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createChemShiftPerSpec <-function(templateOption = 1, dirIP)
{
## written by Dr. Jie Hao, Imperial College London
if(missing(dirIP))
{
return("Please provide input to 'dirIP'.\n")
}
dirA <- dirIP
dirCS<-paste(dirA,"/chemShiftPerSpec.csv",sep="")
dir1<-paste(dirA,"/batmanOptions.txt",sep="")
dir2<-paste(dirA,"/NMRdata.txt",sep="")
#dirL<-paste(dirA,"/metabolitesList.csv",sep="")
dirR<-paste(dirA,"/multi_data.csv",sep="")
dirRU<-paste(dirA,"/multi_data_user.csv",sep="")
if (templateOption == 1)
{
cat("Copying multiplet list from multi_data.csv to chemShiftPerSpec.csv...\n")
b<-read.csv(dirR,header=T,stringsAsFactors=FALSE,colClasses="character")
} else if (templateOption == 2) {
cat("Copying multiplet list from multi_data_user.csv to chemShiftPerSpec.csv...\n")
b<-read.csv(dirRU,header=T,stringsAsFactors=FALSE,colClasses="character")
} else if (templateOption == 3) {
cat("Copying multiplet list from multi_data.csv and multi_data_user.csv to chemShiftPerSpec.csv...\n")
b1<-read.csv(dirR,header=T,stringsAsFactors=FALSE,colClasses="character")
b2<-read.csv(dirRU,header=T,stringsAsFactors=FALSE,colClasses="character")
b<-rbind(b1,b2)
}
## prepare template file for c++
bn<-nrow(b)
ind <-6:8
for (i in ind)
{
check<-b[,i]=='n'
b[check,i]=-50
}
##D<-order(b[,1])
tempData<-b
## read in batman optitons
con <- file(dir1, open = "r")
oneLine <- readLines(con, n = 30, warn = FALSE)
fL<-substr(oneLine,1,1)
nL<-which(is.na(match(fL,"%")))
myVector <- strsplit(oneLine[nL[2]], ":")
#ranges <- strsplit(myVector[[1]][2],",")
sno <- NULL
sno <-getSpectraRange(myVector)
## sNo <- as.numeric(myVector[[1]][2])
close(con)
sNo <- length(sno)
sa<-read.table(dir2, header=TRUE,sep="\t",comment.char = "")
if ((ncol(sa)-1)<sNo)
return(cat("No. of spectra included smaller than input spectra.\n"))
if (!is.null(colnames(sa))) {
saname<-colnames(sa)
saname<-saname[2:length(saname)]
sTitle<-rbind(1:length(saname),saname)
} else {
sTitle<-rbind(1:(ncol(sa)-1),1:(ncol(sa)-1))
}
chemlist <- NULL
#for (n in 1:length(metaList))
#{
#chemlist<-rbind(chemlist,tempData[which(tempData[,1] == metaList[n,]),1:2])
#}
chemlist<-tempData[,1:2]
#dim(chemlist)<-c(length(chemlist),1)
nlist <- matrix("n", dim(chemlist)[1], 1)
for (n in 1:dim(sTitle)[2])
{
chemlist<-cbind(chemlist, nlist)
}
#return(list(chemlist = chemlist, sTitle = sTitle[2,]))
names(chemlist)<-c("multiplets","pos_in_ppm", sTitle[2,])
write.table(chemlist,file=dirCS,sep = ",",row.names = FALSE,col.names = TRUE)
}
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