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mikekuceramikekucera
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GeneListTunable for use with GeneMANIA task
1 parent a9d47cb commit 9e0f602

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8 files changed

+486
-5
lines changed

8 files changed

+486
-5
lines changed

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java‎

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@@ -27,6 +27,8 @@
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import org.baderlab.csplugins.enrichmentmap.style.ChartFactoryManager;
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import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
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import org.baderlab.csplugins.enrichmentmap.style.charts.radialheatmap.RadialHeatMapChartFactory;
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import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListGUITunableHandler;
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import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
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import org.baderlab.csplugins.enrichmentmap.view.EMColumnPresentation;
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import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
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import org.baderlab.csplugins.enrichmentmap.view.creation.CreationDialogShowAction;
@@ -40,6 +42,8 @@
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import org.cytoscape.view.presentation.customgraphics.CyCustomGraphics2Factory;
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import org.cytoscape.work.ServiceProperties;
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import org.cytoscape.work.TaskFactory;
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import org.cytoscape.work.swing.GUITunableHandlerFactory;
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import org.cytoscape.work.swing.SimpleGUITunableHandlerFactory;
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import org.ops4j.peaberry.osgi.OSGiModule;
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import org.osgi.framework.BundleContext;
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@@ -117,6 +121,11 @@ public void start(BundleContext bc) {
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Properties colProps = new Properties();
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colProps.put(CyColumnPresentation.NAMESPACE, EMStyleBuilder.Columns.NAMESPACE);
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registerService(bc, new EMColumnPresentation(), CyColumnPresentation.class, colProps);
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// gene list GUI tunable handler
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SimpleGUITunableHandlerFactory<GeneListGUITunableHandler> geneListGuiHandler
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= new SimpleGUITunableHandlerFactory<>(GeneListGUITunableHandler.class, GeneListTunable.class);
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registerService(bc, geneListGuiHandler, GUITunableHandlerFactory.class);
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}
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// If the App is updated or restarted then we want to reload the model and view from the tables

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaTask.java‎

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@@ -5,6 +5,7 @@
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import java.util.List;
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import java.util.Map;
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import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
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import org.cytoscape.command.CommandExecutorTaskFactory;
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import org.cytoscape.work.AbstractTask;
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import org.cytoscape.work.FinishStatus;
@@ -29,6 +30,9 @@ public class QueryGeneManiaTask extends AbstractTask {
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public static final String GENEMANIA_ORGANISMS_COMMAND = "organisms";
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public static final String GENEMANIA_SEARCH_COMMAND = "search";
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@Tunable(description = "Genes:")
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public GeneListTunable geneList;
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@Tunable(description = "Organism:")
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public ListSingleSelection<GMOrganism> organisms;
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@@ -38,7 +42,6 @@ public class QueryGeneManiaTask extends AbstractTask {
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@Tunable(description = "Network Weighting:")
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public ListSingleSelection<GMWeightingMethod> weightingMethods;
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private final String query;
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private GMSearchResult result;
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private static long lastTaxonomyId = 9606; // H.sapiens
@@ -51,10 +54,10 @@ public static interface Factory {
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@Inject
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public QueryGeneManiaTask(@Assisted List<String> geneList) {
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query = String.join("|", geneList);
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organisms = new ListSingleSelection<>();
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weightingMethods = new ListSingleSelection<>(GMWeightingMethod.values());
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weightingMethods.setSelectedValue(weightingMethods.getPossibleValues().get(0));
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this.geneList = new GeneListTunable(geneList);
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this.organisms = new ListSingleSelection<>();
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this.weightingMethods = new ListSingleSelection<>(GMWeightingMethod.values());
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this.weightingMethods.setSelectedValue(weightingMethods.getPossibleValues().get(0));
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}
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@ProvidesTitle
@@ -83,6 +86,9 @@ public void run(TaskMonitor tm) throws Exception {
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tm.setTitle("EnrichmentMap");
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tm.setStatusMessage("Querying GeneMANIA...");
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String query = String.join("|", geneList.getSelectedGenes());
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System.out.println(query);
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Map<String, Object> args = new HashMap<>();
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args.put("organism", "" + organisms.getSelectedValue().getTaxonomyId());
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args.put("genes", query);

