ImportFeaturesWindow.java

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */

/*
 * ImportFeaturesWindow.java
 *
 * Created on Jun 24, 2011, 3:22:40 PM
 */
package org.clothocad.tool.sequenceview;

import java.util.ArrayList;
import javax.swing.JProgressBar;
import javax.swing.SwingWorker;
import org.clothocore.api.core.Collector;
import org.clothocore.api.data.ObjLink;
import org.clothocore.api.data.ObjType;
import org.openide.util.Exceptions;

/**
 *
 * @author Henry
 */
public class ImportFeaturesWindow extends javax.swing.JFrame {

    /** Creates new form ImportFeaturesWindow */
    public ImportFeaturesWindow() {
        initComponents();
        this.setVisible(true);
    }

    public ImportFeaturesWindow(String type, String s, SequenceView sv, ArrayList<String> inputLines) {
        initComponents();
        _type = type;
        _sequence = s;
        parseTarget = inputLines;
        _sv = sv;
        ArrayList<ObjLink> collectionLinks = Collector.getAllLinksOf(ObjType.COLLECTION);
        collectionComboBox.removeAllItems();
        for (ObjLink oj : collectionLinks) {
            collectionComboBox.addItem(oj);
        }
        collectionComboBox.setSelectedIndex(-1);
        this.setSize(320, 180);
        this.setVisible(true);
    }

    /** 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() {

        collectionComboBox = new javax.swing.JComboBox();
        yesButton = new javax.swing.JButton();
        cancelButton = new javax.swing.JButton();
        jLabel1 = new javax.swing.JLabel();
        jLabel2 = new javax.swing.JLabel();
        statusLabel = new javax.swing.JLabel();

        setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
        setTitle(org.openide.util.NbBundle.getMessage(ImportFeaturesWindow.class, "ImportFeaturesWindow.title")); // NOI18N
        setAlwaysOnTop(true);
        setMinimumSize(new java.awt.Dimension(223, 135));

        collectionComboBox.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Item 1", "Item 2", "Item 3", "Item 4" }));

        yesButton.setText(org.openide.util.NbBundle.getMessage(ImportFeaturesWindow.class, "ImportFeaturesWindow.yesButton.text")); // NOI18N
        yesButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                yesButtonActionPerformed(evt);
            }
        });

        cancelButton.setText(org.openide.util.NbBundle.getMessage(ImportFeaturesWindow.class, "ImportFeaturesWindow.cancelButton.text")); // NOI18N
        cancelButton.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                cancelButtonActionPerformed(evt);
            }
        });

        jLabel1.setText(org.openide.util.NbBundle.getMessage(ImportFeaturesWindow.class, "ImportFeaturesWindow.jLabel1.text")); // NOI18N

        jLabel2.setText(org.openide.util.NbBundle.getMessage(ImportFeaturesWindow.class, "ImportFeaturesWindow.jLabel2.text")); // NOI18N

        statusLabel.setText(org.openide.util.NbBundle.getMessage(ImportFeaturesWindow.class, "ImportFeaturesWindow.statusLabel.text")); // NOI18N

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
        getContentPane().setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel1)
                    .addGroup(layout.createSequentialGroup()
                        .addComponent(jLabel2)
                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                        .addComponent(statusLabel, javax.swing.GroupLayout.DEFAULT_SIZE, 158, Short.MAX_VALUE))
                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
                        .addComponent(collectionComboBox, javax.swing.GroupLayout.Alignment.LEADING, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                        .addGroup(javax.swing.GroupLayout.Alignment.LEADING, layout.createSequentialGroup()
                            .addComponent(yesButton)
                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                            .addComponent(cancelButton))))
                .addContainerGap())
        );

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

        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addContainerGap()
                .addComponent(jLabel1)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addComponent(collectionComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(yesButton)
                    .addComponent(cancelButton))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addComponent(jLabel2)
                    .addComponent(statusLabel))
                .addContainerGap(31, Short.MAX_VALUE))
        );

        layout.linkSize(javax.swing.SwingConstants.VERTICAL, new java.awt.Component[] {cancelButton, yesButton});

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

    private void yesButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_yesButtonActionPerformed
        if (collectionComboBox.getSelectedIndex() != -1) {
            statusLabel.setText("Parsing for features. Please wait");
            this.repaint();
            try {
                boolean finished = false;
                if (_type.equals("genbank")) {
                    new SwingWorker() {

                        @Override
                        protected Object doInBackground() throws Exception {
                            _sv.parseForGenbankFeatures(_sequence, (ObjLink) collectionComboBox.getSelectedItem(), parseTarget);
                            return null;
                        }
                    }.execute();
                } else if (_type.equals("ApE")) {
                    new SwingWorker() {

                        @Override
                        protected Object doInBackground() throws Exception {
                            _sv.parseForApEFeatures((ObjLink) collectionComboBox.getSelectedItem(), parseTarget);
                            return null;
                        }
                    }.execute();
                }

                    javax.swing.JOptionPane.showMessageDialog(null, "Adding new Clotho Features into " + ((ObjLink) collectionComboBox.getSelectedItem()).name+" in the background.");
                    this.dispose();
                    
            } catch (Exception ex) {
                javax.swing.JOptionPane.showMessageDialog(null, "Error parsing for genbank features. Please check that valid genbank file was used");
                Exceptions.printStackTrace(ex);
            }
        } else {
            statusLabel.setText("Collection not selected.  Please select a Collection \nto save new Features into");
            return;
        }

    }//GEN-LAST:event_yesButtonActionPerformed

    private void cancelButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_cancelButtonActionPerformed
        this.dispose();
    }//GEN-LAST:event_cancelButtonActionPerformed

    /**
     * @param args the command line arguments
     */
    public static void main(String args[]) {
        java.awt.EventQueue.invokeLater(new Runnable() {

            public void run() {
                new ImportFeaturesWindow().setVisible(true);
            }
        });
    }
    // Variables declaration - do not modify//GEN-BEGIN:variables
    private javax.swing.JButton cancelButton;
    private javax.swing.JComboBox collectionComboBox;
    private javax.swing.JLabel jLabel1;
    private javax.swing.JLabel jLabel2;
    private javax.swing.JLabel statusLabel;
    private javax.swing.JButton yesButton;
    // End of variables declaration//GEN-END:variables
    private ArrayList<String> parseTarget; //ArrayList of Strings representing lines from a gen bank file that needs to be parsed
    private SequenceView _sv;
    private String _sequence;
    private String _type; //indicates what type of file is being imported
}