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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| #' Collapse multiple sequences into one | ||
| #' | ||
| #' @description Joins sequences from a vector into a single sequence. Sequence | ||
| #' type remains unchanged. | ||
| #' | ||
| #' @template x | ||
| #' @template NA_letter | ||
| #' @template three-dots | ||
| #' | ||
| #' @return \code{\link[=sq-class]{sq}} object of the same type as input but with | ||
| #' exactly one sequence. | ||
| #' | ||
| #' @details | ||
| #' \code{collapse()} joins sequences from supplied \code{sq} object in the same | ||
| #' order as they appear in said vector. That is, if there are three sequences | ||
| #' AGGCT, ATCCGT and GAACGT, then resulting sequence will be AGGCTATCCGTGAACGT. | ||
| #' This operation does not alter the type of the input object nor its alphabet. | ||
| #' | ||
| #' @examples | ||
| #' # Creating objects to work on: | ||
| #' sq_ami <- sq(c("MIAANYTWIL","TIAALGNIIYRAIE", "NYERTGHLI", "MAYXXXIALN"), | ||
| #' alphabet = "ami_ext") | ||
| #' sq_dna <- sq(c("ATGCAGGA", "GACCGAACGAN", ""), alphabet = "dna_ext") | ||
| #' sq_unt <- sq(c("ATGCAGGA?", "TGACGAGCTTA", "", "TIAALGNIIYRAIE")) | ||
| #' | ||
| #' # Collapsing sequences: | ||
| #' collapse(sq_ami) | ||
| #' collapse(sq_dna) | ||
| #' collapse(sq_unt) | ||
| #' | ||
| #' # Empty sq objects are collapsed as well (into empty string - ""): | ||
| #' sq_empty <- sq(character(), alphabet = "rna_bsc") | ||
| #' collapse(sq_empty) | ||
| #' | ||
| #' @family order_functions | ||
| #' @export | ||
| collapse <- function(x, ...) | ||
| UseMethod("collapse") | ||
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|
||
| #' @export | ||
| collapse.default <- function(x, ...) | ||
| stop("method 'collapse' isn't implemented for this type of object", call. = FALSE) | ||
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| #' @rdname collapse | ||
| #' @export | ||
| collapse.sq <- function(x, ..., | ||
| NA_letter = getOption("tidysq_NA_letter")) { | ||
| assert_string(NA_letter, min.chars = 1) | ||
|
|
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| CPP_collapse(x, NA_letter) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| #' @export | ||
| paste <- function(...) | ||
| UseMethod("paste") | ||
|
|
||
| #' @export | ||
| paste.default <- function(...) { | ||
| base::paste(...) | ||
| } | ||
|
|
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| #' Paste sequences in string-like fashion | ||
| #' | ||
| #' @description Joins multiple vectors of sequences into one vector. | ||
| #' | ||
| #' @param ... [\code{sq}]\cr | ||
| #' Sequences to paste together. | ||
| #' @template NA_letter | ||
| #' | ||
| #' @return \code{\link[=sq-class]{sq}} object of common type of input objects. | ||
| #' Common type is determined in the same process as for | ||
| #' \code{\link[=sq-concatenate]{c.sq}()}. | ||
| #' | ||
| #' @details | ||
| #' \code{paste()} joins sequences in the same way as it does with strings. | ||
| #' All \code{sq} objects must have the same length, that is, contain the same | ||
| #' number of sequences. An exception is made for scalar (length 1) \code{sq} | ||
| #' objects, which are replicated instead. | ||
| #' | ||
| #' @examples | ||
| #' # Creating objects to work on: | ||
| #' sq_dna_1 <- sq(c("TTCAGGGCTAG", "CGATTGC", "CAGTTTA"), | ||
| #' alphabet = "dna_bsc") | ||
| #' sq_dna_2 <- sq(c("ATCTTGAAG", "CATATGCGCTA", "ACGTGTCGA"), | ||
| #' alphabet = "dna_bsc") | ||
| #' sq_unt_1 <- sq(c("ATGCAGGA?", "TGACGAGCTTA", "", "TIAALGNIIYRAIE")) | ||
| #' sq_unt_2 <- sq(c("OVNU!!OK!!J", "GOK!MI!N!BB!", "DPOFIN!!", "??!?")) | ||
| #' | ||
| #' # Pasting sequences: | ||
| #' collapse(sq_dna_1, sq_dna_2) | ||
| #' collapse(sq_unt_1, sq_unt_2) | ||
| #' collapse(sq_dna_2, sq_unt_2, sq_dna_1) | ||
| #' | ||
| #' @family order_functions | ||
| #' @name paste | ||
| #' @export | ||
| paste.sq <- function(..., | ||
| NA_letter = getOption("tidysq_NA_letter")) { | ||
| # Throws error when there is no common size | ||
| vec_size_common(...) | ||
| assert_string(NA_letter, min.chars = 1) | ||
|
|
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| CPP_paste(vec_cast_common(...), NA_letter) | ||
| } |
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