useDynLib(ADaCGH2, .registration = TRUE)
## useDynLib(ADaCGH2, ad_rConvAndPeak, ad_rPulseConv,
##           ad_rWConvAndPeak, ad_rThresAndUnify)

export("pSegmentDNAcopy",
       "pSegmentWavelets",
       "pSegmentHMM",
       "pSegmentBioHMM",
       "pSegmentGLAD",
       "pSegmentCGHseg",
       "pSegmentHaarSeg",
       "pChromPlot",
       "inputToADaCGH",
       "outputToCGHregions",
       "cutFile")

import(ff, ffbase, bit)
## importFrom("bit", intrle, ri)
## importFrom("ffbase", min.ff, max.ff)           
importFrom("parallel", clusterApply, mclapply, stopCluster)
importFrom("DNAcopy", getbdry)
importFrom("tilingArray", segment)
importFrom("snapCGH", fit.model)
importFrom("aCGH", mergeLevels, create.aCGH, find.hmm.states, "hmm<-")
import(GLAD) ## we actually use now a whole bunch of things
## importFrom("GLAD", daglad.profileCGH)
importFrom("waveslim", modwt, imodwt)
importFrom("cluster", pam)


## importFrom("ff",
##            is.ff,
##            is.ffdf,
##            "[[.ff",
##            "[[<-.ff",
##            "[.ff",
##            "[<-.ff",
##            "[.ff_array",
##            "[<-.ff_array",
##vmode,
##as.vmode,
##"vmode<-",
## fforder
##            get.ff,
##            open.ff,
##            close.ff,
##            delete.ff,
##            delete.ffdf,
##            is.open.ff,
##            is.open.ffdf,
##            close.ffdf,
##            open.ffdf,
##            as.ffdf.ff_matrix,
##            as.ffdf,
##            as.ffdf.ff_vector)


