That's great! There's some cleaning up to do there how should we do this post-merge?
On Wed, May 29, 2013 at 4:19 PM, Valerie Obenchain <voben...@fhcrc.org> wrote: > Hi Hector, Michael, > This sounds great. Bringing these into svn is fine with us. Michael, do > you want to merge these in? > Val > On 05/24/2013 07:30 AM, Hector Corrada Bravo wrote: >> 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 >> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