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListGUITunableHandler.java‎

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package org.baderlab.csplugins.enrichmentmap.task.tunables;
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import java.lang.reflect.Field;
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import java.lang.reflect.Method;
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import java.util.List;
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import javax.swing.GroupLayout;
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import javax.swing.JLabel;
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import javax.swing.JPanel;
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import org.baderlab.csplugins.enrichmentmap.view.util.CheckboxData;
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import org.baderlab.csplugins.enrichmentmap.view.util.CheckboxList;
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import org.cytoscape.util.swing.LookAndFeelUtil;
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import org.cytoscape.work.Tunable;
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import org.cytoscape.work.swing.AbstractGUITunableHandler;
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public class GeneListGUITunableHandler extends AbstractGUITunableHandler {
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private JPanel panel;
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private CheckboxList<String> checkBoxList;
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public GeneListGUITunableHandler(Field field, Object instance, Tunable tunable) {
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super(field, instance, tunable);
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init();
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}
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public GeneListGUITunableHandler(Method getter, Method setter, Object instance, Tunable tunable) {
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super(getter, setter, instance, tunable);
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init();
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}
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private GeneListTunable getGeneListTunable() {
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try {
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return (GeneListTunable) getValue();
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} catch(final Exception e) {
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throw new IllegalStateException("bad object", e);
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}
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}
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private void init() {
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panel = createGeneListPanel();
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}
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private JPanel createGeneListPanel() {
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JLabel title = new JLabel(getDescription());
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GeneListPanel<String> checkboxPanel = new GeneListPanel<>();
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for(String gene : getGeneListTunable().getGenes()) {
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checkboxPanel.getModel().addElement(new CheckboxData<>(gene));
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}
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JPanel panel = new JPanel();
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final GroupLayout layout = new GroupLayout(panel);
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panel.setLayout(layout);
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layout.setAutoCreateContainerGaps(true);
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layout.setAutoCreateGaps(true);
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layout.setHorizontalGroup(layout.createParallelGroup()
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.addComponent(title)
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.addGroup(layout.createSequentialGroup()
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.addComponent(checkboxPanel)
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)
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);
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layout.setVerticalGroup(layout.createSequentialGroup()
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.addComponent(title)
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.addGroup(layout.createParallelGroup()
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.addComponent(checkboxPanel)
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)
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);
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if(LookAndFeelUtil.isAquaLAF())
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panel.setOpaque(false);
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return panel;
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}
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@Override
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public JPanel getJPanel() {
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return panel;
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}
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@Override
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public void handle() {
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List<String> selectedGenes = checkBoxList.getSelectedData();
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getGeneListTunable().setSelectedGenes(selectedGenes);
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}
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@Override
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public void update() {
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}
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}

