[Biojava-dev] Proliferation of Sequence Utility Classes

[Peter Troshin]

Hi Andreas,

I will try looking at it when I have time, hopefully some time in November.

See you on the summit,
Peter

On 20/10/2011 04:04, Andreas Prlic wrote:
> 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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>>
>
>