# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# IMPORTS
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
importFrom("R.methodsS3", "setMethodS3")
importFrom("R.methodsS3", "appendVarArgs")
importFrom("R.methodsS3", "isGenericS3")
importFrom("R.oo", "setConstructorS3")
importFrom("R.oo", "extend")
importFrom("R.oo", "throw")
importFrom("R.oo", "uses")

## Importing Class:es
importFrom("R.oo", "BasicObject")
importFrom("R.oo", "Interface")
importFrom("R.oo", "Object")
importFrom("R.oo", "Class")
importFrom("R.utils", "GenericSummary")
importFrom("R.utils", "System")
importFrom("R.filesets", "GenericDataFile")
importFrom("R.filesets", "GenericDataFileList")
importFrom("R.filesets", "GenericDataFileSet")
importFrom("R.filesets", "GenericDataFileSetList")
importFrom("R.filesets", "GenericTabularFile")
importFrom("R.filesets", "GenericTabularFileSet")
importFrom("R.filesets", "TabularTextFile")
importFrom("R.filesets", "TabularTextFileSet")

## Importing generics
importFrom("matrixStats", "anyMissing")
importFrom("matrixStats", "colAlls")
importFrom("matrixStats", "colWeightedMeans")
importFrom("matrixStats", "colWeightedMedians")
importFrom("matrixStats", "rowCollapse")
importFrom("matrixStats", "rowMads")
importFrom("matrixStats", "rowSds")
importFrom("matrixStats", "rowSums2")
importFrom("matrixStats", "colMedians")
importFrom("matrixStats", "rowMedians")
importFrom("R.filesets", "append") ## Multi-sources: R.filesets, PSCBS, base
importFrom("R.filesets", "byName")
importFrom("R.filesets", "byPath")
importFrom("R.filesets", "clearCache") ## Multi-sources: R.filesets, R.oo, R.cache
importFrom("R.filesets", "clone") ## Multi-sources: R.filesets, R.oo
importFrom("R.filesets", "extractMatrix")
importFrom("R.filesets", "findByName")
importFrom("R.filesets", "fromFile")
importFrom("R.filesets", "getAsteriskTags")
importFrom("R.filesets", "getColumnNames")
importFrom("R.filesets", "getColumnNamesTranslator")
importFrom("R.filesets", "getDefaultColumnNames")
importFrom("R.filesets", "getDefaultFullName")
importFrom("R.filesets", "getExtensionPattern")
importFrom("R.filesets", "getFilenameExtension")
importFrom("R.filesets", "getFullName")
importFrom("R.filesets", "getFullNames")
importFrom("R.filesets", "getName") ## Multi-sources: R.filesets, R.oo
importFrom("R.filesets", "getNames")
importFrom("R.filesets", "getPath") ## Multi-sources: R.filesets, R.oo
importFrom("R.filesets", "getSets")
importFrom("R.filesets", "getTags")
importFrom("R.filesets", "indexOf")
importFrom("R.filesets", "nbrOfColumns")
importFrom("R.filesets", "nbrOfRows")
importFrom("R.filesets", "readColumns")
importFrom("R.filesets", "readDataFrame")
importFrom("R.filesets", "setAttributes") ## Multi-sources: R.filesets, R.rsp
importFrom("R.filesets", "setAttributesBy")
importFrom("R.filesets", "setAttributesByTags")
importFrom("R.filesets", "setColumnNamesTranslator")
importFrom("R.filesets", "setName")
importFrom("R.filesets", "setTags")
importFrom("R.filesets", "translateColumnNames")
importFrom("R.oo", "equals")
importFrom("R.oo", "getVersion")
importFrom("R.oo", "newInstance")
importFrom("R.oo", "save") ## Multi-sources: R.oo, base
importFrom("R.utils", "downloadFile")
importFrom("R.utils", "getVerbose")
importFrom("R.utils", "hsize")
importFrom("R.utils", "isDone")
importFrom("R.utils", "validate") ## Multi-sources: R.utils, R.filesets
importFrom("R.utils", "writeDataFrame")
importFrom("utils", "str")

## Importing functions
## importFrom("aroma.light", "robustSmoothSpline") ## Only suggested for now
importFrom("PSCBS", "plotTracksManyChromosomes")
importFrom("R.cache", "loadCache")
importFrom("R.cache", "saveCache")
importFrom("R.devices", "png2")
importFrom("R.filesets", "dropRootPathTags")
importFrom("R.filesets", "getAttribute") ## Multi-sources: R.filesets, R.rsp
importFrom("R.filesets", "getChecksum") ## Multi-sources: R.filesets, R.cache
importFrom("R.filesets", "getFile") ## Multi-sources: R.filesets, R.rsp
importFrom("R.filesets", "getFileList")
importFrom("R.filesets", "getFileSize")
importFrom("R.filesets", "getHeader") ## Multi-sources: R.filesets, R.rsp
importFrom("R.filesets", "getOneFile")
importFrom("R.filesets", "getPathname")
importFrom("R.filesets", "getPathnames")
importFrom("R.filesets", "hasTag")
importFrom("R.filesets", "indexOf.GenericDataFileSet")
importFrom("R.filesets", "setAttribute") ## Multi-sources: R.filesets, R.rsp
importFrom("R.oo", "attachLocally")
importFrom("R.oo", "getDate")
importFrom("R.oo", "getKnownSubclasses")
importFrom("R.oo", "getPosition")
importFrom("R.oo", "getStaticInstance")
importFrom("R.oo", "isVisible")
importFrom("R.oo", "ll")
importFrom("R.oo", "objectSize")
importFrom("R.oo", "Package")
importFrom("R.oo", "startupMessage")
importFrom("R.oo", "trim")
importFrom("R.rsp", "rfile")
importFrom("R.utils", "callHooks")
importFrom("R.utils", "capitalize")
importFrom("R.utils", "cat") ## Multi-sources: R.utils, base
importFrom("R.utils", "copyDirectory")
importFrom("R.utils", "copyFile")
importFrom("R.utils", "dataFrame")
importFrom("R.utils", "draw")
importFrom("R.utils", "enter")
importFrom("R.utils", "exit")
importFrom("R.filesets", "extract") ## Multi-sources: R.utils, R.filesets
importFrom("R.utils", "filePath")
importFrom("R.utils", "findFiles")
importFrom("R.utils", "getAbsolutePath")
importFrom("R.utils", "getFilename") ## Multi-sources: R.utils, R.filesets
importFrom("R.utils", "getOption") ## Multi-sources: R.utils, base
importFrom("R.utils", "getParent")
importFrom("R.utils", "gunzip") ## Multi-sources: R.utils, R.filesets
importFrom("R.utils", "hpaste")
importFrom("R.utils", "insert")
importFrom("R.utils", "isDirectory")
importFrom("R.utils", "isFile") ## Multi-sources: R.utils, R.filesets
importFrom("R.utils", "isPackageInstalled")
importFrom("R.utils", "isPackageLoaded")
importFrom("R.utils", "isZero")
importFrom("R.utils", "less")
importFrom("R.utils", "loadObject")
importFrom("R.utils", "mergeByCommonTails")
importFrom("R.utils", "moveInSearchPath")
importFrom("R.utils", "popState")
importFrom("R.utils", "popTemporaryFile")
importFrom("R.utils", "printf")
importFrom("R.utils", "pushState")
importFrom("R.utils", "pushTemporaryFile")
importFrom("R.utils", "queryRCmdCheck")
importFrom("R.utils", "readTable")
importFrom("R.utils", "removeDirectory")
importFrom("R.utils", "resample")
importFrom("R.utils", "saveObject")
importFrom("R.utils", "seqToHumanReadable")
importFrom("R.utils", "setOption")
importFrom("R.utils", "Settings")
importFrom("R.utils", "loadAnywhere")
importFrom("R.utils", "stext")
importFrom("R.utils", "toCamelCase")
importFrom("R.utils", "use")
importFrom("utils", "browseURL")
importFrom("utils", "capture.output")
importFrom("utils", "data")
importFrom("utils", "download.file")
importFrom("utils", "getFromNamespace")
importFrom("utils", "head")
importFrom("utils", "object.size")
importFrom("utils", "packageDescription")
importFrom("utils", "write.table")

