libpappsomspp
Library for mass spectrometry
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pappso::TimsMsRunReaderDia Class Reference

#include <timsmsrunreaderdia.h>

Inheritance diagram for pappso::TimsMsRunReaderDia:
pappso::TimsMsRunReaderBase pappso::MsRunReader

Public Member Functions

 TimsMsRunReaderDia (MsRunIdCstSPtr &msrun_id_csp)
 
 TimsMsRunReaderDia (const TimsMsRunReaderBase &msrun_reader_base)
 
virtual ~TimsMsRunReaderDia ()
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index) override
 get a MassSpectrumSPtr class given its spectrum index
 
virtual MassSpectrumCstSPtr massSpectrumCstSPtr (std::size_t spectrum_index) override
 
virtual QualifiedMassSpectrum qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const override
 get a QualifiedMassSpectrum class given its scan number
 
virtual XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum index
 
virtual XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum
 
virtual std::size_t spectrumListSize () const override
 get the totat number of spectrum conained in the MSrun data file
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
 
virtual void readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
 
virtual void readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
 
virtual bool acquireDevice () override
 acquire data back end device
 
- Public Member Functions inherited from pappso::TimsMsRunReaderBase
 TimsMsRunReaderBase (MsRunIdCstSPtr &msrun_id_csp)
 
 TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base)
 
virtual ~TimsMsRunReaderBase ()
 
virtual TimsDataSp getTimsDataSPtr ()
 give an access to the underlying raw data pointer
 
virtual bool hasScanNumbers () const override
 tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file
 
virtual bool releaseDevice () override
 release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object
 
virtual Trace getTicChromatogram () override
 get a TIC chromatogram
 
virtual std::vector< double > getRetentionTimeLine () override
 retention timeline get retention times along the MSrun in seconds
 
- Public Member Functions inherited from pappso::MsRunReader
 MsRunReader (const MsRunIdCstSPtr &ms_run_id)
 
 MsRunReader (const MsRunReader &other)
 
virtual ~MsRunReader ()
 
const MsRunIdCstSPtrgetMsRunId () const
 
virtual std::size_t scanNumber2SpectrumIndex (std::size_t scan_number)
 if possible, converts a scan number into a spectrum index This is a convenient function to help transition from the old scan number (not implemented by all vendors) to more secure spectrum index (not vendor dependant). It is better to not rely on this function.
 
void setMonoThread (bool is_mono_thread)
 set only one is_mono_thread to true
 
bool isMonoThread () const
 

Protected Member Functions

virtual void initialize () override
 
- Protected Member Functions inherited from pappso::TimsMsRunReaderBase
virtual bool accept (const QString &file_name) const override
 tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format
 
- Protected Member Functions inherited from pappso::MsRunReader

Private Attributes

TimsDiaSlicesmp_timsDiaSlices = nullptr
 

Friends

class MsFileAccessor
 

Additional Inherited Members

- Protected Attributes inherited from pappso::TimsMsRunReaderBase
TimsDataSp msp_timsData = nullptr
 
- Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr mcsp_msRunId
 
MsRunReaderScanNumberMultiMapmpa_multiMapScanNumber = nullptr
 

Detailed Description

Definition at line 44 of file timsmsrunreaderdia.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderDia() [1/2]

pappso::TimsMsRunReaderDia::TimsMsRunReaderDia ( MsRunIdCstSPtr & msrun_id_csp)

Default constructor

Definition at line 38 of file timsmsrunreaderdia.cpp.

39 : TimsMsRunReaderBase(msrun_id_csp)
40{
41 // qInfo() << msp_timsData.get();
42 initialize();
43}
TimsMsRunReaderBase(MsRunIdCstSPtr &msrun_id_csp)
virtual void initialize() override

References initialize().

◆ TimsMsRunReaderDia() [2/2]

pappso::TimsMsRunReaderDia::TimsMsRunReaderDia ( const TimsMsRunReaderBase & msrun_reader_base)

Definition at line 46 of file timsmsrunreaderdia.cpp.

48 : TimsMsRunReaderBase(msrun_reader_base)
49{
50 initialize();
51}

References initialize().

◆ ~TimsMsRunReaderDia()

pappso::TimsMsRunReaderDia::~TimsMsRunReaderDia ( )
virtual

Destructor

Definition at line 53 of file timsmsrunreaderdia.cpp.

