/** Create an mzIdentML file **/
MzIdentMLControllerImpl mzIdentMlController = new MzIdentMLControllerImpl(inputFile, true);
/** Create the Spectra files **/
List<File> fileList = new ArrayList<File>();
fileList.add(filems);
/** Add MS files **/
mzIdentMlController.addMSController(fileList);
/** Read the spectra **/
for(Comparable id: mzIdentMlController.getSpectrumIds()){
Spectrum spectrum = mzIdentMlController.getSpectrumById(id);
if(spectrum != null)
System.out.println("Spectrum id: " + id + " Number of Peaks: " + spectrum.getMassIntensityMap().length);
}
/** Print Peptide sequence for all Peptides for every protein identification **/
Collection<Comparable> proteinIds = mzIdentMlController.getProteinIds();
for(Comparable proteinID: proteinIds){
Collection<Comparable> peptideIds = mzIdentMlController.getPeptideIds(proteinID);
for(Comparable peptideId: peptideIds)
System.out.println(mzIdentMlController.getPeptideSequence(proteinID,peptideId));
}