Added check for circular genomes
Adding findOverlaps tests for GIntervalTrees
Merge branch 'master' into cleanup
correct documentation of assay(...)

- withDimnames, not withNames, allowed in ...


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78251 bc3139a8-67e5-0310-9ffc-ced21a209358
tweak GRanges test to avoid what seems like an unwanted warning


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78274 bc3139a8-67e5-0310-9ffc-ced21a209358
add pintersect,GAlignments,GAlignments


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78275 bc3139a8-67e5-0310-9ffc-ced21a209358
fix seqinfo bug related to RangesLists/RangedData


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78276 bc3139a8-67e5-0310-9ffc-ced21a209358
rip out the S4 update stuff that was pushed up to BiocGenerics


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78277 bc3139a8-67e5-0310-9ffc-ced21a209358
rip out the matrix-style pretty printing (moved to IRanges)


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78283 bc3139a8-67e5-0310-9ffc-ced21a209358
POSSIBLY CONTROVERSIAL (you knew something like this was coming).

Add ability for GenomicRanges subclasses to list the names of slots
that should be treated as "columns" in the virtual GRanges table. This
is implemented by adding a method on the extraColumnSlotNames
generic. Then, the GenomicRanges methods take care of subsetting,
replacement, showing, some validity checking, etc, for those
slots. This greatly facilitates implementing subclasses with
additional fixed columns. Just overload extraColumnSlotNames, write
your constructor and slot accessors, and whatever else makes your
class special. Every attempt was made to implement this in a way that
does not negatively affect the performance of GRanges. If we had
shallow-R, this attention would not have been necessary.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78284 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'
Merge branch 'master' into cleanup

Conflicts:
	DESCRIPTION
revert commit 78275

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78305 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'
Merge branch 'master' into cleanup
unit tests for 'GIntervalTree-class' and 'findOverlaps,GenomicRanges,GIntervalTree-method' completed
'GIntervalTree' man page
fix extra column slot handling in 'show'


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78348 bc3139a8-67e5-0310-9ffc-ced21a209358
add an 'update' method for GAlignments; needed because clone now
depends on update (for efficiency)


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@78349 bc3139a8-67e5-0310-9ffc-ced21a209358
'GIntervalTree' documentation completed