duplicate code related to msfinder

[hechth]

RAMClustR/R/import.MSFinder.structures.R

Lines 35 to 98 in 36fce5b

	if(is.null(mat.dir)) {
	mat.dir = paste0(home.dir, "/spectra/mat")
	}
	if(is.null(msp.dir)) {
	msp.dir = paste0(home.dir, "/spectra/msp")
	}
	usemat = TRUE
	usemsp = TRUE
	if(!dir.exists(mat.dir)) {
	usemat = FALSE
	}
	if(!dir.exists(msp.dir)) {
	usemsp = FALSE
	}
	if(!usemsp & !usemat) {
	stop("neither of these two directories exist: ", '\n',
	" ", mat.dir, '\n',
	" ", msp.dir, '\n')
	}
	if(usemsp & usemat) {
	msps<-list.files(msp.dir, recursive = TRUE)
	mats<-list.files(mat.dir, recursive = TRUE)
	if(length(mats) > length(msps)) {usemsp <- FALSE}
	if(length(msps) > length(mats)) {usemat <- FALSE}
	if(length(msps) == length(mats)) {
	feedback<-readline(prompt="Press 1 for .mat or 2 for .msp to continue")
	if(feedback == 1) {usemsp <- FALSE}
	if(feedback == 2) {usemat <- FALSE}
	}
	}
	mat.dir <- c(mat.dir, msp.dir)[c(usemat, usemsp)]
	do <- ramclustObj$cmpd
	### retrieve parameter file from mat directory and parse to save with results.
	params <- list.files(mat.dir, pattern = "batchparam", full.names = TRUE)
	if(length(params) == 0) {
	params <- list.files(mat.dir, pattern = "MSFINDER.INI", full.names = TRUE)
	}
	if(length(params) > 0) {
	mtime <- rep(NA, length(params))
	for(i in 1:length(mtime)) {
	mtime[i] <- format(file.info(params[i])$mtime, format = '%y%m%d%H%M%S')
	}
	params <- params[which.max(mtime)]
	params <- readLines(params)
	breaks <- which(nchar(params)==0)
	## structure inference parameters
	st <- grep ("Structure finder parameters", params)+1
	end <- breaks[which(breaks > st)[1]]-1
	if(end <= st) {stop('parsing of parameter file has failed')}
	tmp <- strsplit(params[st:end], "=")
	nms <- sapply(1:length(tmp), FUN = function(x) {tmp[[x]][1]})
	vals <- sapply(1:length(tmp), FUN = function(x) {tmp[[x]][2]})
	names(vals) <- nms
	ramclustObj$msfinder.structure.parameters <- vals

This code section reading data from MSfinder outputs is duplicated in import.MSFinder.formulas.R

RAMClustR/R/import.MSFinder.formulas.R

Lines 45 to 107 in 36fce5b

	if (is.null(mat.dir)) {
	mat.dir = paste0(getwd(), "/spectra/mat")
	}
	if (is.null(msp.dir)) {
	msp.dir = paste0(getwd(), "/spectra/msp")
	}
	usemat = TRUE
	usemsp = TRUE
	if (!dir.exists(mat.dir)) {
	usemat = FALSE
	}
	if (!dir.exists(msp.dir)) {
	usemsp = FALSE
	}
	if (!usemsp & !usemat) {
	stop("neither of these two directories exist: ", "\n",
	" ", mat.dir, "\n", " ", msp.dir, "\n")
	}
	if (usemsp & usemat) {
	msps <- list.files(msp.dir, recursive = TRUE)
	mats <- list.files(mat.dir, recursive = TRUE)
	if (length(mats) > length(msps)) {
	usemsp <- FALSE
	}
	if (length(msps) > length(mats)) {
	usemat <- FALSE
	}
	if (length(msps) == length(mats)) {
	feedback <- readline(prompt = "Press 1 for .mat or 2 for .msp to continue")
	if (feedback == 1) {
	usemsp <- FALSE
	}
	if (feedback == 2) {
	usemat <- FALSE
	}
	}
	}
	mat.dir <- c(mat.dir, msp.dir)[c(usemat, usemsp)]
	do <- list.files(mat.dir, pattern = ".fgt", full.names = TRUE)
	### retrieve parameter file from mat directory and parse to save with results.
	params <- list.files(mat.dir, pattern = "batchparam", full.names = TRUE)
	if(length(params) == 0) {
	params <- list.files(mat.dir, pattern = "MSFINDER.INI", full.names = TRUE)
	}
	if(length(params) > 0) {
	mtime <- rep(NA, length(params))
	for(i in 1:length(mtime)) {
	mtime[i] <- format(file.info(params[i])$mtime, format = '%y%m%d%H%M%S')
	}
	params <- params[which.max(mtime)]
	params <- readLines(params)
	breaks <- which(nchar(params)==0)
	## formula inference parameters
	st <- grep ("Formula finder parameters", params)+1
	end <- breaks[which(breaks > st)[1]]-1
	if(end <= st) {stop('parsing of parameter file has failed')}
	tmp <- strsplit(params[st:end], "=")
	nms <- sapply(1:length(tmp), FUN = function(x) {tmp[[x]][1]})
	vals <- sapply(1:length(tmp), FUN = function(x) {tmp[[x]][2]})
	names(vals) <- nms
	ramclustObj$msfinder.formula.parameters <- vals