[Biojava-dev] Proliferation of Sequence Utility Classes

[Andy Yates]

Thank you if anything it makes it easier for me to remember where the utility methods are :)

On 20 Oct 2011, at 10:02, Peter Troshin wrote:

> 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/
>>> 
>>> 
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> 
>> 
>> 
> 

---
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/