/usr/share/doc/libbiojava-java-demos/examples/performance/ReadFastaX.java is in libbiojava-java-demos 1:1.7.1-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 | /*
* 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.BufferedInputStream;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.net.URLConnection;
import java.util.zip.GZIPInputStream;
import org.biojavax.SimpleNamespace;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;
/** Read a FASTA file and print the length of all sequences in the file.
* Uses the slower biojavax implementation.
*
* @author Andreas Prlic
* @since 1.7
* @date Jun 19, 2008
*/
public class ReadFastaX {
public static void main (String[] args){
try {
UserDisplay display = new UserDisplay();
display.setTitle("BioJava performance example - BioJavaX");
display.setVisible(true);
StringBuffer txt = new StringBuffer("<body>");
txt.append("<h1>BioJava performance example</h1> Read all chromosomes of Drosophila and print the length of each using BioJavaX.<br> ");
long start = System.currentTimeMillis();
// setup file input
String fileName = "/dmel-all-chromosome-r5.8.fasta.gz";
URL u = ReadFastaX.class.getResource(fileName);
System.out.println(u);
txt.append( "reading " + fileName + " (47 MB)");
System.out.println(txt);
display.setText(txt + "</body>");
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 + "</body>");
return;
}
GZIPInputStream gzip = new GZIPInputStream(inStream);
InputStream is = new BufferedInputStream(gzip);
BufferedReader br = new BufferedReader(new InputStreamReader(is));
SimpleNamespace ns = null;
ns = new SimpleNamespace("biojava");
// You can use any of the convenience methods found in the BioJava 1.6 API
RichSequenceIterator rsi = RichSequence.IOTools.readFastaDNA(br,ns);
long total = 0;
long maxMem = 0;
// Since a single file can contain more than a sequence, you need to iterate over
// rsi to get the information.
txt.append( "<table><tr><td><b>name</b></td><td><b>length</b></td></th>");
while(rsi.hasNext()){
RichSequence seq = rsi.nextRichSequence();
total += seq.length();
System.out.println(seq.getName() + "\t" + seq.length());
txt.append( "<tr><td>" + seq.getName() + "</td><td>" + seq.length() + "</td></tr>");
display.setText(txt + "</body>");
long mem0 = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
if (mem0 > maxMem)
maxMem = mem0;
}
txt.append( "</table>");
txt.append( "Total length is " + total + "<br>");
long time = System.currentTimeMillis() - start;
txt.append( "total processing time: " + (time / 1000) + " sec. " + "<br>");
txt.append("mamimum memory: " + (maxMem /1024/1024) + " MB" + "<br>");
display.setText(txt + "</body>");
}
catch(Exception be){
be.printStackTrace();
System.exit(-1);
}
}
}
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