####################################################################################################
####################################################################################################
## 	function to convert an instance of class "Factorization" from 
##	package fabia to an instance of class "biclust" from package biclust
##
##  minr: 	define the minimum number of row cluster members, clusters with less members will not be extracted 
##			(minr=30 was used in the Hochreiter et al. 2010)
##  minc: 	define the minimum number of column cluster members, clusters with less members will not be extracted 
##			(minc=5 was used in the Hochreiter et al. 2010)
##  resFab: results of a fabia run -> instance of class "Factorization"
##	thresZ: threshold for sample belonging to bicluster; default 0.5. 
##	thresL: threshold for loading belonging to bicluster (if not given it is estimated).
##			For additional information on thresZ and thresL please see the extractBic man-page  via "? extractBic"
##
##	example:
##		dat <- makeFabiDataBlocks(n = 100,l= 50,p = 3,f1 = 5,f2 = 5,
##	     		of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
##	       		sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)
##
##		X <- dat[[1]]
##		Y <- dat[[2]]
##
##		resEx <- fabia(X,3,0.1,20,1.0,1.0)
##
##		res_biclust  <- convertFABIA2biclust(resEx,minc=2, minr=2,thresZ=0.5,thresL=NULL)
##
## 	for previous fabia versions please use "convertFABIA2biclust_previousVersions"
##
##		res_biclust  <- convertFABIA2biclust_previousVersions(resEx,minc=2, minr=2,thresZ=0.5,thresL=NULL)
##
##
##
##	======NEW VERSION======
##
##  Users reported an issue with the recent biclust package, which could be reproduced with version biclust_1.0.1:
##		
##		res_biclust  <- convertFABIA2biclust(resEx,minc=2, minr=2,thresZ=0.5,thresL=NULL)
##  	Error in initialize(value, ...) : 
## 		argument "d" is missing, with no default
##
##	The new function convertFABIA2biclustNewVersion solves this issue:   
##
##		res_biclust  <- convertFABIA2biclustNewVersion(resEx,minc=2, minr=2,thresZ=0.5,thresL=NULL)
##
##
##
##
##
##
####################################################################################################
####################################################################################################



library(fabia)

convertFABIA2biclust <- function(resFab, minc=2, minr=2,thresZ=0.5,thresL=NULL){

    require(biclust)
    method <- resFab@parameters[[1]]
    cyc <- resFab@parameters[[2]]
	alpha <- resFab@parameters[[3]]
	spl <- resFab@parameters[[4]]
	spz <- resFab@parameters[[5]]
	p <- resFab@parameters[[6]]
	sL <- resFab@parameters[[7]]
	sZ <- resFab@parameters[[8]]
	n <- resFab@n
	l <- resFab@l
	La <- NULL
	Za <- NULL
	lapla <- NULL
	Psi <- NULL
	
	rFab <- extractBic(resFab,thresZ=thresZ,thresL=thresL)
	
    p <- length(rFab$bic[,1])
	
    pp <- 0
    for (i in 1:p) {
        if (rFab$bic[i,1]$binp[1]>=minr)
        {
            if (rFab$bic[i,1]$binp[2]>=minc) {
                pp <- pp + 1
            }
        }
    }
	
	if ((p==0)||(pp==0)) {
        L <- matrix(0,n,1)
        Z <- matrix(0,1,l)
        pp <- 0
    } else {
		
		
        L <- matrix(0,n,pp)
        Z <- matrix(0,pp,l)
		
        j <- 0
		
        for (i in 1:p) {
			
            if (rFab$bic[i,1]$binp[1]>=minr)
            {
                if (rFab$bic[i,1]$binp[2]>=minc) {
                    j <- j + 1
                    for (k in 1:rFab$bic[i,1]$binp[2]) {
                        Z[j,rFab$numn[i,2]$numnp[k]] <- 1
                    }
                    for (k in 1:rFab$bic[i,1]$binp[1]) {
                        L[rFab$numn[i,1]$numng[k],j] <- 1
                    }
                }
            }
        }
    }
	
    lp<- list()
    lp[[1]]=method
    lp[[2]]=cyc
    lp[[3]]=alpha
    lp[[4]]=spl
    lp[[5]]=spz
    lp[[6]]=p
    lp[[7]]=sL
    lp[[8]]=sZ
    lp[[9]]=La
    lp[[10]]=Za
    lp[[11]]=lapla
    lp[[12]]=Psi
	
