import(methods)
import(Biostrings)
import(GenomicAlignments)
import(caTools)
import(BSgenome.Ecoli.NCBI.20080805)
import(RCircos)
import(GenomicRanges)
importFrom("grDevices", "dev.off", "heat.colors", "pdf", "tiff")
importFrom("graphics", "axis", "lines", "par", "plot", "plot.window",
    "points", "polygon", "rect", "text")
importFrom("stats", "loess", "predict", "runmed")
importFrom("utils", "read.table", "write.table")

exportClasses(
    Data4Cseq)

exportMethods(
    prepare4CseqData,
    createVirtualFragmentLibrary,
    printBEDFragmentLibrary,
    checkRestrictionEnzymeSequence,
    giveEnzymeSequence,
    readPointsOfInterestFile,

    readsToFragments,
    chooseNearCisFragments,
    normalizeFragmentData,
    getReadDistribution,
    visualizeViewpoint,
    drawHeatmap,

    exportVisualizationFragmentData,
    importVisualizationFragmentData,
    printWigFile,
    simulateDigestion,
    drawDigestionFragmentHistogram,
    plotTransInteractions,

    Data4Cseq,
    viewpointChromosome, "viewpointChromosome<-",
    viewpointInterval, "viewpointInterval<-",
    readLength, "readLength<-",
    pointsOfInterest, "pointsOfInterest<-",
    rawReads, "rawReads<-",
    rawFragments, "rawFragments<-",
    nearCisFragments, "nearCisFragments<-"
)


