facility for grouping bam's

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

+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
+
+import uk.ac.sanger.artemis.components.Utilities;
+
+class GroupBamFrame extends JFrame
+{
+  private static final long serialVersionUID = 1L;
+  private String[] groups = new String[]{ "Default" };
+  private JPanel groupPanel = new JPanel(new GridBagLayout());
+  private JPanel bamPanel = new JPanel(new GridBagLayout());
+  private HashMap<JCheckBoxMenuItem, JComboBox> bamGroupMap = 
+      new HashMap<JCheckBoxMenuItem, JComboBox> ();
+  
+  private HashMap<String, JCheckBox> groupList = 
+      new HashMap<String, JCheckBox>();
+  private static final int PAD = 2;
+  
+  private BamView bamView;
+  private JMenu bamFilesMenu;
+
+  GroupBamFrame(final BamView bamView, final JMenu bamFilesMenu)
+  {
+    super("Alignment Groups");
+    
+    this.bamView = bamView;
+    this.bamFilesMenu = bamFilesMenu;
+    
+    final JPanel centerPanel = new JPanel(new GridBagLayout());
+    final JScrollPane jsp = new JScrollPane(centerPanel);
+    getContentPane().add(jsp, BorderLayout.CENTER);
+    centerPanel.setBackground(Color.WHITE);
+
+    ///
+    /// number of groups
+    Box xBox = Box.createHorizontalBox();
+    xBox.add(new JLabel("Add Group:"));
+    final JTextField newGroup = new JTextField(10);
+    xBox.add(newGroup);
+    newGroup.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent e)
+      {
+        addGroup(bamView, bamFilesMenu, newGroup, jsp);
+      }
+    });
+    newGroup.addFocusListener(new java.awt.event.FocusAdapter() {
+      public void focusGained(java.awt.event.FocusEvent evt) {
+        SwingUtilities.invokeLater( new Runnable() {
+          public void run() {
+            newGroup.selectAll();              
+          }
+        });
+      }
+    });
+
+    final JButton addGroupButton = new JButton("ADD");
+    xBox.add(addGroupButton);
+    addGroupButton.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent e)
+      {
+        if(newGroup.getText() == null ||
+           newGroup.getText().trim().equals(""))
+        {
+          JOptionPane.showMessageDialog(GroupBamFrame.this, 
+              "Type in the name for the new group.", "Group name missing", 
+              JOptionPane.INFORMATION_MESSAGE);
+          return;
+        }
+        addGroup(bamView, bamFilesMenu, newGroup, jsp);
+      }
+    });
+    xBox.add(Box.createHorizontalGlue());
+    getContentPane().add(xBox, BorderLayout.NORTH);
+    
+    //
+    xBox = Box.createHorizontalBox();
+    final JButton close = new JButton("CLOSE");
+    close.addActionListener(new ActionListener(){
+      public void actionPerformed(ActionEvent arg0)
+      {
+        setVisible(false);
+      }
+    });
+    xBox.add(close);
+    xBox.add(Box.createHorizontalGlue());
+    getContentPane().add(xBox, BorderLayout.SOUTH); 
+
+    
+    ///
+    ///
+    final GridBagConstraints c = new GridBagConstraints();
+    c.gridy = 0;
+    c.gridx = 0;
+    c.ipadx = PAD;
+    c.ipady = PAD;
+    c.anchor = GridBagConstraints.WEST;
+    c.gridwidth = 2;
+    final JLabel alignLabel = new JLabel("ALIGNMENTS:");
+    alignLabel.setFont(alignLabel.getFont().deriveFont(Font.BOLD));
+    centerPanel.add(alignLabel, c);
+    c.gridwidth = 1;
+    c.gridy += 1;
+    centerPanel.add(Box.createVerticalStrut(5), c);
