/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.gui;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.gui.MenuCreator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.swing.*;
import java.awt.*;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
public class JmolViewerImpl implements StructureViewer {
private static final Logger logger = LoggerFactory.getLogger(JmolViewerImpl.class);
public static final String viewer = "org.jmol.api.JmolSimpleViewer";
public static final String adapter = "org.jmol.api.JmolAdapter";
public static final String smartAdapter = "org.jmol.adapter.smarter.SmarterJmolAdapter";
Structure structure;
JmolPanel jmolPanel;
JFrame frame;
public JmolViewerImpl() {
frame = new JFrame();
JMenuBar menu = MenuCreator.initJmolMenu(frame, null, null, null);
frame.setJMenuBar(menu);
frame.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
frame.dispose();
//System.exit(0);
}
});
Container contentPane = frame.getContentPane();
Box vBox = Box.createVerticalBox();
try {
jmolPanel = new JmolPanel();
} catch (ClassNotFoundException e) {
e.printStackTrace();
System.err.println("Could not find Jmol in classpath, please install first. http://www.jmol.org");
return;
}
jmolPanel.setPreferredSize(new Dimension(500, 500));
vBox.add(jmolPanel);
JTextField field = new JTextField();
field.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
field.setText("enter RASMOL like command...");
// RasmolCommandListener listener = new RasmolCommandListener(jmolPanel, field);
// field.addActionListener(listener);
// field.addMouseListener(listener);
// field.addKeyListener(listener);
vBox.add(field);
contentPane.add(vBox);
frame.pack();
frame.setVisible(true);
}
public void setTitle(String label) {
frame.setTitle(label);
frame.repaint();
}
@Override
public void setStructure(Structure structure) {
if (jmolPanel == null) {
System.err.println("please install Jmol first");
return;
}
setTitle(structure.getPDBCode());
// actually this is very simple
// just convert the structure to a PDB file
String pdb = structure.toPDB();
//System.out.println(s.isNmr());
//System.out.println(pdb);
// Jmol could also read the file directly from your file system
//viewer.openFile("/Path/To/PDB/1tim.pdb");
//System.out.println(pdb);
jmolPanel.openStringInline(pdb);
// send the PDB file to Jmol.
// there are also other ways to interact with Jmol, e.g make it directly
// access the biojava structure object, but they require more
// code. See the SPICE code repository for how to do this.
}
@Override
public void clear() {
// TODO Auto-generated method stub
}
@Override
public Color getColor() {
// TODO Auto-generated method stub
return null;
}
@Override
public Selection getSelection() {
// TODO Auto-generated method stub
return null;
}
@Override
public void repaint() {
// TODO Auto-generated method stub
}
@Override
public void setColor(Color red) {
// TODO Auto-generated method stub
}
@Override
public void setSelection(Selection selection) {
// TODO Auto-generated method stub
}
@Override
public void setStyle(RenderStyle wireframe) {
// TODO Auto-generated method stub
}
@Override
public void setZoom(int i) {
// TODO Auto-generated method stub
}
@SuppressWarnings("rawtypes")
static class JmolPanel extends JPanel {
/**
*
*/
private static final long serialVersionUID = -3661941083797644242L;
Class viewerC;
Class adapterC;
Class smartAdapterC;
Object viewerO;
Object adapterO;
Method evalString;
Method renderScreenImage;
Method openStringInline;
//JmolSimpleViewer viewer;
//JmolAdapter adapter;
@SuppressWarnings("unchecked")
JmolPanel() throws ClassNotFoundException {
try {
viewerC = Class.forName(viewer);
adapterC = Class.forName(adapter);
smartAdapterC = Class.forName(smartAdapter);
Method m = viewerC.getMethod("allocateSimpleViewer", new Class[]{Component.class, adapterC});
Constructor constructor = smartAdapterC.getConstructor(new Class[]{});
adapterO = constructor.newInstance(new Object[]{});
//viewerC = JmolSimpleViewer.allocateSimpleViewer(this, adapter);
viewerO = m.invoke(viewerC, this, adapterO);
evalString = viewerC.getMethod("evalString", String.class);
renderScreenImage = viewerC.getMethod("renderScreenImage",
new Class[]{Graphics.class, Dimension.class, Rectangle.class});
openStringInline = viewerC.getMethod("openStringInline", new Class[]{String.class});
} catch (InstantiationException ex) {
logger.error("Exception caught", ex);
} catch (IllegalAccessException ex) {
logger.error("Exception caught", ex);
} catch (IllegalArgumentException ex) {
logger.error("Exception caught", ex);
} catch (InvocationTargetException ex) {
logger.error("Exception caught", ex);
} catch (NoSuchMethodException e) {
logger.error("Exception caught", e);
}
evalString("set scriptQueue on;");
}
public Class getViewer() {
return viewerC;
}
public void evalString(String rasmolScript) {
try {
evalString.invoke(viewerO, rasmolScript);
} catch (Exception e) {
e.printStackTrace();
}
}
public void openStringInline(String pdbFile) {
try {
openStringInline.invoke(viewerO, pdbFile);
} catch (Exception e) {
e.printStackTrace();
}
}
public void executeCmd(String rasmolScript) {
try {
evalString.invoke(viewerO, rasmolScript);
} catch (Exception e) {
e.printStackTrace();
}
}
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);
try {
renderScreenImage.invoke(viewerO, g, currentSize, rectClip);
} catch (Exception e) {
e.printStackTrace();
}
}
}
}