/* * 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( "