LineAttributes.java

/* LineAttributes.java
 *
 * created: 2010
 *
 * This file is part of Artemis
 *
 * Copyright (C) 2010  Genome Research Limited
 *
 * This program 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 2
 * of the License, or (at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 **/


package uk.ac.sanger.artemis.components.alignment;

import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.List;
import java.util.Random;

import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.ListCellRenderer;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;

/**
 * Define line attributes for graphs lines
 */
public class LineAttributes
{
  /** defines the colour */
  private Color lineColour = Color.black;
  /** defines the line Stroke - size and style */
  private BasicStroke stroke;
  
  private static float dotDash[] = {10.f, 5.f, 3.f, 5.f};
  private static float dash[] = {10.f};
  
  private static BasicStroke style1 = 
      new BasicStroke(1.f);
  private static BasicStroke style2 = 
      new BasicStroke(1.f, BasicStroke.CAP_BUTT,
                      BasicStroke.JOIN_MITER, 
                      1.f, dash, 0.f);
  private static BasicStroke style3 = 
      new BasicStroke(1.f, BasicStroke.CAP_BUTT, 
                      BasicStroke.JOIN_MITER, 
                      1.f, dotDash, 0.f);
  
  /** available stroke types */
  private static BasicStroke[] STROKES = 
       new BasicStroke[]{ style1, style2, style3 };
  
  /** fill in underneath wiggle plots */
  public static String PLOT_TYPES[]    = 
          { "Open", "Filled" };
  private String plotType = PLOT_TYPES[0];

  /**
   * Contruct a LineAttributes instance
   * @param lineColour
   */
  public LineAttributes(Color lineColour)
  {
    this.lineColour = lineColour;
    this.stroke = new BasicStroke(1.f);
  }
  
  public Color getLineColour()
  {
    return lineColour;
  }

  public void setLineColour(Color lineColour)
  {
    this.lineColour = lineColour;
  }

  public BasicStroke getStroke()
  {
    return stroke;
  }

  public void setStroke(BasicStroke stroke)
  {
    this.stroke = stroke;
  }
  
  protected static BasicStroke[] getStrokes()
  {
    return STROKES;
  }
  
  /**
   * Given a stroke return the index for it based on the style.
   * @param stroke
   * @return
   */
  private static int getStyleIndex(BasicStroke stroke)
  {
    float myDash[] = stroke.getDashArray();
    if(myDash != null && 
       myDash.length == dotDash.length)
      return 2;
    else if(myDash != null && 
            myDash.length == dash.length &&
            myDash[0] == dash[0])
      return 1;
    else
      return 0;
  }
  
  public String getPlotType()
  {
    return plotType;
  }

  public static LineAttributes[]  init(int numPlots)
  {
    final Color frameColour[] = { 
        Color.red, 
        new Color(0,200,0), 
        Color.blue,
        Color.magenta,
        new Color(100, 100, 0),
        new Color(0, 100, 100),
        new Color(50, 0, 50),
        new Color(255, 102, 0),
        Color.black };
    final LineAttributes lines[] = new LineAttributes[numPlots];
    
    if(numPlots == 1)
    {
      lines[0] = new LineAttributes(Color.black);
      return lines;
    }
    
    final Random rand = new Random();
    for(int i=0; i<numPlots; i++)
    {
      if(i < frameColour.length)
        lines[i] = new LineAttributes(frameColour[i]);
      else
        lines[i] = new LineAttributes(
            new Color(rand.nextFloat(), rand.nextFloat(), rand.nextFloat()));
    }
    return lines;
  }

  
  /**
   * Utility used by uk.ac.sanger.artemis.components.Plot
   * @param numPlots
   * @param lines
   * @param plot
   * @return
   */
  public static LineAttributes[] configurePlots(
                                    final List<String> bamList, 
                                    final LineAttributes[] lines,
                                    final JPanel covergePanel)
  {
    JPanel panel = new JPanel(new GridBagLayout());
    GridBagConstraints c = new GridBagConstraints();

    final int numPlots = bamList.size();
    final LineAttributes[] thislines;
    if(lines.length < numPlots)
      thislines = init(numPlots);
    else
      thislines = lines;
    
    int gridx = 0;
    int gridy = 0;
    c.gridy = gridy++;
    c.gridx = gridx;
    // open / filled    
    panel.add(new JLabel("Plot Options:"), c);
    final JComboBox openPlot = new JComboBox(PLOT_TYPES);
    openPlot.setSelectedItem(thislines[0].plotType);
    openPlot.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        for(int i=0; i<numPlots; i++)
          thislines[i].plotType =    
            (String) openPlot.getSelectedItem();
        covergePanel.repaint();
      }
    });
    c.gridy = gridy++;
    panel.add(openPlot, c);
    
    c.gridy = gridy++;
    panel.add(new JLabel("Line Options:"), c);
    c.gridx = gridx++;
    c.gridy = gridy++;
    gridx++;
    
    final JCheckBox applyToAll = new JCheckBox("Apply colour to all");

