Add Reset button to mastermap dialog.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/actions/ShowEnrichmentMapDialogAction.java

@@ -7,7 +7,6 @@
 import org.baderlab.csplugins.enrichmentmap.view.mastermap.MasterMapDialogParameters;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialog;
 import org.cytoscape.application.swing.CySwingApplication;
-import org.cytoscape.util.swing.IconManager;
 
 import com.google.inject.Inject;
 import com.google.inject.Provider;
@@ -16,7 +15,6 @@
 public class ShowEnrichmentMapDialogAction extends AbstractAction {
 
 	@Inject private Provider<MasterMapDialogParameters> dialogParametersProvider;
-	@Inject private IconManager iconManager;
 	@Inject private CySwingApplication application;
 
 	private CardDialog masterMapDialog;
@@ -29,7 +27,7 @@ public ShowEnrichmentMapDialogAction() {
 	public void actionPerformed(ActionEvent e) {
 		if (masterMapDialog == null) {
 			MasterMapDialogParameters params = dialogParametersProvider.get();
-			masterMapDialog = new CardDialog(application.getJFrame(), iconManager, params);
+			masterMapDialog = new CardDialog(application.getJFrame(), params);
 		}
 
 		masterMapDialog.open();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/mastermap/CombinedConstantSlider.java

@@ -10,12 +10,14 @@
 public class CombinedConstantSlider extends JPanel {
 
 	private JSlider slider;
+	private final int defaultValue;
 
 	public CombinedConstantSlider(int defaultValue) {
 		if(defaultValue < 0)
 			defaultValue = 0;
 		if(defaultValue > 100)
 			defaultValue = 100;
+		this.defaultValue = defaultValue;
 
 		JLabel jaccardLabel = new JLabel(mkLabel("Jaccard", 100-defaultValue));
 		JLabel overlapLabel = new JLabel(mkLabel("Overlap", defaultValue));
@@ -46,6 +48,9 @@ public int getValue() {
 		return slider.getValue();
 	}
 
+	public void reset() {
+		slider.setValue(defaultValue);
+	}
 
 	private static String mkLabel(String name, int percent) {
 		return name + " (" + percent + "%)";

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

@@ -114,6 +114,7 @@ public void createContents() {
    		);
 	}
 
+	
 	private JPanel createFilterNodesPanel() {
 		JPanel panel = new JPanel();
 		panel.setBorder(LookAndFeelUtil.createTitledBorder("Gene-Set Filtering (Nodes)"));
@@ -294,6 +295,24 @@ private JPanel createFilterEdgesPanel() {
 	}
 
 
+	public void reset() {
+		pvalueText.setValue(propertyManager.getDefaultPvalue());
+		qvalueText.setValue(propertyManager.getDefaultQvalue());
+		nesFilterCombo.setSelectedItem(ComboItem.of(NESFilter.ALL));
+		shouldFilterMinCheckbox.setSelected(false);
+		minExperimentsText.setValue(3);
+		minExperimentsLabel.setEnabled(false);
+		minExperimentsText.setEnabled(false);
+		
+		cutoffValues = new EnumMap<>(SimilarityMetric.class);
+		cutoffValues.put(SimilarityMetric.JACCARD,  propertyManager.getDefaultCutOff(SimilarityMetric.JACCARD));
+		cutoffValues.put(SimilarityMetric.OVERLAP,  propertyManager.getDefaultCutOff(SimilarityMetric.OVERLAP));
+		cutoffValues.put(SimilarityMetric.COMBINED, propertyManager.getDefaultCutOff(SimilarityMetric.COMBINED));
+		cutoffMetricCombo.setSelectedItem(ComboItem.of(SimilarityMetric.JACCARD));
+		combinedConstantSlider.reset();
+	}
+	
+	
 	private void showAdvancedOptions(boolean show) {
 		pvalueLabel.setVisible(show);
 		pvalueText.setVisible(show);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/mastermap/EditCommonPanel.java

