Clean up genemania dialog. Refs #377

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/LoadEnrichmentsFromGenemaniaTask.java

@@ -57,6 +57,7 @@ public void run(TaskMonitor tm) {
 		tm.setProgress(0.7);
 
 		createDataSet(genemaniaNetwork, geneSets, annotations);
+		dataset.getMap().getParams().setFDR(true);
 
 		tm.setProgress(1.0);
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/CutoffPropertiesPanel.java

@@ -46,6 +46,7 @@ public class CutoffPropertiesPanel extends JPanel {
 
 	// node filtering
 	private JCheckBox filterGenesCheckbox;
+	private JLabel filterGenesLabel;
 	private JFormattedTextField qvalueText;
 	private JLabel pvalueLabel;
 	private JFormattedTextField pvalueText;
@@ -61,6 +62,7 @@ public class CutoffPropertiesPanel extends JPanel {
 	// edge filtering
 	private JFormattedTextField similarityCutoffText;
 	private JComboBox<ComboItem<SimilarityMetric>> cutoffMetricCombo;
+	private JLabel edgeStrategyLabel;
 	private JComboBox<ComboItem<EdgeStrategy>> edgeStrategyCombo;
 	private CombinedConstantSlider combinedConstantSlider;
 	private SimilaritySlider similaritySlider;
@@ -70,6 +72,8 @@ public class CutoffPropertiesPanel extends JPanel {
 	private JCheckBox notationCheckBox;
 	private JCheckBox advancedCheckBox;
 
+	private boolean isGenemania;
+	
 	private final List<Pair<SimilarityMetric, Double>> sliderTicks = Arrays.asList(
 		Pair.of(SimilarityMetric.JACCARD, 0.35),
 		Pair.of(SimilarityMetric.JACCARD, 0.25),
@@ -90,6 +94,11 @@ private Map<SimilarityMetric,Double> initialCutoffValues() {
 		return values;
 	}
 
+	public void setGeneMania() {
+		this.isGenemania = true;
+		updateVisibility();
+		similaritySlider.setTick(1);
+	}
 
 	@AfterInjection
 	public void createContents() {
@@ -108,11 +117,9 @@ public void createContents() {
 		});
 
 		advancedCheckBox = new JCheckBox("Show Advanced Options");
-		advancedCheckBox.addActionListener(e -> 
-			showAdvancedOptions(advancedCheckBox.isSelected())
-		);
+		advancedCheckBox.addActionListener(e -> updateVisibility());
 
-		showAdvancedOptions(false);
+		updateVisibility();
 
 		SwingUtil.makeSmall(notationCheckBox, advancedCheckBox);
 
@@ -150,7 +157,7 @@ private JPanel createFilterNodesPanel() {
 		panel.setBorder(LookAndFeelUtil.createTitledBorder("Number of Nodes (gene-set filtering)"));
 
 
-		JLabel filterGenesLabel = new JLabel("Filter genes by expressions:");
+		filterGenesLabel = new JLabel("Filter genes by expressions:");
 		JLabel qvalueLabel = new JLabel("FDR q-value cutoff:");
 		pvalueLabel = new JLabel("p-value cutoff:");
 		nesFilterLabel = new JLabel("NES (GSEA only):");
@@ -309,12 +316,12 @@ private JPanel createFilterEdgesPanel() {
 
 
 	private JPanel createFilterEdgesPanel_Top() {
-		JLabel edgesLabel = new JLabel("Data Set Edges:");
+		edgeStrategyLabel = new JLabel("Data Set Edges:");
 		edgeStrategyCombo = new JComboBox<>();
 		edgeStrategyCombo.addItem(new ComboItem<>(EdgeStrategy.AUTOMATIC, "Automatic"));
 		edgeStrategyCombo.addItem(new ComboItem<>(EdgeStrategy.DISTINCT, "Separate edge for each data set (denser)"));
 		edgeStrategyCombo.addItem(new ComboItem<>(EdgeStrategy.COMPOUND, "Combine edges across data sets (sparser)"));
-		SwingUtil.makeSmall(edgeStrategyCombo, edgesLabel);
+		SwingUtil.makeSmall(edgeStrategyCombo, edgeStrategyLabel);
 
 		JPanel panel = new JPanel();
 		final GroupLayout layout = new GroupLayout(panel);
@@ -324,12 +331,12 @@ private JPanel createFilterEdgesPanel_Top() {
 
 		layout.setHorizontalGroup(
 			layout.createSequentialGroup()
-				.addComponent(edgesLabel)
+				.addComponent(edgeStrategyLabel)
 				.addComponent(edgeStrategyCombo)
 		);
 		layout.setVerticalGroup(
 			layout.createParallelGroup(Alignment.BASELINE)
-				.addComponent(edgesLabel)
+				.addComponent(edgeStrategyLabel)
 				.addComponent(edgeStrategyCombo)
 		);
 