## Manually adjusted
importFrom("stats", "reorder")
## Cannot import explicitly from 'base';
## importFrom("base", "flush") ## Multi-sources: R.rsp, base
## importFrom("base", "parse") ## Multi-sources: R.utils, R.rsp, base
## importFrom("base", "readLines") ## Multi-sources: R.filesets, base

importFrom("grDevices",
           "as.raster", "col2rgb", "dev.new", "dev.off",
           "gray.colors", "hsv", "png", "rgb")

importFrom("graphics",
           "abline", "arrows", "axis", "lines", "matplot",
           "par", "plot", "points", "rasterImage", "symbols", "text")

importFrom("stats",
           "aggregate", "coefficients", "density", "dnorm",
           "lm.fit", "mad", "median", "na.omit", "predict", "quantile",
           "rnorm", "sd", "smooth.spline")

## Manual imports
importFrom("R.utils", "Arguments")

importFrom("listenv", "listenv")
importFrom("future", "%<-%")
importFrom("future", "plan")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# EXPORTS
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Object that must exported explicitly
export(.conflicts.OK)
export(.Machine)

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


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# DECLARATIONS
#
# Note: For R (< 3.0.2) only the max. 500 S3 methods are registered.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# AbstractCNData
S3method("findLargeGaps", "AbstractCNData")
S3method("getChipType", "AbstractCNData")
S3method("getLocusData", "AbstractCNData")
S3method("getPlatform", "AbstractCNData")
S3method("hasKnownPositions", "AbstractCNData")
S3method("orderAlongGenome", "AbstractCNData")
S3method("setChipType", "AbstractCNData")
S3method("setPlatform", "AbstractCNData")

# AbstractPSCNData
S3method("callSNPs", "AbstractPSCNData")
S3method("getSNPFields", "AbstractPSCNData")

# Arguments
S3method("getChromosome", "Arguments")
S3method("getChromosomes", "Arguments")

# AromaCellCpgFile
S3method("allocate", "AromaCellCpgFile")
S3method("getDefaultColumnNames", "AromaCellCpgFile")
S3method("getDefaultExtension", "AromaCellCpgFile")
S3method("getFilenameExtension", "AromaCellCpgFile")
S3method("isMissing", "AromaCellCpgFile")
S3method("readCpgs", "AromaCellCpgFile")
S3method("updateCpgs", "AromaCellCpgFile")

# AromaCellPositionFile
S3method("allocate", "AromaCellPositionFile")
S3method("getDefaultColumnNames", "AromaCellPositionFile")
S3method("getDefaultExtension", "AromaCellPositionFile")
S3method("getExtensionPattern", "AromaCellPositionFile")
S3method("getFilenameExtension", "AromaCellPositionFile")
S3method("isMissing", "AromaCellPositionFile")
S3method("readPositions", "AromaCellPositionFile")
S3method("updatePositions", "AromaCellPositionFile")

# AromaCellSequenceFile
S3method("allocate", "AromaCellSequenceFile")
S3method("countBases", "AromaCellSequenceFile")
S3method("countBasesInternal", "AromaCellSequenceFile")
S3method("getDefaultColumnNames", "AromaCellSequenceFile")
S3method("getDefaultExtension", "AromaCellSequenceFile")
S3method("getExtensionPattern", "AromaCellSequenceFile")
S3method("getFilenameExtension", "AromaCellSequenceFile")
S3method("getMaxLengthRepeats", "AromaCellSequenceFile")
S3method("getProbeLength", "AromaCellSequenceFile")
S3method("getSnpNucleotides", "AromaCellSequenceFile")
S3method("getSnpPositions", "AromaCellSequenceFile")
S3method("getSnpShifts", "AromaCellSequenceFile")
S3method("groupBySnpNucleotides", "AromaCellSequenceFile")
S3method("isMissing", "AromaCellSequenceFile")
S3method("readNeighborSequenceMatrix", "AromaCellSequenceFile")
S3method("readPairSequenceMatrix", "AromaCellSequenceFile")
S3method("readSequenceMatrix", "AromaCellSequenceFile")
S3method("readSequences", "AromaCellSequenceFile")
S3method("readTargetStrands", "AromaCellSequenceFile")
S3method("updateSequenceMatrix", "AromaCellSequenceFile")
S3method("updateSequences", "AromaCellSequenceFile")
S3method("updateTargetStrands", "AromaCellSequenceFile")

# AromaCellTabularBinaryFile
S3method("nbrOfCells", "AromaCellTabularBinaryFile")
S3method("byChipType", "AromaCellTabularBinaryFile")

# AromaGenomeTextFile
S3method("byGenome", "AromaGenomeTextFile")
S3method("findByGenome", "AromaGenomeTextFile")
S3method("readDataFrame", "AromaGenomeTextFile")

# AromaMicroarrayDataFile
S3method("getAttributeXY", "AromaMicroarrayDataFile")
S3method("getChipType", "AromaMicroarrayDataFile")
S3method("getPlatform", "AromaMicroarrayDataFile")
S3method("getPloidy", "AromaMicroarrayDataFile")
S3method("getXAM", "AromaMicroarrayDataFile")
S3method("hasAttributeXY", "AromaMicroarrayDataFile")
S3method("isAverageFile", "AromaMicroarrayDataFile")
S3method("setAttributesByTags", "AromaMicroarrayDataFile")
S3method("setAttributeXY", "AromaMicroarrayDataFile")

# AromaMicroarrayDataSet
S3method("as.AromaMicroarrayDataSetList", "AromaMicroarrayDataSet")
S3method("as.AromaMicroarrayDataSetTuple", "AromaMicroarrayDataSet")
S3method("getAromaFullNameTranslatorSet", "AromaMicroarrayDataSet")
S3method("getAverageFile", "AromaMicroarrayDataSet")
S3method("getChipType", "AromaMicroarrayDataSet")
S3method("getDefaultFullName", "AromaMicroarrayDataSet")
S3method("getPlatform", "AromaMicroarrayDataSet")
S3method("setAttributesBy", "AromaMicroarrayDataSet")
S3method("setAttributesBySampleAnnotationFile", "AromaMicroarrayDataSet")
S3method("setAttributesBySampleAnnotationSet", "AromaMicroarrayDataSet")
S3method("validate", "AromaMicroarrayDataSet")

# AromaMicroarrayDataSetTuple
S3method("as.AromaMicroarrayDataSetTuple", "AromaMicroarrayDataSetTuple")
S3method("byPath", "AromaMicroarrayDataSetTuple")
S3method("getAsteriskTags", "AromaMicroarrayDataSetTuple")
S3method("getChipTypes", "AromaMicroarrayDataSetTuple")
S3method("getFullNames", "AromaMicroarrayDataSetTuple")
S3method("getSets", "AromaMicroarrayDataSetTuple")
S3method("getTags", "AromaMicroarrayDataSetTuple")
S3method("indexOf", "AromaMicroarrayDataSetTuple")
S3method("nbrOfChipTypes", "AromaMicroarrayDataSetTuple")

