//  $Id: Explorer.java,v 1.23 2005/01/25 21:24:16 moreland Exp $
//
//  Copyright 2000-2004 The Regents of the University of California.
//  All Rights Reserved.
//
//  Permission to use, copy, modify and distribute any part of this
//  Molecular Biology Toolkit (MBT)
//  for educational, research and non-profit purposes, without fee, and without
//  a written agreement is hereby granted, provided that the above copyright
//  notice, this paragraph and the following three paragraphs appear in all
//  copies.
//
//  Those desiring to incorporate this MBT into commercial products
//  or use for commercial purposes should contact the Technology Transfer &
//  Intellectual Property Services, University of California, San Diego, 9500
//  Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815,
//  FAX: (858) 534-7345, E-MAIL:invent@ucsd.edu.
//
//  IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR
//  DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
//  LOST PROFITS, ARISING OUT OF THE USE OF THIS MBT, EVEN IF THE
//  UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
//  THE MBT PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE
//  UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
//  UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES
//  NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR
//  EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
//  MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE
//  MBT WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.
//  
//  For further information, please see:  http://mbt.sdsc.edu
//  
//  History:
//  $Log: Explorer.java,v $
//  Revision 1.23  2005/01/25 21:24:16  moreland
//  Added menus that globally change the current rendering style.
//
//  Revision 1.22  2004/10/22 23:23:46  moreland
//  Finished and enabled code for printing the 3D/StructureViewer content.
//  Added a menu item and code to control 3D/StructureViewer depth queueing.
//
//  Revision 1.21  2004/07/08 00:42:02  moreland
//  Integreated Dave's new StylesEditorDialog from the gui package.
//
//  Revision 1.20  2004/05/13 17:37:47  moreland
//  Increased inspector frame size to accommodate new StructureInfo data.
//
//  Revision 1.19  2004/04/27 18:18:34  moreland
//  Added edu.sdsc.vis.viewers.Java3dCheck calls to check for Java3D installation.
//
//  Revision 1.18  2004/04/21 23:19:02  moreland
//  Added Java3dCheck code.
//
//  Revision 1.17  2004/04/08 23:55:06  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.16  2004/03/09 17:28:22  moreland
//  Added check to prevent call to System.exit() when running as an applet.
//
//  Revision 1.15  2004/01/31 00:39:01  moreland
//  Updated for release.
//
//  Revision 1.14  2003/12/20 00:32:05  moreland
//  StyleEditor window size increased to accomodate longer combo box items.
//
//  Revision 1.13  2003/12/12 22:46:29  moreland
//  Added editable element styles.
//
//  Revision 1.12  2003/12/09 20:52:42  moreland
//  Enabled preliminary Styles and Selection GUI hooks.
//
//  Revision 1.11  2003/11/10 19:14:57  moreland
//  Added preliminary (disabled) features for printing, exporting images,
//  and editing formatting styles.
//
//  Revision 1.10  2003/07/14 21:31:17  moreland
//  Added "Image Save" feature (see File menu).
//
//  Revision 1.9  2003/07/07 16:20:01  moreland
//  Delay loading PDB ID codes until idCode PopupMenu is first shown.
//
//  Revision 1.8  2003/05/23 20:42:57  moreland
//  Integrated PDB-ID loader GUI above TreeViewer instead of a separate window.
//
//  Revision 1.7  2003/05/20 22:17:50  moreland
//  Enabled PDB ID codes to automatically load in the background via a thread.
//
//  Revision 1.6  2003/05/19 18:15:55  moreland
//  Added FTP-based PDB ID list interface.
//
//  Revision 1.5  2003/05/16 23:34:42  moreland
//  Increased sizes of TreeViewer (in split) and overall Explorer window.
//
//  Revision 1.4  2003/05/16 23:17:00  moreland
//  Enabled "enter" key in PDB ID load text field to trigger loadButton.doClick.
//
//  Revision 1.3  2003/05/16 23:01:10  moreland
//  Changed Inspector menu from a checkbox to a standard menu item.
//  Added several menu accelerator keys.
//  Added RCSB PDB ID loader interface.
//  Added "Close All" menu item.
//
//  Revision 1.2  2003/05/15 23:44:54  moreland
//  Cleaned up code a bit for a preliminary release to obuzko.
//
//  Revision 1.1  2003/05/15 22:42:45  moreland
//  An application which incorporates more MBT GUI layer components.
//
//  Revision 1.0  2003/05/05 16:06:13  moreland
//  First version.
//  


// Core
import java.applet.*;
import java.util.*;
import java.io.*;
import java.net.*;

// GUI
import java.awt.*;
import java.awt.image.*;
import javax.imageio.*;
import java.awt.event.*;
import javax.swing.event.*;
import javax.swing.*;
import javax.swing.filechooser.FileFilter;

// Printing
import java.awt.print.*;
import javax.print.*;

// MBT
import edu.sdsc.mbt.*;
import edu.sdsc.mbt.io.*;
import edu.sdsc.mbt.viewables.*;
import edu.sdsc.mbt.viewers.*;
import edu.sdsc.mbt.gui.*;
import edu.sdsc.mbt.util.*;


