2.2 Read MzML File - PRIDE-Utilities/ms-data-core-api GitHub Wiki

MzMLControllerImpl mzMLController = new MzMLControllerImpl(inputFile);

/** Retrieve the file metadata including contacts File Description, etc**/
ExperimentMetaData metada = mzMLController.getExperimentMetaData();

/** Retrieve the Sample information **/
List<Sample> samples = mzMLController.getSamples();

/** Retrieve the List of Softwares used to generate the file**/
List<Software> softwares = mzMLController.getSoftwares();

/** Retrieve Dta Processing steps **/
List<DataProcessing> dataProcessings = mzMLController.getDataProcessings();
        
/** Retrieve all the MS sptra **/ 
List<Comparable> ids = new ArrayList<Comparable>(mzMLController.getSpectrumIds());

for(Comparable id: ids){
    Spectrum spectrum = mzMLController.getSpectrumById(id);
    /** Print number of Peaks **/
    int numberOfPeaks = spectrum.getMassIntensityMap().length;
    System.out.println(numberOfPeaks);
}       

/** Retrieve all the Chromatograms **/    

ids = new ArrayList<Comparable>(mzMLController.getChromatogramIds());

for(Comparable id: ids){
    Chromatogram chromatogram = mzMLController.getChromatogramById("id");
    /** Print number of Peaks **/
    int numberOfPeaks = chromatogram.getTimeArray().getDoubleArray().length;
    System.out.println(numberOfPeaks);
}       
    
``