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Fixed behavior of testaaGenePopData

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This commit is contained in:
Waldir Leoncio 2020-07-28 11:45:28 +02:00
parent ce3c3b7645
commit ba1573ad59
2 changed files with 22 additions and 18 deletions
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4
R/greedyMix.R
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@ -147,8 +147,8 @@ greedyMix <- function(
# fprintf(1,'Data: %s\n',[pathname filename]); # fprintf(1,'Data: %s\n',[pathname filename]);
# end # end
kunnossa <- testaaGenePopData(pathname_filename) kunnossa <- testaaGenePopData(filename_pathname)
# if (kunnossa == 0) stop("testaaGenePopData returned 0") if (kunnossa == 0) stop("testaaGenePopData returned 0")
# [data,popnames]=lueGenePopData([pathname filename]); # TODO: trans # [data,popnames]=lueGenePopData([pathname filename]); # TODO: trans
# h0 = findobj('Tag','filename1_text'); # h0 = findobj('Tag','filename1_text');

36
R/testaaGenePopData.R
View file

@ -1,15 +1,17 @@
#' @title Tests GenePop data #' @title Tests GenePop data
#' @param tiedostonNimi Filename #' @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) { testaaGenePopData <- function(tiedostonNimi) {
# kunnossa == 0, jos data ei ole kelvollinen genePop data. # kunnossa == 0, jos data ei ole kelvollinen genePop data.
# Muussa tapauksessa kunnossa == 1. # Muussa tapauksessa kunnossa == 1.
kunnossa <- 0 kunnossa <- 0
if (file.exists(paste0(tiedostonNimi, ".rda"))) { if (file.exists(tiedostonNimi)) {
fid <- load(tiedostonNimi) fid <- readLines(tiedostonNimi)
line1 <- readLines(fid)[1] # ensimmäinen rivi line1 <- fid[1] # ensimmäinen rivi
line2 <- readLines(fid)[2] # toinen rivi line2 <- fid[2] # toinen rivi
line3 <- readLines(fid)[3] # kolmas line3 <- fid[3] # kolmas
} else { } else {
fid <- line1 <- line2 <- line3 <- -1 fid <- line1 <- line2 <- line3 <- -1
} }
@ -21,41 +23,43 @@ testaaGenePopData <- function(tiedostonNimi) {
stop('Incorrect file format 1172') stop('Incorrect file format 1172')
} }
if (testaaPop(line3) == 1) { if (testaaPop(line3) == 1) {
# 2 rivi t<>ll<6C>in lokusrivi # 2 rivi t<>ll<6C>in lokusrivi (2 rows then locus row)
nloci <- rivinSisaltamienMjonojenLkm(line2) # TODO: translate function nloci <- rivinSisaltamienMjonojenLkm(line2)
line4 <- readLines(fid)[4] line4 <- fid[4]
if (line4 == -1) stop('Incorrect file format 1180') if (line4 == -1) stop('Incorrect file format 1180')
if (!grepl(',', line4)) { if (!grepl(',', line4)) {
# Rivin nelj?t<>ytyy sis<69>lt<6C><74> pilkku. # Rivin nelj?t<>ytyy sis<69>lt<6C><74> pilkku.
stop('Incorrect file format 1185') stop('Incorrect file format 1185')
} }
pointer <- 1 pointer <- 1
while (line4[pointer] != ',') { # Tiedet<65><74>n, ett?pys<79>htyy while (substring(line4, pointer, pointer) != ',') {
# Tiedet<65><74>n, ett?pys<79>htyy
pointer <- pointer + 1 pointer <- pointer + 1
} }
line4 <- line4[(pointer + 1):nchar(line4)] # pilkun j<>lkeinen osa line4 <- substring(line4, pointer + 1) # pilkun j<>lkeinen osa (the part after the comma)
nloci2 <- rivinSisaltamienMjonojenLkm(line4) nloci2 <- rivinSisaltamienMjonojenLkm(line4)
if (nloci2 != nloci) stop('Incorrect file format 1195') if (nloci2 != nloci) stop('Incorrect file format 1195')
} else { } else {
line <- readLines(fid)[4] line <- fid[4]
lineNumb <- 4 lineNumb <- 4
while (testaaPop(line) != 1 & line != -1) { while (testaaPop(line) != 1 & line != -1) {
line <- readLines(fid)[lineNumb] line <- fid[lineNumb + 1]
lineNumb <- lineNumb + 1 lineNumb <- lineNumb + 1
} }
if (line == -1) stop('Incorrect file format 1206') if (line == -1) stop('Incorrect file format 1206')
nloci <- lineNumb - 2 nloci <- lineNumb - 2
line4 <- readLines(fid)[4] # Eka rivi pop sanan j<>lkeen line4 <- fid[lineNumb + 1] # Eka rivi pop sanan j<>lkeen
if (line4 == -1) stop('Incorrect file format 1212') if (line4 == -1) stop('Incorrect file format 1212')
if (!grepl(',', line4)) { if (!grepl(',', line4)) {
# Rivin t<>ytyy sis<69>lt<6C><74> pilkku. # Rivin t<>ytyy sis<69>lt<6C><74> pilkku. (The line must contain a comma)
stop('Incorrect file format 1217') stop('Incorrect file format 1217')
} }
pointer <- 1 pointer <- 1
while (line4[pointer] != ',') { # Tiedet<65><74>n, ett?pys<79>htyy while (substring(line4, pointer, pointer) != ',') {
# Tiedet<65><74>n, ett?pys<79>htyy
pointer <- pointer + 1 pointer <- pointer + 1
} }
line4 <- line4[(pointer + 1):nchar(line4)] # pilkun j<>lkeinen osa line4 <- substring(line4, pointer + 1) # pilkun j<>lkeinen osa (the part after the comma)
nloci2 <- rivinSisaltamienMjonojenLkm(line4) nloci2 <- rivinSisaltamienMjonojenLkm(line4)
if (nloci2 != nloci) stop('Incorrect file format 1228') if (nloci2 != nloci) stop('Incorrect file format 1228')
} }