org.biojava.nbio.structure.align.gui.StructureLoaderThread Maven / Gradle / Ivy
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/*
* 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.align.gui;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.StructureImpl;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.quaternary.BioAssemblyTools;
import javax.swing.*;
import java.awt.*;
public class StructureLoaderThread extends SwingWorker {
String name;
boolean showBiolAssembly;
UserConfiguration config;
StructureLoaderThread(UserConfiguration config, String name, boolean showBiolAssembly){
this.name = name;
this.showBiolAssembly = showBiolAssembly;
this.config = config;
}
@Override
protected String doInBackground() {
System.out.println("loading " + name );
AtomCache cache = new AtomCache(config.getPdbFilePath(),config.getCacheFilePath());
Structure s = null;
try {
if ( showBiolAssembly) {
s= StructureIO.getBiologicalAssembly(name);
int atomCount = StructureTools.getNrAtoms(s);
if ( atomCount > 200000){
// uh oh, we are probably going to exceed 512 MB usage...
// scale down to something smaller
System.err.println("Structure very large. Reducing display to C alpha atoms only");
s = BioAssemblyTools.getReducedStructure(s);
}
} else {
s = cache.getStructure(name);
}
System.out.println("done loading structure...");
StructureAlignmentJmol jmol = new StructureAlignmentJmol();
jmol.setStructure(s);
jmol.evalString("set antialiasDisplay on; select all;spacefill off; wireframe off; backbone off; cartoon;color cartoon chain; select ligand;wireframe 0.16;spacefill 0.5; select all; color cartoon structure;");
jmol.evalString("save STATE state_1");
} catch (Exception e){
e.printStackTrace();
JOptionPane.showMessageDialog(null, "Error while loading " + name + ":" + e.getMessage());
s = new StructureImpl();
}
hideProgressBar();
return "Done.";
}
public static void showProgressBar() {
if ( progressFrame == null){
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
// TODO Auto-generated method stub
final JFrame frame = new JFrame("Loading ...");
final JProgressBar progressBar = new JProgressBar();
progressBar.setIndeterminate(true);
final JPanel contentPane = new JPanel();
contentPane.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
contentPane.setLayout(new BorderLayout());
contentPane.add(new JLabel("Loading ..."), BorderLayout.NORTH);
contentPane.add(progressBar, BorderLayout.CENTER);
frame.setContentPane(contentPane);
frame.pack();
frame.setLocationRelativeTo(null);
progressFrame = frame;
frame.setVisible(true);
}
});
}
}
static JFrame progressFrame = null;
private void hideProgressBar() {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
if ( progressFrame != null){
progressFrame.dispose();
progressFrame = null;
}
}
});
}
}