PepNovoSettingsDialog.java

package com.compomics.util.gui.parameters.identification_parameters.algorithm_settings;

import com.compomics.util.examples.BareBonesBrowserLaunch;
import com.compomics.util.experiment.identification.identification_parameters.IdentificationAlgorithmParameter;
import com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters;
import com.compomics.util.gui.parameters.identification_parameters.AlgorithmSettingsDialog;
import java.awt.Dialog;
import javax.swing.SwingConstants;

/**
 * Dialog for editing the PepNovo advanced settings.
 *
 * @author Harald Barsnes
 */
public class PepNovoSettingsDialog extends javax.swing.JDialog implements AlgorithmSettingsDialog {

    /**
     * True if the dialog was canceled by the user.
     */
    private boolean canceled = false;
    /**
     * Boolean indicating whether the settings can be edited by the user.
     */
    private boolean editable;

    /**
     * Creates a new PepNovoSettingsDialog with a frame as owner.
     *
     * @param parent the parent frame
     * @param pepNovoParameters the PepNovo parameters
     * @param editable boolean indicating whether the settings can be edited by
     * the user
     */
    public PepNovoSettingsDialog(java.awt.Frame parent, PepnovoParameters pepNovoParameters, boolean editable) {
        super(parent, true);
        this.editable = editable;
        initComponents();
        setUpGUI();
        populateGUI(pepNovoParameters);
        setLocationRelativeTo(parent);
        setVisible(true);
    }

    /**
     * Creates a new PepNovoSettingsDialog with a dialog as owner.
     *
     * @param owner the dialog owner
     * @param parent the parent frame
     * @param pepnovoParameters the PepNovo parameters
     * @param editable boolean indicating whether the settings can be edited by
     * the user
     */
    public PepNovoSettingsDialog(Dialog owner, java.awt.Frame parent, PepnovoParameters pepnovoParameters, boolean editable) {
        super(owner, true);
        this.editable = editable;
        initComponents();
        setUpGUI();
        populateGUI(pepnovoParameters);
        setLocationRelativeTo(owner);
        setVisible(true);
    }

    /**
     * Sets up the GUI.
     */
    private void setUpGUI() {
        correctPrecursorMassCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
        estimateChargeCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
    }

    /**
     * Populates the GUI using the given settings.
     *
     * @param pepnovoParameters the PepNovo parameters
     */
    private void populateGUI(PepnovoParameters pepnovoParameters) {

        hitListLengthSpinner.setValue(pepnovoParameters.getHitListLength());
        if (pepnovoParameters.isCorrectPrecursorMass()) {
            correctPrecursorMassCmb.setSelectedIndex(1);
        } else {
            correctPrecursorMassCmb.setSelectedIndex(0);
        }
        if (pepnovoParameters.isEstimateCharge()) {
            estimateChargeCmb.setSelectedIndex(1);
        } else {
            estimateChargeCmb.setSelectedIndex(0);
        }
    }

    /**
     * This method is called from within the constructor to initialize the form.
     * WARNING: Do NOT modify this code. The content of this method is always
     * regenerated by the Form Editor.
     */
    @SuppressWarnings("unchecked")
    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
    private void initComponents() {

        backgroundPanel = new javax.swing.JPanel();
        pepNovoPanel = new javax.swing.JPanel();
        hitListLengthLabel = new javax.swing.JLabel();
        hitListLengthSpinner = new javax.swing.JSpinner();
        correctPrecursorMassLabel = new javax.swing.JLabel();
        correctPrecursorMassCmb = new javax.swing.JComboBox();
        estimateChargeLabel = new javax.swing.JLabel();
        estimateChargeCmb = new javax.swing.JComboBox();
        openDialogHelpJButton = new javax.swing.JButton();
        okButton = new javax.swing.JButton();
        cancelButton = new javax.swing.JButton();

        setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
        setTitle("PepNovo+ Advanced Settings");
        addWindowListener(new java.awt.event.WindowAdapter() {
            public void windowClosing(java.awt.event.WindowEvent evt) {
                formWindowClosing(evt);
            }
        });

        backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));

        pepNovoPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("PepNovo+ Settings"));
        pepNovoPanel.setOpaque(false);

        hitListLengthLabel.setText("Hit List Length");

        hitListLengthSpinner.setModel(new javax.swing.SpinnerNumberModel(10, 1, 2000, 1));

        correctPrecursorMassLabel.setText("Correct Precursor Mass");

        correctPrecursorMassCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));

        estimateChargeLabel.setText("Estimate Charge");

        estimateChargeCmb.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Yes", "No" }));

