[Biojava-dev] biojava3 sequence tools

[Andy Yates]

Building a Sequence object which can contain AminoAcidCompound or NucleotideCompound is easy; the return types makes this incredibly hard since we'd have to return Sequence<Compound> which forces the user to start casting to a more useful type. Every auto detector I've known gets it wrong since they all apply arbitrary thresholds to decide the switch. 

However if the need is there (which I'm sure for writing some interfaces there are) something can be knocked up quickly I think.

On 11 Aug 2010, at 05:46, Mark Schreiber wrote:

> I think SeqIOTools had a method for this, possible also available in
> RichSequence.IOTools.
> 
> As Richard says, not guaranteed to work in all cases.
> 
> 
> 
> 
> On Wed, Aug 11, 2010 at 12:05 PM, Richard Holland <holland at eaglegenomics.com
>> wrote:
> 
>> You mean an auto-detector that takes a String input, guesses based on
>> content what it is, and returns a Sequence object of the appropriate type,
>> being Protein or DNA etc.? Not that I know of. A bit hard too - if all the
>> letters in the String are a valid subset from two or more alphabets (e.g.
>> ATCG are all in the Protein alphabet as well as being DNA), how do we know
>> which one it is?
>> 
>> On 11 Aug 2010, at 03:24, Andreas Prlic wrote:
>> 
>>> Hi,
>>> 
>>> just wondering if we have already a class that can accept any protein
>>> or DNA sequence as input and can return a Sequence object of the
>>> correct type ?
>>> 
>>> Andreas
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> 
>> --
>> Richard Holland, BSc MBCS
>> Operations and Delivery Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.eaglegenomics.com/
>> 
>> 
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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/