Package: aroma.core
===================

Version: 1.3.1 [2009-11-03]
o Replaced Rd cross references to sfit and HaarSeg packages with
  plain text in order to meet the CRAN requirements that all
  Rd links must exist on the CRAN servers.


Version: 1.3.0 [2009-11-01]
o New public release. 
o More recent dependencies on Bioconductor packages.
o Package passes R CMD check on R v2.10.0 and all redundancy tests.


Version: 1.2.3 [2009-10-25]
o Added getExtensionPattern() to most GenericDataFile classes.


Version: 1.2.2 [2009-10-16]
o Added setName() for RawGenomicSignals.
o Stricter dependencies.


Version: 1.2.1 [2009-10-02]
o CLEAN UP: Updated to use byPath() instead fromFiles().
o CLEAN UP: Move the Interface class to the R.oo package.


Version: 1.2.0 [2009-09-09]
o New public release. 
o Fixed broken/missing Rd links.
o Package passes R CMD check on R v2.9.2 and all redundancy tests.


Version: 1.1.7 [2009-09-07]
o Now getUnitsOnChromosomes() for AromaUnitChromosomeTabularBinaryFile
  returns a vector by default (unlist=TRUE).


Version: 1.1.6 [2009-09-07]
o Added yRange(), yMin() and yMax() for RawGenomicSignals.
o Added extractRawCopyNumbers() for RawSequenceReads.
o BUG FIX/WORKAROUND: smoothScatter(), which is used in for 
  instance aroma.affymetrix, is in the graphics package from 
  R v2.9.0.  It was previously in geneplotter v1.2.4 and before(!).
  The code imported it from geneplotter would therefore give an 
  error of a missing function with geneplotter v1.2.5.  We
  are now assuming R v2.9.0 by default, but if not available,
  but geneplotter v1.2.4 or earlier is, geneplotter is loaded.
  If neither are available, a dummy smoothScatter() is setup
  reporting an error.


Version: 1.1.5 [2009-08-29]
o Added totalAndFracBData/ to the search path of byName() for
  AromaUnit(FracB|Total)CnBinarySet.


Version: 1.1.4 [2009-07-22]
o Added allocateFromUnitAnnotationDataFile() for
  AromaUnitSignalBinaryFile and AromaUnitTabularBinaryFile.
o Added getUnitTypesFile() for AromaPlatform and AromaPlatformInterface.
o Added UnitAnnotationDataFile, which now the UnitNamesFile and the new
  UnitTypesFile inherits from.
o Now uses() for Interface takes multiple Interface:s.


Version: 1.1.3 [2009-07-03]
o Added class RawSequenceReads.
o Added support for argument 'byCount' to binnedSmoothingByState() of 
  SegmentedCopyNumbers.  It is rather complex how it works, but we tried
  to immitate how it works with byCount=FALSE.
o Now binnedSmoothing() of RawGenomicSignals demark locus fields 
  that were not binned to be regular fields.  Ideally all locus fields
  (including custom ones) should be binned, but we leave that for a 
  future implementation.
o Added get-, setStateColorMap(), and getStateColors() for class
  SegmentedGenomicSignalsInterface.


Version: 1.1.2 [2009-06-14]
o Added argument keepUnits=FALSE to extractRawGenomicSignals() of
  AromaUnitSignalBinaryFile.
o Now RawGenomicSignals(y=rgs) sets all locus fields in 'rgs' if it is
  a RawGenomicSignals object.
o BUG FIX: exportTotalCnRatioSet() would return a AromaUnitFracBCnBinarySet.
o Updated examples() that requires "suggested" packages to be ran 
  conditionally, so that it does not throw an error (in R CMD check)
  if the packages is not available.  This is required for a package
  to be put on CRAN.


Version: 1.1.1 [2009-06-10]
o ADDED: Added support for "birdseed" encoding in extractGenotypes() 
  and updateGenotypes() of AromaUnitGenotypeCallFile.
o SPEED UP: updateGenotypes() of AromaUnitGenotypeCallFile is now much
  faster in counting A:s and B:s.
o Added SegmentedGenomicSignalsInterface, which implements all the 
  methods for SegmentedCopyNumbers and the new SegmentedAlleleBFractions.
o Added getFields() to Interface as an ad hoc solutions to avoid
  print(<Interface>) throwing 'Error in UseMethod("getFields") : no 
  applicable method for "getFields"'.
o GRAMMAR FIX: is(Homo|Hetero)zygous(), not is(Homo|Hetero)zygote().
o BUG FIX: isHomozygote() of AromaUnitGenotypeCallFile was not correct.
o BUG FIX: getOutputDataSet() of AromaTransform failed to identify the
  output files if (and only if) a filename translator was applied to
  the input data set.


