# Auxiliary function to delete gap-only columns
# Used inside the functions catfullGenes and catmultGenes
# Author: Domingos Cardoso
.delGaps <- function(x) {
dgaps <- list()
dgaps_temp <- list()
for (j in seq_along(x)) {
temp <- list()
for (i in seq_along(x[[j]][["sequence"]])) {
temp[[i]] <- which(grepl("-", strsplit(x[[j]][["sequence"]], "")[[i]]) == T)
}
dgaps_temp[[j]] <- temp
# List of all columns to be removed
dgaps[[j]] <- .intersectAll(dgaps_temp[[j]])
}
# Removing all gap-only columns
for (j in seq_along(x)) {
if (length(dgaps[[j]]) != 0) {
for (i in seq_along(x[[j]][["sequence"]])) {
s <- strsplit(x[[j]][["sequence"]], "")[[i]][-dgaps[[j]]]
x[[j]][["sequence"]][i] <- paste(s, collapse = "")
}
}
}
return(x)
}
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