/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.gui;

import jalview.io.AlignmentFileReaderI;
import jalview.io.BamFile;
import jalview.util.MessageManager;

import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.util.Arrays;

import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;

/**
 * A dialog where a user can choose import options for a bam file
 */
public class BamFileOptionsChooser extends JPanel
{

  // text field for start of range
  // JFormattedTextField startRange = new JFormattedTextField(
  // new NumberFormatter(NumberFormat.getIntegerInstance()));

  // text field for end of range
  // JFormattedTextField endRange = new JFormattedTextField(
  // new NumberFormatter(NumberFormat.getIntegerInstance()));

  JTextField startRange = new JTextField(10);

  JTextField endRange = new JTextField(10);

  // combo box for chromosome list
  JComboBox<String> chroCombo;

  public BamFileOptionsChooser(AlignmentFileReaderI source)
  {
    Object[] preprocessResult = source.preprocess();
    String[] chromosomes = Arrays.copyOf(preprocessResult,
            preprocessResult.length, String[].class);

    setLayout(new GridBagLayout());
    GridBagConstraints c = new GridBagConstraints();

    setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));

    // set up chromosome input
    JLabel chroLabel = new JLabel(
            MessageManager.getString("label.bam_chromosome"));
    chroCombo = new JComboBox<>(chromosomes);
    
    // set up region input
    JPanel range = new JPanel();
    JLabel rangeLabel = new JLabel(
            MessageManager.getString("label.bam_range"));
    startRange.setColumns(8);
    endRange.setColumns(8);

    JLabel rangeSep = new JLabel("-");
    range.add(startRange);
    range.add(rangeSep);
    range.add(endRange);

    // chromosome label top left
    c.gridx = 0;
    c.gridy = 0;
    c.anchor = GridBagConstraints.WEST;
    c.fill = GridBagConstraints.NONE;
    this.add(chroLabel, c);

    // chromosome combo top right
    c.gridx = 1;
    c.weightx = 1;
    c.anchor = GridBagConstraints.WEST;
    c.fill = GridBagConstraints.HORIZONTAL;
    this.add(chroCombo, c);

    // region label mid left
    c.gridx = 0;
    c.gridy = 1;
    c.anchor = GridBagConstraints.WEST;
    c.fill = GridBagConstraints.NONE;
    this.add(rangeLabel, c);

    // region input mid right
    c.gridx = 1;
    c.weightx = 1;
    c.anchor = GridBagConstraints.WEST;
    c.fill = GridBagConstraints.HORIZONTAL;
    this.add(range, c);
  }

  public void update(AlignmentFileReaderI source)
  {

    int start = Integer.parseInt(startRange.getText());
    int end = Integer.parseInt(endRange.getText());
    ((BamFile) source).setOptions((String) chroCombo.getSelectedItem(),
            start, end);

  }

}