[Biojava-dev] Efficient searching of location objects

[Andy Yates]

I had tried spacial indexes before to some quite good results. When you think about it rtrees are a very good fit for sequence features.

Think I tried jsi from http://jsi.sourceforge.net. 

If I can find my code I will post it up

Andy

Ryan Golhar <ngsbioinformatics at gmail.com> wrote:

>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
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