import(SNPchip, Biobase, oligoClasses)

##classes for HMMs
exportClasses("hSet", "HmmSnpSet", "HmmSnpCallSet", "HmmSnpCopyNumberSet")
exportMethods(
              "[",
              "[<-",
              bind,
              breakpoints,
              byArm,
              calculateEmissionProbability,
              callsIce,
              "callsIce<-",
              copyNumberIce,
              "copyNumberIce<-",
              coerce,
              chromosomeArm, "chromosomeArm<-",
              distance, "distance<-",
              emissionProbability, "emissionProbability<-",
              getBreaks,
              getCopyNumberLocation,
              getCopyNumberScale,
              getInitialStateProbability,
              getLohProbability,
              getTransitionProbability,
              hmm,
              hmmBySample,
              ice2VanillaICE,
              initialize,
              initialStateProbability, "initialStateProbability<-",
              isMissing,
              likelihood, "likelihood<-",
              locationCopyNumber, "locationCopyNumber<-",
              numberStates, ##"numberStates<-",
              pCHOM, "pCHOM<-",
              predictions, "predictions<-",
              scaleCopyNumber, "scaleCopyNumber<-",
              stateNames, "stateNames<-",
              show,
              transitionProbability, "transitionProbability<-",
              .unsplitHmm,
              viterbi)

export(callEmission,
       hapmapProbabilities,
       getHapmapProbabilities,
       getCallEmission)

###########################################################################
##classes for graphical parameters
###########################################################################
exportClasses("ParHSet", "ParHmmSnpSet", "ParHmmSnpCallSet", "ParHmmSnpCopyNumberSet")
###########################################################################
##methods and functions for graphical parameters
###########################################################################
exportMethods(getPar, plotSnp)
export(plotPredictions)

