33 #include "../pappsoexception.h"
48 unsigned int number_of_neutral_phospho_loss)
49 : msp_fragment(sp_fragment), m_ionType(ion_type)
56 QString(
"PeptideIon %1 is not an %2 fragment")
83 : msp_fragment(other.msp_fragment), m_ionType(other.m_ionType)
91 : msp_fragment(std::move(toCopy.msp_fragment)),
92 m_ionType(toCopy.m_ionType),
178 return QColor(
"red");
181 return QColor(
"red");
184 return QColor(
"red");
187 return QColor(
"orange");
190 return QColor(
"orange");
193 return QColor(
"blue");
196 return QColor(
"#ff00ff");
199 return QColor(
"green");
202 return QColor(
"green");
205 return QColor(
"green");
208 return QColor(
"blue");
212 return QColor(
"red");
215 return QColor(
"blue");
218 return QColor(
"blue");
497 QObject::tr(
"PeptideIon name not implemented"));
504 qDebug() <<
"PeptideFragmentIon::getNumberOfAtom(AtomIsotopeSurvey "
505 "atom) NOT IMPLEMENTED";
507 return number + diff;
514 int number =
msp_fragment.get()->getNumberOfIsotope(isotope);
521 return std::make_shared<PeptideFragmentIon>(*
this);
PeptideFragmentIonSp makePeptideFragmentIonSp() const
unsigned int m_neutralPhosphoLossNumber
const QString getPeptideIonName() const
virtual const PeptideFragmentSp & getPeptideFragmentSp() const
PeptideIon getPeptideIonType() const
const PeptideFragmentSp msp_fragment
unsigned int getNumberOfNeutralPhosphoLoss() const
virtual const QString getSequence() const override
amino acid sequence without modification
virtual ~PeptideFragmentIon()
virtual unsigned int size() const override
PeptideFragmentIon(const PeptideFragmentSp &sp_fragment, PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
const PeptideIon m_ionType
static const QColor getPeptideIonColor(PeptideIon ion_type)
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override
get the number of atom C, O, N, H in the molecule
pappso_double getMass() const override
PeptideDirection getPeptideIonDirection() const
virtual bool isPalindrome() const override
tells if the peptide sequence is a palindrome
virtual const QString getName() const override
virtual int getNumberOfIsotope(Isotope isotope) const override
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
static const QString getPeptideIonDirectionName(PeptideDirection direction)
static pappso_double getDeltaMass(PeptideIon ion_type)
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)
@ astar
Nter aldimine ions + NH3 loss.
@ ystar
Cter amino ions + NH3 loss.
@ yo
Cter amino ions + H2O loss.
@ bstar
Nter acylium ions + NH3 loss.
@ bo
Nter acylium ions + H2O loss.
@ ao
Nter aldimine ions + H2O loss.
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
double pappso_double
A type definition for doubles.
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
peptide natural isotope model
class dedicated to raw mass computations of peptide products (fragments)