import(methods)
import(Biostrings)
import(ShortRead)
import(caTools)
import(BSgenome.Ecoli.NCBI.20080805)
import(RCircos)
import(GenomicRanges)


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<-"
)


