Java code with biojava alter program to be able to translate three forwarding op

Question

Java code with biojava

alter program to be able to translate three forwarding open reading frames.its possible to transcribe() method of the GeneticCodes class to transcribe the DNA sequence into a RNA sequence, and then use the translate() method to translate it into a protein sequence.

import org.biojava.bio.BioException;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;
import org.biojavax.bio.seq.RichSequence.IOTools;

import java.io.*;
import java.util.Scanner;
import javax.swing.JFileChooser;

public class readFastaDNA {

private static JFileChooser ourChooser = new JFileChooser(".");

/**
* Open a file through a FileChooser
*/
public static BufferedReader openFile(){
int retval = ourChooser.showOpenDialog(null);
BufferedReader br = null;

if (retval == JFileChooser.APPROVE_OPTION){
File file = ourChooser.getSelectedFile();
try {
br = new BufferedReader(new FileReader(file));
} catch (FileNotFoundException e) {
System.out.println("trouble reading "+file.getName());
e.printStackTrace();
}
}   
return br;
}

public static void main(String[] args) throws BioException{
BufferedReader br = openFile();

RichSequenceIterator it = IOTools.readFastaDNA(br, null);

int count = 0;

while (it.hasNext()){
count++;
RichSequence s = it.nextRichSequence();
System.out.println(s.getAccession());
System.out.println( s.seqString());
}
System.out.println("# sequences read: "+count);   
}
}

Explanation / Answer

Check this... changes made bold and italic

import org.biojava.bio.BioException;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;
import org.biojavax.bio.seq.RichSequence.IOTools;
import java.io.*;
import java.util.Scanner;
import javax.swing.JFileChooser;

public class readFastaDNA {

private static JFileChooser ourChooser = new JFileChooser(".");

/**
* Open a file through a FileChooser
*/
public static BufferedReader openFile() {
int retval = ourChooser.showOpenDialog(null);
BufferedReader br = null;
if (retval == JFileChooser.APPROVE_OPTION) {
File file = ourChooser.getSelectedFile();
try {
br = new BufferedReader(new FileReader(file));
} catch (FileNotFoundException e) {
System.out.println("trouble reading " + file.getName());
e.printStackTrace();
}
}
return br;
}

public static void main(String[] args) throws BioException {
BufferedReader br = openFile();
int count = 0;
RichSequenceIterator seqsData = RichSequence.IOTools.readGenbankDNA(br, null);
while (seqsData.hasNext()) {
count++;
RichSequence _seq = seqsData.nextRichSequence();
System.out.println(_seq.getAccession());
System.out.println(_seq.getDescription());
}
System.out.println("# sequences read: " + count);
}
}

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