[Biojava-l] programming error

[Andy Yates]

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/