add a window,matrix


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78471 bc3139a8-67e5-0310-9ffc-ced21a209358
FilterRules no longer requires its elements to be named


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78472 bc3139a8-67e5-0310-9ffc-ced21a209358
rename castList to asList; should probably export it


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78473 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge IntervalForest by Hector Corrada Bravo


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78475 bc3139a8-67e5-0310-9ffc-ced21a209358
add a summary,FilterMatrix and have summary,FilterRules delegate to it


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78520 bc3139a8-67e5-0310-9ffc-ced21a209358
evalSeparately no longer tries to do any subsetting


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78574 bc3139a8-67e5-0310-9ffc-ced21a209358
fix seqselect,matrix


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78575 bc3139a8-67e5-0310-9ffc-ced21a209358
a couple of minor cosmetic improvements

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@78653 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'

Conflicts:
	DESCRIPTION
	R/IntervalForest-class.R
	R/inter-range-methods.R
	R/intra-range-methods.R
Fix issues with findOverlaps,RangesList,IntervalForest-method

* Empty subject partitions are now handled appropriately
* The CompressedHitsList object is now, correctly, constructed from the query partitioning
* Unit tests for these cases have been added