# AromaMicroarrayTabularBinaryFile
S3method("allocate", "AromaMicroarrayTabularBinaryFile")
S3method("as.character", "AromaMicroarrayTabularBinaryFile")
S3method("byChipType", "AromaMicroarrayTabularBinaryFile")
S3method("findByChipType", "AromaMicroarrayTabularBinaryFile")
S3method("getChipType", "AromaMicroarrayTabularBinaryFile")
S3method("getFilenameExtension", "AromaMicroarrayTabularBinaryFile")
S3method("getPlatform", "AromaMicroarrayTabularBinaryFile")

# AromaPackage
S3method("fixSearchPath", "AromaPackage")
S3method("fixSearchPathInternal", "AromaPackage")

# AromaPlatform
S3method("byName", "AromaPlatform")
S3method("findUnitNamesFile", "AromaPlatform")
S3method("findUnitTypesFile", "AromaPlatform")
S3method("getAromaUgpFile", "AromaPlatform")
S3method("getName", "AromaPlatform")
S3method("getUnitNamesFile", "AromaPlatform")
S3method("getUnitTypesFile", "AromaPlatform")

# AromaPlatformInterface
S3method("getPlatform", "AromaPlatformInterface")
S3method("getChipType", "AromaPlatformInterface")
S3method("isCompatibleWith", "AromaPlatformInterface")
S3method("getAromaPlatform", "AromaPlatformInterface")
S3method("getAromaUgpFile", "AromaPlatformInterface")
S3method("getUnitAnnotationDataFile", "AromaPlatformInterface")
S3method("getUnitNamesFile", "AromaPlatformInterface")
S3method("getUnitTypesFile", "AromaPlatformInterface")

# AromaRepository
S3method("clearCache", "AromaRepository")
S3method("downloadACC", "AromaRepository")
S3method("downloadACM", "AromaRepository")
S3method("downloadACP", "AromaRepository")
S3method("downloadACS", "AromaRepository")
S3method("downloadAll", "AromaRepository")
S3method("downloadCDF", "AromaRepository")
S3method("downloadChipTypeFile", "AromaRepository")
S3method("downloadFile", "AromaRepository")
S3method("downloadProbeSeqsTXT", "AromaRepository")
S3method("downloadTXT", "AromaRepository")
S3method("downloadUFL", "AromaRepository")
S3method("downloadUGC", "AromaRepository")
S3method("downloadUGP", "AromaRepository")
S3method("findAnnotationDataByChipType", "AromaRepository")
S3method("getUrlPath", "AromaRepository")
##S3method("getVerbose", "AromaRepository")
S3method("listFiles", "AromaRepository")
S3method("setVerbose", "AromaRepository")

# AromaSettings
S3method("getRam", "AromaSettings")
##S3method("getVerbose", "AromaSettings")
S3method("setRam", "AromaSettings")
S3method("setVerbose", "AromaSettings")

# AromaTabularBinaryFile
S3method("[", "AromaTabularBinaryFile")
S3method("[[", "AromaTabularBinaryFile")
S3method("[<-", "AromaTabularBinaryFile")
S3method("allocate", "AromaTabularBinaryFile")
S3method("as.character", "AromaTabularBinaryFile")
S3method("colApply", "AromaTabularBinaryFile")
S3method("colMeans", "AromaTabularBinaryFile")
S3method("colStats", "AromaTabularBinaryFile")
S3method("colSums", "AromaTabularBinaryFile")
S3method("dimnames<-", "AromaTabularBinaryFile")
S3method("getBytesPerColumn", "AromaTabularBinaryFile")
S3method("getColClasses", "AromaTabularBinaryFile")
S3method("getDefaultColumnNames", "AromaTabularBinaryFile")
S3method("getRootName", "AromaTabularBinaryFile")
S3method("importFrom", "AromaTabularBinaryFile")
S3method("nbrOfColumns", "AromaTabularBinaryFile")
S3method("nbrOfRows", "AromaTabularBinaryFile")
S3method("readColumns", "AromaTabularBinaryFile")
S3method("readDataFrame", "AromaTabularBinaryFile")
S3method("readFooter", "AromaTabularBinaryFile")
S3method("readHeader", "AromaTabularBinaryFile")
S3method("readRawFooter", "AromaTabularBinaryFile")
S3method("setAttributesByTags", "AromaTabularBinaryFile")
S3method("subset", "AromaTabularBinaryFile")
S3method("summary", "AromaTabularBinaryFile")
S3method("updateData", "AromaTabularBinaryFile")
S3method("updateDataColumn", "AromaTabularBinaryFile")
S3method("writeFooter", "AromaTabularBinaryFile")
S3method("writeRawFooter", "AromaTabularBinaryFile")

# AromaTabularBinarySet
S3method("getDefaultFullName", "AromaTabularBinarySet")
S3method("getRootName", "AromaTabularBinarySet")
S3method("setAttributesBy", "AromaTabularBinarySet")
S3method("setAttributesBySampleAnnotationFile", "AromaTabularBinarySet")
S3method("setAttributesBySampleAnnotationSet", "AromaTabularBinarySet")
S3method("setAttributesByTags", "AromaTabularBinarySet")

# AromaTransform
S3method("as.character", "AromaTransform")
S3method("findFilesTodo", "AromaTransform")
S3method("getAsteriskTags", "AromaTransform")
S3method("getExpectedOutputFiles", "AromaTransform")
S3method("getExpectedOutputFullnames", "AromaTransform")
S3method("getFullName", "AromaTransform")
S3method("getInputDataSet", "AromaTransform")
S3method("getName", "AromaTransform")
S3method("getOutputDataSet", "AromaTransform")
S3method("getOutputDataSet0", "AromaTransform")
S3method("getOutputFiles", "AromaTransform")
S3method("getPath", "AromaTransform")
S3method("getRootPath", "AromaTransform")
S3method("getTags", "AromaTransform")
##S3method("isDone", "AromaTransform")
S3method("process", "AromaTransform")
S3method("setTags", "AromaTransform")

# AromaUcscGenomeTextFile
S3method("findByGenome", "AromaUcscGenomeTextFile")
S3method("readDataFrame", "AromaUcscGenomeTextFile")

# AromaUflFile
S3method("allocate", "AromaUflFile")
S3method("getDefaultColumnNames", "AromaUflFile")
S3method("getDefaultExtension", "AromaUflFile")
S3method("getExtensionPattern", "AromaUflFile")
S3method("getFilenameExtension", "AromaUflFile")
S3method("importFromGenericTabularFile", "AromaUflFile")
S3method("nbrOfEnzymes", "AromaUflFile")
S3method("readDataFrame", "AromaUflFile")
S3method("summaryOfUnits", "AromaUflFile")

# AromaUgpFile
S3method("allocate", "AromaUgpFile")
S3method("getDefaultColumnNames", "AromaUgpFile")
S3method("getDefaultExtension", "AromaUgpFile")
S3method("getExtensionPattern", "AromaUgpFile")
S3method("getFilenameExtension", "AromaUgpFile")
S3method("getPositions", "AromaUgpFile")
S3method("getUnitsAt", "AromaUgpFile")
S3method("getUnitsOnChromosome", "AromaUgpFile")
S3method("importFromGenericTabularFile", "AromaUgpFile")
S3method("plotCoverageMap", "AromaUgpFile")

# AromaUnitCallFile
S3method("allocate", "AromaUnitCallFile")
S3method("extractCallArray", "AromaUnitCallFile")
S3method("extractCalls", "AromaUnitCallFile")
S3method("extractMatrix", "AromaUnitCallFile")
S3method("findUnitsTodo", "AromaUnitCallFile")

# AromaUnitCallSet
S3method("byPath", "AromaUnitCallSet")
S3method("extractCallArray", "AromaUnitCallSet")
S3method("extractCalls", "AromaUnitCallSet")
S3method("extractGenotypeMatrix", "AromaUnitCallSet")
S3method("findByName", "AromaUnitCallSet")
S3method("findUnitsTodo", "AromaUnitCallSet")

