# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# IMPORTS
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
importFrom("R.methodsS3", "setMethodS3")
importFrom("R.oo", "setConstructorS3")
importFrom("R.oo", "extend")
importFrom("R.oo", "uses")
importFrom("R.methodsS3", "throw")

## Importing Class:es
importFrom("R.oo", "Package")
importFrom("aroma.affymetrix", "AffymetrixCelSet")
importFrom("aroma.affymetrix", "AllelicCrosstalkCalibration")
importFrom("aroma.affymetrix", "BasePositionNormalization")
importFrom("aroma.affymetrix", "ProbeLevelModel")
importFrom("aroma.affymetrix", "FragmentLengthNormalization")

## Importing generics
importFrom("aroma.affymetrix", "getFitUnitFunction")
importFrom("aroma.affymetrix", "getProbeAffinityFile")
importFrom("R.filesets", "getAsteriskTags")

## Importing functions
importFrom("aroma.core", "findUnitsTodo")
importFrom("aroma.core", "fit")
importFrom("aroma.core", "process")
importFrom("aroma.affymetrix", "exportTotalAndFracB")
importFrom("aroma.affymetrix", "fitCnProbes")
importFrom("aroma.affymetrix", "getChipEffectSet")
importFrom("aroma.affymetrix", "setDecodeFunction")
importFrom("aroma.affymetrix", "setEncodeFunction")
importFrom("aroma.affymetrix", "SnpPlm")
importFrom("MASS", "ginv")
importFrom("MASS", "rlm")
importFrom("matrixStats", "colMedians")
importFrom("matrixStats", "rowMads")
importFrom("matrixStats", "rowMedians")
importFrom("R.oo", "getDate")
importFrom("R.oo", "getName") ## Multi-sources: R.oo, R.filesets
importFrom("R.oo", "getPosition")
importFrom("R.oo", "getVersion")
importFrom("R.oo", "startupMessage")
importFrom("R.utils", "cat") ## Multi-sources: R.utils, base
importFrom("R.utils", "enter")
importFrom("R.utils", "exit")
importFrom("R.utils", "less")
importFrom("R.utils", "stext")

## Manually imported
importFrom("R.utils", "Arguments")

importFrom("graphics", "abline", "layout", "legend", "lines", "par",
           "plot", "points", "text", "title")
importFrom("stats", "cor", "density", "median", "na.omit")
importFrom("utils", "str")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# EXPORTS
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Export all public methods, that is, those without a preceeding dot
# in their names.
exportPattern("^[^\\.]")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# DECLARATIONS
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# AffymetrixCelSet
S3method("doACNE", "AffymetrixCelSet")

# default
S3method("doACNE", "default")

# NmfPlm
S3method("getAsteriskTags", "NmfPlm")
S3method("getProbeAffinityFile", "NmfPlm")
S3method("getFitUnitFunction", "NmfPlm")

# NmfSnpPlm
S3method("getAsteriskTags", "NmfSnpPlm")

# SnpNmfFit
S3method("plot", "SnpNmfFit")
