- Change default to 'compress=TRUE' for RleList() constructor.
- Replace an lapply() with a more direct subset (thanks Michael)
  in seqselect,Vector-method.
- Make Rle unit tests robust to NA and NaN platform-dependent
  differences.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79850 bc3139a8-67e5-0310-9ffc-ced21a209358
Fix paste,Rle-method to accomodate change of default to RleList(...,
compress=TRUE).


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79896 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify compress_listData() to produce a 'vector()' instead of 'list()' when an empty
list is passed in. This is needed for the RleList() constructor.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79904 bc3139a8-67e5-0310-9ffc-ced21a209358
add trivial comment to NAMESPACE about S3 method exports


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@79919 bc3139a8-67e5-0310-9ffc-ced21a209358
add an internal function for expanding by a DataFrame by set of
columns with identical element lengths.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80045 bc3139a8-67e5-0310-9ffc-ced21a209358
version bump


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80046 bc3139a8-67e5-0310-9ffc-ced21a209358
some documentation


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80089 bc3139a8-67e5-0310-9ffc-ced21a209358
- Fix long standing segfault in "[" method for Rle objects (when doing
  Rle()[0]). 
- Most Vector derivatives now support subsetting by a logical vector longer
  than the object as long as the out of bounds subscript elements are all
  FALSE. Main use case: Rle()[FALSE]
- Start cleaning/reorganizing subsetting code a little bit.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80093 bc3139a8-67e5-0310-9ffc-ced21a209358
More cleaning/reorganizing of subsetting code:
- Rewrite the "[<-" method for Vector objects. Doesn't call .bracket.Index()
  anymore. Delegates the actual work of subsetting to replaceElements().
- Add "replaceElements" method for Vector objects. This default method works
  on any Vector object for which c() and [ work.
- Simplify "[<-" method for List objects. Now it's a 5-liner that basically
  delegates almost everythin to the method for Vector objects.
- Simplify "[<-" method for Rle objects and align its semantic with other
  "[<-" methods for Vector derivatives.
- Remove "[<-" method for CompressedList objects. Not needed anymore.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80119 bc3139a8-67e5-0310-9ffc-ced21a209358
small tweak to man page

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80127 bc3139a8-67e5-0310-9ffc-ced21a209358
Various FilterRules/Matrix fixes. Major change is to the signature of
FilterMatrix constructor.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80130 bc3139a8-67e5-0310-9ffc-ced21a209358
More cleaning/reorganizing of the subsetting code:
- Simplify "seqselect" method for vector objects (doesn't use .bracket.Index()
  anymore).
- Merge and simplify "seqselect<-" methods for vector and factor objects into
  one single method for vectorORfactor objects.
- Support subsetting by empty list.
- Replace "[" method for CompressedList objects with "extractElements" method.
- Add coerce method from RangesList to SimpleRangesList.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80183 bc3139a8-67e5-0310-9ffc-ced21a209358
more doc tweaks


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80187 bc3139a8-67e5-0310-9ffc-ced21a209358
allow zero-row replacement values in [<-,DataFrame


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80189 bc3139a8-67e5-0310-9ffc-ced21a209358
fix typos in some of the extractElements methods


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80190 bc3139a8-67e5-0310-9ffc-ced21a209358
allow logical Rle return values from filter rules


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80191 bc3139a8-67e5-0310-9ffc-ced21a209358
More cleaning/reorganizing of the subsetting code:
- Remove "seqselect" method for CompressedList objects.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80192 bc3139a8-67e5-0310-9ffc-ced21a209358
More cleaning/reorganizing of the subsetting code:
- Remove "seqselect<-" method for CompressedList objects.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80193 bc3139a8-67e5-0310-9ffc-ced21a209358
More cleaning/reorganizing of the subsetting code:
- Remove "seqselect<-" methods for SimpleAtomicList and CompressedAtomicList
  objects.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80194 bc3139a8-67e5-0310-9ffc-ced21a209358
More cleaning/reorganizing of the subsetting code:
- Remove "seqselect" and "seqselect<-" methods for IRanges objects.
- Change signature of subsetByRanges() generic: (x, i) instead of
  (x, start=NULL, end=NULL, width=NULL). Dispatch is still on 1st arg only.
  Unlike seqselect(), subsetByRanges() supports subsetting by a Ranges object
  and nothing else.
- Remove recently added "subsetByRanges" method for List objects.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@80195 bc3139a8-67e5-0310-9ffc-ced21a209358