[Biojava-dev] Proliferation of Sequence Utility Classes

[Andreas Prlic]

Hi Andy and Peter,

Would be great to somehow consolidate these classes. Overall it seems
that the protein disorder package could get a bit better integrated
with -core. Some parts could be replaced with the corresponding - core
methods and some of the unique features could be moved into the core
module to make the generally available. Peter-any chance to take a
look at this at some point when you have time?

Thanks,

Andreas



On Wed, Oct 19, 2011 at 4:44 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi everyone,
>
> I've just noticed from the recent email on biojava-l that we seem to have had a proliferation of Sequence utility classes in the API. At the moment we've got:
>
> * org.biojava3.core.sequence.template.SequenceMixin
> ** Collection of utilities to be used by Sequence implementations rather than re-implementing common logic or using inheritence
>
> * org.biojava3.core.util.SequenceTools
> ** Selection of tools to decipher what a String is & convert it into a Sequence object
> ** Seems to be the same as BioPerl's "decide what this sequence is" tool
>
> * org.biojava3.data.sequence.SequenceUtil
> ** Another String to Sequence utility but a bit more fleshed out
>
> This looks like we need to combine these 3 together into a single place for Sequence based utils otherwise there's a 1 in 3 chance of getting the right set of utilities (plus my naming convention no longer accurately reflects what occurs in that class now)
>
> Andy
>
> ---
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>
>
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>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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