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
>> <[email protected]> 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 - [email protected]
>>> 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 - [email protected]
> 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/
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