/**
 *  Implements an application which incorporates a more complete set of
 *  MBT GUI layer components such as a menubar, TreeViewer, etc...
 *  <P>
 *  @author	John L. Moreland
 */
public class Explorer
	extends Applet
{
	// GUI
	protected JFrame explorerFrame = null;
	protected Container explorerFrameContainer = null;
	private StatusPanel statusPanel = null;
	private JMenuItem toolsInspectorItem = null;
	private final JComboBox pdbIdList = new JComboBox( );
	private Vector idCodes = null;

	// Viewers
	private StructureViewer structureViewer = null;
	private TreeViewer treeViewer = null;

	// Runtime properties (options or parameters)
	private Properties properties = new Properties( );

	// Applet
	private Applet applet = null;

	// Document
	StructureDocument structureDocument = null;


	//
	// Entry Points
	//


	/**
	 * The main program entry point when invoked as an application.
	 */
	public static void main( String[] args )
	{
		Explorer explorer = new Explorer();
		if ( args != null )
		{
			for ( int i=0; i<args.length; i++ )
			{
				if ( args[i].equals( "-f" ) )
					explorer.properties.setProperty( "file", args[++i] );
				if ( args[i].equals( "-u" ) )
					explorer.properties.setProperty( "url", args[++i] );
				if ( args[i].equals( "-p" ) )
					explorer.properties.setProperty( "pdbid", args[++i] );
			}
		}
		explorer.initialize();
	}


	/**
	 * The main program entry point when invoked as an applet.
	 */
	public void init()
	{
		applet = this;
		String value;
		String propertyNames[] = { "file", "url", "pdbid" };

		for ( int i=0; i<propertyNames.length; i++ )
		{
			value = applet.getParameter( propertyNames[i] );
			if ( value != null )
				properties.setProperty( propertyNames[i], value );
		}

		initialize();
	}


	//
	// Initialization
	//


	/**
	 *  Initializes the Explorer.
	 */
	public void initialize()
	{
		// Since this application uses the MBT StructureViewer,
		// make sure that Java3D is installed before continuing.
		if ( ! edu.sdsc.vis.viewers.Java3dCheck.isInstalled() )
		{
			// Display instructions for the user about installing Java3D.
			String urlString =
				edu.sdsc.vis.viewers.Java3dCheck.showInstallInfo( );
			if ( urlString != null )
			{
				try
				{
					edu.sdsc.mbt.util.BrowserLauncher.openURL( urlString );
				}
				catch( java.io.IOException e )
				{
					Status.output( Status.LEVEL_ERROR, "BrowserLauncher.openURL failed: " + e );
				}
			}
			destructor( );
			return;
		}

		// Create a structure document to hold viewers and structures
		structureDocument = new StructureDocument( );

		// Build the frame
		explorerFrame = new JFrame( "MBT Explorer" );
		explorerFrameContainer = explorerFrame.getContentPane();
		explorerFrameContainer.setLayout( new BorderLayout() );

		// Create a StatusPanel
		statusPanel = new StatusPanel( );
		explorerFrameContainer.add( BorderLayout.SOUTH, statusPanel );

		// Create a StructureViewer
		structureViewer = new StructureViewer( );
		structureDocument.addViewer( structureViewer );

		// Create a SequenceViewer
		SequenceViewer sequenceViewer = new SequenceViewer( );
		explorerFrameContainer.add( BorderLayout.NORTH, sequenceViewer );
		structureDocument.addViewer( sequenceViewer );

		// Create a panel to hold the PDB-ID loader widget and the TreeViewer.
		JPanel documentPanel = new JPanel( );
		GridBagLayout gbl = new GridBagLayout( );
		GridBagConstraints gbc = new GridBagConstraints( );
		documentPanel.setLayout( gbl );

		// PDB-ID loader widget (instantiated above since it is "final").
		pdbIdList.setEditable( true );
		ActionListener rcsbClickListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				String cmd = actionEvent.getActionCommand( );
				if ( cmd.equals( "comboBoxChanged" ) )
					doRcsbLoad( );
				// if ( cmd.equals( "comboBoxEdited" ) )
			}
		};
		pdbIdList.addActionListener( rcsbClickListener );

		// Only load the PDB ID code list when the list is first popped up.
		PopupMenuListener idCodePopupListener = new PopupMenuListener( )
		{
			public void popupMenuWillBecomeVisible( PopupMenuEvent e )
			{
				loadIdCodes( );
			}
			public void popupMenuWillBecomeInvisible( PopupMenuEvent e )
			{
			}
			public void popupMenuCanceled( PopupMenuEvent e )
			{
			}
		};
		pdbIdList.addPopupMenuListener( idCodePopupListener );

		JPanel idLoaderPanel = new JPanel( );
		idLoaderPanel.setLayout( new FlowLayout() );
		JLabel idLoaderLabel = new JLabel( "Pdb ID:" );
		idLoaderPanel.add( idLoaderLabel );
		idLoaderPanel.add( pdbIdList );

		gbc.fill = GridBagConstraints.HORIZONTAL;
		gbc.weightx = 1.0;
		gbc.weighty = 0.0;
		gbc.gridwidth = GridBagConstraints.REMAINDER;
		gbc.gridheight = 1;
		gbl.setConstraints( idLoaderPanel, gbc );
		documentPanel.add( idLoaderPanel );

