R/Structstrings-LoopIndexList.R

In Structstrings: Implementation of the dot bracket annotations with Biostrings

#' @include Structstrings.R
NULL

#' @name LoopIndexList
#' 
#' @title LoopIndexList: base pairing information as a list of integer values
#' 
#' @description 
#' With loop indeces base pairing information can be represented by giving each
#' base pair a number and increasing/decreasing it with each opened/closed base
#' pair. This information can be used for further analysis of the represented
#' structure.
#' 
#' @param ... the \code{integer} input vectors.
#' 
#' @return a \code{LoopIndexList} object.
#' 
#' @examples 
#' # if the object is create manually make sure it is a valid structure
#' # information. Otherwise an error is thrown.
#' lil <- LoopIndexList(list(c(1L,2L,3L,3L,3L,2L,1L,0L,5L,6L,6L,5L),
#'                        c(1L,2L,2L,2L,2L,2L,1L,0L,5L,6L,6L,5L)))
NULL

#' @rdname LoopIndexList
#' @export
setClass(Class = "LoopIndexList",
         contains = c("CompressedIntegerList"))

#' @rdname LoopIndexList
#' @export
LoopIndexList <- function(...) as(IRanges::IntegerList(...),"LoopIndexList")

.valid.LoopIndexList <- function(object)
{
  # shift values
  y <- IntegerList(
    mapply(function(i,j){
      c(i,j)
    },
    IntegerList(as.list(rep(0,length(object)))),
    object,
    SIMPLIFY = FALSE))
  z <- IntegerList(
    mapply(function(i,j){
      c(i,j)
    },
    object,
    IntegerList(as.list(rep(0,length(object)))),
    SIMPLIFY = FALSE))
  a <- y - z
  message <- "Unmatched positions."
  # the sumsum of the shift should always be zero
  if(sum(sum(a)) != 0L){
    return(message)
  }
  # ... however there are case were omitting one bracket can cause the sumsum
  # of the shift to be zero as well. In these cases one value occurs only once,
  # which can never be the case (except 0)
  a <- table(unlist(object))
  if(any(a < 2L) && names(a[a < 2L]) != "0"){
    return(message)
  }
  NULL
}

setValidity("LoopIndexList", .valid.LoopIndexList)

#' @name LoopIndexList
#' @export
setAs(
  "IntegerList", "LoopIndexList",
  function(from)
  {
    from <- as(from,"CompressedIntegerList")
    class(from) <- "LoopIndexList"
    validObject(from)
    from
  }
)
#' @name LoopIndexList
#' @export
setAs(
  "CompressedIntegerList", "LoopIndexList",
  function(from)
  {
    class(from) <- "LoopIndexList"
    validObject(from)
    from
  }
)