[Biojava-l] how can i read a genbank
Rajeswari
rajeee_sss at yahoo.com
Wed Oct 11 07:41:21 UTC 2006
Dear developers.,
I got the biojava program to read a genbank file from biojava.org.
it is as follows:
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import java.io.*;
import org.biojava.bio.*;
import java.util.*;
public class genbank1
{
public static void main(String[] args)
{
BufferedReader br = null;
try
{
FileReader f=new FileReader(mygen.java);
br = new BufferedReader(f);
}
catch (FileNotFoundException ex)
{
ex.printStackTrace();
System.exit(-1);
}
SequenceIterator sequences = SeqIOTools.readGenbank(br);
while(sequences.hasNext())
{
try
{
Sequence seq = sequences.nextSequence();
}
catch(BioException ex)
{
ex.printStackTrace();
}
catch(NoSuchElementException ex)
{
ex.printStackTrace();
}
}
}
}
And i saved it as genbank1.java
it was compiled with javac genbank1.java
and when i try to execute it shows no classfoundException.
i run the pro as follows:
c:\jdk1.4\bin\java genbank1 mygen.java
mygen.java consists of the genbank file.
i think the error may be deu to the genbank file.
can anybody tell me how to do this pro correct? and provide me the exact format of a genbank file with extension.
regards
s.rajee
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