libpappsomspp
Library for mass spectrometry
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Classes | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
pappso::masschroq::PeptideMeasurementsBase Class Referenceabstract

#include <peptidemeasurementsbase.h>

Inheritance diagram for pappso::masschroq::PeptideMeasurementsBase:
pappso::masschroq::MbrPeptideMeasurements pappso::masschroq::PeptideMeasurements

Classes

struct  Measurement
 

Public Member Functions

 PeptideMeasurementsBase ()
 
 PeptideMeasurementsBase (const PeptideMeasurementsBase &other)
 
virtual ~PeptideMeasurementsBase ()
 
virtual const std::vector< Measurement > & getMeasurementList () const
 
virtual void pushBackXicCoordList (std::vector< pappso::XicCoordSPtr > &xic_coord_list) const final
 
virtual void detectQuantifyPeaks (const QuantificationMethodSp &quantification_method)=0
 
virtual void flushXics () final
 
virtual void clear () final
 clear the measurement vector
 

Protected Member Functions

virtual void prepareMeasurementsForPeptide (Peptide &the_peptide, const QuantificationMethodSp &quantification_method, const pappso::XicCoordSPtr &best_xic_coord, std::uint8_t charge, double best_rt) final
 
virtual void generateMeasurementsForIsotopeList (PeptideBase &peptide_base, const PeptideLabel *label_p, const QuantificationMethodSp &quantification_method, std::uint8_t charge, double isotope_minimum_ratio, const pappso::XicCoordSPtr &best_xic_coord, double best_rt) final
 

Protected Attributes

std::vector< Measurement > m_measurementList
 

Detailed Description

Todo
write docs

Definition at line 48 of file peptidemeasurementsbase.h.

Constructor & Destructor Documentation

◆ PeptideMeasurementsBase() [1/2]

pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase ( )

Default constructor

Definition at line 34 of file peptidemeasurementsbase.cpp.

35{
36}

Referenced by pappso::masschroq::MbrPeptideMeasurements::MbrPeptideMeasurements(), and pappso::masschroq::PeptideMeasurements::PeptideMeasurements().

◆ PeptideMeasurementsBase() [2/2]

pappso::masschroq::PeptideMeasurementsBase::PeptideMeasurementsBase ( const PeptideMeasurementsBase & other)

Definition at line 42 of file peptidemeasurementsbase.cpp.

44{
45 m_measurementList = other.m_measurementList;
46}

References m_measurementList.

◆ ~PeptideMeasurementsBase()

pappso::masschroq::PeptideMeasurementsBase::~PeptideMeasurementsBase ( )
virtual

Destructor

Definition at line 38 of file peptidemeasurementsbase.cpp.

39{
40}

Member Function Documentation

◆ clear()

void pappso::masschroq::PeptideMeasurementsBase::clear ( )
finalvirtual

clear the measurement vector

Definition at line 199 of file peptidemeasurementsbase.cpp.

200{
201 m_measurementList.clear();
202}

References m_measurementList.

Referenced by detectQuantifyPeaks().

◆ detectQuantifyPeaks()

virtual void pappso::masschroq::PeptideMeasurementsBase::detectQuantifyPeaks ( const QuantificationMethodSp & quantification_method)
pure virtual

Implemented in pappso::masschroq::MbrPeptideMeasurements, and pappso::masschroq::PeptideMeasurements.

References clear(), generateMeasurementsForIsotopeList(), and prepareMeasurementsForPeptide().

◆ flushXics()

void pappso::masschroq::PeptideMeasurementsBase::flushXics ( )
finalvirtual

Definition at line 189 of file peptidemeasurementsbase.cpp.

190{
191
192 for(auto &measure_one : m_measurementList)
193 {
194 measure_one.msp_xicCoord.get()->xicSptr = nullptr;
195 }
196}

References m_measurementList.

◆ generateMeasurementsForIsotopeList()

void pappso::masschroq::PeptideMeasurementsBase::generateMeasurementsForIsotopeList ( PeptideBase & peptide_base,
const PeptideLabel * label_p,
const QuantificationMethodSp & quantification_method,
std::uint8_t charge,
double isotope_minimum_ratio,
const pappso::XicCoordSPtr & best_xic_coord,
double best_rt )
finalprotectedvirtual

Definition at line 56 of file peptidemeasurementsbase.cpp.

64{
65
66 qDebug();
67 const std::vector<pappso::PeptideNaturalIsotopeAverageSp> &natural_isotope_average_list =
68 peptide_base.getPeptideNaturalIsotopeAverageSpList(
69 quantification_method.get()->getXicExtractionMeanPrecisionPtr(),
70 charge,
71 isotope_minimum_ratio);
72
73 for(pappso::PeptideNaturalIsotopeAverageSp isotope_average_sp : natural_isotope_average_list)
74 {
75 pappso::XicCoordSPtr xic_coord = best_xic_coord->initializeAndClone();
76 xic_coord.get()->rtTarget = best_rt;
77 xic_coord.get()->mzRange =
78 quantification_method.get()->getXicExtractionMzRange(isotope_average_sp.get()->getMz());
79
80
81 m_measurementList.push_back(
82 {charge, xic_coord, PeakQualityCategory::nomatch, label_p, nullptr, isotope_average_sp});
83 }
84
85 qDebug() << m_measurementList.size();
86}
pappso::PeptideNaturalIsotopeAverageSp
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp
Definition peptidenaturalisotopeaverage.h:40
pappso::XicCoordSPtr
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:44

References pappso::masschroq::PeptideBase::getPeptideNaturalIsotopeAverageSpList(), pappso::masschroq::QuantificationMethod::getXicExtractionMeanPrecisionPtr(), pappso::masschroq::QuantificationMethod::getXicExtractionMzRange(), m_measurementList, and pappso::masschroq::nomatch.

