/* * 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 org.biojava.bio.seq.impl.RevCompSequence; import org.biojavax.bio.seq.RichSequence; import org.biojavax.bio.seq.RichSequenceIterator; import org.biojavax.bio.seq.io.FastaFormat; import org.biojavax.bio.seq.io.FastaHeader; import java.io.BufferedReader; import java.io.ByteArrayOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.PrintStream; import java.net.URL; import java.net.URLConnection; /** Read DNA sequence and write their reverse complement. * This is based on the benchmark provided at: * http://shootout.alioth.debian.org/gp4/benchmark.php?test=revcomp&lang=all * * @author Andy Yates * @author Andreas Prlic * @date Jun 23, 2008 * @since 1.7 */ public class ReverseComplement { public static void main(String[] args) throws Exception { String fastaLocation; if(args.length > 0) { fastaLocation = args[0]; } else { fastaLocation = "/input.fasta"; } UserDisplay display = new UserDisplay(); display.setTitle("Reverse complement - BioJava"); display.setVisible(true); StringBuffer txt = new StringBuffer(""); txt .append( "

BioJava - Reverse Complement

"); txt.append( "Read DNA sequence and write their reverse complement.
"); txt.append( "This is based on the benchmark provided at:"); txt.append( "http://shootout.alioth.debian.org/gp4/benchmark.php?test=revcomp&lang=all
"); txt.append( " in short the rules are :
"); txt.append( ""); txt.append( "Loading ... " + fastaLocation + "
"); display.setText(txt + ""); long start = System.currentTimeMillis(); FastaHeader fastaHeader = new FastaHeader(); fastaHeader.setShowAccession(true); fastaHeader.setShowDescription(false); fastaHeader.setShowIdentifier(false); fastaHeader.setShowName(false); fastaHeader.setShowNamespace(false); fastaHeader.setShowVersion(false); FastaFormat fastaFormat = new FastaFormat(); fastaFormat.setHeader(fastaHeader); fastaFormat.setLineWidth(60); BufferedReader br = getReader(fastaLocation); RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br, null); ByteArrayOutputStream baos = new ByteArrayOutputStream(); PrintStream ps = new PrintStream(baos); txt.append( "Output:
"); display.setText(txt + ""); while(iter.hasNext()) { RichSequence seq = iter.nextRichSequence(); RevCompSequence rev = new RevCompSequence(seq); rev.setName(seq.getAccession()+" "+seq.getDescription()); fastaFormat.writeSequence(rev, ps); } txt.append( "
" + baos.toString() +"

");		
		long time = System.currentTimeMillis() - start;
		txt.append( "total processing time: " + (time ) + " milli sec. " + "

");
		txt.append( " BioJava provides a very fast and competetive implementation of this benchmark problem.
");
		
		display.setText(txt + "");
		
		
	}
	
	private static BufferedReader getReader(String fileName) throws IOException{
		URL u = ReverseComplement.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;
		
		
	}
}