# AromaUnitChromosomeTabularBinaryFile
S3method("allocate", "AromaUnitChromosomeTabularBinaryFile")
S3method("extractByChromosome", "AromaUnitChromosomeTabularBinaryFile")
S3method("getChromosomes", "AromaUnitChromosomeTabularBinaryFile")
S3method("getDefaultColumnNames", "AromaUnitChromosomeTabularBinaryFile")
S3method("getFilenameExtension", "AromaUnitChromosomeTabularBinaryFile")
S3method("getGenomeVersion", "AromaUnitChromosomeTabularBinaryFile")
S3method("getUnitsOnChromosome", "AromaUnitChromosomeTabularBinaryFile")
S3method("getUnitsOnChromosomes", "AromaUnitChromosomeTabularBinaryFile")
S3method("indexOfColumn", "AromaUnitChromosomeTabularBinaryFile")
S3method("readDataFrame", "AromaUnitChromosomeTabularBinaryFile")

# AromaUnitFracBCnBinaryFile
S3method("extractRawAlleleBFractions", "AromaUnitFracBCnBinaryFile")

# AromaUnitFracBCnBinarySet
S3method("byName", "AromaUnitFracBCnBinarySet")
S3method("exportFracBDiffSet", "AromaUnitFracBCnBinarySet")
##S3method("writeDataFrame", "AromaUnitFracBCnBinarySet")

# AromaUnitGcContentFile
S3method("getDefaultColumnNames", "AromaUnitGcContentFile")
S3method("getExtensionPattern", "AromaUnitGcContentFile")
S3method("getFilenameExtension", "AromaUnitGcContentFile")

# AromaUnitGenotypeCallFile
S3method("allocate", "AromaUnitGenotypeCallFile")
S3method("extractGenotypeMatrix", "AromaUnitGenotypeCallFile")
S3method("extractGenotypes", "AromaUnitGenotypeCallFile")
S3method("isHeterozygous", "AromaUnitGenotypeCallFile")
S3method("isHomozygous", "AromaUnitGenotypeCallFile")
S3method("updateGenotypes", "AromaUnitGenotypeCallFile")

# AromaUnitGenotypeCallSet
S3method("byName", "AromaUnitGenotypeCallSet")
S3method("byPath", "AromaUnitGenotypeCallSet")
S3method("extractGenotypes", "AromaUnitGenotypeCallSet")

# AromaUnitPscnBinaryFile
S3method("allocate", "AromaUnitPscnBinaryFile")
S3method("extractRawCopyNumbers", "AromaUnitPscnBinaryFile")
S3method("getDefaultColumnNames", "AromaUnitPscnBinaryFile")
S3method("hasAlleleBFractions", "AromaUnitPscnBinaryFile")
S3method("hasStrandiness", "AromaUnitPscnBinaryFile")
S3method("hasTotalCopyNumberRatios", "AromaUnitPscnBinaryFile")

# AromaUnitPscnBinarySet
S3method("byName", "AromaUnitPscnBinarySet")
S3method("getAverageFile", "AromaUnitPscnBinarySet")
##S3method("writeDataFrame", "AromaUnitPscnBinarySet")

# AromaUnitSignalBinaryFile
S3method("allocate", "AromaUnitSignalBinaryFile")
S3method("allocateFromUnitAnnotationDataFile", "AromaUnitSignalBinaryFile")
S3method("allocateFromUnitNamesFile", "AromaUnitSignalBinaryFile")

S3method("as.character", "AromaUnitSignalBinaryFile")
S3method("extractMatrix", "AromaUnitSignalBinaryFile")
S3method("extractRawGenomicSignals", "AromaUnitSignalBinaryFile")
S3method("fromFile", "AromaUnitSignalBinaryFile")
##S3method("getAromaUgpFile", "AromaUnitSignalBinaryFile")
S3method("getChipType", "AromaUnitSignalBinaryFile")
S3method("getExtensionPattern", "AromaUnitSignalBinaryFile")
S3method("getFilenameExtension", "AromaUnitSignalBinaryFile")
S3method("getNumberOfFilesAveraged", "AromaUnitSignalBinaryFile")
S3method("getPlatform", "AromaUnitSignalBinaryFile")
S3method("isAverageFile", "AromaUnitSignalBinaryFile")
S3method("nbrOfUnits", "AromaUnitSignalBinaryFile")
S3method("readDataFrame", "AromaUnitSignalBinaryFile")
##S3method("writeDataFrame", "AromaUnitSignalBinaryFile")

# AromaUnitSignalBinarySet
S3method("byName", "AromaUnitSignalBinarySet")
S3method("findByName", "AromaUnitSignalBinarySet")
S3method("getAromaFullNameTranslatorSet", "AromaUnitSignalBinarySet")
S3method("getAromaUgpFile", "AromaUnitSignalBinarySet")
S3method("getChipType", "AromaUnitSignalBinarySet")
S3method("getPlatform", "AromaUnitSignalBinarySet")
S3method("validate", "AromaUnitSignalBinarySet")
##S3method("writeDataFrame", "AromaUnitSignalBinarySet")

# AromaUnitTabularBinaryFile
S3method("allocateFromUnitAnnotationDataFile", "AromaUnitTabularBinaryFile")
S3method("allocateFromUnitNamesFile", "AromaUnitTabularBinaryFile")
S3method("byChipType", "AromaUnitTabularBinaryFile")
S3method("indexOfUnits", "AromaUnitTabularBinaryFile")
S3method("nbrOfUnits", "AromaUnitTabularBinaryFile")
##S3method("writeDataFrame", "AromaUnitTabularBinaryFile")

# AromaUnitTotalCnBinaryFile
S3method("extractPSCNArray", "AromaUnitTotalCnBinaryFile")
S3method("extractPSCNMatrix", "AromaUnitTotalCnBinaryFile")
S3method("extractRawCopyNumbers", "AromaUnitTotalCnBinaryFile")
S3method("getAM", "AromaUnitTotalCnBinaryFile")
S3method("getXAM", "AromaUnitTotalCnBinaryFile")
S3method("hasAlleleBFractions", "AromaUnitTotalCnBinaryFile")
S3method("hasStrandiness", "AromaUnitTotalCnBinaryFile")

# AromaUnitTotalCnBinaryFileList
S3method("extractMergedRawCopyNumbers", "AromaUnitTotalCnBinaryFileList")
S3method("extractRawCopyNumbers", "AromaUnitTotalCnBinaryFileList")
S3method("extractRawGenomicSignals", "AromaUnitTotalCnBinaryFileList")

# AromaUnitTotalCnBinarySet
S3method("as.AromaUnitTotalCnBinarySetTuple", "AromaUnitTotalCnBinarySet")
S3method("as.CopyNumberDataSetTuple", "AromaUnitTotalCnBinarySet")
S3method("byName", "AromaUnitTotalCnBinarySet")
S3method("exportAromaUnitPscnBinarySet", "AromaUnitTotalCnBinarySet")
S3method("exportTotalCnRatioSet", "AromaUnitTotalCnBinarySet")
S3method("extractPSCNArray", "AromaUnitTotalCnBinarySet")
S3method("getAverageFile", "AromaUnitTotalCnBinarySet")
S3method("getUnitNamesFile", "AromaUnitTotalCnBinarySet")
##S3method("writeDataFrame", "AromaUnitTotalCnBinarySet")

# AromaUnitTotalCnBinarySetTuple
S3method("as.AromaUnitTotalCnBinarySetTuple", "AromaUnitTotalCnBinarySetTuple")
S3method("getListOfUnitNamesFiles", "AromaUnitTotalCnBinarySetTuple")

