools.heatmap.header.ColoredLabel;
import org.gitools.heatmap.header.HeatmapColoredLabelsHeader;
import org.gitools.ui.core.Application;
import org.gitools.ui.core.commands.HeaderCommand;
import org.gitools.utils.color.ColorGenerator;
import org.gitools.utils.progressmonitor.DefaultProgressMonitor;
import java.awt.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
public class AddHeaderColoredLabelsCommand extends HeaderCommand {
private final boolean textVisible;
private List<String> colors;
private List<String> ids;
private boolean autoGenerateColors;
public AddHeaderColoredLabelsCommand(String heatmap, MatrixDimensionKey side, String pattern, List<String> colors, List<String> ids,
boolean autoGenerateColors, boolean textVisible, String sort) {
super(heatmap, side, sort, pattern);
this.colors = colors;
this.ids = ids;
this.autoGenerateColors = autoGenerateColors;
this.textVisible = textVisible;
}
@Override
public void execute(IProgressMonitor monitor) throws CommandException {
super.execute(monitor);
if (getExitStatus() > 0) {
return;
}
List<ColoredLabel> cls = new ArrayList<>();
HeatmapColoredLabelsHeader header = new HeatmapColoredLabelsHeader(heatmapDimension);
header.setAnnotationPattern(pattern);
header.setHeatmapDimension(heatmapDimension);
header.setTitle(header.deriveTitleFromPattern());
if (textVisible) {
header.setLabelVisible(true);
}
if (autoGenerateColors) {
cls = header.getClusters();
autoGenerateColoredLabels(header);
}
if (!(colors == null || ids == null)) {
if (colors.size() != ids.size()) {
setExitStatus(1);
throw new CommandException("The number of specified colors and values must match");
}
for (int i = 0; i < colors.size(); i++) {
ColoredLabel cl = new ColoredLabel(ids.get(i), Color.decode(colors.get(i)));
cls = addCluster(cls, cl);
}
if (cls.size() == 0) {
throw new CommandException("No color labels have been created.");
}
header.setClusters(cls);
}
heatmapDimension.addHeader(header);
applySort();
Application.get().refresh();
if (sort != null)
setExitStatus(0);
}
@Deprecated
private List<ColoredLabel> addCluster(List<ColoredLabel> coloredLabels, ColoredLabel cl) {
String key = cl.getValue();
for (int i = 0; i < coloredLabels.size(); i++) {
if (coloredLabels.get(i).getValue().equals(key)) {
coloredLabels.set(i, cl);
break;
}
}
coloredLabels.add(cl);
return coloredLabels;
}
public static void updateFromClusterResults(HeatmapColoredLabelsHeader header, Collection<String> clusters) {
ColorGenerator cg = new ColorGenerator();
List<ColoredLabel> coloredLabels = new ArrayList<>(clusters.size());
for (String cluster : clusters) {
coloredLabels.add(new ColoredLabel(cluster, cg.next(cluster)));
}
header.setClusters(coloredLabels);
}
public static void autoGenerateColoredLabels(HeatmapColoredLabelsHeader header) {
Clusters results = makeAnnotationClustering(header);
updateFromClusterResults(header, results.getClusters());
}
public static Clusters makeAnnotationClustering(HeatmapColoredLabelsHeader header) {
ClusteringData data = new AnnPatClusteringData(header.getHeatmapDimension(), header.getAnnotationPattern());
Clusters results = null;
try {
results = new AnnPatClusteringMethod().cluster(data, new DefaultProgressMonitor());
} catch (ClusteringException e) {
e.printStackTrace();
}
return results;
}
}