[Biojava-dev] Efficient searching of location objects

[Ryan Golhar]

Let me see what I can come up with.


On Wed, Nov 28, 2012 at 3:37 PM, Scooter Willis <HWillis at scripps.edu> wrote:

>  Ryan
>
> Yes a location based search would be a great addition.
>
> Scooter
>
>
> ----- Reply message -----
> From: "Ryan Golhar" <ngsbioinformatics at gmail.com>
> To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>
> Subject: [Biojava-dev] Efficient searching of location objects
> Date: Wed, Nov 28, 2012 3:18 pm
>
>
>
> Hi all - I'm trying to use BioJava3's FeatureList and Location objects.
>  I'm loading a GFF/GTF file and creating a FeatureList.  I don't see a
> mechanism to quickly search the FeatureList by genomic location.
>  Basically, I want to query the FeatureList with specific locations to
> determine if there are features at that location, and what is the next
> feature upstream/downstream from a given location.
>
> It seems to me that a binary tree implementation of the FeatureList may be
> in order, but thought I'd check here first to see what other people
> recommend.
>
> Ryan
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>