def __init__(self,
neutral_mass,
intensity,
charge,
signal_to_noise,
index,
full_width_at_half_max,
a_to_a2_ratio=0,
most_abundant_mass=0,
average_mass=0,
score=0,
envelope=None,
mz=0,
fit=None,
chosen_for_msms=False,
area=0):
if index is None:
index = _Index()
if envelope is None:
envelope = ()
self.neutral_mass = neutral_mass
self.intensity = intensity
self.signal_to_noise = signal_to_noise
self.index = index
self.full_width_at_half_max = full_width_at_half_max
self.charge = charge
self.a_to_a2_ratio = a_to_a2_ratio
self.most_abundant_mass = most_abundant_mass
self.average_mass = average_mass
self.score = score
self.envelope = Envelope(envelope)
self.mz = mz or mass_charge_ratio(self.neutral_mass, self.charge)
self.fit = fit
self.chosen_for_msms = chosen_for_msms
self.area = area
def _reindex(self):
"""
Updates the :attr:`index` of each peak in `self` and updates the
sorted order.
Returns
-------
self: DeconvolutedPeakSet
"""
self.peaks = tuple(sorted(self.peaks, key=operator.attrgetter("neutral_mass")))
self._mz_ordered = tuple(sorted(self.peaks, key=operator.attrgetter("mz")))
for i, peak in enumerate(self.peaks):
peak.index = _Index()
peak.index.neutral_mass = i
for i, peak in enumerate(self._mz_ordered):
peak.index.mz = i
return self
def _reindex(self):
"""
Updates the :attr:`index` of each peak in `self` and updates the
sorted order.
Returns
-------
self: DeconvolutedPeakSet
"""
self.peaks = tuple(
sorted(self.peaks, key=operator.attrgetter("neutral_mass")))
self._mz_ordered = tuple(
sorted(self.peaks, key=operator.attrgetter("mz")))
for i, peak in enumerate(self.peaks):
peak.index = _Index()
peak.index.neutral_mass = i
for i, peak in enumerate(self._mz_ordered):
peak.index.mz = i
return self
def reindex(self):
"""
Updates the :attr:`index` of each peak in `self` and updates the
sorted order.
Returns
-------
self: DeconvolutedPeakSet
"""
self.peaks = tuple(
sorted(self.peaks, key=lambda x: (x.neutral_mass, x.drift_time)))
self._mz_ordered = tuple(
sorted(self.peaks, key=lambda x: (x.mz, x.drift_time)))
for i, peak in enumerate(self.peaks):
peak.index = _Index()
peak.index.neutral_mass = i
for i, peak in enumerate(self._mz_ordered):
peak.index.mz = i
return self
def __init__(self, neutral_mass, intensity, charge, signal_to_noise, index, full_width_at_half_max,
a_to_a2_ratio=None, most_abundant_mass=None, average_mass=None, score=None,
envelope=None, mz=None, fit=None, chosen_for_msms=False, area=0):
if index is None:
index = _Index()
self.neutral_mass = neutral_mass
self.intensity = intensity
self.signal_to_noise = signal_to_noise
self.index = index
self.full_width_at_half_max = full_width_at_half_max
self.charge = charge
self.a_to_a2_ratio = a_to_a2_ratio
self.most_abundant_mass = most_abundant_mass
self.average_mass = average_mass
self.score = score
self.envelope = Envelope(envelope)
self.mz = mz or mass_charge_ratio(self.neutral_mass, self.charge)
self.fit = fit
self.chosen_for_msms = chosen_for_msms
self.area = area