#
# NAMESPACE PING
#
useDynLib(PING,.registration=TRUE)


importFrom(graphics, abline, axis, grid, layout, lines, mtext, par, plot, points, segments, stripchart, symbols, title)
importFrom(grDevices, grey)
importFrom(stats, dt, integrate, kmeans, pt)
importFrom(stats4, summary)

importFrom(Rsamtools, ScanBamParam, scanBamFlag, readBamGappedAlignments)

#importFrom(IRanges, IRanges, RangedData)
#importClassesFrom(IRanges, IRanges, RangedData)
#importMethodsFrom(IRanges, coerce, duplicated, end, levels, lapply, order, score, sort, space, start, width, as.matrix, runValue, elementMetadata, "elementMetadata<-")

#importMethodsFrom(GenomicRanges, coerce, strand, seqnames, width)
#importClassesFrom(GenomicRanges, GRanges)


importClassesFrom(PICS, segReads, segReadsPE, segReadsList, segReadsListPE, pics, picsError, picsList)
importMethodsFrom(PICS, coerce, show, summary, minRange,
	maxRange,
	scoreReverse,
	scoreForward,
	chromosome,
	map,
	score,
	se, seF,seR,sigmaSqF, sigmaSqR, delta, mu, w, K, code, length, "[","[[")
importFrom(PICS, segReads, segReadsPE, segReadsList, segReadsListPE,
	segReadsGeneric, summarySeg, makeRangedDataOutput, setParaEM, setParaPrior,
	candidate.region, segChrRead)
importClassesFrom(Gviz, AnnotationTrack, DataTrack, GenomeAxisTrack, BiomartGeneRegionTrack)
importFrom(Gviz, AnnotationTrack, DataTrack, GenomeAxisTrack, BiomartGeneRegionTrack)
importFrom(Gviz, plotTracks)


exportClasses(ping, pingError, pingList)
exportMethods(show, summary, plot, se, seF, seR, sigmaSqF, sigmaSqR, mu, delta, w, code, length, K,"[","[[",
	chromosome, score)
export("PING","postPING","newPingError",
	"segReads","segReadsPE","segReadsList","segReadsListPE",
	"segmentPING",
	"NucleosomeTrack","CoverageTrack","RawReadsTrack","plotSummary",
	"bam2gr")
#Export imported stuff
export("makeRangedDataOutput","setParaPrior","setParaEM")
