[Biojava-l] programming error

[Andreas Prlic]

Thanks Andy,

yea, would be good to add links on the cookbook front page, otherwise the
sections are hard to find...

Andreas

On Mon, Feb 14, 2011 at 8:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> I've added a bit to the original cookbook page we had. I can migrate these
> changes to the cookbook front page later on in the week
>
> Andy
>
> On 14 Feb 2011, at 15:42, Andreas Prlic wrote:
>
> > Hi Andy,
> >
> > Could we get a Cookbook page for this? sounds like it would be good to
> have a bit more docu on this topic ...
> >
> > Thanks!
> >
> > Andreas
> >
> > On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> > If you want to do frame based translation then there is an easier way of
> accomplishing this. The TranscriptionEngine allows you to translate in
> multiple frames and retrieve that information in a Map such as:
> >
> > TranscriptionEngine te = TranscriptionEngine.getDefault();
> > Frame[] frames = Frame.getForwardFrames();
> > Map<Frame, Sequence<AminoAcidCompound>> results =
> te.multipleFrameTranslation(dna, frames);
> >
> > Change the static call on Frame to Frame.getAllFrames() then you will do
> a full 6 frame translation.
> >
> > Also I would avoid calling the getSequenceAsString() method until you
> need to output it to screen. The Sequence interface provides an adequate set
> of methods for testing length of a sequence. However if you want is the
> longest translation then I would replace that with (assuming the above
> code):
> >
> > List<Sequence<AminoAcidCompound>> translations = new
> ArrayList<Sequence<AminoAcidCompound>>(results.getValues());
> > Collections.sort(translations, new
> Comparator<Sequence<AminoAcidCompound>>() {
> >  public int compare(Sequence<AminoAcidCompound> o1,
> Sequence<AminoAcidCompound> o2) {
> >    Integer o1Length = o1.getLength();
> >    Integer o2Length = o2.getLength();
> >    return o1Length.compareTo(o2Length);
> >  }
> > });
> > Sequence<AminoAcidCompound> longest =
> translations.get(translations.size()-1);
> >
> > However I would like to see what errors you are pulling up from BioJava3
> in case there is a scenario we are not currently taking into account
> >
> > Andy
> >
> > On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote:
> >
> > > On 13-02-11 20:11, Scooter Willis wrote:
> > >> Depending on what you need you may want to try out biojava3.
> > >>
> > >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen
> > >> <mandarijnopw8 at gmail.com>  wrote:
> > >>> hi guys,
> > >>>
> > >>> i made am making a tool to translate dna to protein using biojava.
> > >>> But  i am getting some errors that is do not fully understand.
> > >>> Can somebody please tell me what i am doing wrong?
> > >>>
> > >>>
> > >>> script:
> > >>> http://pastebin.com/TJSjkgqK
> > >>>
> > >>> errors:
> > >>> http://pastebin.com/iFXYWEZB
> > >>> _______________________________________________
> > >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >>>
> > >>>
> > > i a, trying biojava 3 now but i am still doing something wrong.
> > >
> > > http://pastebin.com/uLz934gr
> > > _______________________________________________
> > > 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/
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
> >
> > --
> > -----------------------------------------------------------------------
> > Dr. Andreas Prlic
> > Senior Scientist, RCSB PDB Protein Data Bank
> > University of California, San Diego
> > (+1) 858.246.0526
> > -----------------------------------------------------------------------
>
> --
> 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/
>
>
>
>
>