useDynLib(GeneticsBase)

export(
       "LD",
       "LDband",
       "LDdist",
       "alleleCount",
       "alleleLevels",
       "alleles",
       "alleleSummary",
       "binsearch",
       "callCodes",
       "callCodes<-",
       "carrier",
       "convert",
       "decodeCallCodes",
       "description",
       "description<-",
       "desMarkers",
       "diseq.inner",
       "diseq.ci",
       "dominant",
       "ci.balance",
       "errorMetrics",
       "errorMetrics<-",
       "extractAlleles", #!#
       #"fastGrid",
       "founderGeneSet",
       "geneSet",
       "genotypeFileFormats",
       "genotypeLevels",
       "genotypes",
       "genotypeSummary",
       "gregorius",
       "haplo.score.w",
       "haplo.score.slide.w",
       "haplo.em.w",
       "haplo.scan.w",
       "head",
       "HWE",
       "HWE.chisq", # temporary 
       "HWE.exact",
       "heterozygote",
       "homozygote",
       "html",
       "html.GeneticsBaseSummary",
       "html.markerSummary",
       "html.LD",
       ##"initialize",
       "latex",
       "latex.GeneticsBaseSummary",
       "latex.markerSummary",
       "latex.LD",
       "LDView",
       "left",
       "makeMarkerInfo", 
       "makeTransTable", 
       "makeTransTableList",
       "markerFileFormats",
       "markerInfo",
       "markerInfo<-",
       "markerNames",
       "markerSummary",
       "missingCodes",
       "missingCodes<-",
       "nallele",
       "nmarker",
       "nobs",
       "notes",
       "notes<-",
       "ped2geneSet",
       "PGtables",
       "phase",
       "phase<-",
       "phenotypeFileFormats",
       "ploidy",
       "ploidy<-",
       #"plot",
       "power.casectrl",
       "print.GeneticsBaseSummary",
       "print.markerSummary",
       #"print.LD",
       "read.fbat.phe",
       "read.pbat.phe",
       "read.phe",
       "readGenes",
       "readGenes.fbat.ped",
       "readGenes.hapmap.ped",
       "readGenes.pbat.ped",
       "readGenes.ped",
       "readGenes.perlegen",
       "readGenes.pfizer",
       "read.pfizer.Listing",
       "read.pfizer.Pivot",
       "recessive",
       "right",
       "sampleInfo",
       "sampleInfo<-",
       "studyInfo",
       "studyInfo<-",
       "summary.LD",
       "tail",
       "transTables",
       "transTables<-",
       "txt",
       "txt.default"
)

exportClasses("geneSet")
exportMethods(
              "LD",
              "LDband",
              "LDdist",
              "[",
              "[[",
              "alleleCount",
              "alleleLevels",
              "alleles",
              "callCodes",
              "callCodes<-",
              "carrier",
              "description",
              "description<-",
              "dominant",
              "errorMetrics",
              "errorMetrics<-",
              "genotypeLevels",
              "genotypes",
              "head",
              "heterozygote",
 	      "homozygote",
              "HWE",
              #"initialize",
              #"left",
              "markerInfo",
              "markerInfo<-",
              "markerNames",
              "missingCodes",
              "missingCodes<-",
              "nallele",
              "nmarker",
              "nobs",
              "notes",
              "notes<-",
              "phase",
              "phase<-",
              "ploidy",
              "ploidy<-",
              "plot",
              #"right",
              "recessive",
              "sampleInfo",
              "sampleInfo<-",
              "show",
              "studyInfo",
              "studyInfo<-",
              "tail",
              "transTables",
              "transTables<-"
              )

exportClasses("LD", "LDband", "LDdist")
exportMethods(
              "head",
              "html",
              "latex",
              "left",
              "plot",
              #"print",
              "right",
              "show",
              "tail"
             )

#import(tools)
#importFrom(combinat, rmultz2)
importFrom(gdata, interleave, drop.levels)
importFrom(gdata, nobs)
importFrom(gdata, trim, upperTriangle, "upperTriangle<-")
importFrom(gdata, lowerTriangle, "lowerTriangle<-")
importFrom(gplots, colorpanel)
importFrom(graphics, plot)
importFrom(gtools, odd)
importFrom(methods,show)
importFrom(stats, reshape, na.omit)
importFrom(utils, head, tail)
importFrom(MASS, ginv)
#importFrom(haplo.stats, haplo.score) 
#importFrom(haplo.stats, haplo.score.slide) 
#importFrom(haplo.stats, haplo.em) 
#importFrom(haplo.stats, haplo.scan)
