ourMELONS/R/testaaGenePopData.R

#' @title Tests GenePop data
#' @param tiedostonNimi Filename
#' @return kunnossa (binary "ok" condition value) == 0 if the data is not valid genePop data. Otherwise, kunnossa == 1.
#' @details GenePop data are textfiles that follow the GenePop format. This function checks if such file is properly formatted as GenePop.
testaaGenePopData <- function(tiedostonNimi) {
	# kunnossa == 0, jos data ei ole kelvollinen genePop data.
	# Muussa tapauksessa kunnossa == 1.

	kunnossa <- 0
	if (file.exists(tiedostonNimi)) {
		fid   <- readLines(tiedostonNimi)
		line1 <- fid[1] # ensimmäinen rivi
		line2 <- fid[2] # toinen rivi
		line3 <- fid[3] # kolmas
	} else {
		fid <- line1 <- line2 <- line3 <- -1
	}

	if (line1 == -1 | line2 == -1 | line3 == -1) {
		stop('Incorrect file format 1168')
	}
	if (testaaPop(line1) == 1 | testaaPop(line2) == 1) {
		stop('Incorrect file format 1172')
	}
	if (testaaPop(line3) == 1) {
		# 2 rivi t<>ll<6C>in lokusrivi (2 rows then locus row)
		nloci <- rivinSisaltamienMjonojenLkm(line2)
		line4 <- fid[4]
		if (line4 == -1) stop('Incorrect file format 1180')
		if (!grepl(',', line4)) {
			# Rivin nelj?t<>ytyy sis<69>lt<6C><74> pilkku.
			stop('Incorrect file format 1185')
		}
		pointer <- 1
		while (substring(line4, pointer, pointer) != ',') {
			# Tiedet<65><74>n, ett?pys<79>htyy
			pointer <- pointer + 1
		}
		line4 <- substring(line4, pointer + 1) # pilkun j<>lkeinen osa (the part after the comma)
		nloci2 <- rivinSisaltamienMjonojenLkm(line4)
		if (nloci2 != nloci) stop('Incorrect file format 1195')
	} else {
		line <- fid[4]
		lineNumb <- 4
		while (testaaPop(line) != 1 & line != -1) {
			line <- fid[lineNumb + 1]
			lineNumb <- lineNumb + 1
		}
		if (line == -1) stop('Incorrect file format 1206')
		nloci <- lineNumb - 2
		line4 <- fid[lineNumb + 1] # Eka rivi pop sanan j<>lkeen
		if (line4 == -1) stop('Incorrect file format 1212')
		if (!grepl(',', line4)) {
			# Rivin t<>ytyy sis<69>lt<6C><74> pilkku. (The line must contain a comma)
			stop('Incorrect file format 1217')
		}
		pointer <- 1
		while (substring(line4, pointer, pointer) != ',') {
			# Tiedet<65><74>n, ett?pys<79>htyy
			pointer <- pointer + 1
		}
		line4 <- substring(line4, pointer + 1) # pilkun j<>lkeinen osa (the part after the comma)
		nloci2 <- rivinSisaltamienMjonojenLkm(line4)
		if (nloci2 != nloci) stop('Incorrect file format 1228')
	}
	kunnossa <- 1
	return(kunnossa)
}