52 std::int8_t sequence_database_id,
58 unsigned int missed_cleavage_number,
62 qDebug() <<
"PeptideFixedModificationBuilder::setPeptide begin";
64 std::vector<unsigned int> position_list;
66 peptide_sp_original.get()->getSequence());
68 Peptide peptide(*peptide_sp_original.get());
69 unsigned int size = peptide.
size();
71 for(
unsigned int pos : position_list)
77 else if((
m_isProtCterMod) && (protein_sp.get()->size() == (start + size)))
95 missed_cleavage_number,
97 qDebug() <<
"PeptideFixedModificationBuilder::setPeptide end";
PeptideFixedModificationBuilder(AaModificationP p_mod)
const AaModificationP mp_mod
virtual ~PeptideFixedModificationBuilder()
void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp_original, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
function to give the products of modifications for a digested peptide
PeptideModificatorInterface * m_sink
QString m_aaModificationList
QRegularExpression m_pattern
virtual void getModificationPositionList(std::vector< unsigned int > &position_list, const QString &peptide_str) final
virtual void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
function to give the products of modifications for a digested peptide
PeptideSp makePeptideSp() const
unsigned int size() const override
void addAaModification(AaModificationP aaModification, unsigned int position)
adds a modification to amino acid sequence
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const Peptide > PeptideSp
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object