DataFrame() now automatically derives rownames (from the first
argument that has some). This is a fairly significant change in
behavior, but it probably does better match user behavior. Hopefully
no performance regressions.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79233 bc3139a8-67e5-0310-9ffc-ced21a209358
Reorganize default methods for comparing and/or ordering vector-like objects.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79272 bc3139a8-67e5-0310-9ffc-ced21a209358
merge IntervalForest fixes from Hector


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79278 bc3139a8-67e5-0310-9ffc-ced21a209358
coerce replacement column to original column type during in [<-,DataFrame; supports e.g. Rle into atomic vector

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79289 bc3139a8-67e5-0310-9ffc-ced21a209358
Move findMatches/countMatches generics and default methods from
Ranges-comparison.R to Vector-comparison.R


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79301 bc3139a8-67e5-0310-9ffc-ced21a209358
Add "table" method for Vector objects.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79316 bc3139a8-67e5-0310-9ffc-ced21a209358
- Add selfmatch() generic and default method.
- Add "duplicated" method for Vector objects (implemented on top of
  selfmatch()).


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79318 bc3139a8-67e5-0310-9ffc-ced21a209358
Add "selfmatch" method for Ranges objects.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79319 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix a few broken links.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79320 bc3139a8-67e5-0310-9ffc-ced21a209358
S3 versions of as.data.frame.*


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79368 bc3139a8-67e5-0310-9ffc-ced21a209358
source code tidy -- remove unused variables


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79369 bc3139a8-67e5-0310-9ffc-ced21a209358
Tweak to default "classNameForDisplay" method so it always returns a single
string.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79409 bc3139a8-67e5-0310-9ffc-ced21a209358
only coerce column sub-replacement value to class of column when the
column already exists


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79414 bc3139a8-67e5-0310-9ffc-ced21a209358
as.data.frame.DataFrame now passes stringsAsFactors=FALSE and
check.names=!optional to the underlying data.frame()
call. as(x,"DataFrame") sets optional=TRUE when delegating. Most
places where we called as.data.frame, we now call as(x,"data.frame").


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79637 bc3139a8-67e5-0310-9ffc-ced21a209358
implement and expose S3 equivalent of S4 Rle methods


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79646 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'local-hedgehog'

Conflicts:
	DESCRIPTION