Function testDatastructuresTutorial

src/pyOpenMS/tests/unittests/test_tutorial.py:231–358

()

@report
def testDatastructuresTutorial():

    ###################################
    # Spectrum
    # ********
    ###################################

    spectrum = MSSpectrum()
    mz = range(1500, 500, -100)
    i = [0 for mass in mz]
    spectrum.set_peaks([mz, i])

    # Sort the peaks according to ascending mass-to-charge ratio
    spectrum.sortByPosition()

    # Iterate over spectrum of those peaks
    for p in spectrum:
        print(p.getMZ(), p.getIntensity())

    # More efficient peak access
    for mz, i in zip(*spectrum.get_peaks()):
        print(mz, i)

    # Access a peak by index
    print(spectrum[1].getMZ(), spectrum[1].getIntensity())


    ###################################
    ###################################

    spectrum = MSSpectrum()
    spectrum.setDriftTime(25) # 25 ms
    spectrum.setRT(205.2) # 205.2 s
    spectrum.setMSLevel(3) # MS3
    p = Precursor()
    p.setIsolationWindowLowerOffset(1.5)
    p.setIsolationWindowUpperOffset(1.5) 
    p.setMZ(600) # isolation at 600 +/- 1.5 Th
    p.setActivationEnergy(40) # 40 eV
    p.setCharge(4) # 4+ ion
    spectrum.setPrecursors( [p] )

    fda = FloatDataArray()
    fda.setName("Signal to Noise Array")
    fda.push_back(15)
    sda = StringDataArray()
    sda.setName("Peak annotation")
    sda.push_back("y15++")
    spectrum.setFloatDataArrays( [fda] )
    spectrum.setStringDataArrays( [sda] )
    spectrum.set_peaks( ([401.5], [900]) )

    # Store as mzML
    exp = MSExperiment()
    exp.addSpectrum(spectrum)
    spectrum = MSSpectrum()
    spectrum.set_peaks( ([1, 2], [1, 2]) )
    exp.addSpectrum(spectrum)