/*
* #%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.analysis.combination.editor;
import org.apache.velocity.VelocityContext;
import org.gitools.analysis.combination.CombinationAnalysis;
import org.gitools.analysis.combination.format.CombinationAnalysisFormat;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.heatmap.Heatmap;
import org.gitools.heatmap.decorator.impl.PValueDecorator;
import org.gitools.ui.app.commands.CommandLoadFile;
import org.gitools.ui.app.heatmap.editor.HeatmapEditor;
import org.gitools.ui.core.Application;
import org.gitools.ui.core.components.editor.AnalysisEditor;
import org.gitools.ui.core.components.editor.EditorsPanel;
import org.gitools.ui.platform.IconUtils;
import org.gitools.ui.platform.icons.IconNames;
import org.gitools.ui.platform.progress.JobRunnable;
import org.gitools.ui.platform.progress.JobThread;
import javax.enterprise.context.ApplicationScoped;
import javax.swing.*;
import java.util.Map;
@ApplicationScoped
public class CombinationAnalysisEditor extends AnalysisEditor<CombinationAnalysis> {
public CombinationAnalysisEditor(CombinationAnalysis analysis) {
super(analysis, "/vm/analysis/combination/analysis_details.vm", CombinationAnalysisFormat.EXTENSION);
}
@Override
protected void prepareContext(VelocityContext context) {
final CombinationAnalysis analysis = getModel();
String combOf = "columns";
if (analysis.isTransposeData()) {
combOf = "rows";
}
context.put("combinationOf", combOf);
IResourceLocator resourceLocator = analysis.getData().getLocator();
context.put("dataFile", resourceLocator != null ? resourceLocator.getName() : "Not defined");
resourceLocator = analysis.getGroupsMap().getLocator();
String groupsFile = resourceLocator != null ? resourceLocator.getName() : "Not specified. All " + combOf + " are combined";
context.put("groupsFile", groupsFile);
String sizeAttr = analysis.getSizeLayer();
if (sizeAttr == null || sizeAttr.isEmpty()) {
sizeAttr = "Constant value of 1";
}
context.put("sizeAttr", sizeAttr);
resourceLocator = analysis.getResults().getLocator();
context.put("resultsFile", resourceLocator != null ? resourceLocator.getName() : "Not defined");
resourceLocator = analysis.getLocator();
if (resourceLocator != null) {
context.put("analysisLocation", resourceLocator.getURL());
} else {
setSaveAllowed(true);
}
}
@Override
protected void performUrlAction(String name, Map<String, String> params) {
if ("NewDataHeatmap".equals(name)) {
newDataHeatmap();
} else if ("NewResultsHeatmap".equals(name)) {
newResultsHeatmap();
} else if ("ViewModuleMap".equals(name)) {
newGroupsMap();
}
}
private void newGroupsMap() {
final CombinationAnalysis analysis = getModel();
if (analysis.getGroupsMap() == null) {
Application.get().showNotificationPermanent("Analysis doesn't contain a groups file.");
return;
}
JobThread.execute(Application.get(), new CommandLoadFile(analysis.getGroupsMap()));
}
private void newDataHeatmap() {
final CombinationAnalysis analysis = getModel();
if (analysis.getData() == null) {
Application.get().showNotificationPermanent("Analysis doesn't contain data.");
return;
}
final EditorsPanel editorPanel = Application.get().getEditorsPanel();
JobThread.execute(Application.get(), new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
try {
monitor.begin("Creating new heatmap from data ...", 1);
final HeatmapEditor editor = new HeatmapEditor(createDataHeatmap(analysis));
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
editorPanel.addEditor(editor);
Application.get().showNotification("Combination data heatmap created.");
}
});
} catch (Exception e) {
monitor.exception(e);
}
}
});
}
private void newResultsHeatmap() {
final CombinationAnalysis analysis = getModel();
if (analysis.getResults() == null) {
Application.get().showNotificationPermanent("Analysis doesn't contain results.");
return;
}
final EditorsPanel editorPanel = Application.get().getEditorsPanel();
JobThread.execute(Application.get(), new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
monitor.begin("Creating new heatmap from results ...", 1);
try {
final HeatmapEditor editor = new HeatmapEditor(createResultsHeatmap(analysis));
editor.setIcon(IconUtils.getIconResource(IconNames.analysisHeatmap16));
editor.setName(editorPanel.deriveName(getName(), CombinationAnalysisFormat.EXTENSION, "-results", ""));
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
editorPanel.addEditor(editor);
Application.get().showNotification("Heatmap for combination results created.");
}
});
} catch (Exception e) {
monitor.exception(e);
}
}
});
}
@Deprecated
private Heatmap createDataHeatmap(CombinationAnalysis analysis) {
IMatrix data = analysis.getData().get();
if (Heatmap.class.isAssignableFrom(data.getClass())) {
return (Heatmap) data;
}
Heatmap heatmap = new Heatmap(data);
heatmap.setTitle(analysis.getTitle() + " (data)");
return heatmap;
}
@Deprecated
private Heatmap createResultsHeatmap(CombinationAnalysis analysis) {
Heatmap heatmap = new Heatmap(analysis.getResults().get());
heatmap.getLayers().setTopLayerById("right-p-value");
heatmap.getLayers().getTopLayer().setDecorator(new PValueDecorator());
heatmap.setTitle(analysis.getTitle() + " (results)");
return heatmap;
}
}