[Biojava-l] SequenceFormat.writeSequence with circularlocation

[Schreiber, Mark]

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:yshigemo at genes.nig.ac.jp] 
	Sent: Tue 25/03/2003 10:11 p.m. 
	To: Schreiber, Mark 
	Cc: biojava-l at biojava.org 
	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: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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