53 Peptide &new_peptide,
unsigned int position)
56 Aa &aa = new_peptide.
getAa(position);
69 std::int8_t sequence_database_id,
75 unsigned int missed_cleavage_number,
82 bool modify_this_peptide =
true;
85 modify_this_peptide =
false;
89 modify_this_peptide =
true;
92 (protein_sp.get()->size() ==
93 (start + peptide_sp_original.get()->size())))
96 modify_this_peptide =
true;
100 modify_this_peptide =
true;
104 if(modify_this_peptide)
106 std::vector<unsigned int> position_list;
122 missed_cleavage_number,
126 unsigned int nb_pos = position_list.size();
130 unsigned int comb_size = 1;
137 Peptide new_peptide(*(peptide_sp_original.get()));
138 for(
unsigned int i = 0; i < comb_size; i++)
151 missed_cleavage_number,
155 position_list.begin() + comb_size,
156 position_list.end()));
163 Peptide new_peptide(*(peptide_sp_original.get()));
164 for(
unsigned int i = 0; i < nb_pos; i++)
178 missed_cleavage_number,
192 missed_cleavage_number,
void addAaModification(AaModificationP aaModification)
void removeAaModification(AaModificationP aaModification)
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
Modify a peptide shared pointer with a variable modification on one AA.
unsigned int m_maxNumberMod
PeptideModificatorInterface * m_sink
unsigned int m_modificationCount
static bool next_combination(const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last)
unsigned int m_minNumberMod
virtual ~PeptideVariableModificationReplacement()
PeptideVariableModificationReplacement(AaModificationP mod_before, AaModificationP mod_after)
void replaceModificationsAtPosition(Peptide &new_peptide, unsigned int position)
AaModificationP mp_modAfter
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
PeptideSp makePeptideSp() const
Aa & getAa(unsigned int position)
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
potential replacement of a modification by an other