EnzymeSelectionDialog.java

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

import com.compomics.util.experiment.biology.Enzyme;
import com.compomics.util.experiment.biology.EnzymeFactory;
import java.awt.Dialog;
import java.util.ArrayList;
import java.util.Collections;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JDialog;
import javax.swing.SwingConstants;

/**
 * Simple dialog for mapping a PRIDE enzyme to a utilities enzyme.
 *
 * @author Harald Barsnes
 */
public class EnzymeSelectionDialog extends javax.swing.JDialog {

    /**
     * The enzyme factory.
     */
    private EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
    /**
     * True of the enzyme selection was canceled by the user.
     */
    private boolean selectionCanceled = false;
    /**
     * Boolean indicating whether the settings can be edited by the user.
     */
    private boolean editable;

    /**
     * Creates a new EnzymeSelectionDialog with a frame as owner.
     *
     * @param parent the parent frame
     * @param modal if the dialog is to be modal or not
     * @param enzymeName the PRIDE enzyme name
     * @param editable boolean indicating whether the settings can be edited by
     * the user
     */
    public EnzymeSelectionDialog(java.awt.Frame parent, boolean modal, String enzymeName, boolean editable) {
        super(parent, modal);
        initComponents();
        prideEnzymeNameTextField.setText(enzymeName);
        enzymesCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
        this.editable = editable;
        setLocationRelativeTo(parent);
        setVisible(true);
    }

    /**
     * Creates a new EnzymeSelectionDialog with a dialog as owner.
     *
     * @param owner the dialog owner
     * @param parent the parent frame
     * @param modal if the dialog is to be modal or not
     * @param enzymeName the PRIDE enzyme name
     * @param editable boolean indicating whether the settings can be edited by
     * the user
     */
    public EnzymeSelectionDialog(Dialog owner, java.awt.Frame parent, boolean modal, String enzymeName, boolean editable) {
        super(owner, modal);
        initComponents();
        prideEnzymeNameTextField.setText(enzymeName);
        enzymesCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));
        this.editable = editable;
        setLocationRelativeTo(owner);
        setVisible(true);
    }

    /**
     * Creates a new EnzymeSelectionDialog.
     *
     * @param parent the parent dialog
     * @param modal if the dialog is to be modal or not
     * @param enzymeName the PRIDE enzyme name
     */
    public EnzymeSelectionDialog(JDialog parent, boolean modal, String enzymeName) {
        super(parent, modal);
        initComponents();
        setUpGui();
        populateGui(enzymeName);
        setLocationRelativeTo(parent);
        setVisible(true);
    }

    /**
     * Sets up the GUI.
     */
    private void setUpGui() {

        enzymesCmb.setRenderer(new com.compomics.util.gui.renderers.AlignedListCellRenderer(SwingConstants.CENTER));

        enzymesCmb.setEnabled(editable);

    }

    /**
     * Populates the gui using the given annotation settings.
     *
     * @param annotationSettings the annotation settings to display
     * @param possibleNeutralLosses the possible neutral losses
     */
    private void populateGui(String enzymeName) {
        prideEnzymeNameTextField.setText(enzymeName);
    }

    /**
     * Returns the selected enzyme.
     *
     * @return the selected enzyme
     */
    public Enzyme getEnzyme() {
        if (!selectionCanceled) {
            return enzymeFactory.getEnzyme(enzymesCmb.getSelectedItem().toString());
        } else {
            return null;
        }
    }

