JmolView.java

/*
 * Copyright (c) 2012 European Synchrotron Radiation Facility,
 *                    Diamond Light Source Ltd.
 *
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 */ 
package fable.framework.ui.views;

import java.awt.Container;
import java.awt.Dimension;
import java.awt.Frame;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.io.File;

import javax.swing.JApplet;
import javax.swing.JPanel;

import org.eclipse.swt.SWT;
import org.eclipse.swt.awt.SWT_AWT;
import org.eclipse.swt.layout.GridData;
import org.eclipse.swt.layout.GridLayout;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.FileDialog;
import org.eclipse.swt.widgets.Shell;
import org.eclipse.ui.IWorkbenchWindow;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.part.ViewPart;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAdapter;
import org.jmol.api.JmolSimpleViewer;
import org.jmol.util.Logger;

import fable.framework.toolbox.FableUtils;

/**
 * JmolView is a view for displaying 3d chemical structures using Jmol.
 * 
 * TODO
 * 
 * add controls to change view add support for scripting
 * 
 * @author Andy Gotz
 * 
 */
public class JmolView extends ViewPart {
	public static final String ID = "fable.framework.ui.views.JmolView";
	final static String strScript = "delay; move 360 0 0 0 0 0 0 0 4;";
	public static int viewCount = 0;

	private Composite swtAwtComponent;
	private JApplet container;
	private Frame frame;
	private JmolPanel jmolPanel;
	private JmolSimpleViewer viewer;
	private String fullFileName, fileName;

	@Override
	public void createPartControl(Composite parent) {

		parent.setLayout(new GridLayout(1, false));
		swtAwtComponent = new Composite(parent, SWT.EMBEDDED
				| SWT.NO_BACKGROUND);
		GridData gdlist = new GridData(SWT.FILL, SWT.FILL, true, true);
		gdlist.verticalSpan = 1;
		gdlist.horizontalSpan = 1;
		swtAwtComponent.setLayout(new GridLayout());
		swtAwtComponent.setLayoutData(gdlist);
		frame = SWT_AWT.new_Frame(swtAwtComponent);
		container = new JApplet();
		frame.add(container);
		/* the following code was taken from Integration.java in the jmol svn */
		Container contentPane = container.getContentPane();
		jmolPanel = new JmolPanel();

		contentPane.add(jmolPanel);
		frame.setVisible(true);
		viewer = jmolPanel.getViewer();
		// this initial ZAP command is REQUIRED in Jmol 11.4.
		viewer.evalString("zap");
		// viewer.openFile("/home/goetz/jmol/caffeine.xyz");
		// viewer.openFile("http://chemapps.stolaf.edu/jmol/docs/examples-11/data/caffeine.xyz");
		// viewer.evalString(strScript);
		// viewer.openStringInline(strXyzHOH);
	}

	final static String strXyzHOH = "3\n" + "water\n" + "O  0.0 0.0 0.0\n"
			+ "H  0.76923955 -0.59357141 0.0\n"
			+ "H -0.76923955 -0.59357141 0.0\n";

	static class JmolPanel extends JPanel {
		private static final long serialVersionUID = 1L;
		JmolSimpleViewer viewer;
		JmolAdapter adapter;

		JmolPanel() {
			adapter = new SmarterJmolAdapter();
			viewer = JmolSimpleViewer.allocateSimpleViewer(this, adapter);
		}

		public JmolSimpleViewer getViewer() {
			return viewer;
		}

		final Dimension currentSize = new Dimension();
		final Rectangle rectClip = new Rectangle();

		public void paint(Graphics g) {
			getSize(currentSize);
			g.getClipBounds(rectClip);
			viewer.renderScreenImage(g, currentSize, rectClip);
		}
	}

	@Override
	public void setFocus() {
		// TODO Auto-generated method stub

	}

	/**
	 * Browse for a structure file name and open it with the Jmol viewer.
	 * 
	 */
	public void browseFile() {
		IWorkbenchWindow activeWindow = PlatformUI.getWorkbench()
				.getActiveWorkbenchWindow();
		if (activeWindow != null) {
			try {
				FileDialog fileDlg = new FileDialog(new Shell(), SWT.MULTI);
				fileDlg
						.setText("Select a file containing a structure to display with Jmol");
				String file = fileDlg.open();
				if (file != null) {
					file = fileDlg.getFilterPath() + File.separatorChar
							+ fileDlg.getFileName();
					openFile(file);
				}
			} catch (Exception ex) {
				FableUtils.excMsg(this, "Error opening JMol Viewer", ex);
			}
		}
	}

	/**
	 * Open a structure file and display it with the Jmol viewer. Display the
	 * file name in the view part name.
	 * 
	 * @param fullFileName
	 */
	public void openFile(String _fullFileName) {
		fullFileName = _fullFileName;
		viewer.openFile(fullFileName);
		String strError = viewer.getOpenFileError();
		if (strError != null)
			Logger.error(strError);
		File file = new File(fullFileName);
		fileName = file.getName();
		setPartName("Jmol " + fileName);
	}

	/**
	 * @return the id
	 */
	public static String getID() {
		return ID;
	}
	
}