useDynLib("waveTiling")

## Import Classes
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, MIAxE,
                  Versions)

importClassesFrom(methods, array, character, data.frame, list, matrix,
                  numeric, vector)

importClassesFrom(oligoClasses, TilingFeatureSet)

## Import Methods
importMethodsFrom(affy, pm, pmindex)

importMethodsFrom(Biobase, exprs, "exprs<-", pData, "phenoData<-")

importMethodsFrom(Biostrings, complement, matchPDict, PDict,
                  reverseComplement, startIndex)

importMethodsFrom(GenomicRanges, seqnames)


importMethodsFrom(methods, initialize, show)

importMethodsFrom(oligo, pmChr, pmPosition, pmSequence, pmStrand)

## Import
importFrom(affy, bg.adjust, list.celfiles)

importFrom(preprocessCore, normalize.quantiles)

#importFrom(GenomeGraphs, DisplayPars, gdPlot, makeAnnotationTrack,
#           makeGenericArray, makeGenomeAxis, makeRectangleOverlay,
#           makeTextOverlay)

importFrom(GenomicRanges, GRanges, GRangesList)

import(IRanges)

importFrom(methods, callNextMethod, new)

importFrom(oligo, read.celfiles)

importFrom(stats, contr.helmert, contr.treatment, lm, pnorm, qnorm,
           rnorm)

importFrom(waveslim, wave.filter)

## Export Classes
#exportClasses(WaveTilingFeatureSet, MapFilterProbe, GenomeInfo, WfmFit, WfmInf, WfmFitTime, WfmFitFactor, WfmFitCircadian, WfmFitCustom, WfmInfCompare, WfmInfEffects )
exportClasses(WaveTilingFeatureSet, MapFilterProbe, GenomeInfo, WfmFit, WfmInf)

## Export Methods
exportMethods(show)


## WaveTilingFeatureSet 
exportMethods(addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap, selectProbesFromTilingFeatureSet,bgCorrQn,wfm.fit)

## MapFilterProbe
exportMethods(getFilteredIndices, getPosition, selectProbesFromFilterOverlap)

## WfmFit and WfmInf
exportMethods(getProbePosition, getNoProbes, getBetaWav, getVarBetaWav, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getDesignMatrix, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj,getPrior, getAlpha, getDelta, getTwoSided, getSigProbes,getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff,getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions, plotWfm)

## Other
export(cel2TilingFeatureSet, makeContrasts, makeDesign)

