Merge branch 'fix-handleData' into import-genepop

R/fgetl-fopen.R

@@ -0,0 +1,27 @@
+#' @title Read line from file, removing newline characters
+#' @description Equivalent function to its homonymous Matlab equivalent.
+#' @param file character vector to be read, usually an output of `fopen()`
+#' @return If the file is nonempty, then fgetl returns tline as a character vector. If the file is empty and contains only the end-of-file marker, then fgetl returns tline as a numeric value -1.
+#' @author Waldir Leoncio
+#' @seealso fopen
+#' @export
+fgetl <- function(file) {
+	# ==========================================================================
+	# Validation
+	# ==========================================================================
+	if (length(file) <= 1) return(-1)
+	# ==========================================================================
+	# Returning file minus the first line
+	# ==========================================================================
+	out <- file[-1]
+	return(out)
+}
+
+#' @title Open file
+#' @description Open a text file
+#' @param filename Path and name of file to be open
+#' @return The same as `readLines(filename)`
+#' @author Waldir Leoncio
+#' @seealso fgetl
+#' @export
+fopen <- function(filename) readLines(filename)

R/greedyMix.R

@@ -149,13 +149,26 @@ greedyMix <- function(
 
 			kunnossa <- testaaGenePopData(filename_pathname)
 			if (kunnossa == 0) stop("testaaGenePopData returned 0")
-			# [data,popnames]=lueGenePopData([pathname filename]); # TODO: trans
+			data_popnames <- lueGenePopData(filename_pathname)
+			data          <- data_popnames$data
+			popnames      <- data_popnames$popnames
 
 # 			h0 = findobj('Tag','filename1_text');
 # 			set(h0,'String',filename); clear h0;
 
-# 			[data, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = handleData(data); # TODO:trans
-# 			[Z,dist] = newGetDistances(data,rowsFromInd); # TODO: trans
+			browser()#TEMP
+			list_dranap <- handleData(data) # FIXME: debug
+			data        <- list_dranap$newData
+			rowsFromInd <- list_dranap$rowsFromInd
+			alleleCodes <- list_dranap$alleleCodes
+			noalle      <- list_dranap$noalle
+			adjprior    <- list_dranap$adjprior
+			priorTerm   <- list_dranap$prioterm
+
+			list_Zd <- newGetDistances(data,rowsFromInd) # FIXME: debug
+			Z       <- lizt_Zd$Z
+			dist    <- lizt_Zd$dist
+
 			if (is.null(savePreProcessed)) {
 				save_preproc <- questdlg(
 					quest = 'Do you wish to save pre-processed data?',

R/handleData.R

@@ -20,12 +20,11 @@ handleData <- function(raw_data) {
 	# koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi.
 	# T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j
 	# koodit saavat arvoja v?lill?1,...,noalle(j).
-
 	data <- raw_data
 	nloci <- size(raw_data, 2) - 1
 
 	dataApu <- data[, 1:nloci]
-	nollat <- find(dataApu==0)
+	nollat <- find(dataApu == 0)
 	if (!isempty(nollat)) {
 	   isoinAlleeli <- max(max(dataApu))
 	   dataApu[nollat] <- isoinAlleeli + 1
@@ -39,9 +38,12 @@ handleData <- function(raw_data) {
 	alleelitLokuksessa <- cell(nloci, 1)
 	for (i in 1:nloci) {
 		alleelitLokuksessaI <- unique(data[, i])
-		alleelitLokuksessa[i, 1] <- alleelitLokuksessaI[
-			find(alleelitLokuksessaI >= 0)
-		]
+		alleelitLokuksessaI_pos <- find(alleelitLokuksessaI >= 0)
+		alleelitLokuksessa[i, 1] <- ifelse(
+			test = length(alleelitLokuksessaI_pos) > 0,
+			yes  = alleelitLokuksessaI[alleelitLokuksessaI_pos],
+			no   = 0
+		)
 		noalle[i] <- length(alleelitLokuksessa[i, 1])
 	}
 	alleleCodes <- zeros(max(noalle), nloci)
@@ -65,10 +67,10 @@ handleData <- function(raw_data) {
 	emptyRow <- repmat(a, c(1, ncols))
 	lessThanMax <- find(rowsFromInd < maxRowsFromInd)
 	missingRows <- maxRowsFromInd * nind - nrows
-	data <- as.matrix(c(data, zeros(missingRows, ncols)))
+	data <- rbind(data, zeros(missingRows, ncols))
 	pointer <- 1
 	for (ind in t(lessThanMax)) { #K?y l?pi ne yksil?t, joilta puuttuu rivej?
-		miss = maxRowsFromInd-rowsFromInd(ind); # T?lt?yksil?lt?puuttuvien lkm.
+		miss <- maxRowsFromInd - rowsFromInd(ind) # T?lt?yksil?lt?puuttuvien lkm.
 	}
 	data <- sortrows(data, ncols) # Sorttaa yksil?iden mukaisesti
 	newData <- data
@@ -84,12 +86,12 @@ handleData <- function(raw_data) {
 		priorTerm <- priorTerm + noalle[j] * lgamma(1 / noalle[j])
 	}
 	out <- list(
-		newData = newData,
+		newData     = newData,
 		rowsFromInd = rowsFromInd,
 		alleleCodes = alleleCodes,
-		noalle = noalle,
-		adjprior = adjprior,
-		priorTerm = priorTerm
+		noalle      = noalle,
+		adjprior    = adjprior,
+		priorTerm   = priorTerm
 	)
 	return(out)
 }

man/fgetl.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/fgetl.R
+\name{fgetl}
+\alias{fgetl}
+\title{Read line from file, removing newline characters}
+\usage{
+fgetl(file)
+}
+\arguments{
+\item{file}{character vector to be read, usually an output of `fopen()`}
+}
+\value{
+If the file is nonempty, then fgetl returns tline as a character vector. If the file is empty and contains only the end-of-file marker, then fgetl returns tline as a numeric value -1.
+}
+\description{
+Equivalent function to its homonymous Matlab equivalent.
+}
+\seealso{
+fopen
+}
+\author{
+Waldir Leoncio
+}

man/fopen.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/fgetl.R
+\name{fopen}
+\alias{fopen}
+\title{Open file}
+\usage{
+fopen(filename)
+}
+\arguments{
+\item{filename}{Path and name of file to be open}
+}
+\value{
+The same as `readLines(filename)`
+}
+\description{
+Open a text file
+}
+\seealso{
+fgetl
+}
+\author{
+Waldir Leoncio
+}