[Bioperl-l] Re: No joins

[Brian King]

>  but most fuzzies are
> also joins, (in fact 
> alot of joins have fuzzy ends) so... it became the
> defacto way to handle 
> joins.

If your location class supports fuzzy regions, then
can't you move the fuzzy regions out of a join and
into fuzzy locations of generic sub-features?  If it's
the end regions that are fuzzy, then the parent has to
retain the fuzzyness, but at least you get rid of the
join.  AGAVE has a structure for fuzzy regions, so
I'll look up a GenBank example and make an XML version
again.  Probably next week.


> Practical question - what does BioJava do with the
> Fuzzies?
> 

BioJava has a base Location class that has
getMin()/getMax() methods to handle the simple case of
a contiguous region.  The are sub-classes to handle
the more complex locations, such as a FuzzyLocation. 
FuzzyLocation takes outerMin, outerMax, innerMin,
innerMax,  isMinFuzzy, isMaxFuzzy arguments in the
constructor.  There is a default policy that tells how
the fuzzy ends get interpreted in getMin()/getMax(),
and the policy is settable.  So for any location you
can deal with a simple range, or request all the gory
detail.  It's complicated, but true to the input data.

Regards,
Brian 

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