*Added bioc-devel; hope you don't mind* Hector,
This is great stuff. The overall design is on the right track. As you said, there's a bit of cleaning to do, but I think we should merge this into svn and work the rest out from there. This will really benefit performance, especially for visualization. Of course, I can't speak for the others. Michael On Tue, May 21, 2013 at 11:52 AM, Hector Corrada Bravo < hcorr...@umiacs.umd.edu> wrote: > Since the semester is over I finally finished this... > > Recall that I wanted a persistent set of IntervalTrees for GRanges objects > for repeated querying. (The application is this: > http://epiviz.cbcb.umd.edu/help/?page_id=62 which I hope to get out > soon). Folding this into IRanges and GenomicRanges would make our life > easier come installation time. > > I've implemented class 'IntervalForest' within IRanges following Michael's > suggestion of storing this as an array of rbTree on the C side. I've > implemented findOverlaps that operates with this array in C. There is code > duplication in IntervalTree.c that could be reduced but that's if this > makes it into the package. > > I've also implemented a 'GIntervalTree' that uses 'IntervalForest' > underneath. findOverlaps-GenomicRanges-GIntervalTree-method is implemented > for this class. I didn't touch the existing > findOverlaps-GenomicRanges-GenomicRanges-method. > > You can pull these here: > http://github.com/hcorrada/IRanges > http://github.com/hcorrada/GenomicRanges > > These track the devel branch of the two packages. Let me know the best way > to propagate to svn if you guys want this. It needs documentation, but I'll > add that once implementation is settled. > > Kasper, I'm not sure if this would help with the 'too many seqlevels' > problem but I'd be curious to know if you try it. > > Cheers, > Hector > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
