# Requirements: None

##########################################################################
# COLOR.CODING				attributes: v, color, mark
#
#	color.coding				constructor from a logical vector and a scalar

color.coding <- function(v, color, mark=1) {
	val <- list(v=v, color=color, mark=mark)
	class(val) <- 'color.coding'
	val
}

is.color.coding <- function(x) inherits(x, 'color.coding')

confidence.curve.color <- 3
bad.channel.replicate.color <- 4
bad.replicate.ratio.color <- 5
central.line.color <- 6
top.ten.color <- 7
significant.color <- 8
bottom.ten.solo.color <- 9
bottom.ten.color <- 10
boring.point.color <- 11
top.ten.solo.color <- 12
fold.difference.color <- 13
worst.channel.replicate.color <- 16

##########################################################################
# COLOR.CODED.PAIR				attributes: x, y, ccl
#
#	color.coded.pair				constructor from two vectors and a list
#										that contains color.codings
#	plot							scatter plot with colors

color.coded.pair <- function(x, y, ccl) {
	val <- list(x=x, y=y, color.code.list=ccl)
	class(val) <- 'color.coded.pair'
	val
}

plot.color.coded.pair <- function(ob, pch=1, ...) {
	plot(ob$x, ob$y, type='n', ...)
	points(ob$x, ob$y, col=boring.point.color, pch=pch)
	if (is.list(ob$color.code.list)) {
		lapply(ob$color.code.list, function(cc, x, y) {
			if (sum(cc$v) > 0) {
				points(x[cc$v], y[cc$v], col=cc$color, pch=cc$mark)
			}
		}, ob$x, ob$y)
	} else if (is.color.coding(ob$color.code.list)) {
		v <- ob$color.code.list$v
		if (sum(v) > 0) {
			points(ob$x[v], ob$y[v], col=ob$color.code.list$color, pch=ob$color.code.list$mark)
		}
	}
	invisible(ob)
}