R/AromaMicroarrayDataFile.ATTRS.R

In HenrikBengtsson/aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

setMethodS3("setAttributeXY", "AromaMicroarrayDataFile", function(this, value, ...) {
  # Argument 'value':
  if (is.null(value)) {
    # Nothing todo?
    return()
  }

  pattern <- "^(X*)(Y*)$"
  if (regexpr(pattern, value) == -1) {
    throw("The value of argument 'value' is unrecognized: ", value)
  }

  # Parse and count
  n23 <- gsub(pattern, "\\1", value)
  n24 <- gsub(pattern, "\\2", value)
  n23 <- nchar(n23)
  n24 <- nchar(n24)
  setAttributes(this, n23=n23, n24=n24)
}, protected=TRUE)

setMethodS3("getAttributeXY", "AromaMicroarrayDataFile", function(this, ...) {
  n23 <- getAttribute(this, "n23", 0)
  n24 <- getAttribute(this, "n24", 0)
  xyTag <- paste(c(rep("X", n23), rep("Y", n24)), collapse="")
  xyTag
}, protected=TRUE)

setMethodS3("hasAttributeXY", "AromaMicroarrayDataFile", function(this, values, ...) {
   xyTag <- getAttributeXY(this)
   (xyTag %in% values)
}, protected=TRUE)


setMethodS3("setAttributesByTags", "AromaMicroarrayDataFile", function(this, tags=getTags(this), ...) {
  # Split tags
  tags <- Arguments$getTags(tags, collapse=NULL)

  newAttrs <- NextMethod("setAttributesByTags", tags=tags)

  # Parse XY, XX, XXX etc tags
  values <- grep("^X*Y*$", tags, value=TRUE)
  if (length(values) > 0) {
    newAttrs <- c(newAttrs, setAttributeXY(this, values))
  }

  # Parse tri<chromosome> tags
  values <- grep("^tri([1-9]|[0-9][0-9]|X|Y)$", tags, value=TRUE)
  if (length(values) > 0) {
    values <- gsub("^tri", "", values)
    chromosomes <- Arguments$getChromosomes(values)
    keys <- sprintf("n%02d", chromosomes)
    newAttrs <- c(newAttrs, lapply(keys, FUN=function(key) {
      setAttribute(this, key, 3)
    }))
  }

  # Return nothing
  invisible(newAttrs)
}, protected=TRUE)




setMethodS3("getPloidy", "AromaMicroarrayDataFile", function(this, chromosome, defaultValue=NA, ...) {
  # Argument 'chromosome':
  chromosome <- Arguments$getChromosome(chromosome)

  key <- sprintf("n%02d", chromosome)
  value <- getAttribute(this, key, defaultValue=defaultValue)
  value
}, protected=TRUE)