/* * 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 25, 2008 * */ package performance; import java.io.BufferedReader; import java.io.FileNotFoundException; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.net.URL; import java.net.URLConnection; import java.util.NoSuchElementException; import org.biojava.bio.BioException; import org.biojava.bio.alignment.SequenceAlignment; import org.biojava.bio.alignment.SmithWaterman; import org.biojava.bio.alignment.SubstitutionMatrix; import org.biojava.bio.symbol.FiniteAlphabet; import org.biojavax.RichObjectFactory; import org.biojavax.bio.seq.RichSequence; import org.biojavax.bio.seq.RichSequenceIterator; import org.biojavax.bio.seq.RichSequence.IOTools; /** * @author Andreas Dräger (draeger) * @date Jun 25, 2008 * @since 1.7 * @author Andreas Prlic */ public class SmithWatermanExample { /** * This method computes a pairwise local alignment between two given sequences * and prints the result on the standard output stream. The sequences must be * genbank files and the substitution matrix must be defined for the same * alphabet than both sequences. * * @param args * query sequence file (genbank), subject sequence file (genbank), * substitution matrix file */ public static void main(String[] args) { try { String file1 = "/file1.gb"; String file2 = "/file2.gb"; String file3 = "/dna.mat" ; long start = System.currentTimeMillis(); long maxMem = 0; UserDisplay display = new UserDisplay(); display.setTitle("BioJava performance example - Smith Waterman"); display.setVisible(true); StringBuffer txt = new StringBuffer(); txt.append(""); txt.append( "

BioJava performance example

"); txt.append("Align two sequences of approx 3000 nucleotides length using Smith Waterman.

"); txt.append("Reading sequence 1...
"); display.setText(txt + ""); BufferedReader b1 = getReader(file1); RichSequenceIterator rsiQuery = IOTools.readGenbankDNA(b1, RichObjectFactory.getDefaultNamespace()); txt.append("Reading sequence 2...
"); display.setText(txt + ""); BufferedReader b2 = getReader(file2); RichSequenceIterator rsiSubject = IOTools.readGenbankDNA(b2, RichObjectFactory.getDefaultNamespace()); if (rsiQuery.hasNext() && rsiSubject.hasNext()) { RichSequence query = rsiQuery.nextRichSequence(); RichSequence subject = rsiSubject.nextRichSequence(); String matrix = getMatrxiFromFile(file3); txt.append("Using matrix:

" + matrix + "

"); txt.append("Calculating SmithWaterman of
" ); txt.append("query : " +query.getDescription() +" (" + query.getName()+")
"); txt.append("subject: " +subject.getDescription() +" (" + subject.getName()+")
"); short match = 0; short replace = 5; short insert = 2; short delete = 2; short gapExtend = 1; txt.append("using penalties: match ("+match +"), replace ("+ replace+"),"+ " insert ("+ insert +" ) delete (" + delete + ")," + " gapExtend (" +gapExtend +")
"); display.setText(txt + ""); SubstitutionMatrix smax = new SubstitutionMatrix( (FiniteAlphabet) query.getAlphabet(), matrix,file3); long mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); if (mem0 > maxMem) maxMem = mem0; SequenceAlignment sa = new SmithWaterman(match, replace, insert, delete, gapExtend, smax); mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); if (mem0 > maxMem) maxMem = mem0; sa.pairwiseAlignment(query, subject); mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory(); if (mem0 > maxMem) maxMem = mem0; txt.append("done...

");
				txt.append(sa.getAlignmentString());

				long time = System.currentTimeMillis() - start;

				mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
				if (mem0 >  maxMem) 
					maxMem = mem0;	

				txt.append("");

				txt.append( "total processing time: " + (time / 1000) + " sec. " + "
");
				txt.append( "mamimum memory: " + (maxMem /1024/1024) + " MB" + "
");


				display.setText(txt + "");



			}
		} catch (FileNotFoundException e) {
			e.printStackTrace();
		} catch (NoSuchElementException e) {
			e.printStackTrace();
		} catch (BioException e) {
			e.printStackTrace();
		} catch (IOException e) {
			e.printStackTrace();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	private static BufferedReader getReader(String fileName) throws IOException{
		URL u = SmithWatermanExample.class.getResource(fileName);

		System.out.println(u);
		if (u == null){
			System.err.println("could not find file " + fileName);

			throw new IOException("could not find file " + fileName);
		}
		URLConnection urlc = u.openConnection();

		InputStream inStream = urlc.getInputStream();

		BufferedReader r = new BufferedReader(new InputStreamReader(inStream));
		return r;


	}

	private static String getMatrxiFromFile(String fileName) throws IOException{
		BufferedReader reader = getReader(fileName);
		StringBuffer matString = new StringBuffer();

		while (reader.ready())
			matString.append(reader.readLine() + System.getProperty("line.separator"));
		reader.close();
		return matString.toString();

	}

}