import(
    LowMACAAnnotation,
    methods,
    cgdsr,
    parallel,
    RColorBrewer,
    BiocParallel
)
importFrom(stringr, str_extract)
importFrom(reshape2, melt)
importFrom(data.table, rbindlist)
importFrom(motifStack , plotMotifLogo , pcm2pfm , colorset)
importFrom(Biostrings , consensusMatrix , readAAMultipleAlignment)
importFrom(Biostrings , AAMultipleAlignment, as.matrix)
importClassesFrom(Biostrings , AAMultipleAlignment)
exportPattern("^[[:alpha:]]+")
exportMethods(
    "alignSequences",
    "bpAll",
    "entropy",
    "getMutations",
    "mapMutations",
    "nullProfile",
    "parallelize",
    "parallelize<-",
    "lmAlignment",
    "lmEntropy",
    "lmMutations",
    "lmParams",
    "lmParams<-",
    "lmPlot",
    "protter",
    "setup",
    "show",
    "lfm",
    "lfmSingleSequence",
    "lmPlotSingleSequence"
)
export("allPfamAnalysis")
exportClasses(
    "LowMACA" 
)