I have a DNAMultipleAlignment object. In R, the show function displays the head and tail of the aligned sequences, with nice colors. And I can cut-paste it as plain text as show below.

> seqs_aln
DNAMultipleAlignment with 5 rows and 230 columns
     aln                                                                                                   names               
[1] -----ATTGTTTAGTCTGGGGTTTACAGAAGAGTTGTTTCTTCATGGAA...TTTCGCCGAAAAATCAAG------------------GTTCCATTGAGT- Oki
[2] -----ATTGTTTAGTCTGCTG-TCACAGTAGAGTTGTTGCTTCATGGAA...TTTCGCCGAATAATCACTCAATTGAAAGACG-----GTTCCATTGAGT- Osa
[3] -----ATTGTTTAGTCTGCTG-TCACAGTAGAGTTGTTGCTTCATGGAA...ATTCGCCGAATAATCACTCAATTGAAAGACGCGATTGTTCCATTGAGT- Aom
[4] ---TTATTGTTTAGTCTGCAG-TCACAGTAGAGTTGTTGCTTCATGGAA...TTTCGCCGAATAATCACTGAATCGC-----------GTTCCATCGAATG Bar
[5] AGATTATTGTTTAGTCTGCAG-TCACAGTAGAGTTGTTGCTTCATGGAA...TTTCGCCGAATAATCACTGAATCGG-----------GTTCCATCGAATG Nor

This is neat but I also would like to output the full alignment in my _RMarkdown_ notebook. I wonder why there is no equivalent of writePairwiseAlignment() for mutliple alignment sequences?

After inspecting selectMethod("detail", "DNAMultipleAlignment"), I found that I can use a slightly customised version of Biostrings:::.write.MultAlign to display

