[Biojava-l] SequenceFormat.writeSequence with circularlocation

[Schreiber, Mark]

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
	
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