R/PeakML.Methods.mzML.startTimeStamp.R

In andzajan/mzmatch.R: mzmatch and PeakML integration for XCMS.

PeakML.Methods.mzML.startTimeStamp <- function(filename){
	
	# Binary file like cdf format, can't be parsed by XML.
	tryCatch(mzMLtree <- xmlParse(filename), 
		error= function(e) {cat ("Measurement date and time information can be extracted only from mzML data files. \n")
		mzMLtree <- NULL}
	)

	if (!is.null(mzMLtree))
	{
		#x reffers there to the default namespace of the document				
		startTimeStamp <- unlist(getNodeSet(xmlRoot(mzMLtree), "//x:run/@startTimeStamp", "x"))
		startTimeStamp <- sub ("T"," ",startTimeStamp)
		rm (mzMLtree)
		gc ()
	} else
	{
		startTimeStamp <- NA
	}
	if (length(startTimeStamp)==0)
	{
		# mzXML is XML file (so will be parsed by xmlParse), but does not contain time stamp.
		cat ("Measurement date and time information can be extracted only from mzML data files. \n")
		startTimeStamp <- NA
	}
	startTimeStamp
}