        javax.swing.GroupLayout pepNovoPanelLayout = new javax.swing.GroupLayout(pepNovoPanel);
        pepNovoPanel.setLayout(pepNovoPanelLayout);
        pepNovoPanelLayout.setHorizontalGroup(
            pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(pepNovoPanelLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(pepNovoPanelLayout.createSequentialGroup()
                        .addGroup(pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(correctPrecursorMassLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addComponent(estimateChargeLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE))
                        .addGap(18, 18, 18)
                        .addGroup(pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(estimateChargeCmb, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addComponent(correctPrecursorMassCmb, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
                    .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, pepNovoPanelLayout.createSequentialGroup()
                        .addComponent(hitListLengthLabel, javax.swing.GroupLayout.PREFERRED_SIZE, 180, javax.swing.GroupLayout.PREFERRED_SIZE)
                        .addGap(18, 18, 18)
                        .addComponent(hitListLengthSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );
        pepNovoPanelLayout.setVerticalGroup(
            pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(pepNovoPanelLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(hitListLengthSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(hitListLengthLabel))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(correctPrecursorMassCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(correctPrecursorMassLabel))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(pepNovoPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(estimateChargeCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(estimateChargeLabel))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        openDialogHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help.GIF"))); // NOI18N
        openDialogHelpJButton.setToolTipText("Open the PepNovo+ web page");
        openDialogHelpJButton.setBorder(null);
        openDialogHelpJButton.setBorderPainted(false);
        openDialogHelpJButton.setContentAreaFilled(false);
        openDialogHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
            public void mouseEntered(java.awt.event.MouseEvent evt) {
                openDialogHelpJButtonMouseEntered(evt);
            }
            public void mouseExited(java.awt.event.MouseEvent evt) {
                openDialogHelpJButtonMouseExited(evt);
            }
        });
        openDialogHelpJButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                openDialogHelpJButtonActionPerformed(evt);
            }
        });

        okButton.setText("OK");
        okButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                okButtonActionPerformed(evt);
            }
        });

        cancelButton.setText("Cancel");
        cancelButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                cancelButtonActionPerformed(evt);
            }
        });

        javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
        backgroundPanel.setLayout(backgroundPanelLayout);
        backgroundPanelLayout.setHorizontalGroup(
            backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(backgroundPanelLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(backgroundPanelLayout.createSequentialGroup()
                        .addGap(10, 10, 10)
                        .addComponent(openDialogHelpJButton)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                        .addComponent(okButton)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(cancelButton))
                    .addComponent(pepNovoPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                .addContainerGap())
        );

        backgroundPanelLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {cancelButton, okButton});

        backgroundPanelLayout.setVerticalGroup(
            backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(backgroundPanelLayout.createSequentialGroup()
                .addContainerGap()
                .addComponent(pepNovoPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                    .addComponent(openDialogHelpJButton)
                    .addComponent(okButton)
                    .addComponent(cancelButton))
                .addContainerGap())
        );

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
        getContentPane().setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addComponent(backgroundPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addComponent(backgroundPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
        );

        pack();
    }// </editor-fold>//GEN-END:initComponents

    /**
     * Save the settings and close the dialog.
     *
     * @param evt
     */
    private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
        boolean valid = validateParametersInput(true);
        if (valid) {
            dispose();
        }
    }//GEN-LAST:event_okButtonActionPerformed

    /**
     * Close the dialog without saving the settings.
     *
     * @param evt
     */
    private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
        canceled = true;
        dispose();
    }//GEN-LAST:event_cancelButtonActionPerformed

    /**
     * Change the cursor into a hand cursor.
     *
     * @param evt
     */
    private void openDialogHelpJButtonMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonMouseEntered
        setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
    }//GEN-LAST:event_openDialogHelpJButtonMouseEntered

    /**
     * Change the cursor back to the default cursor.
     *
     * @param evt
     */
    private void openDialogHelpJButtonMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonMouseExited
        setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
    }//GEN-LAST:event_openDialogHelpJButtonMouseExited

    /**
     * Open the PepNovo+ web page.
     *
     * @param evt
     */
    private void openDialogHelpJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_openDialogHelpJButtonActionPerformed
        setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
        BareBonesBrowserLaunch.openURL("http://proteomics.ucsd.edu/Software/PepNovo/");
        setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
    }//GEN-LAST:event_openDialogHelpJButtonActionPerformed

    /**
     * Close the dialog without saving the settings.
     *
     * @param evt
     */
    private void formWindowClosing(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_formWindowClosing
        cancelButtonActionPerformed(null);
    }//GEN-LAST:event_formWindowClosing

    // Variables declaration - do not modify//GEN-BEGIN:variables
    private javax.swing.JPanel backgroundPanel;
    private javax.swing.JButton cancelButton;
    private javax.swing.JComboBox correctPrecursorMassCmb;
    private javax.swing.JLabel correctPrecursorMassLabel;
    private javax.swing.JComboBox estimateChargeCmb;
    private javax.swing.JLabel estimateChargeLabel;
    private javax.swing.JLabel hitListLengthLabel;
    private javax.swing.JSpinner hitListLengthSpinner;
    private javax.swing.JButton okButton;
    private javax.swing.JButton openDialogHelpJButton;
    private javax.swing.JPanel pepNovoPanel;
    // End of variables declaration//GEN-END:variables

    /**
     * Inspects the parameters validity.
     *
     * @param showMessage if true an error messages are shown to the users
     * @return a boolean indicating if the parameters are valid
     */
    public boolean validateParametersInput(boolean showMessage) {
        boolean valid = true;
        okButton.setEnabled(valid);
        return valid;
    }

    /**
     * Returns the PepNovo+ parameters as set by the user.
     *
     * @return the PepNovo+ parameters
     */
    public PepnovoParameters getInput() {

        PepnovoParameters pepNovoParameters = new PepnovoParameters();
        pepNovoParameters.setHitListLength((Integer) hitListLengthSpinner.getValue());
        pepNovoParameters.setCorrectPrecursorMass(correctPrecursorMassCmb.getSelectedIndex() == 1);
        pepNovoParameters.setEstimateCharge(estimateChargeCmb.getSelectedIndex() == 0);

        return pepNovoParameters;
    }

    @Override
    public boolean isCancelled() {
        return canceled;
    }

    @Override
    public IdentificationAlgorithmParameter getParameters() {
        return getInput();
    }
}