@@ -472,17 +479,23 @@ public void reset() {
 	}
 
 
-	private void showAdvancedOptions(boolean show) {
-		pvalueLabel.setVisible(show);
-		pvalueText.setVisible(show);
-		nesFilterLabel.setVisible(show);
-		nesFilterCombo.setVisible(show);
-		minExperimentsLabel.setVisible(show);
-		minExperimentsText.setVisible(show);
-		shouldFilterMinLabel.setVisible(show);
-		shouldFilterMinCheckbox.setVisible(show);
-		parseBaderlabLabel.setVisible(show);
-		parseBaderlabCheckbox.setVisible(show);
+	private void updateVisibility() {
+		boolean show = advancedCheckBox.isSelected();
+		pvalueLabel.setVisible(show && !isGenemania);
+		pvalueText.setVisible(show && !isGenemania);
+		nesFilterLabel.setVisible(show && !isGenemania);
+		nesFilterCombo.setVisible(show && !isGenemania);
+		minExperimentsLabel.setVisible(show && !isGenemania);
+		minExperimentsText.setVisible(show && !isGenemania);
+		shouldFilterMinLabel.setVisible(show && !isGenemania);
+		shouldFilterMinCheckbox.setVisible(show && !isGenemania);
+		parseBaderlabLabel.setVisible(show && !isGenemania);
+		parseBaderlabCheckbox.setVisible(show && !isGenemania);
+		
+		filterGenesCheckbox.setVisible(!isGenemania);
+		filterGenesLabel.setVisible(!isGenemania);
+		edgeStrategyLabel.setVisible(!isGenemania);
+		edgeStrategyCombo.setVisible(!isGenemania);
 
 		CardLayout cardLayout = (CardLayout)cardPanel.getLayout();
 		cardLayout.show(cardPanel, show ? "advanced" : "simple");

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/SimilaritySlider.java

@@ -43,6 +43,9 @@ public SimilaritySlider(List<Pair<SimilarityMetric, Double>> cutoffs, int defaul
 		add(slider, BorderLayout.SOUTH);
 	}
 
+	public void setTick(int tick) {
+		slider.setValue(tick);
+	}
 
 	public Pair<SimilarityMetric,Double> getTickValue() {
 		return cutoffs.get(slider.getValue()-1);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/genemania/GenemaniaDialogPage.java

@@ -5,7 +5,6 @@
 import java.util.Collections;
 import java.util.List;
 
-import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 
@@ -57,20 +56,17 @@ private String getOrganismName() {
 	@Override
 	public JPanel createBodyPanel(CardDialogCallback callback) {
 		this.callback = callback;
+		cutoffPanel.setGeneMania();
 
 		// Assume GenemaniaDialogShowAction did its job of validating the current network.
 		genemaniaNetwork = applicationManager.getCurrentNetwork();
 
 		networkNamePanel = new NamePanel("Network Name");
-		
-		String name = genemaniaNetwork.getRow(genemaniaNetwork).get(CyNetwork.NAME, String.class);
-		String text = "Create an EnrichmentMap network from the Genemania network '" + name + "'?";
-		JLabel label = new JLabel(text);
+		networkNamePanel.setAutomaticName(getOrganismName());
 
 		JPanel panel = new JPanel(new GridBagLayout());
-		panel.add(label, GBCFactory.grid(0,0).insets(0).weightx(1.0).fill(GridBagConstraints.HORIZONTAL).get());
-		panel.add(networkNamePanel, GBCFactory.grid(0,1).insets(0).weightx(1.0).fill(GridBagConstraints.HORIZONTAL).get());
-		panel.add(cutoffPanel, GBCFactory.grid(0,2).insets(0).weightx(1.0).fill(GridBagConstraints.HORIZONTAL).get());
+		panel.add(networkNamePanel, GBCFactory.grid(0,0).insets(0).weightx(1.0).fill(GridBagConstraints.HORIZONTAL).get());
+		panel.add(cutoffPanel, GBCFactory.grid(0,1).insets(0).weightx(1.0).fill(GridBagConstraints.HORIZONTAL).get());
 		return panel;
 	}
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/genemania/GenemaniaDialogParameters.java

@@ -31,12 +31,12 @@ public List<CardDialogPage> getPages() {
 
 	@Override
 	public Dimension getPreferredSize() {
-		return new Dimension(820, 700);
+		return new Dimension(820, 320);
 	}
 
 	@Override
 	public Dimension getMinimumSize() {
-		return new Dimension(650, 550);
+		return new Dimension(650, 320);
 	}
 
 	@Override

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/genemania/GenemaniaDialogShowAction.java

@@ -43,23 +43,9 @@ public void showDialog() {
 			showNotGenemaniaNetworkError();
 			return;
 		}
-		
-//		String networkName = network.getRow(network).get(CyNetwork.NAME, String.class);
-//		boolean confirm = showConfirmDialog(networkName);
-//		if(confirm) {
-//			createEMNetworkFrom(network);
-//		}
 		super.showDialog();
 	}
 
-//	private boolean showConfirmDialog(String networkName) {
-//		int r = JOptionPane.showConfirmDialog(jframeProvider.get(), 
-//				"Create an EnrichmentMap network from the Genemania network '" + networkName + "'?", 
-//				"EnrichmentMap: Create from Genemania", 
-//				JOptionPane.OK_CANCEL_OPTION);
-//		return r == JOptionPane.OK_OPTION;
-//	}
-	
 	private void showNoNetworkError() {
 		JOptionPane.showMessageDialog(jframeProvider.get(), 
 				"Please select a network first.", 
@@ -74,11 +60,6 @@ private void showNotGenemaniaNetworkError() {
 				JOptionPane.ERROR_MESSAGE);
 	}
 
-//	private void createEMNetworkFrom(CyNetwork genemaniaNetwork) {
-//		
-//		
-//	}
-	
 	private boolean hasRequiredData(CyNetwork network) {
 		CyTable table = network.getDefaultNetworkTable();
 
@@ -100,8 +81,6 @@ private boolean hasRequiredData(CyNetwork network) {
 			List<GenemaniaAnnotation> fromJson = gson.fromJson(jsonString, listType);
 			if(fromJson == null || fromJson.isEmpty()) {
 				return false;
-			} else {
-				System.out.println("found it: " + fromJson.get(0));
 			}
 		} catch(JsonParseException e) {
 			return false;