import(methods)
import(IRanges)
import(Biostrings)
import(DECIPHER)
import(S4Vectors)

importFrom("utils", "setTxtProgressBar", "txtProgressBar", "data", 
           "object.size", "getS3method","read.table")
importFrom("stats", "predict", "runif", "setNames", "rnorm", "optim")
importFrom("parallel", "mclapply", "detectCores")
importFrom("graphics", "hist")
importFrom("grDevices", "topo.colors")

export(NucleotideOverlap)
export(gffToDataFrame)
export(PairSummaries)
export(FindSets)
export(DisjointSet)
export(ExtractBy)
export(SequenceSimilarity)
export(SubSetPairs)
export(EstimRearrScen)
export(BlockExpansion)
export(BlockReconciliation)
export(BlastSeqs)
export(GetProtWebData)

S3method(`[`, "LinkedPairs")
S3method(print, "LinkedPairs")

S3method(print, 'GenRearr')

export(ProtWeaver)
S3method(show, 'ProtWeaver')
S3method(print, 'ProtWeaver')
S3method(`[`, 'ProtWeaver')
S3method(predict, 'ProtWeaver')
S3method(PAProfiles, 'ProtWeaver')
S3method(CophProfiles, 'ProtWeaver')
S3method(Jaccard, 'ProtWeaver')
S3method(Hamming, 'ProtWeaver')
S3method(MutualInformation, 'ProtWeaver')
S3method(MirrorTree, 'ProtWeaver')
S3method(ContextTree, 'ProtWeaver')
S3method(ProfileDCA, 'ProtWeaver')
S3method(Coloc, 'ProtWeaver')
S3method(Behdenna, 'ProtWeaver')
S3method(Ensemble, 'ProtWeaver')

S3method(GetProtWebData, 'ProtWeb')
S3method(plot, 'ProtWeb')
S3method(summary, 'ProtWeb')
S3method(show, 'ProtWeb')
S3method(print, 'ProtWeb')