		// Create a TreeViewer
		treeViewer = new TreeViewer( );
		structureDocument.addViewer( treeViewer );
		gbc.fill = GridBagConstraints.BOTH;
		gbc.weightx = 1.0;
		gbc.weighty = 1.0;
		gbc.gridwidth = GridBagConstraints.REMAINDER;
		gbc.gridheight = 1;
		gbl.setConstraints( treeViewer, gbc );
		documentPanel.add( treeViewer );

		// Create a JSplitPane to hold the documentPanel and structureViewer
		JSplitPane splitPane = new JSplitPane( JSplitPane.HORIZONTAL_SPLIT,
			documentPanel, structureViewer );
		splitPane.setOneTouchExpandable( true );
		splitPane.setDividerLocation( 210 );
		explorerFrameContainer.add( BorderLayout.CENTER, splitPane );

		// Java3D's Canvas3D is heavyweight, so menus must be also
		// be so that they can draw over the top of the 3D content...
		JPopupMenu.setDefaultLightWeightPopupEnabled( false );
		ToolTipManager.sharedInstance().setLightWeightPopupEnabled( false );

		// Create a menu area
		JMenuBar menuBar = createMenuBar( );
		explorerFrame.setJMenuBar( menuBar );

		// Create a toolbar area
		// explorerFrameContainer.add( "East", new JLabel( "Toolbar" ) );

		// Pack the frame
		explorerFrame.pack();
		explorerFrame.validate();
		explorerFrame.setSize( 800, 550 );
		explorerFrame.setVisible( true );

		// Make sure we clean up if the user hits the close box
		WindowAdapter closer = new WindowAdapter()
		{
			public void windowClosing( WindowEvent event )
			{
				destructor();
			}
		};
		explorerFrame.addWindowListener( closer );

		//
		// See if the runtime properties specify any Structures to load.
		//

		Structure structure = null;
		String dataset = null;
		if ( properties.getProperty( "file" ) != null )
		{
			dataset = properties.getProperty( "file" );
			structure = StructureFactory.load( new File( dataset ) );
		}
		else if ( properties.getProperty( "url" ) != null )
		{
			dataset = properties.getProperty( "url" );
			try
			{
				structure = StructureFactory.load( new URL( dataset ) );
			}
			catch ( MalformedURLException e )
			{
				Status.output( Status.LEVEL_ERROR, e.toString() );
			}
		}
		else if ( properties.getProperty( "pdbid" ) != null )
		{
			dataset = properties.getProperty( "pdbid" );
			String urlString = "ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/" + dataset.toLowerCase() + ".cif.gz";
			try
			{
				structure = StructureFactory.load( new URL( urlString ) );
			}
			catch ( MalformedURLException e )
			{
				Status.output( Status.LEVEL_ERROR, e.toString() );
			}


			if ( structure == null )
				Status.output( Status.LEVEL_ERROR, "Load failed: " + dataset );
		}

		if ( structure != null )
			addStructure( structure );
		structure = null;
	}


	private boolean destroyed = false;
	/**
	 * Quits the application.
	 */
	public void destructor()
	{
		if ( ! destroyed )
		{
			destroyed = true;
			// Do cleanup here...
		}
		if ( applet == null )
			System.exit( 0 );
	}


	/**
	 * Creates the menu bar for the application.
	 */
	public JMenuBar createMenuBar( )
	{
		JMenuBar menuBar = new JMenuBar( );

		//
		// File Menu
		//

		JMenu fileMenu = new JMenu( "File" );

		JMenuItem fileOpenItem = new JMenuItem( "Open..." );
		ActionListener fileOpenListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				fileOpen( );
			}
		};
		fileOpenItem.addActionListener( fileOpenListener );
		fileOpenItem.setAccelerator(
			KeyStroke.getKeyStroke( KeyEvent.VK_O, Event.CTRL_MASK ) );
		fileMenu.add( fileOpenItem );

		JMenuItem fileCloseAllItem = new JMenuItem( "Close All" );
		ActionListener fileCloseAllListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				closeAll( );
			}
		};
		fileCloseAllItem.addActionListener( fileCloseAllListener );
		fileMenu.add( fileCloseAllItem );

		JMenuItem fileSaveImageItem = new JMenuItem( "Save Image..." );
		fileSaveImageItem.setEnabled( true );
		ActionListener fileSaveImageListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				saveImage( );
			}
		};
		fileSaveImageItem.addActionListener( fileSaveImageListener );
		fileMenu.add( fileSaveImageItem );

		JMenuItem fileSaveImagesItem = new JMenuItem( "Save Images..." );
		fileSaveImagesItem.setEnabled( true );
		ActionListener fileSaveImagesListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				saveImages( 9, 30.0 );
			}
		};
		fileSaveImagesItem.addActionListener( fileSaveImagesListener );
		fileMenu.add( fileSaveImagesItem );
		fileSaveImagesItem.setEnabled( false ); // JLM DEBUG: Feature not complete.

