Nothing
Mafft <- function(file.name, file.path="", type="DNA", aln.filetype="FASTA", args=NULL,
out.name=NULL, print.curl=FALSE, job.name=NULL, email=TRUE,
shared.username=NULL, suppress.Warnings=FALSE) {
type <- match.arg(type, c("DNA", "PROTEIN"))
aln.filetype <- match.arg(aln.filetype, c("CLUSTALW", "FASTA"))
if (rplant.env$api == "f") {
privAPP=FALSE
version="mafftDispatcher-1.0.13100u1"
if (!is.null(args)) {
args <- c(args)
}
if (type == "DNA"){
args <- append(args, "--nuc")
} else {
args <- append(args, "--amino")
}
if (aln.filetype == "CLUSTALW"){
args <- append(args, "--clustalout")
}
args <- paste(args, collapse=" ") # make a single statement
args <- list(c("arguments",args))
} else {
privAPP=TRUE
version="mafft-beta-7.221"
options=NULL
if (type == "DNA"){
options <- append(options, list(c("T", "--nuc")))
} else {
options <- append(options, list(c("T", "--amino")))
}
if (aln.filetype == "CLUSTALW"){
options <- append(options, list(c("format", "--clustalout")))
}
if (!is.null(out.name)){
options <- append(options, list(c("outname", outname)))
}
if (!is.null(args)){
args <- c(args)
args <- append(options, list(c("arguments",args)))
} else {
args <- options
}
}
nprocs <- 1
App <- GetAppInfo(version)[[3]]
input.list <- vector("list",1)
input.list[[1]] <- App[,2][1]
if (is.null(job.name)){
# job.name <- paste(rplant.env$user,"_",version,"_viaR", sep="")\
job.name <- version
}
myJob<-SubmitJob(application=version, job.name=job.name, nprocs=nprocs,
file.list=list(file.name), file.path=file.path, email=email,
input.list=input.list, suppress.Warnings=suppress.Warnings,
print.curl=print.curl, shared.username=shared.username,
args.list=args, private.APP=privAPP)
if ((!is.null(out.name)) && (rplant.env$api == "a")){
cat(paste("Result file:", out.name, "\n"))
} else if (rplant.env$api == "f"){
cat("Result file: mafft.fa\n")
} else {
cat("Result file: mafft.aln\n")
}
return(myJob)
}
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