# High-level function to get the *FULL* HPO annotation matrix (i.e. labels matrix) w.r.t. a given weighted adiacency matrix
# Input:
# anc.file.name: name of the list of ancestors to load (without rda extension). 
#				 It must be an rda file containing for each node the list of all its ancestor (def: anc.name) 
# anc.dir: relative path to directory where the ancestor file is stored (def: anc.dir)
# net : name of the dataset to load (without rda extension). It must be an .rda file containing the weighted adjiacency matrix of the graph. (def: net)
# net.dir: relative path to directory where the weighted adjiacency matrix is stored (def: net.dir)
# ann.file.name:
# ann.dir: 
# output.name : name of the output file without rda extension (def: output.name)
# output.dir: relative path to directory where the final HPO annotation matrix is stored  (def: output)
# Output:
# a matrix with annotations gene-phenotype stored in an .rda file in "/output" directory. 
# Rows correspond to genes and columns to phenotpyes. Let's denote "hpo.ann" the annotation matrix, the entries hpo.ann[i,j] 
# correspond to the i-th gene and j-th phenotype. hpo.ann[i,j]=1 means that gene i is annotated with phenotype j, O otherwise.
Do.full.HPO.annotation.matrix <- function(anc.file.name=anc.file.name, anc.dir="/anc.dir" ,net=net, net.dir="/net.dir", 
										  ann.file.name=ann.file.name, ann.dir="/ann.dir", output.name=output.name, output.dir="/output"){
	## loading list of ancestors
	anc.path <- paste0(anc.dir, anc.file.name, ".rda");
	anc.name <- load(anc.path);
	anc <- eval(parse(text=anc.name));  

	## loading wadj matrix
	net.path <- paste0(net.dir, net, ".rda");
	net.name <- load(net.path);
	W <- eval(parse(text=net.name));  

	## loading the specific annotation matrix
	ann.path <- paste0(ann.dir, ann.file.name, ".rda");
	ann.name <- load(ann.path);
	ann.spec <- eval(parse(text=ann.name));

	## costruction of full HPO annotation matrix
	hpo.ann <- full.annotation.matrix(W=W, anc=anc, ann.spec=ann.spec);
	
	## saving labels matrix
	hpo.ann.file <- paste0(output.dir, output.name, ".rda");
	save(hpo.ann, file=hpo.ann.file, compress=TRUE);
}