		fileMenu.add( new JSeparator() );

		JMenuItem filePrefItem = new JMenuItem( "Preferences..." );
		filePrefItem.setEnabled( false );
		fileMenu.add( filePrefItem );

		fileMenu.add( new JSeparator() );

		JMenuItem filePageSetupItem = new JMenuItem( "Page Setup..." );
		ActionListener filePageSetupListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				pageSetup( true );
			}
		};
		filePageSetupItem.addActionListener( filePageSetupListener );
		filePageSetupItem.setEnabled( true );
		fileMenu.add( filePageSetupItem );

		JMenuItem filePrintItem = new JMenuItem( "Print..." );
		ActionListener filePrintListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				print( );
			}
		};
		filePrintItem.addActionListener( filePrintListener );
		filePrintItem.setAccelerator(
			KeyStroke.getKeyStroke( KeyEvent.VK_P, Event.CTRL_MASK ) );
		fileMenu.add( filePrintItem );
		filePrintItem.setEnabled( true );

		fileMenu.add( new JSeparator() );

		JMenuItem fileQuitItem = new JMenuItem( "Quit" );
		ActionListener fileQuitListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				destructor( );
			}
		};
		fileQuitItem.addActionListener( fileQuitListener );
		fileQuitItem.setAccelerator(
			KeyStroke.getKeyStroke( KeyEvent.VK_Q, Event.CTRL_MASK ) );
		fileMenu.add( fileQuitItem );

		menuBar.add( fileMenu );

		//
		// Edit Menu
		//

		JMenu editMenu = new JMenu( "Edit" );

		JMenuItem editUndoItem = new JMenuItem( "Undo" );
		editUndoItem.setEnabled( false );
		editMenu.add( editUndoItem );

		editMenu.add( new JSeparator() );

		JMenuItem editCutItem = new JMenuItem( "Cut" );
		editCutItem.setEnabled( false );
		editMenu.add( editCutItem );

		JMenuItem editCopyItem = new JMenuItem( "Copy" );
		editCopyItem.setEnabled( false );
		editMenu.add( editCopyItem );

		JMenuItem editPasteItem = new JMenuItem( "Paste" );
		editPasteItem.setEnabled( false );
		editMenu.add( editPasteItem );

		JMenuItem editClearItem = new JMenuItem( "Clear" );
		editClearItem.setEnabled( false );
		editMenu.add( editClearItem );

		editMenu.add( new JSeparator() );

		JMenuItem editSelectAllItem = new JMenuItem( "Select All" );
		ActionListener selectAllListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				selectAll( );
			}
		};
		editSelectAllItem.addActionListener( selectAllListener );
		editSelectAllItem.setEnabled( false );
		editMenu.add( editSelectAllItem );

		JMenuItem editUnselectAllItem = new JMenuItem( "Unselect All" );
		ActionListener unselectAllListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				unselectAll( );
			}
		};
		editUnselectAllItem.addActionListener( unselectAllListener );
		editUnselectAllItem.setEnabled( false );
		editMenu.add( editUnselectAllItem );

		JMenuItem editSelectItem = new JMenuItem( "Select..." );
		editSelectItem.setEnabled( false );
		editMenu.add( editSelectItem );

	/* TODO: Need to add global toolkit parameters.
		JMenu editPickLevelMenu = new JMenu( "Pick Level" );
		ButtonGroup pickLevelButtonGroup = new ButtonGroup( );
		editMenu.add( editPickLevelMenu );
		JRadioButtonMenuItem editPickDefaultItem =
			new JRadioButtonMenuItem( "Default" );
		pickLevelButtonGroup.add( editPickDefaultItem );
		editPickDefaultItem.setSelected( true );
		editPickLevelMenu.add( editPickDefaultItem );
		editPickLevelMenu.add( new JSeparator() );
		JRadioButtonMenuItem editPickStructuresItem =
			new JRadioButtonMenuItem( "Structures" );
		pickLevelButtonGroup.add( editPickStructuresItem );
		editPickLevelMenu.add( editPickStructuresItem );
		JRadioButtonMenuItem editPickChainsItem =
			new JRadioButtonMenuItem( "Chains" );
		pickLevelButtonGroup.add( editPickChainsItem );
		editPickLevelMenu.add( editPickChainsItem );
		JRadioButtonMenuItem editPickFragmentsItem =
			new JRadioButtonMenuItem( "Fragments" );
		pickLevelButtonGroup.add( editPickFragmentsItem );
		editPickLevelMenu.add( editPickFragmentsItem );
		JRadioButtonMenuItem editPickResiduesItem =
			new JRadioButtonMenuItem( "Residues" );
		pickLevelButtonGroup.add( editPickResiduesItem );
		editPickLevelMenu.add( editPickResiduesItem );
	*/

		menuBar.add( editMenu );

		//
		// View Menu
		//

		JMenu viewMenu = new JMenu( "View" );

		JMenuItem viewResetItem = new JMenuItem( "Reset View" );
		ActionListener viewResetListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				resetView( );
			}
		};
		viewResetItem.addActionListener( viewResetListener );
		viewMenu.add( viewResetItem );

