Examples with CySwingApplication org.cytoscape.application.swing.CySwingApplication used on opensource projects

Example 1 with CySwingApplication

use of org.cytoscape.application.swing.CySwingApplication in project EnrichmentMapApp by BaderLab.

the class PostAnalysisWeightPanel method createHypergeomPanel.

private JPanel createHypergeomPanel() {
    ActionListener universeSelectActionListener = e -> {
        boolean enable = e.getActionCommand().equals("User Defined");
        universeSelectionTextField.setEnabled(enable);
    };
    gmtRadioButton = new JRadioButton();
    gmtRadioButton.setActionCommand("GMT");
    gmtRadioButton.addActionListener(universeSelectActionListener);
    gmtRadioButton.setSelected(true);
    expressionSetRadioButton = new JRadioButton();
    expressionSetRadioButton.setActionCommand("Expression Set");
    expressionSetRadioButton.addActionListener(universeSelectActionListener);
    intersectionRadioButton = new JRadioButton();
    intersectionRadioButton.setActionCommand("Intersection");
    intersectionRadioButton.addActionListener(universeSelectActionListener);
    userDefinedRadioButton = new JRadioButton("User Defined:");
    userDefinedRadioButton.setActionCommand("User Defined");
    userDefinedRadioButton.addActionListener(universeSelectActionListener);
    ButtonGroup buttonGroup = new ButtonGroup();
    buttonGroup.add(gmtRadioButton);
    buttonGroup.add(expressionSetRadioButton);
    buttonGroup.add(intersectionRadioButton);
    buttonGroup.add(userDefinedRadioButton);
    DecimalFormat intFormat = new DecimalFormat();
    intFormat.setParseIntegerOnly(true);
    universeSelectionTextField = new JFormattedTextField(intFormat);
    universeSelectionTextField.addPropertyChangeListener("value", e -> {
        Number val = (Number) universeSelectionTextField.getValue();
        if (val == null || val.intValue() < 0) {
            universeSelectionTextField.setValue(1);
            CySwingApplication application = serviceRegistrar.getService(CySwingApplication.class);
            JOptionPane.showMessageDialog(application.getJFrame(), "Universe value must be greater than zero", "Parameter out of bounds", JOptionPane.WARNING_MESSAGE);
        }
    });
    universeSelectionTextField.setEnabled(false);
    gmtRadioButton.setText("GMT");
    expressionSetRadioButton.setText("Expression Set");
    intersectionRadioButton.setText("Intersection");
    universeSelectionTextField.setValue(0);
    makeSmall(gmtRadioButton, expressionSetRadioButton, intersectionRadioButton, userDefinedRadioButton, universeSelectionTextField);
    JPanel panel = new JPanel();
    panel.setBorder(LookAndFeelUtil.createTitledBorder("Advanced Hypergeometric Universe"));
    final GroupLayout layout = new GroupLayout(panel);
    panel.setLayout(layout);
    layout.setAutoCreateContainerGaps(true);
    layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
    layout.setHorizontalGroup(layout.createParallelGroup(Alignment.LEADING, true).addComponent(gmtRadioButton).addComponent(expressionSetRadioButton).addComponent(intersectionRadioButton).addGroup(layout.createSequentialGroup().addComponent(userDefinedRadioButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addPreferredGap(ComponentPlacement.RELATED).addComponent(universeSelectionTextField, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)));
    layout.setVerticalGroup(layout.createSequentialGroup().addComponent(gmtRadioButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(expressionSetRadioButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(intersectionRadioButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(userDefinedRadioButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(universeSelectionTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)));
    if (LookAndFeelUtil.isAquaLAF())
        panel.setOpaque(false);
    return panel;
}

Example 2 with CySwingApplication

use of org.cytoscape.application.swing.CySwingApplication in project EnrichmentMapApp by BaderLab.

the class PostAnalysisWeightPanel method createRankTestSelectPanel.