@@ -104,5 +104,10 @@ public String getGmtFile() {
 	public String getExpressionFile() {
 		return expressionsText.getText();
 	}
+
+	public void reset() {
+		gmtText.setText("");
+		expressionsText.setText("");
+	}
 
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/mastermap/MasterDetailDialogPage.java

@@ -21,6 +21,7 @@
 import javax.swing.JCheckBox;
 import javax.swing.JLabel;
 import javax.swing.JList;
+import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.ListCellRenderer;
@@ -236,9 +237,9 @@ private JPanel createTitlePanel() {
 		JLabel label = new JLabel("Data Sets:");
 		SwingUtil.makeSmall(label);
 
-		JButton addButton = SwingUtil.createIconButton(iconManager, IconManager.ICON_PLUS,     "Add Data Set");
+		JButton addButton = SwingUtil.createIconButton(iconManager, IconManager.ICON_PLUS, "Add Data Set");
 		scanButton = SwingUtil.createIconButton(iconManager, IconManager.ICON_FOLDER_O, "Scan Folder for Data Sets");
-		deleteButton = SwingUtil.createIconButton(iconManager, IconManager.ICON_TRASH_O,  "Delete Data Set");
+		deleteButton = SwingUtil.createIconButton(iconManager, IconManager.ICON_TRASH_O, "Delete Data Set");
 
 		addButton.addActionListener(e -> addNewDataSetToList());
 		deleteButton.addActionListener(e -> deleteSelectedItems());
@@ -307,6 +308,30 @@ private void updateButtonEnablement() {
 	}
 
 
+	@Override
+	public void extraButtonClicked(String actionCommand) {
+		if(MasterMapDialogParameters.RESET_BUTTON_ACTION_COMMAND.equals(actionCommand)) {
+			reset();
+		}
+	}
+	
+	private void reset() {
+		int result = JOptionPane.showConfirmDialog(callback.getDialogFrame(), 
+				"Clear inputs and restore default values?", "EnrichmentMap: Reset", JOptionPane.OK_CANCEL_OPTION);
+		if(result == JOptionPane.OK_OPTION) {
+			distinctEdgesCheckbox.setSelected(false);
+			cutoffPanel.reset();
+			commonPanel.reset();
+			for(DataSetListItem item : dataSetListModel.toList()) {
+				if(item != commonParams) {
+					dataSetListModel.removeElement(item);
+					dataSetDetailPanel.remove(item.getDetailPanel().getPanel());
+				}
+			}
+			callback.setFinishButtonEnabled(false);
+		}
+	}
+	
 	private void scan() {
 		Optional<File> rootFolder = FileBrowser.browseForRootFolder(callback.getDialogFrame());
 		if(rootFolder.isPresent()) {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/mastermap/MasterMapDialogParameters.java

@@ -6,8 +6,10 @@
 import java.util.Arrays;
 import java.util.List;
 
+import javax.swing.AbstractButton;
 import javax.swing.Icon;
 import javax.swing.ImageIcon;
+import javax.swing.JButton;
 
 import org.baderlab.csplugins.enrichmentmap.view.AboutDialog;
 import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogPage;
@@ -18,8 +20,11 @@
 
 public class MasterMapDialogParameters implements CardDialogParameters {
 
+	static final String RESET_BUTTON_ACTION_COMMAND = "reset";
+	
 	@Inject private Provider<MasterDetailDialogPage> masterDetailDialogPage;
 
+	
 	@Override
 	public List<CardDialogPage> getPages() {
 		return Arrays.asList(
@@ -54,4 +59,11 @@ public Icon getIcon() {
 		Image scaled = original.getImage().getScaledInstance(80, 49, Image.SCALE_SMOOTH);
 		return new ImageIcon(scaled);
 	}
+	
+	@Override
+	public AbstractButton[] getAdditionalButtons() {
+		JButton resetButton = new JButton("Reset");
+		resetButton.setActionCommand(RESET_BUTTON_ACTION_COMMAND);
+		return new JButton[] { resetButton };
+	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/util/CardDialog.java