Version: 1.1.0 [2009-05-29]
o New public release. No updates.
o Package passes R CMD check on R v2.9.0 and all redundancy tests.


Version: 1.0.8 [2009-05-25]
o GENERALIZATION: The AromaTransforms class was generalized further
  to handle cases where the number of output files does not map
  one to one to the input files.


Version: 1.0.7 [2009-05-18]
o Added extractRawAlleleBFractions() for AromaUnitFracBCnBinaryFile.
o Added exportFracBDiffSet() for AromaUnitFracBCnBinarySet.
o Moved the Explorer class and its support files under inst/ from
  aroma.affymetrix to aroma.core.
o Moved the AromaCellPositionFile class from aroma.affymetrix 
  to aroma.core.
o ADDED: Now all segmentByNnn() for RawGenomicSignals also returns
  so called 'aromaEstimates', which are additional parameter 
  estimates, e.g. robust estimates of the standard deviation of
  all full-resolution CNs as well as per identified region.
o CLEAN UP: Moved all file set specific classes and methods to
  the new R.filesets package.
o MEMORY OPTIMIZATION: Where ever possible/applicable, we now use
  Arguments$getNumerics(), which, in R utils v1.1.5 and new, corces
  to doubles only if the input is not already doubles.  This will 
  lower the memory usage in some cases since an integers use 4 bytes
  and doubles 8 bytes.  This also save disk space if object is saved
  to disk, e.g. a DNAcopy fit object with integer genomic positions 
  instead of double ones, save approx 5-7% disk space.
o ROBUSTNESS: Now allocate() for AromaTabularBinaryFile first allocates
  a temporary file which is then renamed.  This makes the file allocation
  more atomic, and therefore less error prone to interrupts etc.
o ROBUSTNESS: Now indexOf() for UnitNamesFile assert that exactly one
  of the 'pattern' and 'names' arguments is given.  It also gives an 
  informative error message if 'pattern' is a vector.
o ROBUSTNESS: Now all arguments that are expected to be exactly one
  character string (not an empty vector or a vector of length two)
  are asserted to be that too.  This closes some potential bugs.
o EXCEPTION HANDLING: All methods that modifies an existing file, are 
  now asserting that the file permissions allow modifying it, and if not
  gives a clear error message that this is the case.
o BUG FIX: allocateFromUnitNamesFile() for AromaUnitSignalBinaryFile
  would not call generic allocate() but the one for this class.
o BUG FIX: extractMergedRawCopyNumbers(..., unshift=TRUE) would estimate
  the relative shifts between platforms using smoothed CNs over the
  genomic region defined by the first data set.  Now it is done over the
  region defined by the union of all data sets.  The impact of this
  bug should be neglectable or zero.


Version: 1.0.6 [2009-05-14]
o Now binnedSmoothing() of RawGenomicSignals uses weighted estimates
  (by default) if weights exists.
o Added RawAlleleBFractions() extending RawGenomicSignals.
o Added extractCopyNumberRegions() for profileCGH, DNAcopy, and 
  HaarSeg segmentation object. Before they were in aroma.affymetrix.
o Added segmentByCBS(), segmentByGLAD(), and segmentByHarSeeg() 
  to RawGenomicSignals, which all support weights if the underlying
  segmentation method does.  To date, it is only CBS and HaarSeg
  that supports weights.  These methods also support memoization.
o Added extractRegion() to RawGenomicSignals.
o Added getWeights() and hasWeights() to RawGenomicSignals.
o Added {add,subtract,multiply,divide}By() for RawGenomicSignals all
  utilizing support method applyBinaryOperator().
o ALPHA: Added classes GenericDataFile{Set}List.
o ALPHA: Added class AromaUnitTotalCnBinaryFileList with methods 
  extractRawCopyNumbers() and extractMergedRawCopyNumbers().
o SPEED UP: Now TextUnitNamesFile caches all unit names in memory.
o BUG FIX: Now aroma.core works with the IRanges and grid packages,
  regardless on the order they were loaded.
o BUG FIX: getPlatform() of TextUnitNamesFile would sometimes return
  a list of length one, instead of an single character string.
o BUG FIX: extractSubset() of RawGenomicSignals did not recognize all
  locus fields.


