Hi -
It would be a good idea to check your biojava version. This was definitely a bug
before 1.3 I think it should have been fixed in bj1.3pre1
- Mark
-----Original Message-----
From: Yasumasa Shigemoto [mailto:[EMAIL PROTECTED]
Sent: Sun 23/03/2003 7:33 p.m.
To: [EMAIL PROTECTED]
Cc:
Subject: [Biojava-l] SequenceFormat.writeSequence with circularlocation
Hi,
I use a SequenceFormat.writeSequence(Sequence seq, java.io.PrintStream os)
and it seems to have a bug in some case.
The simple code reads entry of accession "J01566"
and write a file.
But circular location is changed as follows.
Original
CDS join(5140..6646,1..62)
Generated
CDS join(1..62,5140..6646)
public class FFWriteTest {
public static void main(String[] args) throws Exception {
SequenceFormat gFormat = new GenbankFormat();
BufferedReader gReader = new BufferedReader(new
FileReader("J015
66"));
SequenceBuilderFactory sbFact = new
GenbankProcessor.Factory(Sim
pleSequenceBuilder.FACTORY);
Alphabet alpha = DNATools.getDNA();
SymbolTokenization rParser = alpha.getTokenization("token");
SequenceIterator seqI = new StreamReader(gReader, gFormat,
rPars
er, sbFact);
Sequence seq = seqI.nextSequence();
PrintStream ps = new PrintStream(new
FileOutputStream("J01566.ma
ke"));
gFormat.writeSequence(seq, ps);
ps.close();
}
}
Regards,
Yasumasa Shigemoto
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