/*
* #%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.overlapping;
import org.apache.velocity.VelocityContext;
import org.gitools.analysis.overlapping.OverlappingAnalysis;
import org.gitools.analysis.overlapping.format.OverlappingAnalysisFormat;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.api.resource.ResourceReference;
import org.gitools.heatmap.Heatmap;
import org.gitools.heatmap.HeatmapLayer;
import org.gitools.heatmap.decorator.impl.LinearDecorator;
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 org.gitools.utils.cutoffcmp.CutoffCmp;
import javax.enterprise.context.ApplicationScoped;
import javax.swing.*;
import java.awt.*;
import java.util.Map;
@ApplicationScoped
public class OverlappingAnalysisEditor extends AnalysisEditor<OverlappingAnalysis> {
public OverlappingAnalysisEditor(OverlappingAnalysis analysis) {
super(analysis, "/vm/analysis/overlapping/analysis_details.vm", OverlappingAnalysisFormat.EXTENSION);
}
@Override
protected void prepareContext(VelocityContext context) {
OverlappingAnalysis analysis = getModel();
ResourceReference<IMatrix> resourceRef = analysis.getFilteredData();
context.put("filteredDataFile", ((resourceRef != null && resourceRef.getLocator() != null) ? resourceRef.getLocator().getURL() : "Not defined"));
String appliedTo = analysis.isTransposeData() ? "rows" : "columns";
context.put("appliedTo", appliedTo);
CutoffCmp cmp = analysis.getBinaryCutoffCmp();
String filterDesc = cmp == null ? "Not filtered" : "Binary cutoff filter for values " + cmp.getLongName() + " " + analysis.getBinaryCutoffValue();
context.put("filterDesc", filterDesc);
resourceRef = analysis.getCellResults();
context.put("resultsFile", (resourceRef != null && resourceRef.getLocator() != null) ? resourceRef.getLocator().getURL() : "Not defined");
IResourceLocator analysisLocator = analysis.getLocator();
if (analysisLocator != null) {
context.put("analysisLocation", analysisLocator.getURL());
if (analysisLocator.isWritable()) {
setSaveAllowed(true);
}
}
}
@Override
protected void performUrlAction(String name, Map<String, String> params) {
if ("NewDataHeatmap".equals(name)) {
newDataHeatmap();
} else if ("NewResultsHeatmap".equals(name)) {
newResultsHeatmap();
}
}
private void newDataHeatmap() {
final OverlappingAnalysis analysis = getModel();
if (analysis.getSourceData() == 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) {
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("Heatmap from data created.");
}
});
}
});
}
private void newResultsHeatmap() {
final OverlappingAnalysis analysis = getModel();
if (analysis.getCellResults() == 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);
Heatmap heatmap = new Heatmap(analysis.getCellResults().get());
heatmap.setTitle(analysis.getTitle() + " (results)");
final HeatmapEditor editor = new HeatmapEditor(createResultsHeatmap(analysis));
editor.setIcon(IconUtils.getIconResource(IconNames.analysisHeatmap16));
editor.setName(editorPanel.deriveName(getName(), OverlappingAnalysisFormat.EXTENSION, "-results", ""));
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
editorPanel.addEditor(editor);
Application.get().showNotification("Heatmap for results created.");
}
});
}
});
}
@Deprecated
private Heatmap createDataHeatmap(OverlappingAnalysis analysis) {
IMatrix data = analysis.getSourceData().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(OverlappingAnalysis analysis) {
IMatrix results = analysis.getCellResults().get();
if (Heatmap.class.isAssignableFrom(results.getClass())) {
return (Heatmap) results;
}
Heatmap heatmap = new Heatmap(results, true);
heatmap.setTitle(analysis.getTitle() + " (results)");
for (HeatmapLayer layer : heatmap.getLayers()) {
LinearDecorator dec = new LinearDecorator();
Color minColor = new Color(0x63, 0xdc, 0xfe);
Color maxColor = new Color(0xff, 0x00, 0x5f);
dec.setMinValue(0.0);
dec.setMinColor(minColor);
dec.setMidValue(1.0);
dec.setMidColor(maxColor);
dec.setMaxValue(1.0);
dec.setMaxColor(maxColor);
dec.setEmptyColor(Color.WHITE);
layer.setDecorator(dec);
}
heatmap.getLayers().setTopLayerIndex(heatmap.getLayers().indexOf("jaccard-index"));
heatmap.setTitle(analysis.getTitle());
return heatmap;
}
}