Examples with GroupLayout javax.swing.GroupLayout used on opensource projects

Example 16 with GroupLayout

use of javax.swing.GroupLayout in project EnrichmentMapApp by BaderLab.

the class AddRanksDialog method createContents.

private void createContents() {
    JPanel textFieldPanel = createTextFieldPanel();
    JPanel buttonPanel = createButtonPanel();
    Container contentPane = this.getContentPane();
    GroupLayout layout = new GroupLayout(contentPane);
    contentPane.setLayout(layout);
    layout.setHorizontalGroup(layout.createParallelGroup().addComponent(textFieldPanel).addComponent(buttonPanel));
    layout.setVerticalGroup(layout.createSequentialGroup().addComponent(textFieldPanel).addGap(0, 0, Short.MAX_VALUE).addComponent(buttonPanel));
}

Example 17 with GroupLayout

use of javax.swing.GroupLayout in project EnrichmentMapApp by BaderLab.

the class ControlPanel method createContents.

@AfterInjection
private void createContents() {
    setMinimumSize(new Dimension(390, 400));
    setPreferredSize(new Dimension(390, 600));
    JButton helpButton = SwingUtil.createOnlineHelpButton(EnrichmentMapBuildProperties.USER_MANUAL_URL, "Online Manual...", serviceRegistrar);
    makeSmall(getAboutButton(), getClosePanelButton());
    final GroupLayout layout = new GroupLayout(this);
    setLayout(layout);
    layout.setAutoCreateContainerGaps(LookAndFeelUtil.isWinLAF());
    layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
    layout.setHorizontalGroup(layout.createParallelGroup(CENTER, true).addGroup(layout.createSequentialGroup().addComponent(getEmViewCombo(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addPreferredGap(ComponentPlacement.RELATED).addComponent(getCreateEmButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addPreferredGap(ComponentPlacement.RELATED).addComponent(getOptionsButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addComponent(getCtrlPanelsContainer(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addGroup(layout.createSequentialGroup().addComponent(helpButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getAboutButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addGap(0, 0, Short.MAX_VALUE).addComponent(getClosePanelButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)));
    layout.setVerticalGroup(layout.createSequentialGroup().addGroup(layout.createParallelGroup(CENTER, false).addComponent(getEmViewCombo(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getCreateEmButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getOptionsButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addComponent(getCtrlPanelsContainer(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addGroup(layout.createParallelGroup(CENTER, false).addComponent(helpButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getAboutButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getClosePanelButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)));
    if (LookAndFeelUtil.isAquaLAF())
        setOpaque(false);
}

Example 18 with GroupLayout

use of javax.swing.GroupLayout in project EnrichmentMapApp by BaderLab.

the class DataSetSelector method init.

private void init() {
    LookAndFeelUtil.equalizeSize(getAddButton(), getRemoveButton());
    LookAndFeelUtil.equalizeSize(getSelectAllButton(), getSelectNoneButton());
    final GroupLayout layout = new GroupLayout(this);
    setLayout(layout);
    layout.setAutoCreateContainerGaps(false);
    layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
    layout.setHorizontalGroup(layout.createParallelGroup(CENTER, true).addComponent(getTableScrollPane(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addGroup(layout.createSequentialGroup().addComponent(getAddButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getRemoveButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addGap(20, 20, Short.MAX_VALUE).addComponent(getSelectAllButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(getSelectNoneButton(), PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)));
    layout.setVerticalGroup(layout.createSequentialGroup().addComponent(getTableScrollPane(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addGroup(layout.createParallelGroup(CENTER, false).addComponent(getAddButton(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(getRemoveButton(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(getSelectAllButton(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(getSelectNoneButton(), DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE)));
    if (isAquaLAF())
        setOpaque(false);
}

Example 19 with GroupLayout

use of javax.swing.GroupLayout in project EnrichmentMapApp by BaderLab.

the class PostAnalysisKnownSignaturePanel method createKnownSignatureGMTPanel.

