Nothing
### --- Test setup ---
if(FALSE) {
## Not really needed, but can be handy when writing tests
library("RUnit")
library("DatABEL")
}
#test.empty <- function(){}
### do not run
#stop("SKIP THIS TEST")
###
### load shared functions
#source("../inst/unitTests/shared_functions.R")
source(paste(path,"/shared_functions.R",sep=""))
quiet <- TRUE
### test functions
test.text2databel <- function()
{
# library("RUnit")
# library("DatABEL")
# source("shared_functions.R")
unlink("test_matrix*")
# create matrix
# data <- make_random_matrix(range_dim1 = c(5,20), range_dim2 = c(5,20))
data <- make_matrix_of_type_with_NA()
NR <- dim(data)[1]
NC <- dim(data)[2]
# create text files
cat("\nDIM data:",dim(data),"\n")
write.table(data,file="test_matrix_dimnames.dat",row.names=TRUE,col.names=TRUE,quote=FALSE)
write.table(data,file="test_matrix_dimnames_TAB.dat",row.names=TRUE,col.names=TRUE,quote=FALSE,sep="\t")
write.table(data,file="test_matrix_colnames.dat",row.names=FALSE,col.names=TRUE,quote=FALSE)
write.table(data,file="test_matrix_rownames.dat",row.names=TRUE,col.names=FALSE,quote=FALSE)
write.table(data,file="test_matrix_NOnames.dat",row.names=FALSE,col.names=FALSE,quote=FALSE)
write(colnames(data),file="test_matrix.colnames")
write(rownames(data),file="test_matrix.rownames")
# generate identical data and check
a <- text2databel(infile="test_matrix_dimnames.dat",outfile="test_matrix_dimnames",R_matrix=TRUE)
x <- databel("test_matrix_dimnames")
tmp <- as(x,"matrix")
if (!quiet) print(data)
if (!quiet) print(tmp)
checkEquals(data,tmp)
data <- tmp
# test standard options
text2databel(infile="test_matrix_dimnames.dat",outfile="test_matrix_dimnames_T",
R_matrix=TRUE,transpose=TRUE)
x <- databel("test_matrix_dimnames_T")
checkIdentical(t(data),as(x,"matrix"))
# test with TAB separator
text2databel(infile="test_matrix_dimnames_TAB.dat",outfile="test_matrix_dimnames_TTAB",
R_matrix=TRUE,transpose=TRUE)
x <- databel("test_matrix_dimnames_TTAB")
checkIdentical(t(data),as(x,"matrix"))
# convert text two filevector format
text2databel(infile="test_matrix_NOnames.dat",outfile="test_matrix_NOnames",
colnames="test_matrix.colnames",rownames="test_matrix.rownames")
x <- databel("test_matrix_NOnames")
checkIdentical(data,as(x,"matrix"))
text2databel(infile="test_matrix_NOnames.dat",outfile="test_matrix_NOnames_T",
colnames="test_matrix.colnames",rownames="test_matrix.rownames",transpose=TRUE)
x <- databel("test_matrix_NOnames_T")
checkIdentical(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_NOnames.dat",outfile="test_matrix_NOnames_NOnames")
x <- databel("test_matrix_NOnames_NOnames")
checkEqualsNumeric(data,as(x,"matrix"))
text2databel(infile="test_matrix_NOnames.dat",outfile="test_matrix_NOnames_NOnames_T",transpose=TRUE)
x <- databel("test_matrix_NOnames_NOnames_T")
checkEqualsNumeric(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_rownames.dat",outfile="test_matrix_rownames",
rownames=1,colnames="test_matrix.colnames")
x <- databel("test_matrix_rownames")
checkIdentical(data,as(x,"matrix"))
text2databel(infile="test_matrix_rownames.dat",outfile="test_matrix_rownames_T",
rownames=1,colnames="test_matrix.colnames",transpose=TRUE)
x <- databel("test_matrix_rownames_T")
checkIdentical(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_rownames.dat",outfile="test_matrix_rownames_NoColNames",
rownames=1)
x <- databel("test_matrix_rownames_NoColNames")
checkEqualsNumeric(data,as(x,"matrix"))
text2databel(infile="test_matrix_rownames.dat",outfile="test_matrix_rownames_NoColNames_T",
rownames=1,transpose=TRUE)
x <- databel("test_matrix_rownames_NoColNames_T")
checkEqualsNumeric(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_colnames.dat",outfile="test_matrix_colnames",
colnames=1,rownames="test_matrix.rownames")
x <- databel("test_matrix_colnames")
checkIdentical(data,as(x,"matrix"))
text2databel(infile="test_matrix_colnames.dat",outfile="test_matrix_colnames_T",
colnames=1,rownames="test_matrix.rownames",transpose=TRUE)
x <- databel("test_matrix_colnames_T")
checkIdentical(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_colnames.dat",outfile="test_matrix_colnames_NoRowNames",
colnames=1)
x <- databel("test_matrix_colnames_NoRowNames")
checkEqualsNumeric(data,as(x,"matrix"))
text2databel(infile="test_matrix_colnames.dat",outfile="test_matrix_colnames_NoRowNames_T",
colnames=1,transpose=TRUE)
x <- databel("test_matrix_colnames_NoRowNames_T")
checkEqualsNumeric(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_dimnames.dat",outfile="test_matrix_dimnames",R_matrix=TRUE)
x <- databel("test_matrix_dimnames")
checkIdentical(data,as(x,"matrix"))
text2databel(infile="test_matrix_dimnames.dat",outfile="test_matrix_dimnames_T",
R_matrix=TRUE,transpose=TRUE)
x <- databel("test_matrix_dimnames_T")
checkIdentical(t(data),as(x,"matrix"))
text2databel(infile="test_matrix_NOnames.dat",outfile="test_matrix_sub",
skipcols=3,skiprows=2)
x <- databel("test_matrix_sub")
checkEqualsNumeric(data[c(3:dim(data)[1]),c(4:dim(data)[2])],as(x,"matrix"))
# stupid extended matrix in non-R format
newmat <- make_matrix_of_type_with_NA(range_dim1 = c(NR+2,NR+2), range_dim2 = c(NC+3,NC+3))
newmat[3:(NR+2),4:(NC+3)] <- data
newmat[2,4:(NC+3)] <- colnames(data)
newmat[3:(NR+2),3] <- rownames(data)
newmat
write.table(newmat,file="test_matrix_strange.dat",col.names=FALSE,row.names=FALSE,quote=FALSE)
text2databel(infile="test_matrix_strange.dat",outfile="test_matrix_strange",
colnames=2,rownames=3)
x <- databel("test_matrix_strange")
checkEquals(data,as(x,"matrix"))
rm(list=ls());gc()
unlink("test_matrix*")
}
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