		JCheckBoxMenuItem viewStereoItem = new JCheckBoxMenuItem( "Toggle Stereo" );
		ActionListener viewStereoListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				structureViewer.setStereoEnable( ! structureViewer.getStereoEnable( ) );
			}
		};
		viewStereoItem.addActionListener( viewStereoListener );
		viewMenu.add( viewStereoItem );

		viewMenu.add( new JSeparator() );

		ButtonGroup viewerButtonGroup = new ButtonGroup( );

		JRadioButtonMenuItem viewExamineItem = new JRadioButtonMenuItem( "Examine Viewer" );
		ActionListener viewExamineListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				setNavigationType( 0 );
			}
		};
		viewExamineItem.addActionListener( viewExamineListener );
		viewMenu.add( viewExamineItem );
		viewerButtonGroup.add( viewExamineItem );
		viewExamineItem.setSelected( true );
		viewExamineItem.setEnabled( false ); // JLM DEBUG: Feature not complete.

		JRadioButtonMenuItem viewWalkItem = new JRadioButtonMenuItem( "Walk Viewer" );
		ActionListener viewWalkListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				setNavigationType( 1 );
			}
		};
		viewWalkItem.addActionListener( viewWalkListener );
		viewMenu.add( viewWalkItem );
		viewerButtonGroup.add( viewWalkItem );
		viewWalkItem.setEnabled( false ); // JLM DEBUG: Feature not complete.

		JRadioButtonMenuItem viewNoneItem = new JRadioButtonMenuItem( "None Viewer" );
		ActionListener viewNoneListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				setNavigationType( 2 );
			}
		};
		viewNoneItem.addActionListener( viewNoneListener );
		viewMenu.add( viewNoneItem );
		viewerButtonGroup.add( viewNoneItem );
		viewNoneItem.setEnabled( false ); // JLM DEBUG: Feature not complete.

		menuBar.add( viewMenu );

		//
		// Format Menu
		//

		JMenu formatMenu = new JMenu( "Format" );

		JMenuItem formatStylesItem = new JMenuItem( "Edit Styles..." );
		ActionListener formatStylesListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				showStyleEditorDialog( );
			}
		};
		formatStylesItem.addActionListener( formatStylesListener );
		formatMenu.add( formatStylesItem );

		JMenuItem structureViewerPrefsItem = new JMenuItem(
			"Structure Viewer Preferences..." );
		ActionListener structureViewerPrefsListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				showStructureViewerPrefsFrame( );
			}
		};
		structureViewerPrefsItem.addActionListener(
			structureViewerPrefsListener );
		formatMenu.add( structureViewerPrefsItem );

		JMenuItem structureViewerDepthItem = new JMenuItem(
			"Structure Viewer Depth Queueing..." );
		ActionListener structureViewerDepthListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				showStructureViewerDepthDialog( );
			}
		};
		structureViewerDepthItem.addActionListener(
			structureViewerDepthListener );
		formatMenu.add( structureViewerDepthItem );

		formatMenu.add( new JSeparator() );

		//
		// Predefined scene styles.
		//

		JMenuItem comboStyleItem = new JMenuItem( "Combo Style" );
		ActionListener comboStyleListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				buildView( StructureViewer.VIEW_COMBO );
			}
		};
		comboStyleItem.addActionListener( comboStyleListener );
		formatMenu.add( comboStyleItem );


		JMenuItem ballStickStyleItem = new JMenuItem( "Ball-and-Stick" );
		ActionListener ballStickStyleListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				buildView( StructureViewer.VIEW_BALL_AND_STICK );
			}
		};
		ballStickStyleItem.addActionListener( ballStickStyleListener );
		formatMenu.add( ballStickStyleItem );


		JMenuItem stickStyleItem = new JMenuItem( "Stick Bonds" );
		ActionListener stickStyleListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				buildView( StructureViewer.VIEW_STICKS );
			}
		};
		stickStyleItem.addActionListener( stickStyleListener );
		formatMenu.add( stickStyleItem );


		JMenuItem backboneStyleItem = new JMenuItem( "Backbone Trace" );
		ActionListener backboneStyleListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				buildView( StructureViewer.VIEW_BACKBONE_LINE );
			}
		};
		backboneStyleItem.addActionListener( backboneStyleListener );
		formatMenu.add( backboneStyleItem );


		JMenuItem ribbonStyleItem = new JMenuItem( "Ribbons" );
		ActionListener ribbonStyleListener = new ActionListener( )
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				buildView( StructureViewer.VIEW_BACKBONE_RIBBON );
			}
		};
		ribbonStyleItem.addActionListener( ribbonStyleListener );
		formatMenu.add( ribbonStyleItem );


		menuBar.add( formatMenu );

		//
		// Tools Menu
		//

		JMenu toolsMenu = new JMenu( "Tools" );

		toolsInspectorItem = new JMenuItem( "Show Inspector" );
		ActionListener toolsInspectorListener = new ActionListener()
		{
			public void actionPerformed( ActionEvent actionEvent )
			{
				showInspector( );
			}
		};
		toolsInspectorItem.addActionListener( toolsInspectorListener );
		toolsInspectorItem.setAccelerator(
			KeyStroke.getKeyStroke( KeyEvent.VK_I, Event.CTRL_MASK ) );
		toolsMenu.add( toolsInspectorItem );

		menuBar.add( toolsMenu );

