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(IRanges, as.matrix, cbind, findOverlaps, ifelse, intersect,
                  lapply, mad, Map, mean, median, ncol, nrow, order, paste,
                  pintersect, pmin,queryHits, rbind, reduce, Reduce, Rle, 
                  rownames,"rownames<-", sapply, stack, start, subjectHits,
                  subseq, t, table, tapply, unique, unlist, values,
                  "values<-", which, width)

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)

importFrom(IRanges, 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)

