R/print.r

In coil: Contextualization and Evaluation of COI-5P Barcode Data

#' 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 = "")
}