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/*
* PDB web 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.
*
*
* Created on Jun 13, 2009
* Created by Andreas Prlic
*
*/
package org.biojava.nbio.structure.align.webstart;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
import org.biojava.nbio.structure.align.ce.CeCPMain;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.client.FarmJobParameters;
import org.biojava.nbio.structure.align.client.JFatCatClient;
import org.biojava.nbio.structure.align.client.PdbPair;
import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;
import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
import org.biojava.nbio.structure.align.gui.AlignmentGui;
import org.biojava.nbio.structure.align.gui.ChooseDirAction;
import org.biojava.nbio.structure.align.gui.DisplayAFP;
import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import javax.swing.*;
import java.io.File;
public class WebStartMain
{
static UserConfiguration userConfig;
/**
* If no arguments, shows AlignmentGui for pairwise alignments.
* if 1 argument: dbmenu shows the DBSearchGUI, otherwise the AlignentGUI is shown.
*
* if more than 3 arguments takes the following arguments
* arg0 : fatcat or biojava .
* arg1 : pdb1.X
* arg2 ; pdb2.X
*
* The 4th argument is optional and it could be the serverLocation which the client should talk to.
*
* @param args
*/
public static void main(String[] args){
AligUIManager.setLookAndFeel();
if ( args.length == 0){
//JOptionPane.showMessageDialog(null,
// "Not enough arguments. Need at least 3, but only got " + args.length);
// we did not get enough arguments, show the general user interface...
javax.swing.SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
AlignmentGui.getInstance();
}
});
return;
}
else if ( args.length < 3){
//String arg0 = args[0];
javax.swing.SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
AlignmentGui.getInstance();
}
});
return;
}
String arg0 = args[0];
if (! (arg0.equals("fatcat") ||
arg0.equals("biojava") ||
arg0.equals("fatcat_flexible") ||
arg0.equals("ce") ||
arg0.equals("ce_cp") ||
arg0.equals("sw")
)){
JOptionPane.showMessageDialog(null,
"Wrong arguments. First argument has to be \"fatcat\", \"ce\", \"ce_cp\", \"sw\", \"fatcat_flexible\", or \"biojava\", but got " + arg0);
return;
}
String serverLocation = FarmJobParameters.DEFAULT_SERVER_URL;
if ( args.length > 3 ) {
// we have 4 arguments.
// in this case the 4th has to be the server URL
serverLocation = args[3];
}
try {
String name1 = args[1];
String name2 = args[2];
PdbPair pair = new PdbPair(name1, name2);
System.out.println("### user provided: " + pair);
UserConfiguration config = getWebStartConfig();
System.setProperty(UserConfiguration.PDB_DIR,config.getPdbFilePath());
System.out.println("using PDB file path: " + config.getPdbFilePath());
AtomCache cache = new AtomCache(config);
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
showProgressBar(frame,"Loading PDB files...", "Loading files from local directory or via FTP.");
Atom[] ca1 = cache.getAtoms(pair.getName1());
Atom[] ca2 = cache.getAtoms(pair.getName2());
frame.dispose();
System.out.println("done reading structures");
if (arg0.equalsIgnoreCase("ce") ||
arg0.equalsIgnoreCase("ce_cp") ||
arg0.equalsIgnoreCase("sw") ||
arg0.equalsIgnoreCase("fatcat") ||
arg0.equalsIgnoreCase("fatcat_flexible")){
try {
StructureAlignment algorithm ;
if ( arg0.equalsIgnoreCase("ce"))
algorithm = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);
else if ( arg0.equalsIgnoreCase("ce_cp"))
algorithm = StructureAlignmentFactory.getAlgorithm(CeCPMain.algorithmName);
else if ( arg0.equalsIgnoreCase("fatcat"))
algorithm = StructureAlignmentFactory.getAlgorithm(FatCatRigid.algorithmName);
else if ( arg0.equalsIgnoreCase("fatcat_flexible"))
algorithm = StructureAlignmentFactory.getAlgorithm(FatCatFlexible.algorithmName);
else
algorithm = new SmithWaterman3Daligner();
showStructureAlignment(serverLocation,algorithm ,ca1,ca2,pair.getName1(),pair.getName2());
} catch (Exception e){
e.printStackTrace();
JOptionPane.showMessageDialog(null,
"Something went wrong! : " + e.getMessage());
}
} else if ( arg0.equalsIgnoreCase("biojava")){
try {
//showBiojava(ca1,ca2);
} catch (Exception e){
e.printStackTrace();
JOptionPane.showMessageDialog(null,
"Something went wrong! : " + e.getMessage());
System.exit(0);
}
}
} catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(null,
"Error: " + e.getMessage());
System.exit(0);
return;
}
}
private static JProgressBar showProgressBar(JFrame frame, String title, String displayTxt){
frame.setTitle(title);
JProgressBar progressBar;
JPanel content = new JPanel();
content.setOpaque(true);
//Where the GUI is constructed:
progressBar = new JProgressBar();
progressBar.setToolTipText(title);
progressBar.setValue(0);
progressBar.setStringPainted(true);
progressBar.setIndeterminate(true);
JTextField txt = new JTextField(displayTxt);
txt.setEditable(false);
