Read group options

uk/ac/sanger/artemis/components/alignment/ReadGroupsFrame.java

+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Point;
+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.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import net.sf.samtools.SAMReadGroupRecord;
+
+class ReadGroupFrame extends JFrame
+{
+  private static final long serialVersionUID = 1L;
+  private LineAttributes[] colours;
+  private List<SAMReadGroupRecord> hideReadGroups = new Vector<SAMReadGroupRecord>();
+  
+  ReadGroupFrame(List<SAMReadGroupRecord> readGroups, BamView bamView)
+  {
+    super("Read Groups");
+    
+    colours = LineAttributes.init(readGroups.size()); 
+    update(readGroups, bamView);
+    
+    JFrame f = (JFrame) SwingUtilities.getAncestorOfClass(JFrame.class, bamView);
+    
+    int hgt = 250;
+    if(hgt < f.getHeight()/2)
+      hgt = f.getHeight()/2;
+    setPreferredSize(new Dimension(300, hgt));
+    
+    pack();
+    
+    final Point p = f.getLocationOnScreen();
+    final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+    int y = (screen.height-getSize().height)/2;
+    if(y < 10) 
+      y = 10;
+    int x = p.x-getSize().width;
+    if(x < 10)
+      x = 10;
+    setLocation(new Point(x, y));
+    
+    setDefaultCloseOperation(HIDE_ON_CLOSE);
+  }
+  
+  private void update(final List<SAMReadGroupRecord> readGroups, 
+                      final BamView bamView)
+  {
+    final JPanel mainPanel = new JPanel(new BorderLayout());
+    final JPanel panel = new JPanel(new GridBagLayout());
+    final JScrollPane jsp = new JScrollPane(panel);
+    mainPanel.add(jsp, BorderLayout.CENTER);
+    getContentPane().add(mainPanel);
+    
+    final JButton close = new JButton("CLOSE");
+    close.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent arg0)
+      {
+        setVisible(false);
+      }
+    });
+    mainPanel.add(close, BorderLayout.SOUTH);
+    
+    final GridBagConstraints c = new GridBagConstraints();
+    c.gridy = 0;
+    c.anchor = GridBagConstraints.WEST;
+
+    if(readGroups.size() == 0)
+    {
+      panel.add(new JLabel("No read groups"), c);
+      return;
+    }
+    
+    c.gridx = 0;
+    JLabel rgLab = new JLabel("Read Groups");
+    rgLab.setFont(rgLab.getFont().deriveFont(Font.BOLD));
+    panel.add(rgLab, c);
+    
+    c.gridx = 1;
+    JLabel colLab = new JLabel("Colour");
+    colLab.setFont(rgLab.getFont().deriveFont(Font.BOLD));
+    panel.add(colLab, c);
+    
+    final JButton toggle = new JButton("Toggle");
+    final List<JCheckBox> checkBoxes = new Vector<JCheckBox>();
+    c.gridx = 2;
+    panel.add(toggle, c);
+    toggle.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent arg0)
+      {
+        for(JCheckBox cb: checkBoxes)
+          cb.setSelected(!cb.isSelected());
+      }      
+    });
+    
+    c.gridy = 1;
+    for(int i=0; i<readGroups.size(); i++)
+    {
+      final SAMReadGroupRecord grp = readGroups.get(i);
+
+      c.gridx = 0;
+      final JLabel lab = new JLabel(grp.getId());
+      lab.setToolTipText(grp.getDescription());
+      panel.add(lab, c);
+      
+      c.gridx = 1;
+      final LineAttributes lnAttr = colours[i];
+      final JButton butt = new JButton("Select", bamView.getImageIcon(lnAttr.getLineColour()));
+      butt.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent _)
+        {
+          Color newColour = JColorChooser.showDialog(null, "Colour Chooser",
+              lnAttr.getLineColour());
+          
+          lnAttr.setLineColour(newColour); 
+          butt.setIcon(bamView.getImageIcon(lnAttr.getLineColour()));
+          bamView.repaint();
+        }
+      });
+      panel.add(butt, c);
+      
+      c.gridx = 2;
+      final JCheckBox show = new JCheckBox("Show", true);
+      checkBoxes.add(show);
+      show.addItemListener(new ItemListener(){
+        public void itemStateChanged(ItemEvent arg0)
+        {
+          if(show.isSelected())
+            hideReadGroups.remove(grp);
+          else
+            hideReadGroups.add(grp);
+          bamView.repaintBamView();
+        }
+      });
+      panel.add(show, c);
+      
+      c.gridy+=1;
+    }
+  }
+  
+  protected Color getReadGroupColour(final List<SAMReadGroupRecord> readGroups, final SAMReadGroupRecord rg)
+  {
+    if(rg == null)
+      return Color.BLACK;
+    final String rgId = rg.getId();
+    for(int i=0; i<readGroups.size(); i++)
+    {
+      final SAMReadGroupRecord grp = readGroups.get(i);
+      if(grp.getId().equals(rgId))
+        return colours[i].getLineColour();
+    }
+    return Color.BLACK;
+  }
+  
+  protected boolean isReadGroupVisible(final SAMReadGroupRecord rg)
+  {
+    return !hideReadGroups.contains(rg);
+  }
+}
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