		//
		// Return the menu bar.
		//

		return menuBar;
	}


	/**
	 * Reset the 3D StructureViewer viewpoint so that all geometry is visible.
	 */
	public void buildView( int viewType )
	{
		structureViewer.buildView( viewType );
	}

	/**
	 * Reset the 3D StructureViewer viewpoint so that all geometry is visible.
	 */
	public void resetView( )
	{
		structureViewer.resetView( );
	}

	private JFileChooser jFileChooser = null;

	/**
	 * Present a file "open..." dialog box in order to load a data set
	 * from local disk.
	 */
	public void fileOpen( )
	{
		if ( jFileChooser == null )
		{
			jFileChooser = new JFileChooser();
			String loaders[] = StructureFactory.getFileStructureLoaderNames( );
			for ( int i=0; i<loaders.length; i++ )
			{
				final FileStructureLoader loader =
					StructureFactory.getFileStructureLoader( loaders[i] );
				final String loaderName = loader.getLoaderName( );

				FileFilter structureFilter = new FileFilter( )
				{
					private FileStructureLoader fsLoader = null;
					private String fslName = null;

					// public FileFilter( ) // anonymous constructor
					{
						fsLoader = loader;
						fslName = loaderName;
					}

					public boolean accept( File file )
					{
						if ( loader.canLoad( file ) ) return true;
						if ( file.isDirectory() ) return true;
						return false;
					}
					public String getDescription( )
					{
						return loaderName;
					}
				};
				jFileChooser.addChoosableFileFilter( structureFilter );
			}
			// jFileChooser.setFileFilter( structureFilter );
		}

		int returnVal = jFileChooser.showOpenDialog( explorerFrame );
		if ( returnVal == JFileChooser.APPROVE_OPTION )
		{
			File file = jFileChooser.getSelectedFile( );
			addStructure( StructureFactory.load( file ) );
		}
	}


	private void doRcsbLoad( )
	{
		String str = (String) pdbIdList.getSelectedItem( );
		if ( str == null ) return;
		if ( str.equals( "" ) ) return;
		String id = str.toLowerCase( );
		try
		{
			addStructure( StructureFactory.load( new URL( "ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/" + id + ".cif.gz" ) ) );
		}
		catch ( MalformedURLException e )
		{
			Status.output( Status.LEVEL_ERROR, e.toString() );
		}
	}

	/**
	 * Add a structure to the default document.
	 */
	public void addStructure( Structure structure )
	{
		if ( structure == null ) return;
		structureDocument.addStructure( structure );
	}

	/**
	 * Remove a structure from the default document.
	 */
	public void removeStructure( Structure structure )
	{
		if ( structure == null ) return;
		structureDocument.removeStructure( structure );
	}

	/**
	 * Remove (close) all structures from the default document.
	 */
	public void closeAll( )
	{
		structureDocument.removeAllStructures( );
	}


	private JFrame inspectorFrame = null;
	private StructureComponentInspector inspector = null;

	/**
	 * Show or hide the inspector window.
	 */
	public void showInspector( )
	{
		if ( inspectorFrame == null )
		{
			// Open an inpsector window
			inspectorFrame = new JFrame( "MBT Inspector" );
			Container inspectorFrameContainer =
				inspectorFrame.getContentPane( );
			inspectorFrame.setSize( 700, 374 );
			inspector = new StructureComponentInspector( );
			inspectorFrameContainer.add( inspector );
			WindowAdapter closer = new WindowAdapter()
			{
				public void windowClosing( WindowEvent event )
				{
					structureDocument.removeViewer( inspector );
				}
			};
			inspectorFrame.addWindowListener( closer );
		}

		if ( ! inspectorFrame.isVisible() )
			structureDocument.addViewer( inspector );

		inspectorFrame.setVisible( true );
	}

	/**
	 * Go fetch a list of PDB ID codes from the RCSB ftp site
	 * and return the short names in a Vector.
	 */
	public void loadIdCodes( )
	{
		if ( idCodes != null ) return;
		Cursor oldCursor = pdbIdList.getCursor( );
		pdbIdList.setCursor( Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR) );

		URL url = null;
		try
		{
			url = new URL( "ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/" );
		}
		catch ( MalformedURLException e )
		{
			System.err.println( e );
			pdbIdList.setCursor( oldCursor );
			return;
		}

		InputStream inputStream = null;
		try
		{
			inputStream = url.openStream( );
		}
		catch ( java.io.IOException e )
		{
			System.err.println( e );
			pdbIdList.setCursor( oldCursor );
			return;
		}