# AromaUnitTypesFile
S3method("allocate", "AromaUnitTypesFile")
S3method("getChipType", "AromaUnitTypesFile")
S3method("getPlatform", "AromaUnitTypesFile")
S3method("getUnitTypes", "AromaUnitTypesFile")
S3method("importFromUnitTypesFile", "AromaUnitTypesFile")

# BasicObject
S3method("asThis", "BasicObject")

# BinnedScatter
S3method("plot", "BinnedScatter")
S3method("points", "BinnedScatter")
S3method("reorder", "BinnedScatter")
S3method("subsample", "BinnedScatter")
S3method("subset", "BinnedScatter")

# CacheKeyInterface
S3method("getCacheKey", "CacheKeyInterface")

# CbsModel
S3method("getFitFunction", "CbsModel")
S3method("getRandomSeed", "CbsModel")
S3method("setRandomSeed", "CbsModel")

# CbsSegmentationDataFile
S3method("loadFit", "CbsSegmentationDataFile")

# CbsSegmentationDataSet
S3method("byName", "CbsSegmentationDataSet")
S3method("byPath", "CbsSegmentationDataSet")

# character
S3method("getAromaFullNameTranslatorSet", "character")
S3method("getFullNameTranslatorSet", "character")
S3method("getProbePositionEffectDesignMatrix", "character")
S3method("xmlToList", "character")

# ChromosomalModel
S3method("as.character", "ChromosomalModel")
S3method("fit", "ChromosomalModel")
S3method("getAlias", "ChromosomalModel")
S3method("getAromaGenomeTextFile", "ChromosomalModel")
S3method("getArrays", "ChromosomalModel")
S3method("getAsteriskTags", "ChromosomalModel")
S3method("getChipType", "ChromosomalModel")
S3method("getChipTypes", "ChromosomalModel")
S3method("getChromosomes", "ChromosomalModel")
S3method("setChromosomes", "ChromosomalModel")
S3method("getFullName", "ChromosomalModel")
S3method("getFullNames", "ChromosomalModel")
S3method("getGenome", "ChromosomalModel")
S3method("getGenomeData", "ChromosomalModel")
S3method("getGenomeFile", "ChromosomalModel")
S3method("getListOfAromaUgpFiles", "ChromosomalModel")
S3method("getName", "ChromosomalModel")
S3method("getNames", "ChromosomalModel")
S3method("getParentPath", "ChromosomalModel")
S3method("getPath", "ChromosomalModel")
S3method("getReportPath", "ChromosomalModel")
S3method("getRootPath", "ChromosomalModel")
S3method("getSets", "ChromosomalModel")
S3method("getSetTuple", "ChromosomalModel")
S3method("getTableOfArrays", "ChromosomalModel")
S3method("getTags", "ChromosomalModel")
S3method("indexOf", "ChromosomalModel")
S3method("nbrOfArrays", "ChromosomalModel")
S3method("nbrOfChipTypes", "ChromosomalModel")
S3method("setGenome", "ChromosomalModel")

# ChromosomeExplorer
S3method("addIndexFile", "ChromosomeExplorer")
S3method("as.character", "ChromosomeExplorer")
S3method("display", "ChromosomeExplorer")
S3method("getArraysOfInput", "ChromosomeExplorer")
S3method("getChromosomeLabels", "ChromosomeExplorer")
S3method("getChromosomes", "ChromosomeExplorer")
S3method("getFullNames", "ChromosomeExplorer")
S3method("getModel", "ChromosomeExplorer")
S3method("getNameOfInput", "ChromosomeExplorer")
S3method("getNames", "ChromosomeExplorer")
S3method("getPath", "ChromosomeExplorer")
S3method("getSampleLabels", "ChromosomeExplorer")
S3method("getTagsOfInput", "ChromosomeExplorer")
S3method("getZooms", "ChromosomeExplorer")
S3method("indexOf", "ChromosomeExplorer")
S3method("process", "ChromosomeExplorer")
S3method("setArrays", "ChromosomeExplorer")
S3method("setCytoband", "ChromosomeExplorer")
S3method("setZooms", "ChromosomeExplorer")
S3method("updateSetupExplorerFile", "ChromosomeExplorer")

# CopyNumberChromosomalModel
S3method("as.character", "CopyNumberChromosomalModel")
S3method("calculateChromosomeStatistics", "CopyNumberChromosomalModel")
S3method("calculateRatios", "CopyNumberChromosomalModel")
S3method("estimateSds", "CopyNumberChromosomalModel")
S3method("extractRawCopyNumbers", "CopyNumberChromosomalModel")
S3method("fit", "CopyNumberChromosomalModel")
S3method("getChromosomeLength", "CopyNumberChromosomalModel")
S3method("getDataFileMatrix", "CopyNumberChromosomalModel")
S3method("getMaxNAFraction", "CopyNumberChromosomalModel")
S3method("getNames", "CopyNumberChromosomalModel")
S3method("getOptionalArguments", "CopyNumberChromosomalModel")
S3method("getPairedNames", "CopyNumberChromosomalModel")
S3method("getReference", "CopyNumberChromosomalModel")
S3method("getReferenceSetTuple", "CopyNumberChromosomalModel")
S3method("getRefSetTuple", "CopyNumberChromosomalModel")
S3method("isPaired", "CopyNumberChromosomalModel")
S3method("newPlot", "CopyNumberChromosomalModel")
S3method("plotAxesLayers", "CopyNumberChromosomalModel")
S3method("plotChromosomesLayers", "CopyNumberChromosomalModel")
S3method("plotCytobandLayers", "CopyNumberChromosomalModel")
S3method("plotFitLayers", "CopyNumberChromosomalModel")
S3method("plotGridHorizontalLayers", "CopyNumberChromosomalModel")
S3method("plotRawCopyNumbers", "CopyNumberChromosomalModel")
S3method("plotSampleLayers", "CopyNumberChromosomalModel")
S3method("setReference", "CopyNumberChromosomalModel")

# CopyNumberDataFile
S3method("as.CopyNumberDataFile", "CopyNumberDataFile")
S3method("getNumberOfFilesAveraged", "CopyNumberDataFile")
S3method("hasAlleleBFractions", "CopyNumberDataFile")
S3method("hasStrandiness", "CopyNumberDataFile")

# CopyNumberDataSet
S3method("as.CopyNumberDataSet", "CopyNumberDataSet")
S3method("doCBS", "CopyNumberDataSet")
S3method("hasAlleleBFractions", "CopyNumberDataSet")
S3method("hasStrandiness", "CopyNumberDataSet")

# CopyNumberDataSetTuple
S3method("as.CopyNumberDataSetTuple", "CopyNumberDataSetTuple")
S3method("doCBS", "CopyNumberDataSetTuple")
S3method("hasAlleleBFractions", "CopyNumberDataSetTuple")
S3method("hasStrandiness", "CopyNumberDataSetTuple")

# CopyNumberOutliers
S3method("applyRegions", "CopyNumberOutliers")
S3method("as.character", "CopyNumberOutliers")
S3method("as.data.frame", "CopyNumberOutliers")
S3method("drawLevels", "CopyNumberOutliers")
S3method("lines", "CopyNumberOutliers")
S3method("nbrOfRegions", "CopyNumberOutliers")