@@ -5,10 +5,11 @@
 
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
-import java.awt.Color;
-import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
 import java.util.List;
 
+import javax.swing.AbstractAction;
+import javax.swing.AbstractButton;
 import javax.swing.BorderFactory;
 import javax.swing.GroupLayout;
 import javax.swing.GroupLayout.Alignment;
@@ -18,14 +19,13 @@
 import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.UIManager;
+import javax.swing.border.Border;
 
-import org.baderlab.csplugins.enrichmentmap.view.util.CardDialogCallback.Message;
-import org.cytoscape.util.swing.IconManager;
 import org.cytoscape.util.swing.LookAndFeelUtil;
 
 public class CardDialog {
 
-	private JPanel message;
 	private JDialog dialog;
 
 	private JComboBox<ComboItem<CardDialogPage>> pageChooserCombo;
@@ -34,17 +34,13 @@ public class CardDialog {
 	private JButton finishButton;
 
 	private final CardDialogParameters params;
-	private final IconManager iconManager;
 
 
-	public CardDialog(JFrame parent, IconManager iconManager, CardDialogParameters params) {
-		if (iconManager == null)
-			throw new IllegalArgumentException("'iconManager' must not be null.");
+	public CardDialog(JFrame parent, CardDialogParameters params) {
 		if (params == null)
 			throw new IllegalArgumentException("'params' must not be null.");
 
 		this.params = params;
-		this.iconManager = iconManager;
 
 		dialog = new JDialog(parent);
 		createComponents();
@@ -66,12 +62,14 @@ private void createComponents() {
 		dialog.setPreferredSize(params.getPreferredSize());
 		dialog.setTitle(params.getTitle());
 
-		// Create message and button panel first because 
-		// the controller can call callbacks from inside createBodyPanel()
-		JPanel buttonPanel  = createButtonPanel();
-		JPanel bodyPanel    = createBodyPanel();
+		// Create message and button panel first because the controller can call callbacks from inside createBodyPanel()
+		JPanel buttonPanel = createButtonPanel();
+		JPanel bodyPanel   = createBodyPanel();
 
-	    buttonPanel .setBorder(BorderFactory.createMatteBorder(1, 0, 0, 0, Color.LIGHT_GRAY));
+		Border padding   = BorderFactory.createEmptyBorder(5,5,5,5);
+		Border separator = BorderFactory.createMatteBorder(1,0,0,0,UIManager.getColor("Separator.foreground"));
+		Border border    = BorderFactory.createCompoundBorder(separator, padding);
+	    buttonPanel.setBorder(border);
 
 	    dialog.add(bodyPanel,    BorderLayout.CENTER);
 	    dialog.add(buttonPanel,  BorderLayout.SOUTH);
@@ -162,74 +160,37 @@ private JPanel createChooserPanel(List<CardDialogPage> pages) {
    		return panel;
 	}
 
