libpappsomspp
Library for mass spectrometry
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pappso::specglob::PeptideSpectrum Class Reference

#include <peptidespectrum.h>

Inheritance diagram for pappso::specglob::PeptideSpectrum:

Public Member Functions

 PeptideSpectrum (const pappso::PeptideSp peptide_sp)
 
 PeptideSpectrum (const PeptideSpectrum &other)
 
virtual ~PeptideSpectrum ()
 
std::vector< double > getMassList () const
 
pappso::PeptideSp getPeptideSp () const
 

Private Attributes

pappso::PeptideSp msp_peptide
 

Detailed Description

Todo:
write docs

Definition at line 60 of file peptidespectrum.h.

Constructor & Destructor Documentation

◆ PeptideSpectrum() [1/2]

pappso::specglob::PeptideSpectrum::PeptideSpectrum ( const pappso::PeptideSp  peptide_sp)

Default constructor

Definition at line 46 of file peptidespectrum.cpp.

47 : std::vector<PeptideSpectrumDataPoint>()
48{
50 msp_peptide = peptide_sp;
51 std::list<pappso::PeptideIon> ion_list;
52 ion_list.push_back(ion_type);
53
54
55 pappso::PeptideFragmentIonListBase fragmented_ion_list(msp_peptide, ion_list);
56
57 std::list<pappso::PeptideFragmentIonSp> peptide_ion_list =
58 fragmented_ion_list.getPeptideFragmentIonSp(pappso::PeptideIon::b);
59
60 push_back({pappso::MHPLUS, 0});
61 // qDebug() << pappso::PeptideRawFragmentMasses::getDeltaMass(ion_type);
62 for(auto &peptide_ion : peptide_ion_list)
63 {
64 push_back({peptide_ion.get()->getMz(1), 0});
65 }
66 push_back({(msp_peptide.get()->getMz(1) - pappso::MASSH2O +
68 0});
69 for(std::size_t i = 1; i < size(); i++)
70 {
71 at(i).diff_mz = (at(i).mz - at(i - 1).mz);
72 }
73}
static pappso_double getDeltaMass(PeptideIon ion_type)
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:425
@ b
Nter acylium ions.
const pappso_double MHPLUS(1.007276466879)
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)

References pappso::b, pappso::PeptideRawFragmentMasses::getDeltaMass(), pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp(), pappso::MASSH2O(), pappso::MHPLUS(), and msp_peptide.

◆ PeptideSpectrum() [2/2]

pappso::specglob::PeptideSpectrum::PeptideSpectrum ( const PeptideSpectrum other)

Copy constructor

Parameters
otherTODO

Definition at line 75 of file peptidespectrum.cpp.

76 : std::vector<PeptideSpectrumDataPoint>(other)
77{
78 msp_peptide = other.msp_peptide;
79}

References msp_peptide.

◆ ~PeptideSpectrum()

pappso::specglob::PeptideSpectrum::~PeptideSpectrum ( )
virtual

Destructor

Definition at line 81 of file peptidespectrum.cpp.

82{
83}

Member Function Documentation

◆ getMassList()

std::vector< double > pappso::specglob::PeptideSpectrum::getMassList ( ) const

Definition at line 86 of file peptidespectrum.cpp.

87{
88 std::vector<double> mass_list;
89 for(const PeptideSpectrumDataPoint &n : *this)
90 {
91 mass_list.push_back(n.mz);
92 };
93
94 return mass_list;
95}

◆ getPeptideSp()

pappso::PeptideSp pappso::specglob::PeptideSpectrum::getPeptideSp ( ) const

Definition at line 98 of file peptidespectrum.cpp.

99{
100 return msp_peptide;
101}

References msp_peptide.

Referenced by pappso::specglob::SpectralAlignment::fillMatricesWithScores().

Member Data Documentation

◆ msp_peptide

pappso::PeptideSp pappso::specglob::PeptideSpectrum::msp_peptide
private

Definition at line 86 of file peptidespectrum.h.

Referenced by PeptideSpectrum(), PeptideSpectrum(), and getPeptideSp().


The documentation for this class was generated from the following files: