###################################################
### chunk number 1: setup
###################################################
#line 18 "NetCDF-lab.Rnw"
options(width = 40)


###################################################
### chunk number 2: scanIntro
###################################################
#line 61 "NetCDF-lab.Rnw"
library(AdvancedR2011Data)
pth <- system.file("extdata", "snpData.csv", package = "AdvancedR2011Data")
dat <- scan(pth, what = character(0), sep =",",
                               skip = 600, nlines = 1, quiet = TRUE)


###################################################
### chunk number 3: rowAccess
###################################################
#line 95 "NetCDF-lab.Rnw"
library(ncdf)
st <- system.time
ncFile <- system.file("extdata", "snpData.nc", package = "AdvancedR2011Data")
nc <- open.ncdf(ncFile, write = FALSE)
st(dat <- get.var.ncdf(nc, varid = "snpData", start= c(601,1), count = c(1, 113735)))
csvFile <- system.file("extdata", "snpData.csv", package = "AdvancedR2011Data")
st(origDat <- scan(csvFile, what = integer(0), sep =",", skip = 600, nlines = 1,
            quiet = TRUE))
identical(as.vector(dat), origDat)
invisible(close.ncdf(nc))


###################################################
### chunk number 4: colAccess eval=FALSE
###################################################
## #line 160 "NetCDF-lab.Rnw"
## library(StudentGWAS)
## getNcdfVarSummary <- StudentGWAS:::getNcdfVarSummary
## getGWAScols <- function(nc, first, last = first)
## {
##     if (!is.numeric(first) || length(first) != 1 || is.na(first))
##         stop("'first' must be a single integer")
##     if (!is.numeric(last) || length(last) != 1 || is.na(last))
##         stop("'last' must be a single integer")
##     ncInfo <- getNcdfVarSummary(nc, "snpData")
##     nrows <- ncInfo$dim1
##     ncols <- ncInfo$dim2
##     if (first < 1 || last < first || last > ncols)
##         stop("we need to have 1 <= 'first' <= 'last' <= nb col in NetCDF file")
##     dat <- get.var.ncdf(nc, varid = "snpData", start= c(1,first),
##             count = c(nrows, last - first + 1))
##     structure(as.raw(dat), dim = dim(dat))
## }
## 
## pth <- system.file("extdata", "small_snpData.nc", package = "StudentGWAS")
## nc <- open.ncdf(pth)
## dat <- getGWAScols(nc, 1, 4)
## invisible(close.ncdf(nc))


###################################################
### chunk number 5: unitTest eval=FALSE
###################################################
## #line 216 "NetCDF-lab.Rnw"
## library(ncdf)
## testGWAScols <- function() 
## {   
##     pth <- system.file("extdata", "small_snpData.nc", package = "StudentGWAS")
##     nc <-  open.ncdf(pth, write = FALSE)
##     ncols <- getNcdfVarSummary(nc, "snpData")$dim2
##     current <- getGWAScols(nc, 1, ncols)
##     load(system.file("extdata", "small_snpData.rda", package = "StudentGWAS"))
##     identical(current, small_snpData)  
## }
## testGWAScols()