// FG: this function is used to call this class from outside the library
public void useMzIdentMLToCSV(String mzid, String out, String option, boolean verbose) {
isVerbose = verbose;
MzIdentMLUnmarshaller mzIdentMLUnmarshaller = new MzIdentMLUnmarshaller(new File(mzid));
MzIdentMLToCSV mzidToCsv = new MzIdentMLToCSV();
mzidToCsv.unmarshaller = mzIdentMLUnmarshaller;
mzidToCsv.init(out, option);
}
public static void main(String[] args) {
MzIdentMLToCSV mzidToCsv = new MzIdentMLToCSV();
// TODO - Undecided which if any command line arguments to include - minimally need to know
// whether to export Peptides or PAGs
if (args != null && args.length == 3) {
mzidToCsv.unmarshaller = new MzIdentMLUnmarshaller(new File(args[0]));
mzidToCsv.init(args[1], args[2]);
} else {
mzidToCsv.unmarshaller = new MzIdentMLUnmarshaller(new File(mzidToCsv.xmlFile));
mzidToCsv.init("out.csv", "exportPSMs");
// mzidToCsv.init("out.csv","exportProteinGroups");
// System.out.println("Error - correct usage MzIdentMLToCSV inputFile.mzid outputFile.csv
// [exportProteinGroups|exportPSMs|exportProteinsOnly]");
}
}