	
	
    bicB <- BiclustResult(lp,L,Z,pp)
	
    return(bicB)
}

convertFABIA2biclust_previousVersions <- function(resFab, minc=2, minr=2,thresZ=0.5,thresL=NULL){

    require(biclust)
    method <- resFab@parameters[[1]]
    cyc <- resFab@parameters[[2]]
	alpha <- resFab@parameters[[3]]
	spl <- resFab@parameters[[4]]
	spz <- resFab@parameters[[5]]
	p <- resFab@parameters[[6]]
	sL <- resFab@parameters[[7]]
	sZ <- resFab@parameters[[8]]
	n <- resFab@n
	l <- resFab@l
	La <- NULL
	Za <- NULL
	lapla <- NULL
	Psi <- NULL
	
	rFab <- extract_bic(resFab,thresZ=thresZ,thresL=thresL)
	
    p <- length(rFab$bic[,1])
	
    pp <- 0
    for (i in 1:p) {
        if (rFab$bic[i,1]$binp[1]>=minr)
        {
            if (rFab$bic[i,1]$binp[2]>=minc) {
                pp <- pp + 1
            }
        }
    }
	
	if ((p==0)||(pp==0)) {
        L <- matrix(0,n,1)
        Z <- matrix(0,1,l)
        pp <- 0
    } else {
		
		
        L <- matrix(0,n,pp)
        Z <- matrix(0,pp,l)
		
        j <- 0
		
        for (i in 1:p) {
			
            if (rFab$bic[i,1]$binp[1]>=minr)
            {
                if (rFab$bic[i,1]$binp[2]>=minc) {
                    j <- j + 1
                    for (k in 1:rFab$bic[i,1]$binp[2]) {
                        Z[j,rFab$numn[i,2]$numnp[k]] <- 1
                    }
                    for (k in 1:rFab$bic[i,1]$binp[1]) {
                        L[rFab$numn[i,1]$numng[k],j] <- 1
                    }
                }
            }
        }
    }
	
    lp<- list()
    lp[[1]]=method
    lp[[2]]=cyc
    lp[[3]]=alpha
    lp[[4]]=spl
    lp[[5]]=spz
    lp[[6]]=p
    lp[[7]]=sL
    lp[[8]]=sZ
    lp[[9]]=La
    lp[[10]]=Za
    lp[[11]]=lapla
    lp[[12]]=Psi
	
	
	
    bicB <- BiclustResult(lp,L,Z,pp)
	
    return(bicB)
}



convertFABIA2biclustNewVersion <- function(resFab, minc=2, minr=2,thresZ=0.5,thresL=NULL){

    require(biclust)
    method <- resFab@parameters[[1]]
    cyc <- resFab@parameters[[2]]
	alpha <- resFab@parameters[[3]]
	spl <- resFab@parameters[[4]]
	spz <- resFab@parameters[[5]]
	p <- resFab@parameters[[6]]
	sL <- resFab@parameters[[7]]
	sZ <- resFab@parameters[[8]]
	n <- resFab@n
	l <- resFab@l
	La <- NULL
	Za <- NULL
	lapla <- NULL
	Psi <- NULL
	
	rFab <- extractBic(resFab,thresZ=thresZ,thresL=thresL)
	
    p <- length(rFab$bic[,1])
	
    pp <- 0
    for (i in 1:p) {
        if (rFab$bic[i,1]$binp[1]>=minr)
        {
            if (rFab$bic[i,1]$binp[2]>=minc) {
                pp <- pp + 1
            }
        }
    }
	
	if ((p==0)||(pp==0)) {
        L <- matrix(0,n,1)
        Z <- matrix(0,1,l)
        pp <- 0
    } else {
		
		
        L <- matrix(0,n,pp)
        Z <- matrix(0,pp,l)
		
        j <- 0
		
        for (i in 1:p) {
			
            if (rFab$bic[i,1]$binp[1]>=minr)
            {
                if (rFab$bic[i,1]$binp[2]>=minc) {
                    j <- j + 1
                    for (k in 1:rFab$bic[i,1]$binp[2]) {
                        Z[j,rFab$numn[i,2]$numnp[k]] <- 1
                    }
                    for (k in 1:rFab$bic[i,1]$binp[1]) {
                        L[rFab$numn[i,1]$numng[k],j] <- 1
                    }
                }
            }
        }
    }
	
    lp<- list()
    lp[[1]]=method
    lp[[2]]=cyc
    lp[[3]]=alpha
    lp[[4]]=spl
    lp[[5]]=spz
    lp[[6]]=p
    lp[[7]]=sL
    lp[[8]]=sZ
    lp[[9]]=La
    lp[[10]]=Za
    lp[[11]]=lapla
    lp[[12]]=Psi
	
	
	
    bicB <- BiclustResult(lp,L,Z,pp, d=list(info="fabia biclusters"))
	
    return(bicB)
}