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;
68 Peptide peptide(*peptide_sp_original.get());
69 unsigned int size = peptide.
size();
71 for(
unsigned int pos : position_list)
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
const QString getSequence() const override
print amino acid sequence without modifications
void addAaModification(AaModificationP aaModification, unsigned int position)
adds a modification to amino acid sequence
unsigned int size() const
protein amino acid sequence size
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