[Biojava-l] biojava3 and symbol

[Francois Le Fevre]

perfect thank a lot.
Have a good day
Francois

2011/2/28 Andy Yates <ayates at ebi.ac.uk>

> 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
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> 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/
>
>
>
>
>


-- 


Francois Le Fevre
Management Informatique Innovation Biotechnologies
Paris, France
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