scagnostics.trace <- function(df, trace) {
	n <- length(trace$index)
	res <- numeric(n*9)
	res <- matrix(res, ncol=9)
	
	df <- as.matrix(df)

	colnames(res) <- colnames(scagnostics(as.data.frame(df %*% trace$projs[[1]])))
	for (i in 1:n) {
		res[i,] <- scagnostics(as.data.frame(df %*% trace$projs[[i]]))
	}
	
	return(res)	
} 


scagnostics.anneal <- function(df, idx, cool=0.99, temp=1, start=NULL, show.index=TRUE, gg=FALSE, stop.it="MAXRUNS", ...) {
	checkstop <- function() {
		if (stop.it=="MAXRUNS") return (i >= maxRuns)
		if (stop.it=="NRUNS") {
			if (i==maxRuns) {
				print("continue? (y/n)")
				key <- readLines(,1)
				continue <- !(key[1] != "y")
				if (continue) maxRuns <- maxRuns + runs
			}
			return (i >= maxRuns)
		}	
		if (stop.it=="CONV") return (abs(deltaI) <= absDelta)

		return (I0>1)
	}


	i <- 1
	df <- as.matrix(df)

	if (is.null(start)) {
		A0 <- proj(df)

	} else {
		A0 <- ortho(start)
	}
	
	res <- scagnostics(as.data.frame(df %*% A0))
	I0 <- res[idx]
	method <- colnames(res)[idx]
	
	index <- I0
	projs <- list()
	projs[[1]] <- A0
	print(c("start index: ",I0))
	if (gg) ggobi_display_set_tour_projection(d,A0)
	
	if (stop.it == "MAXRUNS") {
		pull.break=FALSE
		maxRuns=500
	}
	if (stop.it == "NRUNS") {
		pull.break=TRUE
		maxRuns=30
		runs=30
	}
	if (stop.it == "CONV") {
		deltaI <- 1
		absDelta=0.001
	}


	while (!checkstop()) {
		B <- proj(df)
		Ai <- ortho(A0+cool^i*B)
		Ii <- scagnostics(as.data.frame(df %*% Ai))[idx]
		Ti <- temp/log(i+1)
		deltaI <- Ii-I0
		rho <- min(exp(deltaI/(Ii*Ti)),1)
		if (is.na(rho)) rho <- 0
	#	print(c(i, I0,Ii,deltaI/(Ii*Ti), rho))
	
		if (rbinom(1,1,rho)>0) {
			A0 <- Ai
			I0 <- Ii
			if (gg) ggobi_display_set_tour_projection(d,Ai)
			i <- i+1
			projs[[i]] <- A0
	
			index <- c(index,I0)
			if (show.index) plot(index, pch=20, ylab=method)
		}

	}
	res <- list(index=index, projs = projs)
	print(c("end index: ", I0))
	return(res)
}