/*
* 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 19, 2008
*
*/
package performance;
import java.io.*;
import java.net.URL;
import java.net.URLConnection;
import java.util.zip.GZIPInputStream;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;
/** Read a FASTA file and print the length of all sequences in the file.
*
* @author David Huen
* @author Andreas Prlic
* @since 1.7
* @date Jun 19, 2008
*
*/
public class ReadFasta {
/**
* The program takes two args: the first is the file name of the Fasta file.
* The second is the name of the Alphabet. Acceptable names are DNA RNA or PROTEIN.
* @param args parameter array
**/
public static void main(String[] args) {
try {
UserDisplay display = new UserDisplay();
display.setTitle("BioJava performance example");
display.setVisible(true);
StringBuffer txt = new StringBuffer();
txt.append("");
txt.append("BioJava performance example
Read all chromosomes of Drosophila and print the length of each.
");
long start = System.currentTimeMillis();
// setup file input
String fileName = "/dmel-all-chromosome-r5.8.fasta.gz";
URL u = ReadFasta.class.getResource(fileName);
System.out.println(u);
String alphabet = "DNA";
txt.append("reading " + fileName + " (47 MB)");
System.out.println(txt);
display.setText(txt + "");
URLConnection urlc = u.openConnection();
InputStream inStream = urlc.getInputStream();
if (inStream == null){
System.err.println("could not find file " + fileName);
txt.append("could not find file " + fileName);
display.setText(txt + " ");
return;
}
display.setText(txt + "");
GZIPInputStream gzip = new GZIPInputStream(inStream);
BufferedInputStream is = new BufferedInputStream(gzip);
//get the appropriate Alphabet
Alphabet alpha = AlphabetManager.alphabetForName(alphabet);
//get a SequenceDB of all sequences in the file
SequenceDB db = SeqIOTools.readFasta(is, alpha);
long maxMem = 0;
//list sequences and length
SequenceIterator sI = db.sequenceIterator();
long total = 0;
txt.append("