org.biojava.nbio.structure.gui.util.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.gui.util;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.ClusterAltAligs;
import org.biojava.nbio.structure.align.StructurePairAligner;
import org.biojava.nbio.structure.align.gui.AlignmentGui;
import org.biojava.nbio.structure.align.pairwise.AlternativeAlignment;
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 Runnable {
private static final Logger logger = LoggerFactory.getLogger(AlignmentCalc.class);
boolean interrupted = false;
String pdb1;
String pdb2;
String chain1;
String chain2;
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 ) {
this.parent= parent;
structure1 = s1;
structure2 = s2;
}
@Override
public void run() {
// both structure have been downloaded, now calculate the alignment ...
StructurePairAligner aligner = new StructurePairAligner();
try {
aligner.align(structure1,structure2);
} catch (StructureException e){
logger.warn(e.getMessage());
}
AlternativeAlignment[] aligs = aligner.getAlignments();
//cluster similar results together
ClusterAltAligs.cluster(aligs);
showAlignment(aligner,aligs);
//logger.info("done!");
parent.notifyCalcFinished();
}
private void showAlignment(StructurePairAligner alignment, AlternativeAlignment[] aligs) {
AlternativeAlignmentFrame frame = new AlternativeAlignmentFrame(structure1, structure2);
frame.setStructurePairAligner(alignment);
frame.setAlternativeAlignments(aligs);
frame.pack();
frame.setVisible(true);
}
/** stops what is currently happening and does not continue
*
*
*/
public void interrupt() {
interrupted = true;
}
public void cleanup() {
parent.notifyCalcFinished();
parent=null;
// cleanup...
structure1 = null;
structure2 = null;
}
}