[Biojava-l] SequenceFormat.writeSequence with circularlocation

[Yasumasa Shigemoto]

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:yshigemo at genes.nig.ac.jp]
>         Sent: Sun 23/03/2003 7:33 p.m.
>         To: biojava-l at biojava.org
>         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
>
>         _______________________________________________
>         Biojava-l mailing list  -  Biojava-l at biojava.org
>         http://biojava.org/mailman/listinfo/biojava-l
>
>
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