/*
* #%L
* org.gitools.mutex
* %%
* Copyright (C) 2013 - 2014 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.plugins.mutex.ui;
import com.jgoodies.binding.adapter.ComboBoxAdapter;
import com.jgoodies.binding.beans.PropertyAdapter;
import com.jgoodies.binding.list.SelectionInList;
import org.gitools.heatmap.Heatmap;
import org.gitools.heatmap.decorator.impl.NonEventToNullFunction;
import org.gitools.ui.platform.dialog.MessageStatus;
import org.gitools.ui.platform.wizard.AbstractWizardPage;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Collection;
public class MutualExclusiveAnalysisPage extends AbstractWizardPage {
private JComboBox columnAnnotationCombo;
private JPanel rootPanel;
private JComboBox rowAnnotationCombo;
private JCheckBox allColumnsCheckBox;
private JCheckBox columnAnnotationGroupingBox;
private JComboBox eventsFunctionComboBox;
private JLabel eventsFunctionDescription;
private JSpinner permutationSpinner;
private JCheckBox discardEmpty;
private JLabel testDescription;
private Heatmap heatmap;
public MutualExclusiveAnalysisPage(Heatmap heatmap) {
super("Mutual exclusion & Co-occurrence analysis");
this.heatmap = heatmap;
setTitle("Mutual Exclusion & Co-occurrence analysis");
setMessage("Select which groups of columns and rows you want to test");
Collection<String> colAnnlabels = heatmap.getColumns().getAnnotations().getLabels();
Collection<String> rowAnnlabels = heatmap.getRows().getAnnotations().getLabels();
columnAnnotationCombo.setModel(new DefaultComboBoxModel(
colAnnlabels.toArray(new String[colAnnlabels.size()])
));
rowAnnotationCombo.setModel(new DefaultComboBoxModel(
rowAnnlabels.toArray(new String[rowAnnlabels.size()])
));
ActionListener actionListener = new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
updateControls();
}
};
eventsFunctionComboBox.addActionListener(actionListener);
eventsFunctionComboBox.setModel(
new ComboBoxAdapter<>(
new SelectionInList<NonEventToNullFunction>(
heatmap.getLayers().getTopLayer().getDecorator().getEventFunctionAlternatives(),
new PropertyAdapter<>(heatmap.getLayers().getTopLayer(), "eventFunction")
)
)
);
allColumnsCheckBox.addActionListener(actionListener);
columnAnnotationGroupingBox.addActionListener(actionListener);
permutationSpinner.setModel(new SpinnerNumberModel(10000, 100, 10000000, 1000));
testDescription.setText("All " + heatmap.getContents().getRows().size() + " " + heatmap.getRows().getId().getLabel() + "s will be taken into account " +
"for a weighted permutation test to assess probability of mutual exclusion and co-occurence");
updateControls();
}
public String getRowsGroupsPattern() {
return "${" + rowAnnotationCombo.getSelectedItem() + "}";
}
public boolean isAllColumnsGroup() {
return allColumnsCheckBox.isSelected();
}
public String getColumnGroupsPattern () {
if (columnAnnotationGroupingBox.isSelected()) {
return "${" + columnAnnotationCombo.getSelectedItem() + "}";
} else {
return null;
}
}
@Override
public void updateControls() {
boolean hasColAnnotation = columnAnnotationCombo.getModel().getSize() > 0;
boolean hasRowAnnotation = rowAnnotationCombo.getModel().getSize() > 0;
if (!hasColAnnotation) {
columnAnnotationGroupingBox.setEnabled(false);
columnAnnotationGroupingBox.setSelected(false);
allColumnsCheckBox.setSelected(true);
}
if (!hasRowAnnotation) {
setComplete(false);
setMessage(MessageStatus.ERROR, "No row annotation available for grouping. For all rows, use Edit > Row > Sort by Mut.Ex.");
}
columnAnnotationCombo.setEnabled(columnAnnotationGroupingBox.isSelected());
if (eventsFunctionDescription!=null && eventsFunctionComboBox.getSelectedItem() != null) {
eventsFunctionDescription.setText(((NonEventToNullFunction) eventsFunctionComboBox.getSelectedItem()).getDescription());
}
setComplete(columnAnnotationGroupingBox.isSelected() || isAllColumnsGroup());
}
@Override
public JComponent createControls() {
return rootPanel;
}
public int getPermutations() {
return Integer.parseInt(permutationSpinner.getValue().toString());
}
public boolean getDiscardEmpty() {
return discardEmpty.isSelected();
}
}