# Generated by roxygen2: do not edit by hand

export("end<-")
export("mcols<-")
export("start<-")
export("strand<-")
export(AAMultipleAlignment)
export(AAStringSet)
export(CodonMatrix)
export(DNAMultipleAlignment)
export(DNAStringSet)
export(GENETIC_CODE_TABLE)
export(GRangesList)
export(GRangesMatrixSeq)
export(ListCodonMatrix)
export(MatrixSeq)
export(aa_index)
export(aa_mutmat)
export(aa_phychem_index)
export(aminoacid_dist)
export(as.AutomorphismList)
export(aut3D)
export(autZ125)
export(autZ5)
export(autZ64)
export(automorphismByRanges)
export(automorphism_bycoef)
export(automorphism_prob)
export(automorphisms)
export(base2codon)
export(base2int)
export(base_coord)
export(base_matrix)
export(base_seq2string_set)
export(codon_coord)
export(codon_dist)
export(codon_dist_matrix)
export(codon_matrix)
export(colMeans2)
export(colSds)
export(colSums2)
export(colVars)
export(conserved_regions)
export(dna_phychem)
export(end)
export(getAutomorphisms)
export(getGeneticCode)
export(get_coord)
export(get_mutscore)
export(makeGRangesFromDataFrame)
export(matrices)
export(mcols)
export(mod)
export(modeq)
export(modlin)
export(modlineq)
export(modq)
export(mut_type)
export(peptide_phychem_index)
export(readDNAMultipleAlignment)
export(rowMeans2)
export(rowSds)
export(rowSums2)
export(rowVars)
export(seq2granges)
export(seqranges)
export(setValidity2)
export(slapply)
export(sortByChromAndEnd)
export(sortByChromAndStart)
export(start)
export(str2chr)
export(str2dig)
export(strand)
export(subseq)
export(translate)
export(translation)
export(unmasked)
export(width)
exportClasses(Automorphism)
exportClasses(AutomorphismByCoef)
exportClasses(AutomorphismByCoefList)
exportClasses(AutomorphismList)
exportClasses(BaseGroup)
exportClasses(BaseGroup_OR_CodonGroup)
exportClasses(BaseSeq)
exportClasses(BaseSeqMatrix)
exportClasses(CodonGroup)
exportClasses(CodonMatrix)
exportClasses(CodonSeq)
exportClasses(ConservedRegion)
exportClasses(ConservedRegionList)
exportClasses(DNAStringSet_OR_DNAMultipleAlignment)
exportClasses(DNAStringSet_OR_NULL)
exportClasses(DataFrame_OR_data.frame)
exportClasses(GRangesMatrixSeq)
exportClasses(GRanges_OR_NULL)
exportClasses(ListCodonMatrix)
exportClasses(MatrixList)
exportClasses(MatrixSeq)
exportMethods("$")
exportMethods("[")
exportMethods("[[")
exportMethods("names<-")
exportMethods(as.AutomorphismList)
exportMethods(as.list)
exportMethods(automorphismByRanges)
exportMethods(automorphism_bycoef)
exportMethods(automorphism_prob)
exportMethods(automorphisms)
exportMethods(base2codon)
exportMethods(base2int)
exportMethods(base_coord)
exportMethods(base_matrix)
exportMethods(base_seq2string_set)
exportMethods(codon_matrix)
exportMethods(conserved_regions)
exportMethods(coordList)
exportMethods(dna_phychem)
exportMethods(getAutomorphisms)
exportMethods(get_coord)
exportMethods(get_mutscore)
exportMethods(matrices)
exportMethods(names)
exportMethods(peptide_phychem_index)
exportMethods(seq2granges)
exportMethods(seqRanges)
exportMethods(seqranges)
exportMethods(show)
exportMethods(str2chr)
exportMethods(str2dig)
exportMethods(translation)
import(BiocGenerics)
import(Biostrings)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(foreach)
importFrom(BiocGenerics,"end<-")
importFrom(BiocGenerics,"start<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,width)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,multicoreWorkers)
importFrom(Biostrings,AAMultipleAlignment)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,DNAMultipleAlignment)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,GENETIC_CODE_TABLE)
importFrom(Biostrings,getGeneticCode)
importFrom(Biostrings,readDNAMultipleAlignment)
importFrom(Biostrings,translate)
importFrom(Biostrings,unmasked)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(IRanges,IRanges)
importFrom(IRanges,ranges)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,setValidity2)
importFrom(Seqinfo,"seqlevels<-")
importFrom(Seqinfo,Seqinfo)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(XVector,subseq)
importFrom(data.table,data.table)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,"%>%")
importFrom(dplyr,lag)
importFrom(dplyr,mutate)
importFrom(foreach,"%:%")
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(matrixStats,colMeans2)
importFrom(matrixStats,colSds)
importFrom(matrixStats,colSums2)
importFrom(matrixStats,colVars)
importFrom(matrixStats,rowMeans2)
importFrom(matrixStats,rowSds)
importFrom(matrixStats,rowSums2)
importFrom(matrixStats,rowVars)
importFrom(methods,as)
importFrom(methods,coerce)
importFrom(methods,extends)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,show)
importFrom(methods,validObject)
importFrom(numbers,modlin)
importFrom(numbers,modq)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(stats,as.dist)
importFrom(stats,optim)
importFrom(stats,setNames)
importFrom(utils,data)
