
import("Biobase")

import("BiocGenerics")

import("ProtGenerics")

import("methods")

import("stats4")

importFrom("grid",
	"grid.raster")

importFrom("irlba",
	"irlba")

importFrom("lattice",
	"xyplot",
	"levelplot",
	"panel.abline",
	"panel.xyplot",
	"panel.levelplot",
	"simpleKey")

importFrom("signal",
	"interp1",
	"kaiser",
	"pchip",
	"sgolayfilt")

importFrom("sp",
	"point.in.polygon")

importFrom("utils",
	"sessionInfo",
	"setTxtProgressBar",
	"txtProgressBar")

exportClasses(
	"Binmat",
	"Hashmat",
	"IAnnotatedDataFrame",
	"ImageData",
	"MIAPE-Imaging",
	"MSImageData",
	"MSImageProcess",
	"MSImageSet",
	"ResultSet",
	"SImageData",
	"SImageSet",
	"iSet")

export(
	"Binmat",
	"ImageData",
	"IAnnotatedDataFrame",
	"Hashmat",
	"MSImageData",
	"MSImageSet",
	"SImageData",
	"SImageSet")

export(
	"alpha.colors",
	"generateImage",
	"generateSpectrum",
	"gradient.colors",
	"intensity.colors",
	"readAnalyze",
	"readImzML",
	"readMSIData",
	"risk.colors")

export(
	"print.summary.iSet",
	"print.summary.PCA",
	"print.summary.PLS",
	"print.summary.OPLS",
	"print.summary.SpatialKMeans",
	"print.summary.SpatialShrunkenCentroids",
	"print.summary.CrossValidated")

export(
	"plot.summary.PCA",
	"plot.summary.PLS",
	"plot.summary.OPLS",
	"plot.summary.SpatialKMeans",
	"plot.summary.SpatialShrunkenCentroids",
	"plot.summary.CrossValidated")

exportMethods(
	"as.array",
	"as.matrix",
	"length",
	"names",
	"names<-",
	"rownames",
	"rownames<-",
	"colnames",
	"colnames<-",
	"cbind",
	"rbind",
	"summary")

exportMethods(
	"image",
	"image3D",
	"plot")

exportMethods(
	"fitted",
	"predict",
	"residuals",
	"coef")

exportMethods("logLik")

exportMethods(
	"$",
	"$<-",
	"[",
	"[<-",
	"[[",
	"[[<-",
	"annotatedDataFrameFrom",
	"combine",
	"coord",
	"coord<-",
	"coordinates",
	"coordinates<-",
	"coordLabels",
	"coordLabels<-",
	"dim",
	"dim<-",
	"dims",
	"dimnames",
	"dimnames<-",
	"features",
	"fData",
	"fData<-",
	"featureData",
	"featureData<-",
	"featureNames",
	"featureNames<-",
	"fvarLabels",
	"fvarLabels<-",
	"fvarMetadata",
	"fvarMetadata<-",
	"iData",
	"iData<-",
	"imageData",
	"imageData<-",
	"initialize",
	"keys",
	"keys<-",
	"modelData",
	"modelData<-",
	"mz",
	"mz<-",
	"mzData",
	"mzData<-",
	"pData",
	"pData<-",
	"peaks",
	"peaks<-",
	"peakData",
	"peakData<-",
	"pixels",
	"pixelData",
	"pixelData<-",
	"pixelNames",
	"pixelNames<-",
	"positionArray",
	"positionArray<-",
	"processingData",
	"processingData<-",
	"regeneratePositions",
	"resultData",
	"resultData<-",
	"sampleNames",
	"sampleNames<-",
	"show",
	"spectra",
	"spectra<-",
	"storageMode",
	"storageMode<-",
	"varLabels",
	"varLabels<-",
	"varMetadata",
	"varMetadata<-")

exportMethods(
	"embeddingMethod",
	"embeddingMethod<-",
	"imageShape",
	"imageShape<-",
	"instrumentModel",
	"instrumentModel<-",
	"instrumentVendor",
	"instrumentVendor<-",
	"inSituChemistry",
	"inSituChemistry<-",
	"ionizationType",
	"ionizationType<-",
	"lineScanDirection",
	"lineScanDirection<-",
	"massAnalyzerType",
	"massAnalyzerType<-",
	"matrixApplication",
	"matrixApplication<-",
	"msiInfo",
	"pixelSize",
	"pixelSize<-",
	"scanDirection",
	"scanDirection<-",
	"scanPattern",
	"scanPattern<-",
	"scanPolarity<-",
	"scanPolarity<-",
	"scanType",
	"scanType<-",
	"softwareName",
	"softwareName<-",
	"softwareVersion",
	"softwareVersion<-",
	"specimenOrigin",
	"specimenOrigin<-",
	"specimenType",
	"specimenType<-",
	"stainingMethod",
	"stainingMethod<-",
	"tissueThickness",
	"tissueThickness<-",
	"tissueWash",
	"tissueWash<-")

exportMethods(
	"baselineReduction",
	"baselineReduction<-",
	"centroided",
	"centroided<-",
	"prochistory",
	"prochistory<-",
	"files",
	"files<-",
	"normalization",
	"normalization<-",
	"peakPicking",
	"peakPicking<-",
	"smoothing",
	"smoothing<-",
	"spectrumRepresentation",
	"spectrumRepresentation<-")

exportMethods(
	"cvApply",
	"featureApply",
	"pixelApply")

exportMethods(
	"batchProcess",
	"normalize",
	"peakPick",
	"peakAlign",
	"peakFilter",
	"reduceBaseline",
	"reduceDimension",
	"smoothSignal",
	"standardizeSamples")

exportMethods("coregister")

exportMethods(
	"OPLS",
	"PCA",
	"PLS",
	"spatialKMeans",
	"spatialShrunkenCentroids")

exportMethods("topLabels")

exportMethods("select")

useDynLib("Cardinal")
