[Biojava-dev] Proliferation of Sequence Utility Classes

[Andy Yates]

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/