# Generated by roxygen2: do not edit by hand

export()
export(ModDNAString)
export(ModDNAStringSet)
export(ModDNAStringSetList)
export(ModRNAString)
export(ModRNAStringSet)
export(ModRNAStringSetList)
export(QualityScaledModDNAStringSet)
export(QualityScaledModRNAStringSet)
export(combineIntoModstrings)
export(combineModifications)
export(fullName)
export(incompatibleModifications)
export(letterFrequency)
export(modifyNucleotides)
export(nomenclature)
export(readModDNAStringSet)
export(readModRNAStringSet)
export(readQualityScaledModDNAStringSet)
export(readQualityScaledModRNAStringSet)
export(removeIncompatibleModifications)
export(replaceLetterAt)
export(sanitizeFromModomics)
export(sanitizeFromtRNAdb)
export(sanitizeInput)
export(separate)
export(shortName)
export(writeModStringSet)
export(writeQualityScaledModStringSet)
exportClasses(ModDNAString)
exportClasses(ModDNAStringSet)
exportClasses(ModDNAStringSetList)
exportClasses(ModRNAString)
exportClasses(ModRNAStringSet)
exportClasses(ModRNAStringSetList)
exportClasses(QualityScaledModDNAStringSet)
exportClasses(QualityScaledModRNAStringSet)
exportMethods("==")
exportMethods("seqtype<-")
exportMethods(Views)
exportMethods(XString)
exportMethods(XStringSet)
exportMethods(alphabet)
exportMethods(alphabetFrequency)
exportMethods(as.character)
exportMethods(combineIntoModstrings)
exportMethods(combineModifications)
exportMethods(consensusMatrix)
exportMethods(consensusString)
exportMethods(fullName)
exportMethods(hasOnlyBaseLetters)
exportMethods(incompatibleModifications)
exportMethods(letterFrequency)
exportMethods(modifyNucleotides)
exportMethods(nomenclature)
exportMethods(removeIncompatibleModifications)
exportMethods(replaceLetterAt)
exportMethods(separate)
exportMethods(seqtype)
exportMethods(shortName)
import(BiocGenerics)
import(Biostrings)
import(GenomicRanges)
import(S4Vectors)
import(methods)
importFrom(Biostrings,xscodes)
importFrom(crayon,make_style)
importFrom(grDevices,rgb)
importFrom(stringi,stri_enc_get)
importFrom(stringi,stri_enc_toascii)
importFrom(stringi,stri_enc_tonative)
importFrom(stringi,stri_enc_toutf8)
importFrom(stringi,stri_locate_all_fixed)
importFrom(stringi,stri_locate_all_regex)
importFrom(stringi,stri_sub)
importFrom(stringr,str_detect)
importFrom(stringr,str_sub)
importFrom(stringr,str_trim)