public static void main(String[] args) throws IOException {
Modification methylH = Modification.parseModification("CH2");
Modification methylD = Modification.parseModification("CH[2]3H-1");
PeakProcessorChain<PeakAnnotation> ppc = new PeakProcessorChain<>();
SpectraPairExtractor mse = new SpectraPairExtractor(methylH, methylD);
FilenameFilter filter = new SuffixFileFilter(".mgf", IOCase.INSENSITIVE);
File specFile = new File(args[0]);
if (specFile.isDirectory()) {
File[] files = specFile.listFiles(filter);
for (File aFile : files) {
System.out.println("Processing File:" + aFile.getName());
mse.process(aFile.getAbsolutePath(), ppc, 6);
}
} else {
System.out.println("Processing File:" + specFile.getName());
mse.process(specFile.getAbsolutePath(), ppc, 10);
}
}
