useDynLib(Biobase, sublist_extract)

import(methods)

importFrom(BiocGenerics,
    dims,
    combine,
    updateObject, updateObjectFromSlots, getObjectSlots,
    annotation, "annotation<-"
)

importFrom(utils, head, tail, menu, packageDescription, read.table,
           write.table, .DollarNames)

exportClasses(aggregator, container, eSet,
              MIAxE, MIAME, characterORMIAME,
              annotatedDataset, AssayData, data.frameOrNULL,
              AnnotatedDataFrame,
              Versions, VersionsNull, Versioned, VersionedBiobase,
              ExpressionSet, MultiSet, SnpSet, NChannelSet,
              ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric,
              ScalarCharacter)

exportMethods("[", "[[", "$", abstract, aggenv, aggfun,
              annotatedDataFrameFrom, annotation,
              channel, channelNames, coerce,
              combine, content, contents, description, dimnames, "dimnames<-",
              dims, experimentData, expinfo, exprs,
              featureNames, featureData, fData, fvarLabels, fvarMetadata,
              hybridizations, initfun,
              length, locked, makeDataPackage, normControls, notes, otherInfo,
              pData,
              phenoData, preproc, protocolData, sampleNames, samples, se.exprs,
              selectChannels, snpCall, snpCallProbability, storageMode,
              varLabels, varMetadata,
              "annotation<-", "channelNames<-", "description<-", "dimLabels<-",
              "experimentData<-", "exprs<-",
              "featureNames<-", "featureData<-", "fData<-", "fvarLabels<-",
              "fvarMetadata<-",
              "notes<-", "preproc<-", "pData<-",
              "phenoData<-", "protocolData<-", "sampleNames<-",
              "snpCall<-", "snpCallProbability<-", "varLabels<-",
              "varMetadata<-", "assayData<-", "se.exprs<-",  "storageMode<-",
              "write.exprs", dim, dimLabels, assayData,
              pubMedIds, "pubMedIds<-",
              isVersioned, isCurrent, classVersion, "classVersion<-",
              updateObject, updateObjectTo,
              initialize, show, Compare,

              AnnotatedDataFrame,
              ExpressionSet)

export(Aggregate, addVigs2WinMenu, anyMissing,
       as.data.frame.ExpressionSet, assayDataNew,
       assayDataValidMembers, assayDataElementNames, assayDataElement,
       assayDataElementReplace, "assayDataElement<-", cache, copyEnv,
       copySubstitute, createPackage, dumpPackTxt, esApply,
       getPkgVigs, isUnique, listLen, matchpt, mkScalar, multiassign,
       NChannelSet, note, openPDF,openVignette, package.version,
       reverseSplit, rowMax, rowMedians, rowMin, rowQ,
       readExpressionSet, read.AnnotatedDataFrame, read.MIAME, MIAME,
       selectSome, strbreak, subListExtract, testBioCConnection,
       lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery,
       validMsg, write.AnnotatedDataFrame)
S3method(.DollarNames, "eSet")
S3method(.DollarNames, "ExpressionSet")
S3method(head, "AnnotatedDataFrame")
S3method(tail, "AnnotatedDataFrame")
S3method(as.data.frame, "ExpressionSet")