# CopyNumberRegions
S3method("-", "CopyNumberRegions")
S3method("*", "CopyNumberRegions")
S3method("+", "CopyNumberRegions")
S3method("append", "CopyNumberRegions")
S3method("applyRows", "CopyNumberRegions")
S3method("as.character", "CopyNumberRegions")
S3method("as.data.frame", "CopyNumberRegions")
S3method("drawDensity", "CopyNumberRegions")
S3method("drawLevels", "CopyNumberRegions")
S3method("equals", "CopyNumberRegions")
S3method("extractIGV", "CopyNumberRegions")
S3method("getChromosomes", "CopyNumberRegions")
S3method("getDensity", "CopyNumberRegions")
S3method("getLength", "CopyNumberRegions")
S3method("getMeanAt", "CopyNumberRegions")
S3method("getValueAt", "CopyNumberRegions")
S3method("lines", "CopyNumberRegions")
S3method("nbrOfChromosomes", "CopyNumberRegions")
S3method("nbrOfRegions", "CopyNumberRegions")
S3method("prune", "CopyNumberRegions")
S3method("simulateRawCopyNumbers", "CopyNumberRegions")
S3method("subset", "CopyNumberRegions")
S3method("unique", "CopyNumberRegions")
S3method("xMax", "CopyNumberRegions")
S3method("xMin", "CopyNumberRegions")
S3method("xRange", "CopyNumberRegions")

# CopyNumberSegmentationModel
S3method("fit", "CopyNumberSegmentationModel")
S3method("getAsteriskTags", "CopyNumberSegmentationModel")
S3method("getFitFunction", "CopyNumberSegmentationModel")
S3method("getFullNames", "CopyNumberSegmentationModel")
S3method("getRegions", "CopyNumberSegmentationModel")
S3method("getTags", "CopyNumberSegmentationModel")
S3method("plot", "CopyNumberSegmentationModel")
S3method("plotCopyNumberRegionLayers", "CopyNumberSegmentationModel")
S3method("writeRegions", "CopyNumberSegmentationModel")

# data.frame
S3method("as.NonPairedPSCNData", "data.frame")
S3method("as.PairedPSCNData", "data.frame")

# default
S3method("colMeans", "default")
S3method("colSums", "default")
S3method("convertTable", "default")
S3method("doCBS", "default")
S3method("drawExtraAnnotations", "default")
S3method("extractCNRs", "default")
S3method("extractCopyNumberRegions", "default")
S3method("extractRawAlleleBFractions", "default")
S3method("extractRawCNs", "default")
S3method("extractRawCopyNumbers", "default")
S3method("extractRawGenomicSignals", "default")
S3method("extractRawMirroredAlleleBFractions", "default")
S3method("findAnnotationData", "default")
S3method("findAnnotationDataByChipType", "default")
S3method("findPngDevice", "default")
S3method("getDeviceResolution", "default")
S3method("locallyUnique", "default")
S3method("onFitAddGenotypeCalls", "default")
S3method("pointsRawCNs", "default")
S3method("remap", "default")
S3method("shakyText", "default")

# DNAcopy
S3method("drawCnRegions", "DNAcopy")
S3method("extractCopyNumberOutliers", "DNAcopy")
S3method("extractCopyNumberRegions", "DNAcopy")
S3method("extractRawCopyNumbers", "DNAcopy")

# Explorer
S3method("addIncludes", "Explorer")
S3method("addIndexFile", "Explorer")
S3method("as.character", "Explorer")
S3method("display", "Explorer")
S3method("getAlias", "Explorer")
S3method("getArrays", "Explorer")
S3method("getArraysOfInput", "Explorer")
S3method("getAsteriskTags", "Explorer")
S3method("getFullName", "Explorer")
S3method("getIncludePath", "Explorer")
S3method("getMainPath", "Explorer")
S3method("getName", "Explorer")
S3method("getNameOfInput", "Explorer")
S3method("getNames", "Explorer")
S3method("getPath", "Explorer")
S3method("getReportPathPattern", "Explorer")
S3method("getRootPath", "Explorer")
S3method("getSampleLayerPrefix", "Explorer")
S3method("getSubname", "Explorer")
S3method("getTags", "Explorer")
S3method("getTagsOfInput", "Explorer")
S3method("getTemplatePath", "Explorer")
##S3method("getVersion", "Explorer")
S3method("nbrOfArrays", "Explorer")
S3method("process", "Explorer")
S3method("setAlias", "Explorer")
S3method("setArrays", "Explorer")
S3method("setReportPathPattern", "Explorer")
S3method("setSubname", "Explorer")
S3method("setup", "Explorer")
S3method("splitByReportPathPattern", "Explorer")
S3method("updateSetupExplorerFile", "Explorer")

# FileCacheKeyInterface
S3method("getCacheKey", "FileCacheKeyInterface")

# GenericDataFile
S3method("getParentName", "GenericDataFile")

# GenericDataFileSet
S3method("getFullNameTranslatorSet", "GenericDataFileSet")
S3method("getParentName", "GenericDataFileSet")

# GenericTabularFileSet
S3method("calculateAverageColumnAcrossFiles", "GenericTabularFileSet")

# GladModel
S3method("getFitFunction", "GladModel")
S3method("onFitAddGenotypeCalls", "GladModel")
S3method("writeRegions", "GladModel")

# HaarSeg
S3method("drawCnRegions", "HaarSeg")
S3method("extractCopyNumberRegions", "HaarSeg")
S3method("extractRawCopyNumbers", "HaarSeg")

# HaarSegModel
S3method("getAsteriskTags", "HaarSegModel")
S3method("getFitFunction", "HaarSegModel")

# Image
S3method("colorize", "Image")
S3method("display", "Image")
S3method("getImageData", "Image")
S3method("interleave", "Image")
S3method("rescale", "Image")
S3method("setImageData", "Image")
S3method("writeImage", "Image")

# list
S3method("as.CopyNumberDataSetTuple", "list")
S3method("exportAromaUnitPscnBinarySet", "list")
##S3method("listToXml", "list")
S3method("mergeBoxplotStats", "list")

# matrix
S3method("as.GrayscaleImage", "matrix")
S3method("backtransformGenotypeCone", "matrix")
S3method("backtransformMultiDimensionalCone", "matrix")
S3method("binScatter", "matrix")
S3method("colBinnedSmoothing", "matrix")
S3method("colGaussianSmoothing", "matrix")
S3method("colKernelSmoothing", "matrix")
S3method("createImage", "matrix")
S3method("fitGenotypeCone", "matrix")
S3method("fitSplineBlockPolish", "matrix")
S3method("fitWHLAPLM", "matrix")
S3method("fitWHRCModel", "matrix")
S3method("fitWLAPLM", "matrix")
S3method("fitWRCModel", "matrix")
S3method("fitWRMA", "matrix")
S3method("gaussianSmoothing", "matrix")
S3method("getImage", "matrix")
S3method("matrixBlockPolish", "matrix")
S3method("smoothWRMA", "matrix")
S3method("smoothWSA", "matrix")

# MPCBS
S3method("drawCnRegions", "MPCBS")
S3method("extractCopyNumberRegions", "MPCBS")

# NonPairedPSCNData
S3method("as.NonPairedPSCNData", "NonPairedPSCNData")
S3method("as.PairedPSCNData", "NonPairedPSCNData")
S3method("callNaiveGenotypes", "NonPairedPSCNData")
S3method("callSegmentationOutliers", "NonPairedPSCNData")
S3method("dropSegmentationOutliers", "NonPairedPSCNData")
S3method("getSignalColumnNames", "NonPairedPSCNData")
S3method("segmentByCBS", "NonPairedPSCNData")

# numeric
S3method("binnedSmoothing", "numeric")
S3method("fitProbePositionEffects", "numeric")
S3method("gaussianSmoothing", "numeric")
S3method("kernelSmoothing", "numeric")
S3method("lapplyInChunks", "numeric")
S3method("splitInChunks", "numeric")