Referenced by detectQuantifyPeaks(), and prepareMeasurementsForPeptide().

◆ getMeasurementList()

const std::vector< pappso::masschroq::PeptideMeasurementsBase::Measurement > & pappso::masschroq::PeptideMeasurementsBase::getMeasurementList ( ) const
virtual

Definition at line 50 of file peptidemeasurementsbase.cpp.

51{
52 return m_measurementList;
53}

References m_measurementList.

Referenced by pappso::masschroq::CborOutputStream::writeMbrPeptideMeasurements(), and pappso::masschroq::CborOutputStream::writePeptideMeasurements().

◆ prepareMeasurementsForPeptide()

void pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide ( Peptide & the_peptide,
const QuantificationMethodSp & quantification_method,
const pappso::XicCoordSPtr & best_xic_coord,
std::uint8_t charge,
double best_rt )
finalprotectedvirtual

Definition at line 89 of file peptidemeasurementsbase.cpp.

95{
96
97 double isotope_minimum_ratio = quantification_method.get()->getIsotopeMinimumRatio();
98
99
100 auto label_map = the_peptide.getPeptideLabelMap();
101
102 if(isotope_minimum_ratio > 0)
103 {
104 // isotope
105 if(label_map.size() > 0)
106 {
107 // isotope, label
108
109 for(auto &peptide_label_pair : label_map)
110 {
111 // for each label
112 qDebug();
113 generateMeasurementsForIsotopeList(*(peptide_label_pair.second.get()),
114 peptide_label_pair.second.get(),
115 quantification_method,
116 charge,
117 isotope_minimum_ratio,
118 best_xic_coord,
119 best_rt);
120 }
121 }
122 else
123 {
124 // isotope, no label
125 generateMeasurementsForIsotopeList(the_peptide,
126 nullptr,
127 quantification_method,
128 charge,
129 isotope_minimum_ratio,
130 best_xic_coord,
131 best_rt);
132 }
133 }
134 else
135 {
136 // no isotope
137 if(label_map.size() > 0)
138 {
139 // no isotope, label
140 for(auto &peptide_label_pair : label_map)
141 {
142 // for each label
143 qDebug();
144 double mz = peptide_label_pair.second->getPappsoPeptideSp().get()->getMz(charge);
145 pappso::XicCoordSPtr xic_coord = best_xic_coord->initializeAndClone();
146 xic_coord.get()->rtTarget = best_rt;
147 xic_coord.get()->mzRange = quantification_method.get()->getXicExtractionMzRange(mz);
148
149
150 m_measurementList.push_back({charge,
151 xic_coord,
152 PeakQualityCategory::nomatch,
153 peptide_label_pair.second.get(),
154 nullptr,
155 nullptr});
156 }
157 }
158 else
159 {
160 // no isotope, no label
161 double mz = the_peptide.getPappsoPeptideSp().get()->getMz(charge);
162 pappso::XicCoordSPtr xic_coord = best_xic_coord->initializeAndClone();
163 xic_coord.get()->rtTarget = best_rt;
164 xic_coord.get()->mzRange = quantification_method.get()->getXicExtractionMzRange(mz);
165
166
167 m_measurementList.push_back(
168 {charge, xic_coord, PeakQualityCategory::nomatch, nullptr, nullptr, nullptr});
169 }
170 }
171}
pappso::masschroq::PeptideMeasurementsBase::generateMeasurementsForIsotopeList
virtual void generateMeasurementsForIsotopeList(PeptideBase &peptide_base, const PeptideLabel *label_p, const QuantificationMethodSp &quantification_method, std::uint8_t charge, double isotope_minimum_ratio, const pappso::XicCoordSPtr &best_xic_coord, double best_rt) final
Definition peptidemeasurementsbase.cpp:56

References generateMeasurementsForIsotopeList(), pappso::masschroq::QuantificationMethod::getIsotopeMinimumRatio(), pappso::masschroq::PeptideBase::getPappsoPeptideSp(), pappso::masschroq::Peptide::getPeptideLabelMap(), pappso::masschroq::QuantificationMethod::getXicExtractionMzRange(), m_measurementList, and pappso::masschroq::nomatch.

Referenced by detectQuantifyPeaks(), pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements(), and pappso::masschroq::PeptideMeasurements::prepareMeasurements().

◆ pushBackXicCoordList()

void pappso::masschroq::PeptideMeasurementsBase::pushBackXicCoordList ( std::vector< pappso::XicCoordSPtr > & xic_coord_list) const
finalvirtual

Definition at line 175 of file peptidemeasurementsbase.cpp.

177{
178 for(auto &measure : m_measurementList)
179 {
180 if(measure.msp_xicCoord.get()->rtTarget > 0)
181 {
182 xic_coord_list.push_back(measure.msp_xicCoord);
183 }
184 }
185}

References m_measurementList.

Referenced by pappso::masschroq::MsRunPeptideList::addMbrPeptideMeasurementsSp2XicCoordList(), and pappso::masschroq::MsRunPeptideList::addPeptideObservation2XicCoordList().

Member Data Documentation

◆ m_measurementList

std::vector<Measurement> pappso::masschroq::PeptideMeasurementsBase::m_measurementList
protected

Definition at line 117 of file peptidemeasurementsbase.h.

Referenced by PeptideMeasurementsBase(), clear(), pappso::masschroq::MbrPeptideMeasurements::detectQuantifyPeaks(), pappso::masschroq::PeptideMeasurements::detectQuantifyPeaks(), flushXics(), generateMeasurementsForIsotopeList(), getMeasurementList(), prepareMeasurementsForPeptide(), and pushBackXicCoordList().

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