37 #include "../amino_acid/aa.h"
40 #include "../exportinmportconfig.h"
96 typedef std::shared_ptr<const Peptide>
PeptideSp;
106 Peptide(
const QString &pepstr);
130 void addAaModification(
AaModificationP aaModification,
unsigned int position);
132 std::vector<Aa>::iterator
135 return m_aaVec.begin();
138 std::vector<Aa>::iterator
141 return m_aaVec.end();
144 std::vector<Aa>::const_iterator
147 return m_aaVec.begin();
150 std::vector<Aa>::const_iterator
153 return m_aaVec.end();
156 std::vector<Aa>::const_reverse_iterator
159 return m_aaVec.rbegin();
162 std::vector<Aa>::const_reverse_iterator
165 return m_aaVec.rend();
168 Aa &getAa(
unsigned int position);
169 const Aa &getConstAa(
unsigned int position)
const;
180 virtual int getNumberOfIsotope(
Isotope isotope)
const override;
183 const QString getSequence()
const override;
187 return m_aaVec.size();
202 const std::vector<char> &aa_list)
const;
219 std::vector<unsigned int>
227 std::vector<unsigned int>
229 const std::vector<char> &aa_list)
const;
234 std::vector<unsigned int> getAaPositionList(
char aa)
const;
235 std::vector<unsigned int> getAaPositionList(std::list<char> list_aa)
const;
238 const QString toString()
const;
240 const QString toAbsoluteString()
const;
243 const QString getLiAbsoluteString()
const;
247 void removeInternalNterModification();
248 void removeInternalCterModification();
258 virtual bool isPalindrome()
const override;
259 void replaceLeucineIsoleucine();
260 void removeNterAminoAcid();
261 void removeCterAminoAcid();
std::vector< Aa >::iterator end()
std::vector< Aa >::const_iterator end() const
std::vector< Aa >::const_reverse_iterator rend() const
std::vector< Aa >::const_reverse_iterator rbegin() const
std::vector< Aa >::const_iterator begin() const
unsigned int size() const override
std::vector< Aa >::iterator begin()
pappso_double getMass() const override
friend bool operator==(const Peptide &l, const Peptide &r)
std::vector< Aa > m_aaVec
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
bool operator<(Aa const &l, Aa const &r)
std::shared_ptr< const Peptide > PeptideSp
double pappso_double
A type definition for doubles.
bool peptideIonTypeIsComplement(PeptideIon ion_type_ref, PeptideIon ion_type)
tells if an ion type is the complement ion of the other
bool peptideIonIsNter(PeptideIon ion_type)
tells if an ion is Nter
std::shared_ptr< Peptide > NoConstPeptideSp