useDynLib("VanillaICE", .registration=TRUE)

## methods
importMethodsFrom(methods, initialize, show)
importFrom(methods, callNextMethod, new, validObject)

##utils
importFrom(utils, setTxtProgressBar, txtProgressBar, packageDescription)

##Biobase (do we need this)
import(Biobase)

##stats
importFrom(stats, update, sd)

import(IRanges)
importMethodsFrom(IRanges, as.matrix)
import(GenomicRanges)

import(oligoClasses)

##msm
importFrom(msm, rtnorm)

importFrom(matrixStats, colMedians)

## crlmm
##importMethodsFrom(crlmm, calculateRBaf)

##foreach
import(foreach)
import(iterators)

##----------------------------------------------------------------------------
## export
##----------------------------------------------------------------------------
export(BeadStudioSet, robustSds, read.bsfiles, icePlatforms)
exportMethods(hmm)
export(copyNumberLimits, rowMAD, viterbi2Wrapper, rescale)
##export(BeadStudioSetList, constructOligoSetListFrom, constructBafLrrSetListFrom)

## export deprecated classes and functions
exportClasses(HmmOptionList)
export(hmm.setup, HmmOptionList,
       hmmSnpSet2,
       hmmBafLrrSet2, hmmBafLrrSetList2,
       hmmOligoSnpSet2)


