libpappsomspp
Library for mass spectrometry
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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")
74 ion_type = PeptideIon::b;
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),
129 case PeptideIon::ystar:
135 case PeptideIon::bstar:
144 case PeptideIon::astar:
178 return QColor(
"red");
181 return QColor(
"red");
183 case PeptideIon::ystar:
184 return QColor(
"red");
187 return QColor(
"orange");
190 return QColor(
"orange");
192 case PeptideIon::bstar:
193 return QColor(
"blue");
196 return QColor(
"#ff00ff");
199 return QColor(
"green");
201 case PeptideIon::astar:
202 return QColor(
"green");
205 return QColor(
"green");
208 return QColor(
"blue");
212 return QColor(
"red");
215 return QColor(
"blue");
218 return QColor(
"blue");
234 case AtomIsotopeSurvey::C:
242 case PeptideIon::ystar:
248 case PeptideIon::bstar:
276 case PeptideIon::astar:
295 case AtomIsotopeSurvey::H:
304 case PeptideIon::ystar:
312 case PeptideIon::bstar:
347 case PeptideIon::astar:
366 case AtomIsotopeSurvey::N:
375 case PeptideIon::ystar:
382 case PeptideIon::bstar:
413 case PeptideIon::astar:
430 case AtomIsotopeSurvey::O:
440 case PeptideIon::ystar:
447 case PeptideIon::bstar:
481 case PeptideIon::astar:
497 QObject::tr(
"PeptideIon name not implemented"));
501 case AtomIsotopeSurvey::S:
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);
virtual unsigned int size() const override
double pappso_double
A type definition for doubles.
virtual const QString getSequence() const override
amino acid sequence without modification
static pappso_double getDeltaMass(PeptideIon ion_type)
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
virtual const QString getName() const override
const QString getPeptideIonName() const
virtual const PeptideFragmentSp & getPeptideFragmentSp() const
const PeptideFragmentSp msp_fragment
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
unsigned int getNumberOfNeutralPhosphoLoss() const
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
class dedicated to raw mass computations of peptide products (fragments)
static const QString getPeptideIonDirectionName(PeptideDirection direction)
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
pappso_double getMass() const override
PeptideIon getPeptideIonType() const
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
const PeptideIon m_ionType
PeptideDirection getPeptideIonDirection() const
static const QColor getPeptideIonColor(PeptideIon ion_type)
PeptideFragmentIonSp makePeptideFragmentIonSp() const
virtual ~PeptideFragmentIon()
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override
get the number of atom C, O, N, H in the molecule
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
PeptideFragmentIon(const PeptideFragmentSp &sp_fragment, PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
virtual int getNumberOfIsotope(Isotope isotope) const override
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
peptide natural isotope model
unsigned int m_neutralPhosphoLossNumber
virtual bool isPalindrome() const override
tells if the peptide sequence is a palindrome