maintain function name consistency with CHANGED-pre-msa-tree.R and pr…

…e-msa-tree.R while we determine where these functions should live.

NAMESPACE

@@ -104,7 +104,6 @@ export(to_titlecase)
 export(totalGenContextOrDomArchCounts)
 export(validateCountDF)
 export(wordcloud3)
-export(write.MsaAAMultipleAlignment)
 export(writeMSA_AA2FA)
 export(write_proc_medians_table)
 export(write_proc_medians_yml)

R/CHANGED-pre-msa-tree.R

@@ -610,12 +610,12 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSA_AA2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' Write MsaAAMultpleAlignment Objects as algined fasta sequence
+#' writeMSA_AA2FA
 #'
 #' @description
 #' MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
@@ -632,7 +632,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSA_AA2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)