content.add(txt);
content.add(progressBar);
frame.getContentPane().add(content);
frame.pack();
frame.setVisible(true);
return progressBar;
}
public static UserConfiguration getWebStartConfig(){
// check if we could load it (i.e. we are running in web start mode)
if ( userConfig == null ) {
userConfig = WebStartMain.getDefaultConfig();
}
return userConfig;
}
public static UserConfiguration getDefaultConfig(){
userConfig = new UserConfiguration();
String pdbDir = System.getProperty(UserConfiguration.PDB_DIR);
if ( pdbDir != null) {
userConfig.setPdbFilePath(pdbDir);
}
return userConfig;
}
public static UserConfiguration requestUserConfig(){
if ( userConfig == null) {
//UserConfiguration config = new UserConfiguration();
userConfig = new UserConfiguration();
String pdbDir = System.getProperty(UserConfiguration.PDB_DIR);
if ( pdbDir != null) {
userConfig.setPdbFilePath(pdbDir);
return userConfig;
}
}
JTextField textField = new JTextField();
ChooseDirAction action = new ChooseDirAction(textField, userConfig);
action.actionPerformed(null);
if ( textField.getText() == null) {
// accessing temp. OS directory:
String property = "java.io.tmpdir";
String lineSplit = System.getProperty("file.separator");
String tempdir = System.getProperty(property);
if ( !(tempdir.endsWith(lineSplit ) ) )
tempdir = tempdir + lineSplit;
userConfig.setPdbFilePath(tempdir);
return userConfig;
}
File file = new File(textField.getText());
if ( ! file.isDirectory() ){
// should not happen
System.err.println("did not provide directory, going on level higher! " + file.getAbsolutePath());
file = file.getParentFile();
}
System.setProperty(UserConfiguration.PDB_DIR, file.getAbsolutePath());
userConfig.setPdbFilePath(file.getAbsolutePath());
return userConfig;
}
private static void showStructureAlignment(String serverLocation, StructureAlignment algorithm, Atom[] ca1, Atom[] ca2, String name1, String name2) throws StructureException{
JFrame tmpFrame = new JFrame();
tmpFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
String title = "Calculating " + algorithm.getAlgorithmName() + " V." + algorithm.getVersion()+" alignment... ";
showProgressBar(tmpFrame,title, "Calculating the structure alignment.");
//do the actual alignment
AFPChain afpChain = null;
try {
// using 10 sec as timeout on server now, since we expect the server to be able to complete the calculation within that time...
afpChain = JFatCatClient.getAFPChainFromServer(serverLocation,algorithm.getAlgorithmName(), name1, name2, ca1, ca2, 10000);
} catch (Exception e){
e.printStackTrace();
}
if ( afpChain == null ) {
afpChain = algorithm.align(ca1, ca2);
}
afpChain.setName1(name1);
afpChain.setName2(name2);
tmpFrame.dispose();
// show results
StructureAlignmentJmol jmol = StructureAlignmentDisplay.display(afpChain,ca1,ca2);
System.out.println(afpChain.toCE(ca1, ca2));
DisplayAFP.showAlignmentPanel(afpChain,ca1,ca2,jmol);
}
// private static void showBiojava(Atom[] ca1, Atom[] ca2) throws StructureException{
//
// StructurePairAligner aligner = new StructurePairAligner();
//
// StrucAligParameters params = StrucAligParameters.getDefaultParameters();
// //params.setJoinFast(true);
// //params.setMaxIter(1);
// try {
// // align the full 2 structures with default parameters.
// // see StructurePairAligner for more options and how to align
// // any set of Atoms
// long start = System.currentTimeMillis();
//
//
// aligner.align(ca1,ca2,params);
// long end = System.currentTimeMillis();
// System.out.println("calculation time:" + (end-start));
//
// AlternativeAlignment[] aligs = aligner.getAlignments();
// AlternativeAlignment a = aligs[0];
// System.out.println(a);
//
// if (! BiojavaJmol.jmolInClassPath()){
// System.err.println("Could not find Jmol in classpath, please install first!");
// return;
// }
// // display the alignment in Jmol
//
//
//
// // first get an artificial structure for the alignment
// Structure artificial = a.getAlignedStructure(structure1, structure2);
//
// // and then send it to Jmol (only will work if Jmol is in the Classpath)
// BiojavaJmol jmol = new BiojavaJmol();
// jmol.setTitle(artificial.getName());
// jmol.setStructure(artificial);
//
// // color the two structures
//
//
// jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; " +
// "select not protein and not solvent; spacefill on;");
// jmol.evalString("select */1 ; color red; model 1; ");
//
//
// // now color the equivalent residues ...
//
// String[] pdb1 = a.getPDBresnum1();
// for (String res : pdb1 ){
// jmol.evalString("select " + res + "/1 ; backbone 0.6; color orange;");
// }
//
// jmol.evalString("select */2; color blue; model 2;");
// String[] pdb2 = a.getPDBresnum2();
// for (String res :pdb2 ){
// jmol.evalString("select " + res + "/2 ; backbone 0.6; color cyan;");
// }
//
//
// // now show both models again.
// jmol.evalString("model 0;");
//
// } catch (StructureException e){
// e.printStackTrace();
// }
//
// }
}
