taverna-workbench-renderers-exts/src/main/java/net/sf/taverna/t2/renderers/JMolRenderer.java

/*******************************************************************************
 * Copyright (C) 2007 The University of Manchester
 *
 *  Modifications to the initial code base are copyright of their
 *  respective authors, or their employers as appropriate.
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public License
 *  as published by the Free Software Foundation; either version 2.1 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
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser 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
 ******************************************************************************/
package net.sf.taverna.t2.renderers;

import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.nio.file.Path;

import javax.swing.JComponent;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextArea;

import org.apache.log4j.Logger;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAdapter;
import org.jmol.api.JmolSimpleViewer;
import org.jmol.api.JmolViewer;
import org.jmol.viewer.Viewer;

import uk.org.taverna.databundle.DataBundles;

/**
 * Renders using the Jmol software for chemical structures
 *
 * @author Tom Oinn
 * @author Ian Dunlop
 * @author Alex Nenadic
 */
public class JMolRenderer implements Renderer {

	private Logger logger = Logger.getLogger(JMolRenderer.class);

	private int MEGABYTE = 1024 * 1024;

	public boolean isTerminal() {
		return true;
	}

	@Override
	public boolean canHandle(String mimeType) {
		if (mimeType.matches(".*chemical/x-pdb.*")
				|| mimeType.matches(".*chemical/x-mdl-molfile.*")
				|| mimeType.matches(".*chemical/x-cml.*")) {
			return true;
		}

		return false;
	}

	static final String proteinScriptString = "wireframe off; spacefill off; select protein; cartoon; colour structure; select ligand; spacefill; colour cpk; select dna; spacefill 0.4; wireframe on; colour cpk;";

	static final String scriptString = "select *; spacefill 0.4; wireframe 0.2; colour cpk;";

	@Override
	public String getType() {
		return "Jmol";
	}

	@Override
	public JComponent getComponent(Path path) throws RendererException {
		if (DataBundles.isValue(path) || DataBundles.isReference(path)) {
			long approximateSizeInBytes = 0;
			try {
				approximateSizeInBytes = RendererUtils.getSizeInBytes(path);
			} catch (Exception ex) {
				logger.error("Failed to get the size of the data", ex);
				return new JTextArea(
						"Failed to get the size of the data (see error log for more details): \n"
								+ ex.getMessage());
			}

			if (approximateSizeInBytes > MEGABYTE) {
				int response = JOptionPane
						.showConfirmDialog(
								null,
								"Result is approximately "
										+ bytesToMeg(approximateSizeInBytes)
										+ " MB in size, there could be issues with rendering this inside Taverna\nDo you want to continue?",
								"Render using Jmol?", JOptionPane.YES_NO_OPTION);

				if (response != JOptionPane.YES_OPTION) {
					return new JTextArea(
							"Rendering cancelled due to size of data. Try saving and viewing in an external application.");
				}
			}

			String resolve = null;
			try {
				// Resolve it as a string
				resolve = RendererUtils.getString(path);
			} catch (Exception e) {
				logger.error("Reference Service failed to render data as string", e);
				return new JTextArea(
						"Reference Service failed to render data as string (see error log for more details): \n"
								+ e.getMessage());
			}
			JmolPanel panel = new JmolPanel();
			JmolSimpleViewer viewer = null;
			try {
				viewer = panel.getViewer();
				viewer.openStringInline(resolve);
				if (((JmolViewer) viewer).getAtomCount() > 300) {
					viewer.evalString(proteinScriptString);
				} else {
					viewer.evalString(scriptString);
				}
			} catch (Exception e) {
				logger.error("Failed to create Jmol renderer", e);
				return new JTextArea(
						"Failed to create Jmol renderer (see error log for more details): \n"
								+ e.getMessage());
			}
			return panel;
		} else {
			logger.error("Failed to obtain the data to render: data is not a value or reference");
			return new JTextArea(
					"Failed to obtain the data to render: data is not a value or reference");
		}
	}

	class JmolPanel extends JPanel {
		private static final long serialVersionUID = 1L;

		JmolSimpleViewer viewer;
		JmolAdapter adapter;

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

		public JmolSimpleViewer getViewer() {
			return viewer;
		}

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

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

	/**
	 * Work out size of file in megabytes to 1 decimal place
	 *
	 * @param bytes
	 * @return
	 */
	private int bytesToMeg(long bytes) {
		float f = bytes / MEGABYTE;
		return Math.round(f);
	}
}