@SuppressWarnings("unchecked")
private JPanel createRankTestSelectPanel() {
    JLabel testLabel = new JLabel(LABEL_TEST);
    JLabel cuttofLabel = new JLabel(LABEL_CUTOFF);
    JLabel dataSetLabel = new JLabel("Data Set:");
    DecimalFormat decFormat = new DecimalFormat();
    decFormat.setParseIntegerOnly(false);
    rankTestTextField = new JFormattedTextField(decFormat);
    rankTestTextField.setColumns(6);
    rankTestTextField.setHorizontalAlignment(JTextField.RIGHT);
    rankTestTextField.addPropertyChangeListener("value", e -> {
        StringBuilder message = new StringBuilder("The value you have entered is invalid.\n");
        Number number = (Number) rankTestTextField.getValue();
        PostAnalysisFilterType filterType = getFilterType();
        Optional<Double> value = PostAnalysisInputPanel.validateAndGetFilterValue(number, filterType, message);
        double def = filterType == PostAnalysisFilterType.HYPERGEOM ? HYPERGOM_DEFAULT : filterType.defaultValue;
        savedFilterValues.put(filterType, value.orElse(def));
        if (!value.isPresent()) {
            rankTestTextField.setValue(def);
            CySwingApplication application = serviceRegistrar.getService(CySwingApplication.class);
            JOptionPane.showMessageDialog(application.getJFrame(), message.toString(), "Parameter out of bounds", JOptionPane.WARNING_MESSAGE);
        }
    });
    rankingEnablementRenderer = new EnablementComboBoxRenderer<>();
    rankTestCombo = new JComboBox<>();
    rankTestCombo.setRenderer(rankingEnablementRenderer);
    rankTestCombo.addItem(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED);
    rankTestCombo.addItem(PostAnalysisFilterType.MANN_WHIT_GREATER);
    rankTestCombo.addItem(PostAnalysisFilterType.MANN_WHIT_LESS);
    rankTestCombo.addItem(PostAnalysisFilterType.HYPERGEOM);
    rankTestCombo.addItem(PostAnalysisFilterType.NUMBER);
    rankTestCombo.addItem(PostAnalysisFilterType.PERCENT);
    rankTestCombo.addItem(PostAnalysisFilterType.SPECIFIC);
    rankTestCombo.addActionListener(e -> {
        PostAnalysisFilterType filterType = (PostAnalysisFilterType) rankTestCombo.getSelectedItem();
        rankTestTextField.setValue(savedFilterValues.get(filterType));
        CardLayout cardLayout = (CardLayout) cardPanel.getLayout();
        if (filterType.isMannWhitney() && map.getAllRanks().isEmpty())
            cardLayout.show(cardPanel, "warn");
        else
            cardLayout.show(cardPanel, filterType.name());
    });
    datasetCombo = new JComboBox<>();
    // Dataset model is already initialized
    datasetModel = new DefaultComboBoxModel<>();
    datasetCombo.setModel(datasetModel);
    datasetCombo.addActionListener(e -> {
        updateUniverseSize(getDataSet());
    });
    makeSmall(testLabel, cuttofLabel, rankTestCombo, rankTestTextField);
    makeSmall(dataSetLabel, datasetCombo);
    JPanel panel = new JPanel();
    final GroupLayout layout = new GroupLayout(panel);
    panel.setLayout(layout);
    layout.setAutoCreateContainerGaps(true);
    layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
    layout.setHorizontalGroup(layout.createParallelGroup(Alignment.CENTER, true).addGroup(layout.createSequentialGroup().addGroup(layout.createParallelGroup(Alignment.TRAILING, true).addComponent(testLabel).addComponent(cuttofLabel).addComponent(dataSetLabel)).addGroup(layout.createParallelGroup(Alignment.LEADING, true).addComponent(rankTestCombo, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(rankTestTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(datasetCombo, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE))));
    layout.setVerticalGroup(layout.createSequentialGroup().addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(testLabel).addComponent(rankTestCombo, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(cuttofLabel).addComponent(rankTestTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addPreferredGap(ComponentPlacement.UNRELATED).addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(dataSetLabel).addComponent(datasetCombo, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)));
    if (LookAndFeelUtil.isAquaLAF())
        panel.setOpaque(false);
    return panel;
}