useDynLib("VanillaICE")
import(SNPchip, Biobase, oligoClasses)
exportClasses("HmmParameter", "HmmOptions")
exportMethods("[",
              annotation,
              "annotation<-",
              breakpoints,
	      "breakpoints<-",
              calculateBreakpoints,
	      calculateDistance,
	      physicalDistance,
	      calls.ICE,
	      "calls.ICE<-",
	      copyNumber.ICE,
	      "copyNumber.ICE<-",
              coerce,                            
              db,
	      emission,
	      "emission<-",
              featureNames,
              hmm,
              initialize,
              pData,
              Pi,
              position,
              predictions,
	      "predictions<-",
	      probHomCall,
	      "probHomCall<-",
	      snpset,
	      "snpset<-",
              states,
              "states<-",
              show,
	      summary,
              tau,
	      genomicDistance,
	      "genomicDistance<-",
	      term5,
	      "term5<-",
	      transitionScale,
	      "transitionScale<-")

export(getChromosomeArm,
       addFeatureData,
       calculateCnSE,
       calls.emission,
       copyNumber.emission,
       copynumberEmission,
       findBreaks,
       genotypeEmission,
##       makeTable,
       scaleTransitionProbability,
       viterbi)

##Do not export in released version
##export(.splitAnnotation, .getCallEmission)


