Thanks Michael, It has made significant difference for our visualization project. I would like to merge this into svn asap. Can I get a ruling from the rest of the core group? Please let me know if/when/how to proceed.
Cheers, Hector On Wed, May 22, 2013 at 1:00 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > *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