/**
	 * @return Panel for choosing and loading GMT and SignatureGMT Geneset-Files
	 */
private JPanel createKnownSignatureGMTPanel() {
    knownSignatureGMTFileNameTextField = new JFormattedTextField();
    knownSignatureGMTFileNameTextField.setColumns(15);
    knownSignatureGMTFileNameTextField.setToolTipText(Messages.GMT_INSTRUCTION);
    final Color textFieldForeground = knownSignatureGMTFileNameTextField.getForeground();
    knownSignatureGMTFileNameTextField.addPropertyChangeListener("value", new PropertyChangeListener() {

        @Override
        public void propertyChange(PropertyChangeEvent e) {
            // if the text is red set it back to black as soon as the user starts typing
            knownSignatureGMTFileNameTextField.setForeground(textFieldForeground);
        }
    });
    JButton selectSigGMTFileButton = new JButton("Browse...");
    selectSigGMTFileButton.setToolTipText(Messages.GMT_INSTRUCTION);
    selectSigGMTFileButton.setActionCommand("Known Signature");
    selectSigGMTFileButton.addActionListener(e -> {
        parentPanel.chooseGMTFile(knownSignatureGMTFileNameTextField);
    });
    makeSmall(knownSignatureGMTFileNameTextField, selectSigGMTFileButton);
    JPanel panel = new JPanel();
    panel.setBorder(LookAndFeelUtil.createTitledBorder("SigGMT File (contains signature-genesets)"));
    final GroupLayout layout = new GroupLayout(panel);
    panel.setLayout(layout);
    layout.setAutoCreateContainerGaps(true);
    layout.setAutoCreateGaps(!LookAndFeelUtil.isAquaLAF());
    layout.setHorizontalGroup(layout.createSequentialGroup().addComponent(knownSignatureGMTFileNameTextField, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(selectSigGMTFileButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE));
    layout.setVerticalGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(knownSignatureGMTFileNameTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(selectSigGMTFileButton));
    if (LookAndFeelUtil.isAquaLAF())
        panel.setOpaque(false);
    return panel;
}

Example 20 with GroupLayout

use of javax.swing.GroupLayout in project EnrichmentMapApp by BaderLab.

the class PostAnalysisSignatureDiscoveryPanel method createSignatureDiscoveryGMTPanel.