Version: 1.0.5 [2009-05-10]
o Now getOutputDataSet() of AromaTransform returns a data set with files
  ordered such that the fullnames are ordered the same way as the input
  data set.  Suggested by Xin (Victoria) Wang at UC Berkeley.
o Now getOutputDataSet() of AromaTransform scans for the output data 
  files with fullnames matching those of the input data set.  This is
  one step closer to being able to batch process subsets of data sets
  when the method is, say, a single-array method.
o Now static fromFiles() of GenericDataFileSet supports empty data sets.
o Now readDataFrame() of AromaUgpFile and AromaUnitTabularBinaryFile
  accepts rows=integer(0).
o Added abstract class AromaUnitChromosomeTabularBinaryFile to make it
  easier to setup up new annotation file formats based on chromosomes.
  AromaUgpFile is now inheriting from this class.
  getUnitsOnChromosomes() now returns a list stratified by chromosome.
o Added extractByChromosomes() for AromaUgpFile.
o Added argument 'translate' to getColumnNames() of TabularTextFile.
o UPDATE: Replace argument 'robust' of colBinnedSmoothing()
  with a more generic 'FUN' argument.  The default arguments
  give identical results.
o BUG FIX: Our internal interleave() for Image (defined by EBImage) gave
  'Error in z[idxOdd,, ] : incorrect number of dimensions'. This was
  because internal image structure of the Image class changed (back) to
  being a 2-dim array. Now interleave() handles both 2d and 3d arrays.
o BUG FIX: lines() of RawGenomicSignals did not recognize x/yScale.
o BUG FIX: as.character() of GenericDataFile would throw 
  'Error in sprintf("%d", getFileSize(db, "numeric")) : use 
  format %f, %e, %g or %a for numeric objects' whenever the
  file size is returned as a double, which happens for very
  large files (> 2^31-1 bytes).
o BUG FIX: as.character() of GenericDataFileSet would throw an error if
  the data set was empty, because then there was no path.
o Package passes R CMD check on R v2.9.0.


Version: 1.0.4 [2009-04-07]
o BUG FIX: getUnitNames(..., units=NULL) of TextUnitNamesFile would 
  make the object believe there are zero units in the file. 
  Thanks Shermane Teo at the National University of Singapore 
  for reporting this.
o BUG FIX: binnedSmoothing(..., byCount=TRUE) of RawGenomicSignals 
  would give error "[...] object "ys" not found".
o BUG FIX: When passing a single data points to colBinnedSmoothing(),
  it would throw the exception: "Range of argument 'by' is out 
  of range [0,0]: [<by>,<by>]".


Version: 1.0.3 [2009-03-23]
o Added the TextUnitNamesFile class.


Version: 1.0.2 [2009-02-26]
o Added argument 'units' to extractRawCopyNumbers() of
  AromaUnitSignalBinaryFile.
o Added RawGenomicSignals which RawCopyNumbers now inherits from.
o Added readDataFrame(..., units=NULL) to AromaUnitSignalBinaryFile.
o Added optional argument/field 'name' to RawCopyNumbers, which
  is also used by SegmentedCopyNumbers when querying the "truth"
  function(s) for the copy-number state.  This makes it possible
  to use one (conditional) truth functions for all samples.
o Added hasBeenModified() to GenericDataFile.
o Now hasTags(..., tags) of GenericData{File|Set} splits the
  'tags' argument.
o Now RawCopyNumbers() takes RawCopyNumbers objects as input.
o Now getChecksum() of GenericDataFile caches results unless the 
  file has been modified since last time.
o Now as.character() of GenericDataFile also reports the exact file 
  size in case the file size is reported in kB, MB, etc.  It also 
  tries to report the relative pathname rather than the absolute.



Version: 1.0.1 [2009-02-12]
o Now byName() of AromaUnit(FracB|Total)CnBinarySet searches 
  rawCnData/ then cnData/.
o Added SegmentedCopyNumbers class.
o Added various smoothing methods to RawCopyNumbers.
o Added colBinnedSmoothing() and colKernelSmoothing().
o Added getAromaUgpFile() to UnitNamesFile.
o Added shakyText().
o Added static byChipType() to UnitNamesFile.
o Added argument 'fullname' to getChipType() of AromaUnitSignalBinaryFile.
o Now argument 'files' in extract() of GenericDataFileSet can 
  also be a vector of string.
o ROBUSTNESS: Added support for optional validation/selection by the
  number of units/cells to all static byChipType() methods.  This is
  done by specifying argument nbrOfUnits/nbrOfCells.  This is intend
  for internal use only.
o ROBUSTNESS: Added a sanity check to getAromaUgpFile() of
  UnitNamesFile and AromaUnitSignalBinaryFile, which asserts that 
  the number of units in the located UGP file match that the number
  of units in the data file.
o ROBUSTNESS: Now findAnnotationData() always returns pathnames 
  ordered by the length of their fullnames. Before this was only 
  done if 'firstOnly=TRUE'.
o ALPHA: Added support for "smart" (e.g. "*") subdirectories in static 
  findByName() of GenericDataFileSet.