> #Almost identical to from Biostrings:::.write.MultAlign, except it does not write to a file
> showMultiAlign <- function (x, invertColMask = F, showRowNames = T, hideMaskedCols = T) 
+ {
+         msk <- colmask(x)
+         dims <- dim(x)
+         if (invertColMask == FALSE) {
+             msk <- gaps(msk, start = 1, end = dims[2])
+         }
+         if (hideMaskedCols) {
+             hasMask <- FALSE
+         }
+         else {
+             colmask(x) <- NULL
+             if (length(msk) > 0) {
+                 hasMask <- TRUE
+             }
+             else {
+                 hasMask <- FALSE
+             }
+         }
+         if (hasMask) {
+             dims[1] <- dims[1] + 1
+         }
+         ch <- as.character(x)
+         ch <- unlist(lapply(ch, Biostrings:::.insertSpaces))
+         if (hasMask) {
+             mskInd <- as.integer(msk)
+             mskCh <- paste(as.character(replace(rep(1, dim(x)[2]), 
+                 mskInd, 0)), collapse = "")
+             mskCh <- Biostrings:::.insertSpaces(mskCh)
+         }
+         names <- names(ch)
+         ch <- sapply(ch, Biostrings:::.strChop, chopsize = 55, simplify = FALSE)
+         if (hasMask) {
+             mskCh <- .strChop(mskCh, chopsize = 55)
+             ch <- c(list(Mask = mskCh), ch)
+         }
+         maxLen <- max(nchar(names(ch)))
+         stockSpc <- paste(rep(" ", maxLen), collapse = "")
+         bufferSpacing <- function(name) {
+             spc <- paste(rep(" ", maxLen - nchar(name)), collapse = "")
+             paste(name, spc, sep = "")
+         }
+         ch <- c(ch, list(rep("", length(ch[[1]]))))
+         output <- character(length(ch[[1]]) * length(ch))
+         for (i in seq_len(length(ch[[1]]))) {
+             for (j in seq_len(length(ch))) {
+                 if (i == 1) {
+                   output[j] <- paste(unlist(lapply(names(ch[j]), 
+                     bufferSpacing)), "   ", ch[[j]][i], sep = "")
+                 }
+                 else {
+                   if (showRowNames) {
+                     output[(length(ch) * (i - 1)) + j] <- paste(unlist(lapply(names(ch[j]), 
+                       bufferSpacing)), "   ", ch[[j]][i], sep = "")
+                   }
+                   else {
+                     output[(length(ch) * (i - 1)) + j] <- paste(stockSpc, 
+                       "   ", ch[[j]][i], sep = "")
+                   }
+                 }
+             }
+         }
+         output <- gsub("\\s+$", "", output)
+         output <- output[1:length(output) - 1]
+         if (hasMask) {
+             output <- c(paste("", paste(c(dims, ""), collapse = " "), 
+                 collapse = " "), output)
+         }
+         else {
+             output <- c(paste("", paste(dims, collapse = " "), 
+                 collapse = " "), output)
+         }
+         output
+ }
> seqs_aln |> showMultiAlign()
 [1] " 5 230"                                                      
 [2] "Oki   -----ATTGT TTAGTCTGGG GTTTACAGAA GAGTTGTTTC TTCATGGAAC"
 [3] "Osa   -----ATTGT TTAGTCTGCT G-TCACAGTA GAGTTGTTGC TTCATGGAAC"
 [4] "Aom   -----ATTGT TTAGTCTGCT G-TCACAGTA GAGTTGTTGC TTCATGGAAC"
 [5] "Bar   ---TTATTGT TTAGTCTGCA G-TCACAGTA GAGTTGTTGC TTCATGGAAC"
 [6] "Nor   AGATTATTGT TTAGTCTGCA G-TCACAGTA GAGTTGTTGC TTCATGGAAC"
 [7] ""                                                            
 [8] "Oki   CGGGCTGCTG TAAATCAGAG GACTCGGTCT CGGCCGAGCG CGCGCTGACC"
 [9] "Osa   CAGCCCGCAG TAAATCAGAA GAGTCAGTCG CGGACGAGTG CGCGCTGACC"
[10] "Aom   CAGCCCGCAG TAAATCAGAA GAGTCAGTCG CGGACGAGTG CGCGCTGACC"
[11] "Bar   CAGCCCGCAG TAAATCAGAA GACTAGGTCG CGGGCGACTG CGTGCTGACC"
[12] "Nor   CAGCCCGCAG TAAATCAGAA GACTCGGTCG CGGGCGACTG CGTGCTGACC"
[13] ""                                                            
[14] "Oki   TCTAAAGCGG CGGCCCTAGC GCGCATCGTC AAGCGCAAAT TTTTCAGAAT"
[15] "Osa   TCTAAAGCGG CGGCCCCAAC GCGCATCGTC AAGCGCAACA TTTTCAGAAT"
[16] "Aom   TCTAAAGCGG CGGCCCCAAC GCGCATCGTC AAGCGCAACA TTTTCAGAAT"
[17] "Bar   TCTAAAGCGG CGGCCTCAGC GCGCACCGTC GAGCGCAACA TTTTCAGAAT"
[18] "Nor   TCTAAAGCGG CGGCCTCAGC GCGCACCGTC AAGCGCAACA TTTTCAGAAT"
[19] ""                                                            
[20] "Oki   TGAGCTTCCA AAATCAAACA CCAGAAACGC CTTTCGCCGA AAAATCAAG-"
[21] "Osa   TGAGCTTCTG AAATCAAAAA GCAGAAACA- ATTTCGCCGA ATAATCACTC"
[22] "Aom   TGAGCTTCTG AAATCAAAAA GCAGAAACA- AATTCGCCGA ATAATCACTC"
[23] "Bar   TGAGCTTCTG AAATCAAAAA GCAGAAACA- TTTTCGCCGA ATAATCACTG"
[24] "Nor   TGAGCTTCTG AAATCAAAAA GCAGAAACA- TTTTCGCCGA ATAATCACTG"
[25] ""                                                            
[26] "Oki   ---------- -------GTT CCATTGAGT-"                      
[27] "Osa   AATTGAAAGA CG-----GTT CCATTGAGT-"                      
[28] "Aom   AATTGAAAGA CGCGATTGTT CCATTGAGT-"                      
[29] "Bar   AATCGC---- -------GTT CCATCGAATG"                      
[30] "Nor   AATCGG---- -------GTT CCATCGAATG"

My questions are:

• Is there an easy way to get it in color ?
• Can future versions of _Biostrings_ provide a writeMultipleAlignment function ?