# Object
S3method("asThis", "Object")

# PairedPSCNData
S3method("as.PairedPSCNData", "PairedPSCNData")
S3method("callNaiveGenotypes", "PairedPSCNData")
S3method("callSegmentationOutliers", "PairedPSCNData")
S3method("dropSegmentationOutliers", "PairedPSCNData")
S3method("extractNonPairedPSCNData", "PairedPSCNData")
S3method("getSignalColumnNames", "PairedPSCNData")
S3method("getTCNs", "PairedPSCNData")
S3method("getTotalCopyNumbers", "PairedPSCNData")
S3method("normalizeTumorBoost", "PairedPSCNData")
S3method("plotTracks", "PairedPSCNData")
S3method("segmentByCBS", "PairedPSCNData")
S3method("segmentByPairedPSCBS", "PairedPSCNData")

# ParametersInterface
S3method("getParameters", "ParametersInterface")
S3method("getParametersAsString", "ParametersInterface")
S3method("getParameterSets", "ParametersInterface")

# ProbePositionEffects
S3method("barSequence", "ProbePositionEffects")
S3method("getEffects", "ProbePositionEffects")
S3method("plot", "ProbePositionEffects")
S3method("pointsSequence", "ProbePositionEffects")
S3method("predict", "ProbePositionEffects")
S3method("text", "ProbePositionEffects")
S3method("textSequence", "ProbePositionEffects")

# profileCGH
S3method("drawCnRegions", "profileCGH")
S3method("drawExtraAnnotations", "profileCGH")
S3method("extractCopyNumberOutliers", "profileCGH")
S3method("extractCopyNumberRegions", "profileCGH")
S3method("extractRawCopyNumbers", "profileCGH")
S3method("plotRawCNs", "profileCGH")
S3method("pointsRawCNs", "profileCGH")

# RasterImage
S3method("[", "RasterImage")
S3method("as.character", "RasterImage")
S3method("colorize", "RasterImage")
S3method("display", "RasterImage")
S3method("dropAlpha", "RasterImage")
S3method("getImageData", "RasterImage")
S3method("interleave", "RasterImage")
S3method("read", "RasterImage")
S3method("rescale", "RasterImage")
S3method("save", "RasterImage")
S3method("setImageData", "RasterImage")
S3method("str", "RasterImage")
S3method("write", "RasterImage")
S3method("writeImage", "RasterImage")

# raw
S3method("getProbePositionEffectDesignMatrix", "raw")

# RawAlleleBFractions
S3method("extractRawMirroredAlleleBFractions", "RawAlleleBFractions")
S3method("plot", "RawAlleleBFractions")

# RawCopyNumberModel
S3method("getAsteriskTags", "RawCopyNumberModel")
S3method("getSetTag", "RawCopyNumberModel")

# RawCopyNumbers
S3method("cnRange", "RawCopyNumbers")
S3method("extractRawCopyNumbers", "RawCopyNumbers")
S3method("getCn", "RawCopyNumbers")
S3method("getCNs", "RawCopyNumbers")
S3method("getSignals", "RawCopyNumbers")
S3method("plot", "RawCopyNumbers")

# RawGenomicSignals
S3method("-", "RawGenomicSignals")
S3method("*", "RawGenomicSignals")
S3method("+", "RawGenomicSignals")
S3method("addBy", "RawGenomicSignals")
S3method("append", "RawGenomicSignals")
S3method("applyBinaryOperator", "RawGenomicSignals")
S3method("as.character", "RawGenomicSignals")
S3method("as.data.frame", "RawGenomicSignals")
S3method("assertOneChromosome", "RawGenomicSignals")
S3method("binnedSmoothing", "RawGenomicSignals")
S3method("binnedSmoothingByField", "RawGenomicSignals")
S3method("clearCache", "RawGenomicSignals")
S3method("clone", "RawGenomicSignals")
S3method("divideBy", "RawGenomicSignals")
S3method("drawDensity", "RawGenomicSignals")
S3method("estimateStandardDeviation", "RawGenomicSignals")
S3method("extractChromosome", "RawGenomicSignals")
S3method("extractChromosomes", "RawGenomicSignals")
S3method("extractDataForSegmentation", "RawGenomicSignals")
S3method("extractRegion", "RawGenomicSignals")
S3method("extractRegions", "RawGenomicSignals")
S3method("extractSubset", "RawGenomicSignals")
S3method("gaussianSmoothing", "RawGenomicSignals")
S3method("getBasicField", "RawGenomicSignals")
S3method("getChromosome", "RawGenomicSignals")
S3method("getChromosomes", "RawGenomicSignals")
S3method("getCXY", "RawGenomicSignals")
S3method("getDefaultLocusFields", "RawGenomicSignals")
S3method("getLocusFields", "RawGenomicSignals")
S3method("getPositions", "RawGenomicSignals")
S3method("getSigma", "RawGenomicSignals")
S3method("getSignalColumnName", "RawGenomicSignals")
S3method("getSignalColumnNames", "RawGenomicSignals")
S3method("getSignals", "RawGenomicSignals")
S3method("getWeights", "RawGenomicSignals")
S3method("getXScale", "RawGenomicSignals")
S3method("getXY", "RawGenomicSignals")
S3method("getYScale", "RawGenomicSignals")
S3method("hasWeights", "RawGenomicSignals")
S3method("kernelSmoothing", "RawGenomicSignals")
S3method("lines", "RawGenomicSignals")
S3method("multiplyBy", "RawGenomicSignals")
S3method("nbrOfChromosomes", "RawGenomicSignals")
S3method("nbrOfLoci", "RawGenomicSignals")
S3method("plot", "RawGenomicSignals")
S3method("points", "RawGenomicSignals")
S3method("print", "RawGenomicSignals")
S3method("segmentByCBS", "RawGenomicSignals")
S3method("segmentByGLAD", "RawGenomicSignals")
S3method("segmentByHaarSeg", "RawGenomicSignals")
S3method("segmentByMPCBS", "RawGenomicSignals")
S3method("setBasicField", "RawGenomicSignals")
S3method("setSigma", "RawGenomicSignals")
S3method("setSignals", "RawGenomicSignals")
S3method("setWeights", "RawGenomicSignals")
S3method("setXScale", "RawGenomicSignals")
S3method("setYScale", "RawGenomicSignals")
S3method("signalRange", "RawGenomicSignals")
S3method("sort", "RawGenomicSignals")
S3method("subtractBy", "RawGenomicSignals")
S3method("xMax", "RawGenomicSignals")
S3method("xMin", "RawGenomicSignals")
S3method("xRange", "RawGenomicSignals")
S3method("xSeq", "RawGenomicSignals")
S3method("yMax", "RawGenomicSignals")
S3method("yMin", "RawGenomicSignals")
S3method("yRange", "RawGenomicSignals")

# RawMirroredAlleleBFractions
S3method("plot", "RawMirroredAlleleBFractions")

# RawSequenceReads
S3method("binnedSums", "RawSequenceReads")
S3method("extractRawCopyNumbers", "RawSequenceReads")
S3method("nbrOfReads", "RawSequenceReads")
S3method("plot", "RawSequenceReads")

# RichDataFrame
S3method("$", "RichDataFrame")
S3method("$<-", "RichDataFrame")
S3method("[", "RichDataFrame")
S3method("[[", "RichDataFrame")
S3method("[[<-", "RichDataFrame")
S3method("as.data.frame", "RichDataFrame")
S3method("as.list", "RichDataFrame")
S3method("dim", "RichDataFrame")
S3method("dropVirtualColumn", "RichDataFrame")
S3method("getColumnNames", "RichDataFrame")
S3method("getColumnNamesTranslator", "RichDataFrame")
S3method("getFullName", "RichDataFrame")
S3method("getName", "RichDataFrame")
S3method("getTags", "RichDataFrame")
S3method("getVirtualColumn", "RichDataFrame")
S3method("getVirtualColumnFunction", "RichDataFrame")
S3method("getVirtualColumnNames", "RichDataFrame")
S3method("hasColumn", "RichDataFrame")
S3method("hasColumns", "RichDataFrame")
S3method("hasVirtualColumn", "RichDataFrame")
S3method("hasVirtualColumns", "RichDataFrame")
S3method("length", "RichDataFrame")
S3method("names", "RichDataFrame")
S3method("newInstance", "RichDataFrame")
S3method("print", "RichDataFrame")
S3method("rbind", "RichDataFrame")
S3method("setAttributes", "RichDataFrame")
S3method("setColumnNamesMap", "RichDataFrame")
S3method("setColumnNamesTranslator", "RichDataFrame")
S3method("setName", "RichDataFrame")
S3method("setTags", "RichDataFrame")
S3method("setVirtualColumn", "RichDataFrame")
S3method("subset", "RichDataFrame")
S3method("translateColumnNames", "RichDataFrame")

