## oligoClasses NAMESPACE
##---------------------------------------------------------------------------
## Import
##---------------------------------------------------------------------------
## methods
import(methods)

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

## 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<-')

importMethodsFrom(DBI, dbGetQuery, dbListTables)

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

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

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

## foreach
import(foreach)

## BiocManager
importFrom(BiocManager, repositories)

## utils
importFrom(utils, packageDescription)

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

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

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

## list methods
exportMethods(assayDataList, dims, featureDataList)

## 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,
	      elementNROWS, 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,
	      clone2)

import(S4Vectors)


## 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)
