def protein_relation(self):
if self._protein_relation is None:
peptide = self.peptide
self._protein_relation = PeptideProteinRelation(
peptide.start_position, peptide.end_position,
peptide.protein_id, peptide.hypothesis_id)
return self._protein_relation
def convert(self):
inst = FragmentCachingGlycopeptide(self.glycopeptide_sequence)
inst.id = self.id
peptide = self.peptide
inst.protein_relation = PeptideProteinRelation(peptide.start_position,
peptide.end_position,
peptide.protein_id,
peptide.hypothesis_id)
return inst
def convert(self, peptide_relation_cache=None):
if peptide_relation_cache is None:
session = object_session(self)
peptide_relation_cache = session.info.get("peptide_relation_cache")
if peptide_relation_cache is None:
peptide_relation_cache = session.info['peptide_relation_cache'] = LRUDict(maxsize=1024)
inst = FragmentCachingGlycopeptide(self.glycopeptide_sequence)
inst.id = self.id
try:
inst.protein_relation = peptide_relation_cache[self.peptide_id]
except KeyError:
session = object_session(self)
peptide_props = session.query(
Peptide.start_position, Peptide.end_position,
Peptide.protein_id, Peptide.hypothesis_id).filter(Peptide.id == self.peptide_id).first()
peptide_relation_cache[self.peptide_id] = inst.protein_relation = PeptideProteinRelation(*peptide_props)
return inst
def _build_protein_relation(self, glycopeptide_id_key):
return PeptideProteinRelation(glycopeptide_id_key.start_position,
glycopeptide_id_key.end_position,
glycopeptide_id_key.protein_id,
glycopeptide_id_key.hypothesis_id)