[Biojava-l] Last change to sequence package

[Ewan Birney]

On Tue, 18 Jul 2000, Matthew Pocock wrote:

> 
> 
> Ewan Birney wrote:
> 
> > 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.
> 
> The feature interface hierachy already helps with this
> 
> Feature
>   (location, type, source, annotation, parent, children, sequence)
>    |
>    \ StrandedFeature
>        (Strand { POSITIVE, NEGATIVE, UNKNOWN }
> 
> We do need to make sure that StrandedSequence has the possibility to be UNKNOWN to
> avoid some hoop-jumping, but in general things like low complexity regions should
> be modeled directly as a Feature instance.
> 
> StrandedFeature.Strand would have the methods
>  toString() -- POSITIVE, NEGATIVE or UNKNOWN
>  getValue() -- +1, -1 or 0
>  getToken() -- +, - or .
> 
> What do you think?
> 

Looks ideal.


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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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