[Biojava-dev] Creating SubSequence(s) that are Contained By Location instead of OverlapsLocation

[eduardo.gonzalezcouto at freesurf.ch]

Hello,

As this is my first post to the dev list, I'd like to start by
congratulating everyone for the great work on the project.

I'm currently using the SubSequence class to extract features from a parent
class. This method returns all the translated overlapping features, and
in
my case I have to be more restrictive and only keep the features strictly
contained by the sub-sequence.

Would it be possible to have more flexibility at the level of the protected
method entitled createFeatureHolder() returning a FeatureHolder by allowing
to switch between an OverlapsLocation FeatureFilter and a
ContainedByLocation FeatureFilter? Overloading the whole
createFeatureHolder()method is currently, feasible but it is not very
elegant to copy the whole method just for changing the type of feature
filter. Alternatively, it is possible to filter the features to only keep
the Features that are Projected Features, but I don't know if this will
be
safe in the future.

Thank you in advance for your help.

Best regards,
 Eduardo

--
Eduardo Gonzalez Couto, Ph.D.
Bioinformatician
GeneProt Inc. (Geneva Branch)
Tel. +41 (0)22 719 88 32
Fax. +41 (0)22 719 88 69

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