### This file contains function to show all possible options in phyclust.
.show.option <- function(){
my.cat("Options available in phyclust:", "\n")
my.cat("boundary method: ", paste(.boundary.method, collapse = ", "), "\n")
my.cat("code type: ", paste(.code.type, collapse = ", "), "\n")
my.cat("edist model: ", paste(.edist.model, collapse = ", "), "\n")
my.cat("em method: ", paste(.em.method, collapse = ", "), "\n")
my.cat("identifier: ", paste(.identifier, collapse = ", "), "\n")
my.cat("init method: ", paste(.init.method, collapse = ", "), "\n")
my.cat("init procedure: ", paste(.init.procedure, collapse = ", "), "\n")
my.cat("standard code: \n")
my.print(as.matrix(.nucleotide))
my.print(as.matrix(.snp))
my.cat("substitution model: \n")
my.print(as.matrix(.substitution.model))
invisible()
} # End of .show.option()
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