Version: 1.0.0 [2009-01-12]
o Added getMaxLengthRepeats() to AromaCellSequenceFile.
o Added AromaUnitSignalBinary{File|Set}, AromaUnitTotalCnBinary{File|Set},
  AromaUnitFracBCnFinary{File|Set}, AromaUnitCall{File|Set}, and
  AromaUnitGenotypeCall{File|Set}.
o BUG FIX: readFooter() of AromaTabularBinaryFile did not return the
  correct list for nested structures.
o BUG FIX: groupBySnpNucleotides() of AromaCellSequenceFile would return
  an empty element 'missing' for some chip types, e.g. Mapping10K_Xba142.
  Now that empty elements are dropped.
o BUG FIX: getAttributes() for GenericDataFile:s would give an error
  if there were no attributes.


Version: 0.9.6 [2008-12-04]
o SPEED UP: Now predict() of ProbePositionEffects is 6-7 times faster.
o SPEED UP: Now the result of isMissing() for AromaCellSequenceFile 
  can be cached.
o ALPHA: Added the BinnedScatter class with methods.
o CLEAN UP: readDataFrame() of AromaTabularBinaryFile would forget to
  close the connection if verbose output was activated.  When R later
  would close such connections, a warning would be generated.


Version: 0.9.5 [2008-10-17]
o Package passes R CMD check on R v2.7.2 and R v2.8.0rc.


Version: 0.9.4.5 [2008-10-16]
o BUG FIX: Tried to turn a function passed to as.GrayscaleImage()
  in argument 'transforms' to a list using as.list() and not list().


Version: 0.9.4.4 [2008-09-18]
o Added argument 'skip' to writeChecksum() of GenericDataFile.


Version: 0.9.4.3 [2008-09-03]
o Added getSnpPositions(), getSnpShifts(), getSnpNucleotides() and
  groupBySnpNucleotides() to AromaCellSequenceFile.


Version: 0.9.4.2 [2008-08-31]
o Update fitGenotypeCone() to support both flavors 'sfit' (old)
  and 'expectile' (new).


Version: 0.9.4.1 [2008-08-12]
o Added support for argument 'positions' to countBases() for
  AromaCellSequenceFile.
o ALPHA: Added fitMultiDimensionalCone().
o BUG FIX: readSequences() for AromaCellSequenceFile translated
  raw values to incorrect nucleotides.
o TESTING: Added redundancy tests to aroma.core.


Version: 0.9.4 [2008-08-02]
o Public release.  Package passes R CMD check on R v2.7.1
  and R v2.8.0 devel on WinXP.


Version: 0.9.3.4 [2008-07-24]
o SPEED UP: Added patch for base::serialize() on Windows, 
  which in turn will speed up digest::digest() and all
  methods that use the latter to generate hashcodes.
o SPEED UP: Now as.character() for GenericTabularFile:s
  and TabularTextFile:s reports the number of data rows
  and the number of text lines as NA if the files are too
  large and cached results are not already available.
o SPEED UP: Replaced all which() with faster whichVector().
o Added getCreatedOn(), getLastModifiedOn(), and
  getLastAccessedOn() to GenericDataFile.  These a just
  wrapper accessing file.info() fields.


Version: 0.9.3.3 [2008-07-21]
o Now countBases() of AromaCellSequenceFile returns "raw" 
  counts if argument 'mode="raw"'.
o Now updateDataColumn() coerce values to doubles before 
  censoring them for raw and integer columns.
o Now findByName() assert that the data set name is not empty.
o ALPHA: Added setFullName() and setName() to GenericDataFile
  and GenericDataFileSet. The plan is to have these replace
  what getAlias() and setAlias() do today.
o BETA: Added setFullNameTranslator() to GenericDataFileSet.


Version: 0.9.3.2 [2008-07-16]
o BETA: Added setFullNamesTranslator() (for the files) 
  to AromaGenericFileSet.
o ALPHA: Added protected update2() to GenericDataFileSet.
o ALPHA: Added private ProbePositionEffects et al.