# SampleAnnotationFile
S3method("applyTo", "SampleAnnotationFile")
S3method("fromPath", "SampleAnnotationFile")
S3method("getExtensionPattern", "SampleAnnotationFile")
S3method("getPatterns", "SampleAnnotationFile")
S3method("matchPatterns", "SampleAnnotationFile")
S3method("readDataFrame", "SampleAnnotationFile")

# SampleAnnotationSet
S3method("fromPath", "SampleAnnotationSet")
S3method("loadAll", "SampleAnnotationSet")

# SegmentationDataFile
S3method("extractCopyNumberRegions", "SegmentationDataFile")
S3method("getChromosome", "SegmentationDataFile")
S3method("getReferenceName", "SegmentationDataFile")
S3method("getSampleName", "SegmentationDataFile")
S3method("loadFit", "SegmentationDataFile")

# SegmentationDataSet
S3method("as.character", "SegmentationDataSet")
S3method("byPath", "SegmentationDataSet")
S3method("extractByReferenceName", "SegmentationDataSet")
S3method("extractBySampleName", "SegmentationDataSet")
S3method("extractCopyNumberRegions", "SegmentationDataSet")
S3method("getChipType", "SegmentationDataSet")
S3method("getChromosomes", "SegmentationDataSet")
S3method("getDefaultFullName", "SegmentationDataSet")
S3method("getReferenceNames", "SegmentationDataSet")
S3method("getSampleNames", "SegmentationDataSet")

# SegmentedGenomicSignalsInterface
S3method("as.data.frame", "SegmentedGenomicSignalsInterface")
S3method("binnedSmoothingByState", "SegmentedGenomicSignalsInterface")
S3method("extractSubsetByState", "SegmentedGenomicSignalsInterface")
S3method("getStateColorMap", "SegmentedGenomicSignalsInterface")
S3method("getStateColors", "SegmentedGenomicSignalsInterface")
S3method("getStates", "SegmentedGenomicSignalsInterface")
S3method("getUniqueStates", "SegmentedGenomicSignalsInterface")
S3method("getVirtualField", "SegmentedGenomicSignalsInterface")
S3method("getVirtualLocusFields", "SegmentedGenomicSignalsInterface")
S3method("kernelSmoothingByState", "SegmentedGenomicSignalsInterface")
S3method("plot", "SegmentedGenomicSignalsInterface")
S3method("points", "SegmentedGenomicSignalsInterface")
S3method("setStateColorMap", "SegmentedGenomicSignalsInterface")
S3method("setStates", "SegmentedGenomicSignalsInterface")

# TextUnitNamesFile
S3method("as.character", "TextUnitNamesFile")
S3method("findByChipType", "TextUnitNamesFile")
S3method("getChipType", "TextUnitNamesFile")
S3method("getExtensionPattern", "TextUnitNamesFile")
S3method("getFilenameExtension", "TextUnitNamesFile")
S3method("getPlatform", "TextUnitNamesFile")
S3method("getUnitNames", "TextUnitNamesFile")
S3method("nbrOfUnits", "TextUnitNamesFile")

# UnitAnnotationDataFile
S3method("byChipType", "UnitAnnotationDataFile")
S3method("getAromaUflFile", "UnitAnnotationDataFile")
S3method("getAromaUgpFile", "UnitAnnotationDataFile")
S3method("getChipType", "UnitAnnotationDataFile")
S3method("getDefaultExtension", "UnitAnnotationDataFile")
S3method("getPlatform", "UnitAnnotationDataFile")
S3method("nbrOfUnits", "UnitAnnotationDataFile")

# UnitNamesFile
S3method("getUnitNames", "UnitNamesFile")
S3method("indexOf", "UnitNamesFile")
S3method("nbrOfUnits", "UnitNamesFile")

# UnitTypesFile
S3method("getUnitTypes", "UnitTypesFile")
S3method("nbrOfUnits", "UnitTypesFile")

S3method("stextChipType", "character")
S3method("stringTree", "character")

S3method("drawCytoband2", "default")
S3method("whatDataType", "default")
S3method("write", "default")
S3method("processTime", "default")
S3method("requireWithMemory", "default")

S3method("calcMargins", "matrix")
S3method("fitGenotypeConeByExpectile", "matrix")
S3method("fitGenotypeConeBySfit", "matrix")
S3method("fitMultiDimensionalCone", "matrix")
S3method("fit2d", "matrix")
S3method("norm2d", "matrix")
S3method("normalizeGenotypeCone", "matrix")

S3method("listToXml", "list")

S3method("plotProfile2", "profileCGH")
S3method("drawCytoband", "profileCGH")

S3method("as.character", "AromaMicroarrayDataSetTuple")

S3method("as.character", "AromaPlatform")
S3method("equals", "AromaPlatform")

S3method("getAromaUflFile", "AromaPlatformInterface")

S3method("byPathnames", "SampleAnnotationSet")
S3method("findSAFs", "SampleAnnotationSet")

S3method("fixSearchPath", "AromaCore")

S3method("getLog2Ratios", "CopyNumberSegmentationModel")
S3method("getRawCnData", "CopyNumberChromosomalModel")

S3method("getSampleLayerName", "Explorer")
S3method("getVersion", "Explorer")

S3method("getVerbose", "AromaRepository")

S3method("getVerbose", "AromaSettings")

S3method("getGenericSummary", "RichDataFrame")
S3method("getVirtualColumnFunctions", "RichDataFrame")
S3method("setVirtualColumnFunctions", "RichDataFrame")

S3method("isDone", "AromaTransform")

S3method("stextLabel", "AromaMicroarrayDataFile")
S3method("stextLabels", "AromaMicroarrayDataFile")
S3method("stextSize", "AromaMicroarrayDataFile")
S3method("writeDataFrame", "AromaUnitFracBCnBinarySet")
S3method("writeDataFrame", "AromaUnitPscnBinarySet")
S3method("writeDataFrame", "AromaUnitSignalBinaryFile")
S3method("writeDataFrame", "AromaUnitSignalBinarySet")
S3method("writeDataFrame", "AromaUnitTabularBinaryFile")
S3method("writeDataFrame", "AromaUnitTotalCnBinarySet")

S3method("drawCytoband", "ChromosomalModel")
S3method("getListOfUnitNamesFiles", "ChromosomalModel")
S3method("getListOfUnitTypesFiles", "ChromosomalModel")
S3method("getOutputSet", "ChromosomalModel")
S3method("getSetTag", "ChromosomalModel")

S3method("writeAxesLayers", "ChromosomeExplorer")
S3method("writeCopyNumberRegionLayers", "ChromosomeExplorer")
S3method("writeCytobandLayers", "ChromosomeExplorer")
S3method("writeGraphs", "ChromosomeExplorer")
S3method("writeGridHorizontalLayers", "ChromosomeExplorer")
S3method("writeRawCopyNumberLayers", "ChromosomeExplorer")
S3method("writeRegions", "ChromosomeExplorer")

S3method("findChangePointsByState", "SegmentedGenomicSignalsInterface")
