[Biojava-l] Last change to sequence package

[Ewan Birney]

On Tue, 18 Jul 2000, Matthew Pocock wrote:

> Oops - forgot to mention that this will change the GFF API slightly. The gff
> strand constants (as ints) would be dropped, and replaced by the
> StrandedFeature constants. This way there is only one instance of the strand
> concept in BioJava.
> 
> Scream now or I will change it thursday morning.


Matt - In bioperl/Ensembl we have the concept of strand being one of
"-1,1 or 0" with 0 for strand agnostic things, eg, low complexity regions.
I am not sure that your current scheme supports this. 

It is a useful concept - otherwise you have some nasty code that has to
look at the "type" of sequence feature to realise that you shoudl be
strand agnostic.





> 
> Matthew Pocock wrote:
> 
> > Dear all,
> >
> > The last change that I would like to make to the sequence package is to
> > replace
> >
> > int StrandedFeature.POSITIVE
> > int StrandedFeature.NEGATIVE
> >
> > with identicaly named StrandedFeature.Strand instances. This will make
> > them type-safe enums so you won't be able to do silly things like set
> > the strand to -17. This change will cascade through the StrandedTemplate
> > class and also the GFF package, so that there is a global model of
> > strandedness.
> >
> > Hopefully, this should be a fix-by-recompiling change, unless you
> > explicitly set strands to +1 or -1 (which is exactly the sort of API
> > abuse that I wish to prevent).
> >
> > Comments or flames to the list/me as always
> >
> > Matthew
> >
> > --
> > Joon: You're out of your tree
> > Sam:  It wasn't my tree
> >                                                  (Benny & Joon)
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> 
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> 

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