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListPanel.java‎

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package org.baderlab.csplugins.enrichmentmap.task.tunables;
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import static javax.swing.GroupLayout.DEFAULT_SIZE;
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import static javax.swing.GroupLayout.PREFERRED_SIZE;
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import static javax.swing.GroupLayout.Alignment.CENTER;
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import static org.cytoscape.util.swing.LookAndFeelUtil.isAquaLAF;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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import javax.swing.GroupLayout;
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import javax.swing.JButton;
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import javax.swing.JPanel;
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import javax.swing.JScrollPane;
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import javax.swing.event.ListDataEvent;
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import javax.swing.event.ListDataListener;
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import org.baderlab.csplugins.enrichmentmap.view.util.CheckboxData;
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import org.baderlab.csplugins.enrichmentmap.view.util.CheckboxList;
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import org.baderlab.csplugins.enrichmentmap.view.util.CheckboxListModel;
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import org.cytoscape.util.swing.LookAndFeelUtil;
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@SuppressWarnings("serial")
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public class GeneListPanel<T> extends JPanel {
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private CheckboxList<T> checkboxList;
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private CheckboxListModel<T> checkboxListModel;
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private JButton selectAllButton;
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private JButton selectNoneButton;
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public GeneListPanel() {
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checkboxListModel = new CheckboxListModel<>();
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checkboxList = new CheckboxList<>(checkboxListModel);
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JScrollPane scrollPane = new JScrollPane();
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scrollPane.setViewportView(checkboxList);
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selectAllButton = new JButton("Select All");
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selectNoneButton = new JButton("Select None");
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selectAllButton.addActionListener(e -> {
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List<CheckboxData<T>> oldValue = getSelectedData();
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checkboxListModel.forEach(cb -> cb.setSelected(true));
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checkboxList.invalidate();
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checkboxList.repaint();
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updateSelectionButtons();
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firePropertyChange("selectedData", oldValue, getSelectedData());
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});
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selectNoneButton.addActionListener(e -> {
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List<CheckboxData<T>> oldValue = getSelectedData();
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checkboxListModel.forEach(cb -> cb.setSelected(false));
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checkboxList.invalidate();
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checkboxList.repaint();
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updateSelectionButtons();
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firePropertyChange("selectedData", oldValue, Collections.emptyList());
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});
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selectAllButton.setEnabled(false);
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selectNoneButton.setEnabled(false);
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checkboxListModel.addListDataListener(new ListDataListener() {
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@Override
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public void intervalRemoved(ListDataEvent e) {
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updateSelectionButtons();
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}
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@Override
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public void intervalAdded(ListDataEvent e) {
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updateSelectionButtons();
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}
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@Override
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public void contentsChanged(ListDataEvent e) {
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updateSelectionButtons();
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}
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});
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checkboxList.addListSelectionListener(evt -> {
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if (!evt.getValueIsAdjusting()) {
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updateSelectionButtons();
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firePropertyChange("selectedData", null, getSelectedData());
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}
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});
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if (isAquaLAF()) {
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selectAllButton.putClientProperty("JButton.buttonType", "gradient");
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selectAllButton.putClientProperty("JComponent.sizeVariant", "small");
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selectNoneButton.putClientProperty("JButton.buttonType", "gradient");
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selectNoneButton.putClientProperty("JComponent.sizeVariant", "small");
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}
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LookAndFeelUtil.equalizeSize(selectAllButton, selectNoneButton);
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final GroupLayout layout = new GroupLayout(this);
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setLayout(layout);
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layout.setAutoCreateContainerGaps(false);
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layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
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layout.setHorizontalGroup(layout.createSequentialGroup()
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.addComponent(scrollPane, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
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.addGroup(layout.createParallelGroup(CENTER, true)
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.addComponent(selectAllButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)
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.addComponent(selectNoneButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)
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)
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);
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layout.setVerticalGroup(layout.createParallelGroup()
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.addComponent(scrollPane, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)
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.addGroup(layout.createSequentialGroup()
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.addComponent(selectAllButton)
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.addComponent(selectNoneButton)
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)
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);
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if (LookAndFeelUtil.isAquaLAF())
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setOpaque(false);
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}
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private void updateSelectionButtons() {
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boolean enabled = isEnabled() && !checkboxListModel.isEmpty();
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List<CheckboxData<T>> selectedData = getSelectedData();
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selectAllButton.setEnabled(enabled && selectedData.size() < checkboxListModel.size());
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selectNoneButton.setEnabled(enabled && selectedData.size() > 0);
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}
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public CheckboxList<T> getCheckboxList() {
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return checkboxList;
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}
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public CheckboxListModel<T> getModel() {
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return checkboxListModel;
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}
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public List<T> getSelectedDataItems() {
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return checkboxListModel.stream()
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.filter(CheckboxData::isSelected)
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.map(CheckboxData::getData)
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.collect(Collectors.toList());
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}
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@Override
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public void setEnabled(boolean enabled) {
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super.setEnabled(enabled);
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checkboxList.setEnabled(enabled);
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updateSelectionButtons();
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}
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public List<CheckboxData<T>> getSelectedData() {
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List<CheckboxData<T>> list = new ArrayList<>();
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int size = getModel().getSize();
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for (int i = 0; i < size; i++) {
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CheckboxData<T> data = (CheckboxData<T>) getModel().getElementAt(i);
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if (data.isSelected())
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list.add(data);
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}
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return list;
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}
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}

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListTunable.java‎

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package org.baderlab.csplugins.enrichmentmap.task.tunables;
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import java.util.Collections;
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import java.util.List;
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public class GeneListTunable {
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private List<String> genes;
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private List<String> selectedGenes;
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private List<String> leadingEdgeGenes;
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public GeneListTunable(List<String> genes) {
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this.genes = genes;
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this.selectedGenes = genes;
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this.leadingEdgeGenes = Collections.emptyList();
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}
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public void setLeadingEdgeGenes(List<String> genes) {
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this.leadingEdgeGenes = genes;
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}
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public List<String> getLeadingEdgeGenes() {
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return leadingEdgeGenes;
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}
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public void setSelectedGenes(List<String> selectedGenes) {
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this.selectedGenes = selectedGenes;
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}
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public List<String> getSelectedGenes() {
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return selectedGenes;
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}
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public List<String> getGenes() {
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return genes;
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}
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}

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