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#' Is the text a TMHMM result text?
#'
#' Is the text a TMHMM result text?
#'
#' A TMHMM result text, is similar to a regular FASTA file: it shows the
#' protein names and the locations of the amino acids (instead of the amino
#' acids).
#'
#' Here is an example of a TMHMM result text:
#'
#' \verb{
#' >protein name
#' oMMiii
#' }
#'
#' In this example, \code{protein name} is the name of the protein.
#' The protein consists out of 6 amino acids, of which the first
#' is located outside the cell, the next two are in the membrane,
#' and the last three are inside the (cytosol of) the cell. Note that
#' this is a biologically impossible protein: it takes around 21 amino
#' acids to span the lipid membane.
#' @inheritParams default_params_doc
#' @return TRUE if the text is a TMHMM result text
#' @examples
#' tmhmm_result <- c(
#' ">protein name",
#' "ooooMMMMiiiii"
#' )
#' is_tmhmm_result(tmhmm_result)
#' @export
is_tmhmm_result <- function(tmhmm_result) { # nolint indeed a complex function, no idea how to simplify it
if (class(tmhmm_result) != "character") return(FALSE)
# Must alternate between lines with '>' and a sequence of iMo
n_lines <- length(tmhmm_result)
state <- "need_name"
for (i in seq(1, n_lines)) {
line <- tmhmm_result[i]
if (state == "need_name") {
if (!tmhmm::is_protein_name_line(line)) return(FALSE)
state <- "need_sequence"
} else if (state == "need_sequence") {
if (!tmhmm::is_locatome_line(line)) {
return(FALSE)
}
state <- "need_name_or_sequence"
} else if (state == "need_name_or_sequence") {
if (tmhmm::is_protein_name_line(line)) {
state <- "need_sequence"
} else if (tmhmm::is_locatome_line(line)) {
# Just continue
} else {
return(FALSE)
}
}
}
state == "need_name_or_sequence"
}
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