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Bioconductor Changlog.
Tue, 13 Oct 2009
IRanges
Updating the Rle section of the vignette to reflect the new architecture.
Fixed up the append methods.
Pulled out "c" operator to make class developer explictly create a method for their subclasses.
Pulled out "[" operator to make class developer explictly create a method for their subclasses.
Minor man page reorg.
IRanges
Small addition to the "Auto-Extending buffer" code. Bumped version to 1.3.26
IRanges
Move sequence extraction to Sequence section.
Add stub Rle tips and tricks vignette.
More vignette expansion.
IRanges
Speedup to RleList to RangedData coersion method.
Added grouprank() and togrouprank() for H2LGrouping objects.
Added a method to convert from RleList to RangedData.
IRanges
sync up with the RELEASE_2_3 branch
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Added missing documentation. Bumped version to 0.99.31
Documentation and lots of it. All that remains is the Ranges class and
a couple of related methods. It sounds like Herve is going to handle that.
Fixes to tests. R CMD check can now actually check if the tests
passed. And they actually pass, too.
IRanges
Optimization to Ops methods for Rle objects.
Added a c method for Rle objects and allow logical Rle objects to subscript other Rle objects.
Enhanced the Rle constructors.
Added richer subscript capability to the Rle class.
Minor code change.
Added an Rle class that will be easy to maintain. It is based on the rle function from base and doesn't differentiate values by data type to make it easier to use existing R functions to modify the values.
IRanges
Working on a general conceptual description of the package, could be
worked into a vignette, with a good motivating example.
IRanges
Added functionality in the SplitDataFrameList constructor to accept split columns that will be column bound together.
Bumped version number.
IRanges
Fixed metadata handling of cbind method for XDataFrame objects.
Minor variable name change.
Fixed test name.
Added tests for metadata handling of IntegerList classes.
Fixed metadata handling in c method for IRanges objects.
Minor formatting change.
Fixed metadata handling of FilterRules class.
Fixed a bug related to using '[' as the FUN in lapply.
Major refactor to the IRanges package. The class system became unwieldy and we decided to make the Sequence virtual class the parent of nearly all classes in this package, much like the vector virtual class is the parent of nearly all classes in the S3 world.
Add 'by' method on DataFrame.
IRanges
Added new_IRanges() to the IRanges C interface.
Moved the RoSeq stuff back to Biostrings (where it belongs).
Updated TODO file.
Exported newEmptyNormalIRanges().
IRanges
Fixed the show method for Ranges objects to print a limited number of rows.
Removed another task from list.
Update the TODO list to remove completed tasks.
Added the ability to use the IRanges function to convert logical Rle objects to IRanges.
Added an updateTypedList function to update object that use old TypedList class definition.
Use match.fun in aggregate and shiftApply to find quoted FUN objects.
IRanges
Slight performance tweak to viewRangeMins/Maxs.
Add viewRangeMaxs/Mins on RleViews for finding ranges of continuous maxima/minima
IRanges
Added "as.integer" method for XInteger objects. Bumped version to 0.99.11
Minor code change to coverage function to return the answer rather than NULL.
Not duplicating an SEXP coming from the userspace before passing it to SET_SLOT() is DANGEROUS! Fixed this problem in C implementation of slice().
IRanges
Sped up seqextract and seqextract<- methods for Rle objects.
Renamed term seqblock with subsetbyranges in C interfaces.
Speed up to seqextract<- replacement methods for Sequence and DataTable objects.
Added seqextract<- and window<- replacement methods for vector objects.
Fixed seqextract replacement methods for CompressedList and SimpleList when supplying an IntegerList start argument.
Added the ability to subset by [ and seqextract using a logical RleList on a SimpleList or CompressedList object.
Added seqextract<- replacement methods for SimpleList adn CompressedList objects.
Fixed SimpleRleList -> CompressedIRangesList coercion method.
Added stub methods for window<- and seqextract<- for RangedData stating these operations are not supported.
Import window<- generic from stats package.
IRanges
o Improved the IRanges() constructor:
- revisited handling of the start/end/width arguments for more flexibility
- added 'names' argument
o Views() constructor:
- made treatment of the start/end/width arguments consistent with IRanges()
constructor
o Removed duplicated "Views" method for integer vectors from file
R/XRleIntegerViews-class.R (was already defined in file
R/XIntegerViews-class.R).
o Added coercion methods:
- from Sequence to Views
- from numeric to XInteger
o Defunct views()
Bummped version to 1.1.62
Made "union", "intersect" and "setdiff" methods work as endomorphisms
with respect to their first argument. A few small improvements to various
man pages.
Added a few coercion methods: Rle to NormalIRanges, logical to IRanges,
and logical to NormalIRanges.
Added support for logical input to IRanges() constructor (was already
accepting logical Rle input). Not sure this is good design though.
Note about sorting in overlap() docs.
IRanges
Added AnnotatedCompressedTypedListLike and AnnotatedSimpleTypedListLike to the exported class list.
Made the following changes:
1) Conceptually, a List class is informally defined as a class that inherits from both ListLike and Sequence. To make this distinction clearer I
a) Renamed TypedListV2 to TypedListLike and AnnotatedTypedListV2 to AnnotatedTypedListLike
b) Added Sequence inheritance to "Atomic"List classes as well as XDataFrameList, RangesList, RangedDataList, and RangesMatchingList
Currently DataFrame, Grouping, Views, MaskCollection, FilterRules, and Alignment are ListLike but do not inherit from Sequence.
2) Added a DataFrame virtual class that has a similar interface, but does not inherit from Sequence, where "sequence" operations are performed on the rows.
IRanges
Added append_string_to_CharAE() to the IRanges C interface. Bumped version to 0.99.14
IRanges
Updated TODO file (added the "About renaming/splitting the package" section). Deprecated intToRanges().
