Re^2: A more efficient sort or heap algorithm...

Your advice is fantastic as per usual. The array of arrays does make a lot more sense, suggestion #3 makes even more than the current stuff. I'll try both to get a better feel how each performs, and try and be a little more clever next time. Thanks :).

Bioinformatics

Comment on Re^2: A more efficient sort or heap algorithm...

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Re^3: A more efficient sort or heap algorithm... by stajich (Chaplain) on Jul 19, 2009 at 01:53 UTC
You could also take a look at how GFF files are stored in Bio::DB::GFF or Bio::DB::SeqFeature::Store which use RDMS to handle these types of range queries (mysql,postgres, sqlite) and an in-memory berkeleydb implementation. The get_features_by_location is basically what you'd want to use for your problem.	[reply]


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