/*
* 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 Jun 23, 2008
*
*/
package performance;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.net.URLConnection;
import java.util.zip.GZIPInputStream;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.align.ClusterAltAligs;
import org.biojava.bio.structure.align.StructurePairAligner;
import org.biojava.bio.structure.align.pairwise.AlternativeAlignment;
import org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame;
import org.biojava.bio.structure.io.PDBFileParser;
/** An example that aligns two protein structures.
* @author Andreas Prlic
* @since 1.7
* @date Jun 23, 2008
*
*/
public class AlignProteins {
public static void main (String[] args){
long start = System.currentTimeMillis();
long maxMem = 0;
String fileName1 = "/2hhb.pdb.gz";
String fileName2 = "/pdb2jho.ent.gz";
UserDisplay display = new UserDisplay();
display.setTitle("BioJava performance example");
display.setVisible(true);
StringBuffer txt = new StringBuffer();
txt.append("");
txt.append( "BioJava performance example
");
txt.append("Superimpose the protein structures of Myoglobin (2jho) and Haemoglobin (2hhb)
");
txt.append("20 alternative alignments are calculated and clustered according to the similarity between the alignments.");
txt.append("See how the alternative alignments of the first 4 clusters find the matches of Myoglobin to the different chains of Haemoglobin.
");
txt.append("The algorithm is based on a variation of the PSC++ algorithm provided by Peter Lackner, Univ. Salzburg.");
txt.append("It calculates a a distance matrix based, rigid body protein structure superimposition.
");
txt.append("Loading ... ");
txt.append(fileName1);
txt.append("
");
display.setText(txt + "");
try {
Structure s1 = getStructureFromFile(fileName1);
long mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
if (mem0 > maxMem)
maxMem = mem0;
txt.append("Loading ... " + fileName2 + "
");
display.setText(txt + " ");
Structure s2 = getStructureFromFile(fileName2);
mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
if (mem0 > maxMem)
maxMem = mem0;
StructurePairAligner aligner = new StructurePairAligner();
txt.append("Calculating alignment ... ");
display.setText(txt + "");
aligner.align(s1, s2);
txt.append("done.