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[proforma] Use cache on modification resolvers #147

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[proforma] Use cache on modification resolvers #147

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027eff5
Use cache on modification resolvers
RalfG Apr 16, 2024
97dd010
Fix dummy decorator
RalfG Apr 16, 2024
da1febf
Use built-in pyteomics memoize instead of functools lru_cache
RalfG Apr 16, 2024
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6 changes: 6 additions & 0 deletions pyteomics/proforma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
from .mass import Composition, std_aa_mass, Unimod, nist_mass, calculate_mass, std_ion_comp, mass_charge_ratio
from .auxiliary import PyteomicsError, BasicComposition
from .auxiliary.utils import add_metaclass
from .auxiliary.utils import memoize

try:
import numpy as np
Expand Down Expand Up @@ -343,6 +344,7 @@ def load_database(self):
return obo_cache.resolve("http://www.unimod.org/obo/unimod.obo")
return Unimod()

@memoize(maxsize=10000)
def resolve(self, name=None, id=None, **kwargs):
strict = kwargs.get("strict", self.strict)
exhaustive = kwargs.get("exhaustive", True)
Expand Down Expand Up @@ -398,6 +400,7 @@ def __init__(self, **kwargs):
def load_database(self):
return load_psimod()

@memoize(maxsize=10000)
def resolve(self, name=None, id=None, **kwargs):
if name is not None:
defn = self.database[name]
Expand Down Expand Up @@ -443,6 +446,7 @@ def __init__(self, **kwargs):
def load_database(self):
return load_xlmod()

@memoize(maxsize=10000)
def resolve(self, name=None, id=None, **kwargs):
if name is not None:
defn = self.database[name]
Expand Down Expand Up @@ -562,6 +566,7 @@ def get_mass_from_term(self, term, raw_mass):
"Only a rough approximation is available.") % (term, ))
return rough_mass

@memoize(maxsize=10000)
def resolve(self, name=None, id=None, **kwargs):
if name is not None:
term = self.database[name]
Expand Down Expand Up @@ -613,6 +618,7 @@ def parse_identifier(self, identifier):
"""
return identifier, None

@memoize(maxsize=10000)
def resolve(self, name=None, id=None, **kwargs):
defn = None
for resolver in self.resolvers:
Expand Down