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#' Print a summary of a coi5p object.
#' @param x A coi5p class object.
#' @param ... Additional arguments to be passed between methods.
#' @keywords internal
print.coi5p = function(x, ...){
#header line
l1 = "coi5p barcode sequence"
#line if the sequence has a name
if(length(x$name) != 0 ){
l2 = paste(": ", x$name, "\n",
sep = "")
}else{
l2 = "\n"
}
#line for the sequence
l3 = paste("raw sequence:\n",
substr(x$raw,1, 25), "..." , substr(x$raw, (nchar(x$raw)-24), nchar(x$raw)),
"\n",
sep = "")
lines = c(l1, l2, l3)
#line to add if sequence is framed
if( "framed" %in% names(x) ){
l4 = paste("framed sequence:\n",
substr(x$framed,1, 25), "...", substr(x$framed, (nchar(x$framed)-24), nchar(x$framed)),
"\n",
sep = "")
lines = c(lines, l4)
}
#line to add if sequence is translated
if( "aaSeq" %in% names(x) ){
l5 = paste("Amino acid sequence:\n",
substr(x$aaSeq, 1, 25), "...", substr(x$aaSeq, (nchar(x$aaSeq)-24), nchar(x$aaSeq)),
"\n",
sep = "")
lines = c(lines, l5)
}
if( "was_trimmed" %in% names(x)){
l4a = paste("Raw sequence was trimmed: ", x$was_trimmed, "\n",
sep = "")
lines = c(lines, l4a)
}
#line to add if indel assessment has been performed
if( "indel_likely" %in% names(x) ){
if (x$indel_likely == TRUE){
l6 = paste("Stop codon present: ", x$stop_codons,
", Amino acid PHMM score:", x$aaScore, '\n',
"The sequence likely contains an insertion or deletion.\n",
sep = "")
}else{
l6 = paste("Stop codon present: ", x$stop_codons,
", Amino acid PHMM score:", x$aaScore, '\n',
"The sequence likely does not contain an insertion or deletion.\n",
sep = "")
}
lines = c(lines, l6)
}
if( "align_report" %in% names(x)){
l4b = paste(x$align_report, "\n", sep = "")
lines = c(lines, l4b)
}
#join the lines into a single string
cat(lines,sep = "")
}
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