useDynLib(snapCGH)

import(methods)

importMethodsFrom(tilingArray, logLik)

importFrom(aCGH, clones.info, combine.func, maPalette, states.hmm.func)
importFrom(cluster, clara)
importFrom(DNAcopy, CNA, smooth.CNA)
importFrom(GLAD, glad)
importFrom(graphics, abline, close.screen, identify, image, locator,
           mtext, par, plot, points, rect, screen, segments,
           split.screen, title)
importFrom(grDevices, rainbow)
importFrom(limma, MA.RG, printHead, readGenericHeader)
importFrom(stats, ansari.test, approx, dist, dnorm, hclust, lowess,
           median, rnorm, runif)
importFrom(utils, read.table)

export(findBreakPoints, genomePlot, plotSegmentedGenome, processCGH,
       runBioHMM, runGLAD, runTilingArray, compareSegmentations, 
       zoomChromosome, zoomGenome,read.clonesinfo,runHomHMM,mergeStates,
       runDNAcopy,simulateData, convert.output,filterClones,
       removeByWeights,find.param.five,find.param.four,find.param.three,
       find.param.two,find.param.one,fit.model,run.nelder,IDProbes,
       MergeLevels.new,MergeLevels.old,heatmapGenome,prop.na,
       imputeMissingValues,readPositionalInfo,generate.data,Viterbi.five,
       Viterbi.four,Viterbi.three,Viterbi.two,log2ratios)

exportClasses(SegList)
S3method(dim, SegList)
S3method(length, SegList)
S3method(dimnames, SegList)
S3method(cbind, SegList)
S3method(rbind, SegList)