-	
-	private JPanel createMessage(Message severity, String message) {
-		JPanel panel = new JPanel(new BorderLayout());
-		panel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 0));
-		JLabel icon = getMessageIcon(severity);
-		JLabel messageLabel = new JLabel(message + "  ");
-		panel.add(icon, BorderLayout.WEST);
-		panel.add(messageLabel, BorderLayout.CENTER);
-		panel.setOpaque(false);
-		return panel;
-	}
-	
-	private JLabel getMessageIcon(Message severity) {
-		JLabel icon = new JLabel();
-		switch(severity) {
-			default:
-			case INFO:  
-				icon.setText("");
-				break;
-			case WARN:
-				icon.setText(IconManager.ICON_EXCLAMATION_CIRCLE);
-				icon.setForeground(Color.YELLOW.darker());
-				break;
-			case ERROR:
-				icon.setText(IconManager.ICON_TIMES_CIRCLE);
-				icon.setForeground(Color.RED.darker());
-				break;
-		}
-		
-		icon.setFont(iconManager.getIconFont(16));
-		icon.setBorder(BorderFactory.createEmptyBorder(3,3,3,3));
-		icon.setOpaque(false);
-		return icon;
-	}
-	
+	@SuppressWarnings("serial")
 	private JPanel createButtonPanel() {
-		JPanel panel = new JPanel(new BorderLayout());
-		
-		JPanel buttonPanel = new JPanel(new FlowLayout(FlowLayout.TRAILING));
-		
-		JButton cancelButton = new JButton("Cancel");
-		buttonPanel.add(cancelButton);
-		cancelButton.addActionListener(e -> dialog.setVisible(false));
-		
-		finishButton = new JButton(params.getFinishButtonText());
-		buttonPanel.add(finishButton);
-		finishButton.addActionListener(e -> currentPage.finish());
-		
-		message = new JPanel(new BorderLayout());
-		message.setOpaque(false);
-		
-		panel.add(buttonPanel, BorderLayout.EAST);
-		panel.add(message, BorderLayout.WEST);
+		finishButton = new JButton(new AbstractAction(params.getFinishButtonText()) {
+			public void actionPerformed(ActionEvent e) {
+				currentPage.finish();
+			}
+		});
+		JButton cancelButton = new JButton(new AbstractAction("Cancel") {
+			public void actionPerformed(ActionEvent e) {
+				dialog.setVisible(false);
+			}
+		});
+
+		AbstractButton[] additional = params.getAdditionalButtons();
+		if(additional != null) {
+			for(AbstractButton button : additional) {
+				button.addActionListener(e -> {
+					currentPage.extraButtonClicked(e.getActionCommand());
+				});
+			}
+		}
 
-		return panel;
+		JPanel buttonPanel = LookAndFeelUtil.createOkCancelPanel(finishButton, cancelButton, additional);
+		LookAndFeelUtil.setDefaultOkCancelKeyStrokes(dialog.getRootPane(), finishButton.getAction(), cancelButton.getAction());
+		dialog.getRootPane().setDefaultButton(finishButton);
+		return buttonPanel;
 	}
 
 
 	public class Callback implements CardDialogCallback {
 
-		@Override
-		public void setMessage(Message severity, String text) {
-			JPanel messageContent = createMessage(severity, text);
-			message.removeAll();
-			message.add(messageContent, BorderLayout.CENTER);
-			dialog.revalidate();
-		}
-
 		@Override
 		public void setFinishButtonEnabled(boolean enabled) {
 			finishButton.setEnabled(enabled);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/util/CardDialogCallback.java

@@ -4,20 +4,6 @@
 
 public interface CardDialogCallback {
 
-	public static enum Message {
-		INFO, WARN, ERROR
-	}
-	
-	void setMessage(Message severity, String message);
-	
-	default void clearMessage() {
-		setMessage(Message.INFO, "");
-	}
-	
-	default void setMessage(String message) {
-		setMessage(Message.INFO, message);
-	}
-	
 	void setFinishButtonEnabled(boolean enabled);
 
 	JDialog getDialogFrame();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/util/CardDialogPage.java

@@ -1,5 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.view.util;
 
+import javax.swing.AbstractButton;
 import javax.swing.JPanel;
 
 public interface CardDialogPage {
@@ -16,4 +17,11 @@ default String getPageComboText() {
 
 	void finish();
 
+	/**
+	 * Called when one of the buttons returned by 
+	 * {@link CardDialogParameters#getAdditionalButtons()} is clicked.
+	 * 
+	 * @see AbstractButton#setActionCommand(String)
+	 */
+	default void extraButtonClicked(String actionCommand) { }
 }