    panel.add(new JLabel("Colour"), c);
    c.gridx = gridx++;
    panel.add(new JLabel("Line style"), c);
   
    c.gridx = gridx;
    panel.add(new JLabel("Line size"), c);
    
    for(int i=0; i<numPlots; i++)
    {
      c.gridy = gridy++;
      final int colourNumber = i;
      gridx = 0;

      c.gridx = 0;
      c.gridwidth = GridBagConstraints.REMAINDER;
      c.anchor = GridBagConstraints.NORTHWEST;
      final JLabel bamFileName = new JLabel(bamList.get(i));
      panel.add(bamFileName,c);
      
      c.gridwidth = 1;
      c.gridy = gridy++;
      final JLabel colourLabel = new JLabel("   ");
      colourLabel.setBackground(thislines[i].getLineColour());
      colourLabel.setOpaque(true);
      c.gridx = gridx++;
      panel.add(colourLabel,c);

      JButton butt = new JButton("Select");
      butt.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent _)
        {
          Color newColour = JColorChooser.showDialog(null, "Colour Chooser",
              thislines[colourNumber].getLineColour());
          
          if(applyToAll.isSelected())
          {
            for(int iplot=0; iplot<numPlots; iplot++)
              thislines[iplot].setLineColour(newColour);
          }
          else
            thislines[colourNumber].setLineColour(newColour); 
          colourLabel.setBackground(thislines[colourNumber].getLineColour());
          covergePanel.repaint();
        }
      });
      c.gridx = gridx++;
      panel.add(butt, c);
      
      // line style
      final JSlider slider = new JSlider(1, 10, 
          (int)lines[colourNumber].getStroke().getLineWidth());
      Integer index[] = new Integer[STROKES.length];
      for(int j=0; j<index.length; j++)
        index[j] = j;
      final JComboBox lineStyle = new JComboBox(index);
      lineStyle.setRenderer(new LineStyleListRenderer());
      lineStyle.setSelectedIndex(
          LineAttributes.getStyleIndex(thislines[colourNumber].getStroke()));
      lineStyle.addItemListener(new ItemListener()
      {
        public void itemStateChanged(ItemEvent e)
        {
          thislines[colourNumber].setStroke(
              STROKES[lineStyle.getSelectedIndex()]);
          setLineSize(covergePanel, slider, thislines, colourNumber);
        }
      });
      c.gridx = gridx++;
      panel.add(lineStyle, c);
      
      
      // line size
      slider.addChangeListener(new ChangeListener()
      {
        public void stateChanged(ChangeEvent e)
        {
          setLineSize(covergePanel, slider, thislines, colourNumber);
        }
      });
      c.gridx = gridx;
      panel.add(slider, c);
      
    }
    
    c.gridx = 0;
    c.gridy = gridy++;
    c.gridwidth = GridBagConstraints.REMAINDER;
    c.anchor = GridBagConstraints.WEST;
    panel.add(applyToAll, c);

    JScrollPane jsp = new JScrollPane(panel, 
        JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
        JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
    Dimension d = Toolkit.getDefaultToolkit().getScreenSize();
    
    if(panel.getPreferredSize().height > d.height/2)
    {
      d.setSize(jsp.getPreferredSize().width, d.height/2);
      jsp.setPreferredSize(d);
    }
    
    String config_options[] = { "OK" };
    JOptionPane.showOptionDialog(null,
                                 jsp, "Configure Lines",
                                 JOptionPane.DEFAULT_OPTION,
                                 JOptionPane.QUESTION_MESSAGE,
                                 null, config_options, config_options[0]);
    return thislines;
  }
  
  
  private static void setLineSize(JPanel covergePanel, JSlider slider,
                           LineAttributes[] thislines, int number)
  {
    BasicStroke oldStroke = thislines[number].getStroke();
    BasicStroke newStroke = new BasicStroke(slider.getValue(),
        BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, 
        1.f, oldStroke.getDashArray(), 0.f);
    thislines[number].setStroke(newStroke);
    covergePanel.repaint();
  }
}


/**
 * Renderer for the JComboBox to define different line styles.
 */
class LineStyleListRenderer extends JComponent implements ListCellRenderer
{
  private static final long serialVersionUID = 1L;
  private int selectedIndex = 0;
  public LineStyleListRenderer()
  {
    super();
    setMinimumSize(new Dimension(100, 20));
    setPreferredSize(new Dimension(100, 20));
  }

  /**
   * This method finds the selected index.
   */
  public Component getListCellRendererComponent(JList list, Object value,
      int index, boolean isSelected, boolean cellHasFocus)
  {
    selectedIndex = ((Integer) value).intValue();
    return this;
  }
  
  public void paintComponent(Graphics g)
  {
    super.paintComponent(g);
    Graphics2D g2 = (Graphics2D)g;
    g2.setStroke(LineAttributes.getStrokes()[selectedIndex]);
    g2.drawLine(10, 10, 90, 10);
  }
}