Hmm, sounds like its a bit more of a problem than I thought. Unfortunately I have just
moved locations and networks and don't have any CVS access (or much else). Anyone else
from the list want to volunteer to take a peek at this??
- Mark
-----Original Message-----
From: Yasumasa Shigemoto [mailto:[EMAIL PROTECTED]
Sent: Tue 25/03/2003 10:11 p.m.
To: Schreiber, Mark
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] SequenceFormat.writeSequence with circularlocation
Hi,
I use a biojava-1.3pre1, however the following error occurs.
My environment is as follows.
biojava-1.3pre1 (precompiled version)
java 1.4.1_01
RedHat linux 7.1
Regards,
Yasumasa Shigemoto
"Schreiber, Mark" wrote:
> 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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>
>
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