R/seqbind.R

In bio3d: Biological Structure Analysis

seqbind <- function(..., blank = "-") {
  cl <- match.call()
  
  objs <- list(...)
  are.null <- unlist(lapply(objs, is.null))
  objs <- objs[!are.null]
  
  if(length(objs)==0)
    stop("Incompatible input")
  
  if(length(objs)==1)
    return(unlist(objs))
  
  is.fasta <- function(x)
    return(inherits(x, "fasta"))
           
  are.fas <- unlist(lapply(objs, is.fasta))
  are.vec <- unlist(lapply(objs, is.vector))
  are.mat <- unlist(lapply(objs, is.matrix))
  
  if(!all(are.vec | are.mat | are.fas))
    stop("'Can combine only vectors and/or matrices'")

  objs[are.fas] <- lapply(objs[are.fas], function(x) x$ali)
  objs[are.vec] <- lapply(objs[are.vec], matrix, nrow = 1)
  max.col <- max(unlist(lapply(objs, ncol)))
  extend <- function(x, n, add)
    cbind(x, matrix(add, nrow=nrow(x), ncol=n-ncol(x)))  
  objs <- lapply(objs, extend, n = max.col, add = blank)
  objs <- do.call(rbind, objs)

  out <- as.fasta(objs, id=rownames(objs))
  out$call <- cl
  return(out)
}