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

importFrom("R.oo", "Package")
importFrom("R.oo", "getPosition")
importFrom("R.oo", "startupMessage")

importFrom("R.utils", "Arguments")
importFrom("R.utils", "Verbose")
importFrom("R.utils", "pushState")
importFrom("R.utils", "popState")
importFrom("R.utils", "enter")
importFrom("R.utils", "exit")
importFrom("R.utils", "printf")
importFrom("R.utils", "hpaste")
importFrom("R.utils", "cat") ## Multi-sources: R.utils, base
importFrom("R.utils", "use")

importFrom("matrixStats", "anyMissing")
importFrom("matrixStats", "colMedians")
importFrom("matrixStats", "colMins")
importFrom("matrixStats", "colQuantiles")
importFrom("matrixStats", "rowMedians")
importFrom("matrixStats", "rowWeightedMeans")
importFrom("matrixStats", "rowWeightedMedians")

importFrom("grDevices",
           "xy.coords")
importFrom("graphics",
           "abline", "axis", "box", "lines", "mtext", "par", "plot",
           "points", "polygon")
importFrom("stats",
           "IQR", "approx", "cor", "density", "integrate", "loess",
           "loess.control", "lowess", "mad", "median", "na.omit",
	   "predict", "sd", "smooth.spline", "weighted.mean", "weights")
importFrom("utils",
           "getAnywhere", "packageDescription")


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



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# S3 methods
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# data.frame
S3method("plotDensity", "data.frame")

# default
S3method("distanceBetweenLines", "default")
S3method("normalizeFragmentLength", "default")
S3method("normalizeQuantile", "default")
S3method("robustSmoothSpline", "default")
S3method("sampleTuples", "default")

# density
S3method("findPeaksAndValleys", "density")
S3method("plotDensity", "density")

# list
S3method("averageQuantile", "list")
S3method("normalizeAverage", "list")
S3method("normalizeDifferencesToAverage", "list")
S3method("normalizeQuantileRank", "list")
S3method("normalizeQuantileSpline", "list")
S3method("plotDensity", "list")

# lowess
S3method("predict", "lowess")

# matrix
S3method("averageQuantile", "matrix")
S3method("backtransformAffine", "matrix")
S3method("backtransformPrincipalCurve", "matrix")
S3method("backtransformXYCurve", "matrix")
S3method("calibrateMultiscan", "matrix")
S3method("fitIWPCA", "matrix")
S3method("fitPrincipalCurve", "matrix")
S3method("fitXYCurve", "matrix")
S3method("iwpca", "matrix")
S3method("medianPolish", "matrix")
S3method("normalizeAffine", "matrix")
S3method("normalizeAverage", "matrix")
S3method("normalizeCurveFit", "matrix")
S3method("normalizeLoess", "matrix")
S3method("normalizeLowess", "matrix")
S3method("normalizeQuantileRank", "matrix")
S3method("normalizeQuantileSpline", "matrix")
S3method("normalizeRobustSpline", "matrix")
S3method("normalizeSpline", "matrix")
S3method("plotDensity", "matrix")
S3method("plotMvsA", "matrix")
S3method("plotMvsAPairs", "matrix")
S3method("plotMvsMPairs", "matrix")
S3method("plotXYCurve", "matrix")
S3method("rowAverages", "matrix")
S3method("sampleCorrelations", "matrix")
S3method("wpca", "matrix")

# numeric
S3method("backtransformPrincipalCurve", "numeric")
S3method("callNaiveGenotypes", "numeric")
S3method("findPeaksAndValleys", "numeric")
S3method("fitNaiveGenotypes", "numeric")
S3method("normalizeQuantileRank", "numeric")
S3method("normalizeQuantileSpline", "numeric")
S3method("normalizeTumorBoost", "numeric")
S3method("pairedAlleleSpecificCopyNumbers", "numeric")
S3method("plotDensity", "numeric")
S3method("plotXYCurve", "numeric")

# smooth.spline
S3method("likelihood", "smooth.spline")

# SmoothSplineLikelihood
S3method("print", "SmoothSplineLikelihood")

# XYCurveFit
S3method("lines", "XYCurveFit")
