[Biojava-dev] Efficient searching of location objects

[Scooter Willis]

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
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