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#' @rdname Pajek
#'
#' @description \code{loadnetwork2} - The same as above, but adapted to be called within \code{loadpajek}.
#'
#' @param safe If \code{FALSE} error will occur if not all vertices have labels. If \code{TRUE} reading works faster.
#' @param closeFile Should the connection be closed at the end. Should be always \code{TRUE} if function is used directly.
#' @import Matrix
#' @importFrom utils read.table
#'
#' @export
"loadnetwork2" <-
function(filename,useSparseMatrix=NULL,minN=50,safe=TRUE,closeFile=TRUE){
if(is.character(filename)){
file<-file(description=filename,open="r")
} else file<-filename
while(TRUE){
line<-scan(file = file, nlines =1,what="char",quiet =TRUE, blank.lines.skip=FALSE)
if(substr(line[1],start=1,stop=1)=="%") {print(paste(line,collapse=" "));next}
if(line[1]=="") next
n<-line
break
}
if(length(n)==2){
n<-as.numeric(n[2])
if(safe){
vnames<-rep(as.character(NA),n)
while(TRUE){
line<-scan(file = file, nlines =1,what="char",quiet =TRUE, blank.lines.skip=FALSE)
if(length(line)==0||sum(grep(pattern="^ *$",x=as.character(line))==1)) break
if(line[1]=="") break
if(substr(line[1],start=1,stop=1)=="%") {print(paste(line,collapse=" "));next}
if(substr(line[1],start=1,stop=1)=="*"){
type=line[1]
break
}
vnames[as.integer(line[1])]<-line[2]
}
}else{
vnames<-read.table(file=file,nrows=n,as.is =TRUE)[,2]
type=""
}
if(all(is.na(vnames))){
vnames<-NULL
} else vnames[is.na(vnames)]<-""
if(is.null(useSparseMatrix)){
useSparseMatrix<- n>=50
}
if(useSparseMatrix){
if(requireNamespace("Matrix")){
M<-Matrix::Matrix(0,nrow=n,ncol=n,sparse=TRUE)
}else{
M<-matrix(0,nrow=n,ncol=n)
warning("Matrix package is not installed. Ordanary (dense) matrices will be used instead of sparse onse")
}
}else{
M<-matrix(0,nrow=n,ncol=n)
}
if(type=="*Matrix"){
tmp<-read.table(file=file,nrows=n)
tmp<-as.matrix(tmp)
M[1:n,1:n]<-M
} else while(TRUE){
line<-scan(file = file, nlines =1,what="char",quiet =TRUE, blank.lines.skip=FALSE)
if(length(line)==0||sum(grep(pattern="^ *$",x=as.character(line))==1)) break
if(substr(line[1],start=1,stop=1)=="%") {print(paste(line,collapse=" "));next}
if(substr(line[1],start=1,stop=1)=="*"){
type=line[1]
next
}else line<-as.double(line)
if(tolower(type)=="*arcs"){
M[line[1],line[2]]<-line[3]
}else if(tolower(type)=="*edges") {
M[line[1],line[2]]<-line[3]
M[line[2],line[1]]<-line[3]
}
}
dimnames(M)<-list(vnames,vnames)
} else if(length(n)==3){
n12<-as.numeric(n[2])
n1<-as.numeric(n[3])
n2<-n12-n1
if(safe){
vnames<-rep(as.character(NA),n12)
while(TRUE){
line<-scan(file = file, nlines =1,what="char",quiet =TRUE, blank.lines.skip=FALSE)
if(length(line)==0||sum(grep(pattern="^ *$",x=as.character(line))==1)) break
if(substr(line[1],start=1,stop=1)=="%") {print(paste(line,collapse=" "));next}
if(substr(line[1],start=1,stop=1)=="*"){
type=line[1]
break
}
vnames[as.integer(line[1])]<-line[2]
}
}else{
vnames<-read.table(file=file,nrows=n12,as.is =TRUE)[,2]
type=""
}
if(all(is.na(vnames))){
vnames<-NULL
} else vnames[is.na(vnames)]<-""
if(is.null(useSparseMatrix)){
useSparseMatrix<- n12>50
}
if(useSparseMatrix){
if(requireNamespace("Matrix")){
M<-Matrix::Matrix(0,nrow=n12,ncol=n12,sparse=TRUE)
}else{
warning("Matrix package is not installed. Ordanary (dense) matrices will be used instead of sparse onse")
M<-matrix(0,nrow=n12,ncol=n12)
}
} else {
M<-matrix(0,nrow=n12,ncol=n12)
}
if(type=="*Matrix"){
tmp<-read.table(file=file,nrows=n1)
tmp<-as.matrix(tmp)
M[1:n1,(n1+1):n12]<-tmp
} else while(TRUE){
line<-scan(file = file, nlines =1,what="char",quiet =TRUE, blank.lines.skip=FALSE)
if(length(line)==0||sum(grep(pattern="^ *$",x=as.character(line))==1)) break
if(substr(line[1],start=1,stop=1)=="%") {print(paste(line,collapse=" "));next}
if(substr(line[1],start=1,stop=1)=="*"){
type=line[1]
next
}else line<-as.double(line)
M[line[1],line[2]]<-line[3]
M[line[2],line[1]]<-line[3]
}
dimnames(M)<-list(vnames,vnames)
M<-M[1:n1,(n1+1):n12]
} else stop("Error in line: ", line)
if(closeFile) close(file)
M[is.na(M)]<-1
return(M)
}
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