## oligoClasses NAMESPACE
##---------------------------------------------------------------------------
## Import
##---------------------------------------------------------------------------
## methods
importMethodsFrom(methods, initialize, show)
importFrom(methods, "@<-", callNextMethod, new, validObject, coerce)

## BiocGenerics
importFrom(BiocGenerics, updateObject, annotation, "annotation<-")

## affyio
importFrom(affyio, read.celfile.header, read.celfile)

## Biostrings
importClassesFrom(Biostrings, DNAStringSet)

## graphics
importFrom(graphics, plot)

## Biobase
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
                  NChannelSet, Versions, VersionedBiobase, Versioned, SnpSet)

importFrom(Biobase, assayDataElement, assayDataElementReplace,
           assayDataNew, assayDataValidMembers,
           assayDataElementNames, varLabels, isCurrent,
	   testBioCConnection)

importMethodsFrom(Biobase, annotatedDataFrameFrom, assayData, 
                  "assayData<-", combine, experimentData, 
                  "experimentData<-", exprs, "exprs<-",
		  protocolData,
                  featureData, "featureData<-", featureNames, fData,
		  "fData<-",
                  fvarLabels, pData, "pData<-", phenoData,
                  "phenoData<-", sampleNames, "sampleNames<-", se.exprs,
                  "se.exprs<-", storageMode, "storageMode<-",
                  classVersion,
		  snpCall, snpCallProbability,
                  'snpCall<-', 'snpCallProbability<-')

## IRanges
##importClassesFrom(IRanges, RangedData, DataTable, List, DataTableORNULL, Vector, Annotated)
##importFrom(IRanges, IRanges, RangedData, RangedDataList,
##	   countOverlaps,
##	   ranges, values,
##	   queryHits, subjectHits)
##importMethodsFrom(IRanges, findOverlaps, as.matrix)

##importClassesFrom(GenomicRanges, GRanges)
import(IRanges)
import(GenomicRanges)

## ff
## register open and close methods
importFrom(ff, open.ff, close.ff, ff, ffdf)

## foreach
import(foreach)

## BiocInstaller
importFrom(BiocInstaller, biocinstallRepos)

## utils
importFrom(utils, packageDescription)

##---------------------------------------------------------------------------
## Export
##---------------------------------------------------------------------------
##
##            classes
##
## PDInfo Classes
exportClasses(AffyTilingPDInfo, AffyExpressionPDInfo, AffySNPPDInfo,
              AffySNPCNVPDInfo, AffyGenePDInfo, AffyExonPDInfo,
              NgsExpressionPDInfo, NgsTilingPDInfo, DBPDInfo,
              ExpressionPDInfo, TilingPDInfo)

##Feature-level Classes
exportClasses(FeatureSet, ExpressionFeatureSet, SnpFeatureSet,
              SnpCnvFeatureSet, TilingFeatureSet, ExonFeatureSet,
              GeneFeatureSet)

##SNP-level Classes
exportClasses(AlleleSet, BeadStudioSet, oligoSnpSet, SnpSuperSet, CNSet,
	      gSet, gSetList, RangedDataCopyNumber, RangedDataCNV, RangedDataCBS,
	      RangedDataHMM, CopyNumberSet, GenomeAnnotatedDataFrame,
	      BeadStudioSetList, BafLrrSetList, BafLrrSet,
	      oligoSetList, SnpSet2)

## Ranged-Data methods
exportMethods(numberProbes)

##Misc
exportClasses(ff_or_matrix)


## EXPORTING.....
##             methods
##

## Methods ...
exportMethods(bothStrands, allele, calls, "calls<-", confs, "confs<-",
              chromosome, "chromosome<-", copyNumber,
              "copyNumber<-", cnConfidence, "cnConfidence<-", db, isSnp,
              position, "position<-", sampleNames, A, B, "A<-", "B<-",
	      "genomeBuild<-", getArm)

## FeatureSet methods
exportMethods(exprs)

## PDInfo methods
exportMethods(annotation, db, initialize, genomeBuild,
              geometry, kind, manufacturer)

## Some general methods
exportMethods(getM, getA, annotatedDataFrameFrom, open, close)

## CNSet methods
exportMethods(batch, batchNames, "batchNames<-", coerce, flags, show,
	      nu, phi, batchStatistics, "batchStatistics<-", baf, lrr,
	      "baf<-", "lrr<-", coverage2,
	      findOverlaps, state, openff, closeff, checkOrder,
	      mean, updateObject,
	      "sampleNames<-",
	      GenomeAnnotatedDataFrameFrom,
	      makeFeatureGRanges)

## EXPORTING....
##             functions
##

## Functions for parallel operations
export(pdPkgFromBioC, requireAnnotation, affyPlatforms, celfileDate, celfileName,
       list.celfiles, is.ffmatrix, isPackageLoaded, ldStatus,
       ldSetOptions, parStatus, ocProbesets, ocSamples, ldPath, getBar,
       createFF, ocLapply,
       splitIndicesByLength, splitIndicesByNode, initializeBigMatrix,
       initializeBigVector, initializeBigArray)

export(chromosome2integer, integer2chromosome, i2p, p2i, annotationPackages, checkExists,
       chromosomePositionOrder, integerArray, integerMatrix, findOverlaps,
       RangedDataCNV, RangedDataCBS, RangedDataHMM, library2, AssayDataList,
       getSequenceLengths)


### Deprecated
export(setCluster, getCluster, delCluster, requireClusterPkgSet, requireClusterPkg)
exportMethods(featuresInRange)
