def __get_psm(self, row):
peptide_string = row[self.report_loader.peptide_column_index]
scan_source_name = row[self.report_loader.scan_source_column_index]
scan_source = self.report_loader.scan_source_manager.match_by_name(scan_source_name)
scan_id = row[self.report_loader.scan_id_column_index]
scan_reference = ScanReference(id=scan_id, source=scan_source)
source_statistics = {}
for source_statistic_name in self.source_statistic_names:
try:
source_statistics[source_statistic_name] = \
row[int(source_statistic_name)]
except KeyError:
pass
peptide = Peptide.from_tpp_peptide_string(peptide_string)
psm = Psm(peptide=peptide,
scan_reference=scan_reference,
source_statistics=source_statistics
)
return psm
def from_tpp(self, peptide_string):
return Peptide.from_tpp_peptide_string(peptide_string)