IRanges
Added a function to the debug suite.
Added viewMins, viewMaxs, viewSums functions.
Modified coverage and slice to create XInteger and XIntegerViews respectively.
IRanges
Added the "subseq<-" generic with a method for vector objects (not that I have a serious use-case for this particular method, its purpose is mainly to illustrate the semantic of the generic). Bumped version to 1.1.54
Add missing docs for nearest neighbors, disjoint stuff, mid(), and pgap().
IRanges
Clean up of eval methods in IRanges.
Improved error message handling in "[" method for RangedData object.
Support factor arguments in "[" subscripting.
Fixed a bug in "[" method for RangedData objects when using matrix style subscripting.
Bumped version number.
IRanges
Some speed up improvements to Rle operations, particularly infix operations.
Fixed the Initializer for TypedList to keep previously set slots. Previously old slot values were ignored.
IRanges
Added RangeAE_asIRanges() and CharAEAE_asCHARACTER() to the IRanges C interface.
Merged latest fixes by Michael from 2.3 branch.
time for a version bump -> 1.1.3
IRanges
Added a new Binning class (a subclass of Grouping).
Stripped recently added elementLengths names from CompressedList subset manipulations.
IRanges
Fixed "c" method for XRaw objects (first arg was repeated twice). Bumped version to 1.1.63
o Added "coerce" methods:
- from ANY to vector (as a workaround to a bug in R, see R/utils.R)
- from raw to XRaw
- from raw to XSequence
- from numeric to XRaw
o Added "as.raw" and "as.vector" methods for XRaw objects.
o Removed coerce,integer,XInteger method.
o Removed non-sense "as.integer" methods for XIntegerViews and XRleIntegerViews.
IRanges
Automatically upgrade objects with older TypedList definitions in a lot of key TypedList methods.
Added an updateRangedData function to update older RangedData objects to the newer definition.
Fixed the subscripting of compressed TypedList objects with zero length elements.
IRanges
Added a split method for IRanges objects.
Fixed a bug in the lapply method for CompressedList objects when optional arguments are supplied.
IRanges
Simpler implementation of "sapply" method for ListLike objects.
Added the ListLike no-slot virtual class with "lapply", "sapply" and "as.list" methods. This class can be contained by any list-like container (list-like container == container with a "length", "[[" and "names" method) in order to inherit these methods. This immediately applies to the Views and MaskCollections containers in IRanges and the XStringSet container in Biostrings. Bumped version to 1.1.41
IRanges
Fix replacing a non-existent named element with NULL in TypedList [[<-
(should be a no-op, not an error)
Reworking of IRanges TypedList-derived classes. If appropriate, the data in these TypedList classes can be compressed down to a single list element to save space. This had ripple effects to the Biostrings package and the pairwiseAlignment functionality.
IRanges
Optimize RangedData to make subsetting/extraction and dims/dimnames accessors
30X faster. Still slow, but RangedData is now fast enough to not be annoying.
Better tests for nearest neighbor finding.
Fix RangesList show method to accurately report length.
Fix bug in TypedList() when factor is empty (which is not the same as NULL).
Make (Split)XDataFrameList optionally compressible, and take advantage
of compression in dim(names) accessors.
Improved performance of cumsum and cumprod for Rle objects.
IRanges
Fixed unlist function for TypedListV2 objects to return NULL when list is of length 0.
Added a TypedListV2 (TypedList version 2) class to replace TypedList virtual class. It separate implementation from concept and includes the usage of SimpleTypedList and CompressedTypedList virtual classes.
Adding missing doc entries for IntervalTree class.
IRanges
Added verbose argument to shiftApply and switched basesCovered function over to use it.
Added a shiftApply function to facilitate faster than naive shift correlation type operations.
IRanges
Addressed performance issue with IRanges() constructor. Bumped version to 1.3.5
Shuffling the author list.
Update vignette to reflect recent discussions.
IRanges
Small addition to the "Auto-Extending buffer" code. Bumped version to 1.3.26
IRanges
Added another test.
Fixed subseq for Rle objects.
Removed subseq from the Sequence interface.
Split TypedListV2 into two types TypedListV2 and AnnotatedTypedListV2.
RangesMatchingList now tracks the subject names, so that as.matrix
Optimizations to rbind.RangedData
IRanges
Fixed the subscripting of compressed TypedList objects with zero length elements.
Fixed an issue with the window method for Rle objects to work with recently modified subseq method for Rle objects.
Begin adding missing bits of documentation.
- Fixed "show" method for 0-length Ranges object (was not showing the
"names" col), plus other simplifications of the code.
- All "subseq" methods now implement the SEW interface and will raise
a more consistent error message when the user-spplied start/end/width
values are invalid.
IRanges
Added an updateObject man page.
Added the first test of updating old IRanges BioC 2.4 objects to BioC 2.5 framework.
Changed updateObject method for AnnotatedList objects.
Added more information to the list subsection in the vignette.
Minor doc changes.
Removed duplicate description of length function.
Further refinement of isEmpty language.
Fixed the description of isEmpty.
Reorganized Sequence class R code file to make it easier to find code.
Fixed isEmpty methods for CompressedList and SimpleList methods.
Added isEmpty methods for SimpleList and CompressedList objects.
Bumped version number.
Changed sapply Sequence method to use lapply Sequence method.
Added more code to list construction example.
Cleaned up the list section a bit.
Reworked intro to list section.
IRanges
Changed append examples to reflect recent changes in that function.
IRanges
Documentation, without resorting to the T word.
IRanges
Coercion from Ranges to RangedData.
Make coercion from logical/Rle to IRanges also work for the "Ranges" target.
No longer qualify "subsequence" with "mathematical". It's either a
subsequence or a new sequence.