def merge(self, other):
min_mz = min(self[0].start, other[0].start)
max_mz = max(self[0].end, other[0].end)
min_rt = min(self[1].start, other[1].start)
max_rt = max(self[1].end, other[1].end)
return self.__class__(Interval(min_mz, max_mz),
Interval(min_rt, max_rt))
def load_contained(interval_list):
out = []
for item in interval_list:
inner = [Interval(**i) for i in item['members']]
out.append(
Interval(start=item['start'],
end=item['end'],
members=inner))
return out
def extract_intervals(scan_iterator, time_radius=5., mz_lower=2., mz_higher=3.):
intervals = []
for scan, products in scan_iterator:
for product in products:
intervals.append(BoundingBox(
Interval(max(0, product.precursor_information.mz - mz_lower),
product.precursor_information.mz + mz_higher),
Interval(max(0, product.scan_time - time_radius),
product.scan_time + time_radius)))
return intervals
def _locate_pasef_precursor_for(self, scan):
if scan.is_combined():
# raise ValueError("Cannot determine precursor for combined spectra yet")
query_interval = Interval(scan.start_scan, scan.end_scan)
matches = []
for precursor in scan.frame.pasef_precursors:
if query_interval.overlaps(Interval(precursor.start_scan, precursor.end_scan)):
matches.append(precursor)
n_matches = len(matches)
if n_matches == 0:
return None
elif n_matches > 1:
raise ValueError("Multiple precursors found for scan interval!")
else:
return matches[0]
else:
scan_number = scan.start_scan
for precursor in scan.frame.pasef_precursors:
if precursor.start_scan <= scan_number < precursor.end_scan:
return precursor
return None
def to_deconvoluted_peak_set(self, time_bound=None):
if self.deconvoluted_features is None:
raise ValueError(
"Must first deconvolute IMS features before converting to a time-binned peak set!"
)
if time_bound is not None:
cft = IntervalTreeNode.build([
Interval(f.start_time, f.end_time, [f])
for f in self.deconvoluted_features
])
features = chain.from_iterable(cft.overlaps(*time_bound))
else:
features = self.deconvoluted_features
return features_to_peak_set(features)
def combine_intervals(a, b):
min_mz = min(a[0].start, b[0].start)
max_mz = max(a[0].end, b[0].end)
min_rt = min(a[1].start, b[1].start)
max_rt = max(a[1].end, b[1].end)
return (Interval(min_mz, max_mz), Interval(min_rt, max_rt))