[Biojava-l] SortedFeatureHolder (by location)

Keith James kdj@sanger.ac.uk
27 Jun 2002 14:50:50 +0100

>>>>> "pootle" == pootle monster <pootle_monster@hotmail.com> writes:


    pootle> So I made a SortedFeatureHolder that took a Comparator in
    pootle> the constructor (I used an implementation of Comparator
    pootle> for location)

    pootle> I now have two problems: 1: I cant see how to add a
    pootle> FeatureHolder to another FeatureHolder(eg the Sequence)

I think this is due to the design where most (all?) FeatureHolders
expect to get new Features by the createFeature(Feature.Template f)
method. You'd have to ask Matthew Pocock or Thomas Down about the
reasons behind this because I've never been able to "get it" :)

    pootle> 2: Once added I can not see how to speed up the filter
    pootle> method for a location(which was the point of creating this
    pootle> class).

So I take it that your new holder is performing poorly? Do you know
exactly where the bottleneck is?

We need some more information to help you. Have you run a profiler to
find out where all the time is being spent? Also, we can't try to help
on performance issues with out seeing code.



-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK