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(v1.4.0.9011) message formatting

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dr. M.S. (Matthijs) Berends
2020-10-27 15:56:51 +01:00
parent 98773aa859
commit 5a607abb36
27 changed files with 187 additions and 157 deletions
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33
R/mo.R
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@ -1761,9 +1761,7 @@ print.mo_uncertainties <- function(x, ...) {
if (NROW(x) == 0) {
return(NULL)
}
cat(font_blue(strwrap("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. Please see ?mo_matching_score.",
width = 0.98 * getOption("width")),
collapse = "\n"))
message_("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. Please see ?mo_matching_score.", as_note = FALSE)
cat("\n")
msg <- ""
@ -1838,16 +1836,19 @@ print.mo_renamed <- function(x, ...) {
return(invisible())
}
for (i in seq_len(nrow(x))) {
message(font_blue(paste0("NOTE: ",
font_italic(x$old_name[i]), ifelse(x$old_ref[i] %in% c("", NA), "",
paste0(" (", gsub("et al.", font_italic("et al."), x$old_ref[i]), ")")),
" was renamed ",
ifelse(as.integer(gsub("[^0-9]", "", x$new_ref[i])) < as.integer(gsub("[^0-9]", "", x$old_ref[i])),
font_bold("back to "),
""),
font_italic(x$new_name[i]), ifelse(x$new_ref[i] %in% c("", NA), "",
paste0(" (", gsub("et al.", font_italic("et al."), x$new_ref[i]), ")")),
" [", x$mo[i], "]")))
message_(font_italic(x$old_name[i]),
ifelse(x$old_ref[i] %in% c("", NA),
"",
paste0(" (", gsub("et al.", font_italic("et al."), x$old_ref[i]), ")")),
" was renamed ",
ifelse(as.integer(gsub("[^0-9]", "", x$new_ref[i])) < as.integer(gsub("[^0-9]", "", x$old_ref[i])),
font_bold("back to "),
""),
font_italic(x$new_name[i]),
ifelse(x$new_ref[i] %in% c("", NA),
"",
paste0(" (", gsub("et al.", font_italic("et al."), x$new_ref[i]), ")")),
" [", x$mo[i], "]")
}
}
@ -1945,9 +1946,9 @@ replace_ignore_pattern <- function(x, ignore_pattern) {
if (!is.null(ignore_pattern) && !identical(trimws2(ignore_pattern), "")) {
ignore_cases <- x %like% ignore_pattern
if (sum(ignore_cases) > 0) {
message(font_blue(paste0("NOTE: the following input was ignored by `ignore_pattern = \"", ignore_pattern, "\"`: ",
paste0("'", sort(unique(x[x %like% ignore_pattern])), "'", collapse = ", "),
collapse = ", ")))
message_("The following input was ignored by `ignore_pattern = \"", ignore_pattern, "\"`: ",
paste0("'", sort(unique(x[x %like% ignore_pattern])), "'", collapse = ", "),
collapse = ", ")
x[x %like% ignore_pattern] <- NA_character_
}
}