Nothing
### Convert colors.
get.color <- function(u.codon, color = .CF.PT$color){
if(length(u.codon) <= 4){
### Cases of less than or equal to 4 synonymous codon are all fine, but
### the colors should be matched the position. e.g. C = c("TGC", "TGT")
### should be colors 2 and 4 rather than colors 1 and 2.
color <- color[c("A", "C", "G", "T") %in% gsub("..(.)", "\\1", u.codon)]
} else{
if(all(u.codon %in% .CF.GV$synonymous.codon$L)){
### L = c("CTA", "CTC", "CTG", "CTT", "TTA", "TTG")
### Do nothing.
} else if(all(u.codon %in% .CF.GV$synonymous.codon$R)){
### R = c("AGA", "AGG", "CGA", "CGC", "CGG", "CGT")
color <- color[c(5:6, 1:4)]
} else if(all(u.codon %in% .CF.GV$synonymous.codon$S)){
### S = c("AGC", "AGT", "TCA", "TCC", "TCG", "TCT")
### This is for un-split case. The split case is ok in 4 codons case.
color <- color[c(5:6, 1:4)]
} else{
stop("Not in right order nor right unique codon.")
}
}
color
} # End of get.color().
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