org.biojava.nbio.structure.align.gui.AlignmentCalc Maven / Gradle / Ivy
/*
* 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/
*
* Created on Jul 16, 2006
*
*/
package org.biojava.nbio.structure.align.gui;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/** A class that obtains two structures via DAS and aligns them
* This is done in a separate thread.
* It is possible to register Event listeners to get notification of when the download has finished.
*
* @author Andreas Prlic
* @since 1.7
* @version %I% %G%
*/
public class AlignmentCalc implements AlignmentCalculationRunnable {
private static final Logger logger = LoggerFactory.getLogger(AlignmentCalc.class);
boolean interrupted = false;
String pdb1;
String pdb2;
String name1;
String name2;
Structure structure1;
Structure structure2;
AlignmentGui parent;
/** requests an alignment of pdb1 vs pdb 2.
* Chain 1 and chain2 are optional.
* If they are empty strings, they are ignored
* @param parent the alignment gui frame that interacts with this class
* @param s1 structure 1
* @param s2 structure 2
*/
public AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2 , String name1, String name2) {
this.parent= parent;
structure1 = s1;
structure2 = s2;
this.name1 = name1;
this.name2 = name2;
}
@Override
public void run() {
// both structure have been downloaded, now calculate the alignment ...
StructureAlignment algorithm = parent.getStructureAlignment();
//StructurePairAligner aligner = new StructurePairAligner();
//aligner.setDebug(true);
try {
Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure1);
Atom[] ca2 = StructureTools.getRepresentativeAtomArray(structure2);
//System.out.println("ca1 size:" + ca1.length + " ca2 size: " + ca2.length);
AFPChain afpChain = algorithm.align(ca1, ca2);
afpChain.setName1(name1);
afpChain.setName2(name2);
StructureAlignmentJmol jmol = StructureAlignmentDisplay.display(afpChain, ca1, ca2);
String title = jmol.getTitle();
ConfigStrucAligParams params = algorithm.getParameters();
if ( params != null)
title += " " + algorithm.getParameters().toString();
jmol.setTitle(title);
DisplayAFP.showAlignmentPanel(afpChain,ca1,ca2,jmol);
System.out.println(afpChain.toCE(ca1,ca2));
} catch (StructureException e){
e.printStackTrace();
logger.warn(e.getMessage());
}
//logger.info("done!");
parent.notifyCalcFinished();
}
/** stops what is currently happening and does not continue
*
*
*/
@Override
public void interrupt() {
interrupted = true;
}
@Override
public void cleanup() {
parent.notifyCalcFinished();
parent=null;
// cleanup...
structure1 = null;
structure2 = null;
}
/** does not do anything here...
*
*/
@Override
public void setNrCPUs(int useNrCPUs) {
// TODO Auto-generated method stub
//
}
}