Version: 0.9.3.1 [2008-07-12]
o SPEED UP: Now all AromaTabularBinaryFile:s, such as AromaUgpFile,
  read data much faster after two modifications to readDataFrame():
  (i) rownames are no longer generate, if not asked for explicitly,
  and (ii) garbage collection is no longer done after each column.
o Added a general importFrom() for AromaTabularBinaryFile, which
  calls matching importFrom<ClassName>(), if found.
o Added support for 'raw' data columns in AromaTabularBinaryFile.
o BETA: Added readTableHeader().
o BETA: Added AromaCellSequenceFile.
o BETA: Added classes AromaMicroarrayTabularBinaryFile and 
  AromaCellTabularBinaryFile.


Version: 0.9.3 [2008-06-08]
o Package passes R CMD check on R v2.7.0 patched.


Version: 0.9.2.6 [2008-06-07]
o Update filename pattern for getOutputFiles() of AromaTransform.


Version: 0.9.2.5 [2008-05-25]
o Added AromaTransform (extracted from aroma.affymetrix::Transform).
o Added nbrOfArrays() to AromaMicroarrayDataSet.
o Now private xmlToList() handles more complex XML strings.


Version: 0.9.2.4 [2008-05-22]
o Added member 'chromosome' to RawCopyNumbers.
o Added gaussianSmoothing() to RawCopyNumbers.
o Added argument 'xOut' to gaussianSmoothing() in order to specify
  at what loci the smoothed signals should be calculated.


Version: 0.9.2.3 [2008-05-21]
o Now findPngDevice() search for a working PNG device in the following
  order: png(..., type="cairo"), png(..., type="cairo1"), 
  Cairo::CairoPNG(), R.utils::png2(), and finally plain png().
o Added gzip()/gunzip() to GenericDataFile.
o Added static findByName() and byName() to GenericDataFileSet.
o Added static getFileClass() to GenericDataFileSet.  This makes it
  possible to remove most fromFiles() from subclasses but also
  the validation of argument 'files' of their constructors.
o Added validate() to GenericDataFileSet, which is called at the
  end of fromFiles(..., .validate=TRUE).
o Added extractMatrix to GenericTabular(File|Set) and 
  AromaTabularBinary(File|Set).
o Added equals() and hasFile() to GenericDataFileSet.
o Added classes GenericTabularFileSet and AromaTabularBinarySet.
o Added stextChipType() for strings.
o CLEAN UP: Moved more classes and methods from aroma.affymetrix to 
  aroma.core: RawCopyNumbers, CopyNumberRegions, CopyNumberOutliers.
  Moved attribute methods from AffymetrixCel{File|Set} to 
  AromaMicroarrayDataSet.  Moved stextNnn() methods from AffymetrixFile
  to AffymetrixMicroarrayDataSet.
  Created superclass AromaMicroarrayDataSetTuple of AffymetrixCelSetTuple.
o BUG FIX: readDataFrame() did not read the first data row if there 
  was no column header; it was eaten up by a preceeding readHeader().
o BUG FIX: findAnnotationDataByChipType(chipType="GenomeWideSNP_6", 
  pattern="^GenomeWideSNP_6.*[.]ugp$") would find file 
  'GenomeWideSNP_6,Full,na24.ugp' before 'GenomeWideSNP_6,na24.ugp'.
  Now we return the one with the shortest full name.
o ALPHA: Now equals() for GenericDataFile:s uses the class, 
  pathname, file size and file-contents checksum to do the 
  comparison.  Similarly, for GenericDataFileSet:s, the class, 
  path, number of files, pathnames, and finally equals() for 
  each file pair is used for the comparison.  
o ALPHA: Added full name translation for GenericDataFile:s.
o ALPHA: Added UnitNamesFile.
o Package passes R CMD check on R v2.7.0 patched.


Version: 0.9.2 [2008-05-10]
o Took all core classes and core methods in aroma.affymetrix that
  are independent of the Affymetrix platform and placed the here.
o The version is numbered starting from the current version of
  aroma.affymetrix.
o BUG FIX: interleave() for Image gave 'Error in z[idxOdd, ] : 
  incorrect number of dimensions'.  The internal image structure
  is a 3-dim array.
o BUG FIX: When searching with 'firstOnly=FALSE', findAnnotationData() 
  was identifying files that are in "private" directory.  This is how
  affxparser::findFiles() works.  Such files are now filtered out.
o Created.