def _scan_id(self, scan):
scan_number = scan.scan_number
return _make_id(scan_number + 1)
def _pack_index(self):
index = OrderedDict()
for sn in range(self._source.RunHeaderEx.FirstSpectrum - 1,
self._source.RunHeaderEx.LastSpectrum):
index[_make_id(sn)] = sn
return index
def _pack_index(self):
index = OrderedDict()
for sn in range(1, self._source.NumSpectra + 1):
index[_make_id(sn)] = sn
return index
def _precursor_information(self, scan):
if self._ms_level(scan) == 1:
return None
scan_number = scan.scan_number
pinfo_struct = self._source.GetPrecursorInfoFromScanNum(scan_number)
precursor_scan_number = None
labels, _, _ = self._source.GetAllMSOrderData(scan_number)
if pinfo_struct:
# this struct field is unreliable and may fall outside the
# isolation window
mz = pinfo_struct.monoIsoMass
charge = pinfo_struct.chargeState
intensity = float(labels.intensity[0])
# this struct field is unreliable, and simple to infer
# precursor_scan_number = pinfo_struct.scanNumber + 1
else:
mz = labels.mass[0]
intensity = float(labels.intensity[0])
charge = labels.charge[0]
if not charge:
charge = ChargeNotProvided
trailer = self._trailer_values(scan)
_mz = trailer.get('Monoisotopic M/Z', 0.0)
# prefer the trailer m/z if available?
if _mz > 0:
mz = _mz
# imitate proteowizard's firmware bug correction
isolation_window = self._isolation_window(scan)
if (isolation_window.upper + isolation_window.lower) / 2 <= 2.0:
if (isolation_window.target - 3.0 > mz) or (isolation_window.target + 2.5 < mz):
mz = isolation_window.target
elif mz not in isolation_window:
mz = isolation_window.target
_charge = trailer.get('Charge State', 0)
if _charge != 0:
charge = _charge
# Guess which previous scan was the precursor by iterating
# backwards until a scan is found with a lower MS level
if precursor_scan_number is None:
last_index = self._scan_index(scan) - 1
current_level = self._ms_level(scan)
i = 0
while last_index >= 0 and i < 100:
prev_scan = self.get_scan_by_index(last_index)
if prev_scan.ms_level >= current_level:
last_index -= 1
else:
precursor_scan_number = prev_scan._data.scan_number
break
i += 1
if intensity is None:
intensity = 0.0
if mz is None:
mz = 0.0
if charge is None or charge == 0:
charge = ChargeNotProvided
pinfo = PrecursorInformation(
mz, intensity, charge, _make_id(precursor_scan_number),
source=self,
product_scan_id=_make_id(scan.scan_number))
return pinfo
def _scan_id(self, scan):
return _make_id(scan.scan_number)
def _pack_index(self):
index = OrderedDict()
for sn in range(self._source.RunHeaderEx.FirstSpectrum - 1,
self._source.RunHeaderEx.LastSpectrum):
index[_make_id(sn)] = sn
return index
def _scan_id(self, scan):
scan_number = scan.scan_number
return _make_id(scan_number + 1)