+    c.gridy += 1;
+
+    bamPanel.setBackground(Color.WHITE);
+    centerPanel.add(bamPanel, c);
+    
+    c.gridx = 10;
+    c.gridheight = GridBagConstraints.REMAINDER;
+    centerPanel.add(groupPanel, c);
+    groupPanel.setBackground(Color.WHITE);
+
+    Utilities.rightJustifyFrame(this);
+  }
+  
+  protected void updateAndDisplay()
+  {
+    updateBamPanel();
+    updateGroupPanel();
+    pack();
+    setVisible(true);
+  }
+  
+  private void addGroup(final BamView bamView, final JMenu bamFilesMenu,
+                        final JTextField newGroup, final JScrollPane jsp)
+  {
+    final String tmpGroups[] = new String[groups.length+1];
+    for(int i=0; i<groups.length; i++)
+      tmpGroups[i] = groups[i];
+    tmpGroups[tmpGroups.length-1] = newGroup.getText().trim();
+    groups = tmpGroups;
+    
+    updateGroupPanel();
+    updateBamPanel();
+    jsp.validate();
+  }
+  
+  private void updateBamPanel()
+  {
+    final Component cs[] = bamFilesMenu.getMenuComponents();
+    bamPanel.removeAll();
+    final GridBagConstraints c = new GridBagConstraints();
+    c.gridy = 0;
+    c.gridx = 0;
+    c.ipadx = PAD;
+    c.ipady = PAD;
+    c.anchor = GridBagConstraints.WEST;
+    
+    for(Component cp : cs)
+    {
+      if(cp instanceof JCheckBoxMenuItem)
+      {
+        final JCheckBoxMenuItem cbBam = (JCheckBoxMenuItem) cp;
+        final String bam = cbBam.getText();
+        c.gridy += 1;
+        c.gridx = 0;
+        bamPanel.add(new JLabel(bam), c);
+        
+        Color col = bamView.getColorByJCheckBoxMenuItem(cbBam);
+        if(col == null)
+          col = Color.BLACK;
+        
+        c.gridx = 1;
+        bamPanel.add(new JLabel(bamView.getImageIcon(col)), c);
+
+        c.gridx = 2;
+        JComboBox groupList = new JComboBox( groups );
+        bamPanel.add(groupList, c);
+        
+        if(bamGroupMap.containsKey(cbBam))
+          groupList.setSelectedItem(
+              (String) bamGroupMap.get(cbBam).getSelectedItem());
+
+        bamGroupMap.put(cbBam, groupList);
+      }
+    }
+  }
+  
+  private void updateGroupPanel()
+  {
+    groupPanel.removeAll();
+    final GridBagConstraints c = new GridBagConstraints();
+    c.gridy = 0;
+    c.gridx = 0;
+    c.anchor = GridBagConstraints.WEST;
+    
+    final JLabel groupLabel = new JLabel("GROUPS:");
+    groupLabel.setFont(groupLabel.getFont().deriveFont(Font.BOLD));
+    groupPanel.add(groupLabel, c);
+    c.gridy += 2;
+    for(final String group: groups)
+    {
+      c.gridy += 1;
+      
+      final JCheckBox cbox;
+      if(groupList.containsKey(group))
+        cbox = groupList.get(group);
+      else
+      {
+        cbox = new JCheckBox(group, true);
+        groupList.put(group, cbox);
+      }
+      groupPanel.add(cbox, c);
+      cbox.addItemListener(new ItemListener(){
+        public void itemStateChanged(ItemEvent arg0)
+        {
+          Iterator<JCheckBoxMenuItem> it = bamGroupMap.keySet().iterator();
+          while(it.hasNext())
+          {
+            JCheckBoxMenuItem cbs = it.next();
+            String thisGroup = (String) bamGroupMap.get(cbs).getSelectedItem();
+            if(group.equals(thisGroup))
+              cbs.setSelected(cbox.isSelected());
+          }
+        }
+      });
+    }
+  }
+  
+
+}
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