		InputStreamReader inputStreamReader = new InputStreamReader( inputStream );
		BufferedReader bufferedReader = new BufferedReader( inputStreamReader );
		int available = 0;
		idCodes = new Vector( );
		do
		{
			try
			{
				available = inputStream.available( );
				String line = bufferedReader.readLine( );
				if ( ! line.endsWith( ".gz" ) ) continue;
				int lastSpace = line.lastIndexOf( ' ' );
				line = line.substring( lastSpace+1 );
				int period = line.indexOf( '.' );
				line = line.substring( 0, period );
				idCodes.add( line );
			}
			catch ( java.io.IOException e )
			{
				System.err.println( e );
				available = 0;
			}
		} while ( available > 0 );

		pdbIdList.setModel( new DefaultComboBoxModel( idCodes ) );
		pdbIdList.setCursor( oldCursor );
	}

	/**
	 * Save an image file of the 3D StructureViewer rendering.
	 */
	public void saveImage( )
	{
		// http://java.sun.com/j2se/1.4.1/docs/guide/imageio/spec/imageio_guideTOC.fm.html

		int width = structureViewer.getWidth( );
		int height = structureViewer.getHeight( );

		// Ask the user for file name, image file format, and image size.
		ImageFileManager imageFileManager =
			new ImageFileManager( explorerFrame );
		File file = imageFileManager.save( width, height );
		if ( file == null ) return; // User canceled the save.
		width = imageFileManager.getSaveWidth( );
		height = imageFileManager.getSaveHeight( );

		// Ask the StructureViewer to produce a BufferedImage object
		// at the specified resolution.
		BufferedImage bufferedImage =
			structureViewer.getBufferedImage( width, height );

		// Save the image.
		imageFileManager.save( bufferedImage, file );
	}

	/**
	 * Save a series of images using a horizontal rotation left and right of
	 * the current view. This can be used for generating stereo pairs or
	 * higher image counts for lenticular image or hologram generation.
	 *
	 * @param imageCount  How many images will be generated.
	 * @param sweepAngle  The number of degrees swept by the camera.
	 */
	public void saveImages( int imageCount, double sweepAngle )
	{
		if ( imageCount <= 0 ) return;
		if ( sweepAngle <= 0.0 ) return;

		double halfSweep = sweepAngle / 2.0;
		double sweepStep = sweepAngle / (double) (imageCount - 1);
		int width = structureViewer.getWidth( );
		int halfWidth = width / 2;
		int height = structureViewer.getHeight( );
		int halfHeight = height / 2;
		int circleRadius = halfHeight;
		double pixelsPerDegree = (double) circleRadius / 90.0;
		final int matrixSize = 16;
		double newMatrix[] = new double[matrixSize];
		double oldMatrix[] = new double[matrixSize];

		System.err.println( "Explorer.saveImages: " +
			"imageCount = " + imageCount +
			", sweepAngle = " + sweepAngle +
			", sweepStep = " + sweepStep +
			", width = " + width +
			", halfWidth = " + halfWidth +
			", height = " + height +
			", halfHeight = " + halfHeight +
			", pixelsPerDegree = " + pixelsPerDegree
		);
        structureViewer.getViewpoint( oldMatrix );

		edu.sdsc.vis.viewers.VirtualSphere vs =
			new edu.sdsc.vis.viewers.VirtualSphere( );
		vs.setCircle( halfWidth, halfHeight, circleRadius );
		javax.media.j3d.Transform3D transform3D =
			new javax.media.j3d.Transform3D( );

		for ( int i=0; i<imageCount; i++ )
		{
			//
			// Save the old matrix.
			//
        	System.arraycopy( oldMatrix, 0, newMatrix, 0, matrixSize );
			transform3D.set( oldMatrix );

			//
			// Compute a new camera viewpoint.
			//
			double angle = - halfSweep + (double) i * sweepStep;
			int dx = (int) (angle * pixelsPerDegree);
			vs.compute( halfWidth, halfHeight, halfWidth+dx, halfHeight );
			vs.t3d.invert( );
			transform3D.mul( vs.t3d );
			transform3D.get( newMatrix );

			System.err.println( "Explorer.saveImages: " +
				"i = " + i +
				", angle = " + angle +
				", dx = " + dx
			);

			//
			// Set the new camera viewpoint.
			//
        	structureViewer.setViewpoint( newMatrix );

			//
			// Save an image of the new viewpoint.
			//
		
			// System.err.print( "Hit RETURN:" );
			// try { System.in.read(); } catch ( Exception e ) {}

			BufferedImage bufferedImage = structureViewer.getBufferedImage( );
			ImageFileManager imageFileManager =
				new ImageFileManager( explorerFrame );
			imageFileManager.save( bufferedImage );

			//
			// Restore the old matrix.
			//
        	structureViewer.setViewpoint( oldMatrix );
		}

        structureViewer.setViewpoint( oldMatrix );
	}


	private PrinterJob printerJob = null;
	private PageFormat pageFormat = null;

	/**
	 * Configure the printing page set-up with or without a dialog box prompt.
	 */
	public void pageSetup( boolean withDialog )
	{
		// Do we need to create a print job?
		if ( printerJob == null )
			printerJob = PrinterJob.getPrinterJob( );

