[Bioperl-l] computation object

Matthew Pocock mrp@sanger.ac.uk
Tue, 05 Dec 2000 17:32:36 +0000

"Fiers, M.W.E.J." wrote:

> Hi
> <snip/>
> * A way of storing several set's of sub_seqfeature's, much like the current
> 'tags' system, but returning an array of seqfeatures. This is to make it
> easier to parse and separate subsets of sub_seqfeature's. The sub_seqfeature
> method could stay intact and just return all sets.
> Advantages to this structure would be that if somebody inherits from this
> object and stores seqfeature's of children of seqfeature's in this
> structure, it would still be parsable without the parsing having to know
> exactly what subset's are there.

BioJava uses FeatureFilter objects to pull out a sub-set of child features. This
has the added benefit that you can pull out any sub-set, not just those that the
data-publisher thought would be usefull. This ability to arbitrarily filter
features turns out to be a real time-saver. If you code it up right, it doesn't
affect object encapsulation, and the queries can be optimized into SQL, DAS or
whaterver other query languages (can anybody say 'compiler' / 'interpreter' ?).
We have well-known filters for locations, names, key/value pairs and a
collection of boolean operators (and, not, or etc.), but the user can always
supply their own routine.

Just my 2c. Feel free to ignore me - Perl is not Java.


> Mark Fiers
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