    /**
     * 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();
        mappingPanel = new javax.swing.JPanel();
        enzymesCmb = new javax.swing.JComboBox();
        enzymeLabel = new javax.swing.JLabel();
        prideEnzymeNameLabel = new javax.swing.JLabel();
        prideEnzymeNameTextField = new javax.swing.JTextField();
        okButton = new javax.swing.JButton();
        cancelButton = new javax.swing.JButton();

        setDefaultCloseOperation(javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE);
        setTitle("Enzyme");
        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));

        mappingPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Enzyme Selection"));
        mappingPanel.setOpaque(false);

        enzymesCmb.setModel(new DefaultComboBoxModel(loadEnzymes()));
        enzymesCmb.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                enzymesCmbActionPerformed(evt);
            }
        });

        enzymeLabel.setText("Enzyme");

        prideEnzymeNameLabel.setText("PRIDE");

        prideEnzymeNameTextField.setEditable(false);
        prideEnzymeNameTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);

        javax.swing.GroupLayout mappingPanelLayout = new javax.swing.GroupLayout(mappingPanel);
        mappingPanel.setLayout(mappingPanelLayout);
        mappingPanelLayout.setHorizontalGroup(
            mappingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(mappingPanelLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(mappingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(enzymeLabel)
                    .addComponent(prideEnzymeNameLabel))
                .addGap(18, 18, 18)
                .addGroup(mappingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(enzymesCmb, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                    .addComponent(prideEnzymeNameTextField))
                .addContainerGap())
        );
        mappingPanelLayout.setVerticalGroup(
            mappingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(mappingPanelLayout.createSequentialGroup()
                .addContainerGap()
                .addGroup(mappingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(prideEnzymeNameLabel)
                    .addComponent(prideEnzymeNameTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(mappingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(enzymeLabel)
                    .addComponent(enzymesCmb, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        okButton.setText("OK");
        okButton.setEnabled(false);
        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(javax.swing.GroupLayout.Alignment.TRAILING, backgroundPanelLayout.createSequentialGroup()
                .addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                    .addGroup(backgroundPanelLayout.createSequentialGroup()
                        .addContainerGap()
                        .addComponent(mappingPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                    .addGroup(backgroundPanelLayout.createSequentialGroup()
                        .addGap(0, 380, Short.MAX_VALUE)
                        .addComponent(okButton)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                        .addComponent(cancelButton)))
                .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(mappingPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(okButton)
                    .addComponent(cancelButton))
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        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.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
        );

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

    /**
     * Close the dialog.
     *
     * @param evt
     */
    private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_okButtonActionPerformed
        dispose();
        setVisible(false);
    }//GEN-LAST:event_okButtonActionPerformed

    /**
     * Close the dialog.
     *
     * @param evt
     */
    private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
        selectionCanceled = true;
        okButtonActionPerformed(null);
    }//GEN-LAST:event_cancelButtonActionPerformed

    private void formWindowClosing(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_formWindowClosing
        cancelButtonActionPerformed(null);
    }//GEN-LAST:event_formWindowClosing

    /**
     * Enable/disable the OK button.
     *
     * @param evt
     */
    private void enzymesCmbActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_enzymesCmbActionPerformed
        okButton.setEnabled(enzymesCmb.getSelectedIndex() > 0);
    }//GEN-LAST:event_enzymesCmbActionPerformed
    // Variables declaration - do not modify//GEN-BEGIN:variables
    private javax.swing.JPanel backgroundPanel;
    private javax.swing.JButton cancelButton;
    private javax.swing.JLabel enzymeLabel;
    private javax.swing.JComboBox enzymesCmb;
    private javax.swing.JPanel mappingPanel;
    private javax.swing.JButton okButton;
    private javax.swing.JLabel prideEnzymeNameLabel;
    private javax.swing.JTextField prideEnzymeNameTextField;
    // End of variables declaration//GEN-END:variables

    /**
     * Loads the implemented enzymes.
     *
     * @return the list of enzyme names
     */
    private String[] loadEnzymes() {

        ArrayList<String> tempEnzymes = new ArrayList<String>();

        for (int i = 0; i < enzymeFactory.getEnzymes().size(); i++) {
            tempEnzymes.add(enzymeFactory.getEnzymes().get(i).getName());
        }

        Collections.sort(tempEnzymes);

        String[] enzymes = new String[tempEnzymes.size() + 1];

        enzymes[0] = "--- Select ---";

        for (int i = 0; i < tempEnzymes.size(); i++) {
            enzymes[i + 1] = tempEnzymes.get(i);
        }

        return enzymes;
    }
}