/**
     * @return Panel for choosing and loading GMT and SignatureGMT Geneset-Files 
     */
private JPanel createSignatureDiscoveryGMTPanel() {
    signatureDiscoveryGMTFileNameTextField = new JFormattedTextField();
    signatureDiscoveryGMTFileNameTextField.setColumns(15);
    signatureDiscoveryGMTFileNameTextField.setToolTipText(Messages.GMT_INSTRUCTION);
    final Color textFieldForeground = signatureDiscoveryGMTFileNameTextField.getForeground();
    signatureDiscoveryGMTFileNameTextField.addPropertyChangeListener("value", (PropertyChangeEvent e) -> {
        // if the text is red set it back to black as soon as the user starts typing
        signatureDiscoveryGMTFileNameTextField.setForeground(textFieldForeground);
    });
    JButton selectSigGMTFileButton = new JButton("Browse...");
    selectSigGMTFileButton.setToolTipText(Messages.GMT_INSTRUCTION);
    selectSigGMTFileButton.setActionCommand("Signature Discovery");
    selectSigGMTFileButton.addActionListener((ActionEvent evt) -> {
        parentPanel.chooseGMTFile(signatureDiscoveryGMTFileNameTextField);
    });
    JLabel filterLabel = new JLabel("Filter:");
    filterTextField = new JFormattedTextField();
    filterTextField.setColumns(4);
    filterTextField.setHorizontalAlignment(JTextField.RIGHT);
    filterTextField.addPropertyChangeListener("value", (PropertyChangeEvent e) -> {
        StringBuilder message = new StringBuilder("The value you have entered is invalid.\n");
        Number number = (Number) filterTextField.getValue();
        PostAnalysisFilterType filterType = getFilterType();
        Optional<Double> value = PostAnalysisInputPanel.validateAndGetFilterValue(number, filterType, message);
        savedFilterValues.put(filterType, value.orElse(filterType.defaultValue));
        if (!value.isPresent()) {
            filterTextField.setValue(filterType.defaultValue);
            JOptionPane.showMessageDialog(application.getJFrame(), message.toString(), "Parameter out of bounds", JOptionPane.WARNING_MESSAGE);
        }
    });
    // Types of filters:
    // 1. filter by percent, i.e. the overlap between the signature geneset and EM geneset
    //    has to be X percentage of the EM set it overlaps with for at least one geneset in the enrichment map.
    // 2. filter by number, i.e. the overlap between the signature geneset and EM geneset
    //    has to be X genes of the EM set it overlaps with for at least one geneset in the enrichment map.
    // 3. filter by specificity, i.e looking for the signature genesets that are more specific than other genesets
    //    for instance a drug A that targets only X and Y as opposed to drug B that targets X,y,L,M,N,O,P.
    filterTypeCombo = new JComboBox<>();
    // default
    filterTypeCombo.addItem(PostAnalysisFilterType.NO_FILTER);
    //		filterTypeCombo.addItem(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED);
    //		filterTypeCombo.addItem(PostAnalysisFilterType.MANN_WHIT_GREATER);
    //		filterTypeCombo.addItem(PostAnalysisFilterType.MANN_WHIT_LESS);
    filterTypeCombo.addItem(PostAnalysisFilterType.HYPERGEOM);
    filterTypeCombo.addItem(PostAnalysisFilterType.NUMBER);
    filterTypeCombo.addItem(PostAnalysisFilterType.PERCENT);
    filterTypeCombo.addItem(PostAnalysisFilterType.SPECIFIC);
    filterTypeCombo.addActionListener(e -> {
        updateFilterTextField();
    });
    updateFilterTextField();
    //TODO: Maybe move loading SigGMT to File-selection Event add load button
    JButton loadButton = new JButton();
    loadButton.setText("Load Gene Sets");
    loadButton.addActionListener(e -> {
        String filePath = (String) signatureDiscoveryGMTFileNameTextField.getValue();
        if (filePath == null || PostAnalysisInputPanel.checkFile(filePath).equals(Color.RED)) {
            String message = "Signature GMT file name not valid.\n";
            signatureDiscoveryGMTFileNameTextField.setForeground(Color.RED);
            JOptionPane.showMessageDialog(application.getJFrame(), message, "Post Analysis Known Signature", JOptionPane.WARNING_MESSAGE);
            return;
        }
        if (!EnrichmentMapParameters.checkFile(filePath)) {
            String message = "Signature GMT does not exist.\n";
            signatureDiscoveryGMTFileNameTextField.setForeground(Color.RED);
            JOptionPane.showMessageDialog(application.getJFrame(), message, "Post Analysis Known Signature", JOptionPane.WARNING_MESSAGE);
            return;
        }
        FilterMetric filterMetric = createFilterMetric();
        LoadSignatureSetsActionListener action = loadSignatureSetsActionListenerFactory.create(new File(filePath), filterMetric, parentPanel.getEnrichmentMap());
        action.setGeneSetCallback(gs -> {
            this.signatureGenesets = gs;
        });
        action.setFilteredSignatureSetsCallback(selected -> {
            availSigSetsModel.clear();
            selectedSigSetsModel.clear();
            for (String name : selected) availSigSetsModel.addElement(name);
            update();
        });
        action.actionPerformed(null);
    });
    makeSmall(signatureDiscoveryGMTFileNameTextField, selectSigGMTFileButton);
    makeSmall(filterLabel, filterTypeCombo, filterTextField);
    makeSmall(loadButton);
    JPanel panel = new JPanel();
    panel.setBorder(LookAndFeelUtil.createTitledBorder("SigGMT File (contains signature-genesets)"));
    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().addComponent(signatureDiscoveryGMTFileNameTextField, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(selectSigGMTFileButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addGroup(layout.createSequentialGroup().addComponent(filterLabel, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(filterTypeCombo, DEFAULT_SIZE, DEFAULT_SIZE, Short.MAX_VALUE).addComponent(filterTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addComponent(loadButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE));
    layout.setVerticalGroup(layout.createSequentialGroup().addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(signatureDiscoveryGMTFileNameTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(selectSigGMTFileButton)).addGroup(layout.createParallelGroup(Alignment.CENTER, false).addComponent(filterLabel, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(filterTypeCombo, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE).addComponent(filterTextField, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)).addComponent(loadButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE));
    if (LookAndFeelUtil.isAquaLAF())
        panel.setOpaque(false);
    return panel;
}