Nothing
mzmatch.XML.data.base.parser <- function (dbfile,elements=c("name","inchi","class","synonyms"))
{
project <- .jnew("peakml/util/rjava/Project", rep("A",3), rep("A",3), rep("A",3))
DBcontent <- xmlInternalTreeParse (dbfile)
ids <- getNodeSet(DBcontent, "/compounds/compound/id")
ids <- sapply (ids,xmlValue)
formulas <- getNodeSet(DBcontent, "/compounds/compound/formula")
formulas <- sapply (formulas,xmlValue)
OUTPUT <- data.frame (id=ids,formula=formulas)
masses <- rep(NA,length(formulas))
for (formula in 1:length(formulas))
{
masses[formula] <- .jcall (project,returnSig="D",method="formulaToMass",as.character(formulas[formula]))
}
OUTPUT$mass <- masses
OUT <- matrix(ncol=length(elements),nrow=length(ids))
for (element in 1:length(elements))
{
value <- getNodeSet(DBcontent, paste("/compounds/compound/",elements[element],sep=""))
value <- sapply (value,xmlValue)
if (length(value)!=0)
{
OUT[,element] <- value
}
}
colnames(OUT) <- elements
OUTPUT <- cbind (OUTPUT,OUT)
}
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