[Biojava-l] biojava3 and symbol

[Andy Yates]

Hi Francois,

To get a windowed view over any sequence you should use the following:

DNASequence seq = new DNASequence("ATGCTG");
Iterable<SequenceView<NucleotideCompound>> w = new WindowedSequence<NucleotideCompound>(seq, 3);
for(SequenceView<NucelotideCompound> triplet: w) {
  System.out.println(triplet);
}

HTH

Andy

On 25 Feb 2011, at 22:21, François Le Fevre wrote:

> Hello
> I am a newbie in biojava3.
> I have installed the maven version.
> 
> I have a question : is there a way to go from DNASequence to SymbolList?
> I would like to study codons and their frequency in several organisms.
> It was easy with biojava with
> 
> "SymbolList codons  = SymbolListViews.windowedSymbolList(seq, 3);"
> and
> "DistributionTrainerContext"
> 
> But now I am a little lost between maven biojava3 and biojava.
> So if anyone could explain me how to get codons view from DNASequence, it could be great.
> 
> Thanks a lot!
> 
> Francois
> 
> 
> -- 
> ----------------------
> Francois LE FEVRE
> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/