		// Do we need to create an initial page set-up?
		if ( pageFormat == null )
		{
			pageFormat = printerJob.defaultPage( );
			// PrintRequestAttributeSet aset = new HashPrintRequestAttributeSet( );
			// aset.add( OrientationRequested.LANDSCAPE );
			// aset.add( new Copies(1) );
			// aset.add( new JobName( "MBT", null ) );
		}

		if ( withDialog )
			pageFormat = printerJob.pageDialog( pageFormat );
	}


	/**
	 * Print the 3D StructureViewer rendering.
	 */
	public void print( )
	{
		Printable svPrintable = new Printable()
		{
			public int print( Graphics graphics, PageFormat pageFormat, int pageIndex )
			{
				if ( pageIndex >= 0 )
				{
					// Get the printable page's size information.
					int pageX = (int) pageFormat.getImageableX( );
					int pageY = (int) pageFormat.getImageableY( );
					int pageW = (int) pageFormat.getImageableWidth( );
					int pageH = (int) pageFormat.getImageableHeight( );
					float pageAspect = (float) pageW / (float) pageH;

					// Get the veiwer's size information.
					int viewerW = structureViewer.getWidth( );
					int viewerH = structureViewer.getHeight( );
					float viewerAspect = (float) viewerW / (float) viewerH;

					// Get an image that's the same aspect ratio as viewed,
					// but at a "good" resolution for printing.
					int imageW = 1024; // Max resolution
					int imageH = 1024; // Max resolution
					if ( viewerAspect >= 1.0 )
					{
						imageH = (int) ((float) imageW / pageAspect);
					}
					else
					{
						imageW = (int) ((float) imageH * pageAspect);
					}
					BufferedImage bufferedImage =
						structureViewer.getBufferedImage( imageW, imageH );

					graphics.drawImage(
						bufferedImage,
						pageX, pageY, pageW, pageH,
						Color.white,
						null
					);
					return Printable.PAGE_EXISTS;
				}
				else
				{
					return Printable.NO_SUCH_PAGE;
				}
			}
		};

		// Make sure we have a printerJob, and
		// get the Page SetUp (PageFormat) without a dialog box...
		pageSetup( false );

		// Prepare the print job.
		Book book = new Book( );
		book.append( svPrintable, pageFormat );
		printerJob.setPageable( book );

		// If we have a graphics head, show a Print dialog...
		try
		{
			if ( ! printerJob.printDialog() ) return;
		}
		catch( HeadlessException e )
		{
			// Go ahead and print without the print dialog prompt.
		}

		// Print.
		try
		{
			printerJob.print( );
		}
		catch( PrinterException e )
		{
			Status.output( Status.LEVEL_ERROR, "Explorer.print: " + e );
		}
	}


	private StyleEditorDialog styleEditorDialog = null;

	/**
	 * Show or hide the Styles editor frame.
	 */
	public void showStyleEditorDialog( )
	{
		if ( styleEditorDialog == null )
			styleEditorDialog = new StyleEditorDialog( structureDocument );

		styleEditorDialog.show( );
	}

	private DepthCueDialog depthCueDialog = null;

	/**
	 * Show or hide the StructureViewer depth queueing dialog.
	 */
	public void showStructureViewerDepthDialog( )
	{
		if ( depthCueDialog == null )
			depthCueDialog = new DepthCueDialog(
				explorerFrame, structureViewer );
		depthCueDialog.show( );
	}

	private JFrame structureViewerPrefsFrame = null;

	/**
	 * Show or hide the Structure Viewer Preferences frame.
	 */
	public void showStructureViewerPrefsFrame( )
	{
		if ( structureViewerPrefsFrame == null )
		{
			// Open a Structure Viewer Preferences panel in a frame
			structureViewerPrefsFrame = new JFrame(
				"Structure Viewer Preferences" );
			Container structureViewerPrefsContainer =
				structureViewerPrefsFrame.getContentPane( );
			structureViewerPrefsFrame.setSize( 300, 100 );
			StructureViewerPrefs structureViewerPrefs =
				new StructureViewerPrefs( structureViewer );
			structureViewerPrefsContainer.add( structureViewerPrefs );
		}

		structureViewerPrefsFrame.setVisible( true );
	}

	/**
	 * Set the navigation behavior type.
	 */
	public void setNavigationType( int type )
	{
		structureViewer.setNavigationType( type );
	}

	/**
	 * Get the navigation behavior type.
	 */
	public int getNavigationType( )
	{
		return structureViewer.getNavigationType( );
	}

	/**
	 * Select everything in the document.
	 */
	public void selectAll( )
	{
		int structureCount = structureDocument.getStructureCount( );
		for ( int s=0; s<structureCount; s++ )
		{
			Structure structure = structureDocument.getStructure( s );
			StructureMap structureMap = structure.getStructureMap( );
			StructureStyles structureStyles = structureMap.getStructureStyles( );
			structureStyles.selectAll( );
		}
	}

	/**
	 * Unselect everything in the document.
	 */
	public void unselectAll( )
	{
		int structureCount = structureDocument.getStructureCount( );
		for ( int s=0; s<structureCount; s++ )
		{
			Structure structure = structureDocument.getStructure( s );
			StructureMap structureMap = structure.getStructureMap( );
			StructureStyles structureStyles = structureMap.getStructureStyles( );
			structureStyles.unselectAll( );
		}
	}
}