54{
55}

Member Function Documentation

◆ acquireDevice()

bool pappso::TimsMsRunReaderDia::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 168 of file timsmsrunreaderdia.cpp.

169{
171 {
172 qDebug() << msp_timsData.get();
173 mp_timsDiaSlices = msp_timsData.get()->getTimsDiaSlicesPtr();
174 return true;
175 }
176 return false;
177 qDebug();
178}
virtual bool acquireDevice() override
acquire data back end device

References pappso::TimsMsRunReaderBase::acquireDevice(), mp_timsDiaSlices, and pappso::TimsMsRunReaderBase::msp_timsData.

◆ initialize()

void pappso::TimsMsRunReaderDia::initialize ( )
overrideprotectedvirtual

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 59 of file timsmsrunreaderdia.cpp.

60{
61 qDebug();
62
63 if(msp_timsData == nullptr)
65 std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
66
67 if(msp_timsData.get() == nullptr)
68 {
69 throw PappsoException(
70 QObject::tr("ERROR in TimsMsRunReaderDia::initialize "
71 "msp_timsData is null for MsRunId %1")
72 .arg(mcsp_msRunId.get()->toString()));
73 }
74 qDebug();
75 qDebug() << msp_timsData.get();
76 mp_timsDiaSlices = msp_timsData.get()->getTimsDiaSlicesPtr();
77 qDebug();
78}
MsRunIdCstSPtr mcsp_msRunId

Referenced by TimsMsRunReaderDia(), and TimsMsRunReaderDia().

◆ massSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::TimsMsRunReaderDia::massSpectrumCstSPtr ( std::size_t spectrum_index)
overridevirtual

Implements pappso::MsRunReader.

Definition at line 152 of file timsmsrunreaderdia.cpp.

153{
154 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
155 .arg(__FILE__)
156 .arg(__FUNCTION__)
157 .arg(__LINE__));
158}

◆ massSpectrumSPtr()

MassSpectrumSPtr pappso::TimsMsRunReaderDia::massSpectrumSPtr ( std::size_t spectrum_index)
overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 144 of file timsmsrunreaderdia.cpp.

145{
146 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
147 .arg(__FILE__)
148 .arg(__FUNCTION__)
149 .arg(__LINE__));
150}

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

pappso::XicCoordSPtr pappso::TimsMsRunReaderDia::newXicCoordSPtrFromQualifiedMassSpectrum ( const QualifiedMassSpectrum & mass_spectrum,
pappso::PrecisionPtr precision ) const
overridevirtual

get a xic coordinate object from a given spectrum

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 92 of file timsmsrunreaderdia.cpp.

95{
96 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
97 .arg(__FILE__)
98 .arg(__FUNCTION__)
99 .arg(__LINE__));
100}

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr pappso::TimsMsRunReaderDia::newXicCoordSPtrFromSpectrumIndex ( std::size_t spectrum_index,
pappso::PrecisionPtr precision ) const
overridevirtual

get a xic coordinate object from a given spectrum index

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 82 of file timsmsrunreaderdia.cpp.

84{
85 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
86 .arg(__FILE__)
87 .arg(__FUNCTION__)
88 .arg(__LINE__));
89}

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum pappso::TimsMsRunReaderDia::qualifiedMassSpectrum ( std::size_t spectrum_index,
bool want_binary_data = true ) const
overridevirtual

get a QualifiedMassSpectrum class given its scan number

Implements pappso::MsRunReader.

Definition at line 112 of file timsmsrunreaderdia.cpp.

114{
115
116 // spectrum index is a global slice index
117 QualifiedMassSpectrum q_dia_spectrum;
119 getMsRunId(), q_dia_spectrum, spectrum_index, want_binary_data);
120 return q_dia_spectrum;
121}
const MsRunIdCstSPtr & getMsRunId() const
void getMs2QualifiedSpectrumByGlobalSliceIndex(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_slice_index, bool want_binary_data) const

References pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::MsRunReader::getMsRunId(), and mp_timsDiaSlices.

◆ readSpectrumCollection()

void pappso::TimsMsRunReaderDia::readSpectrumCollection ( SpectrumCollectionHandlerInterface & handler)
overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

Implements pappso::MsRunReader.

Definition at line 124 of file timsmsrunreaderdia.cpp.

126{
127 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
128 .arg(__FILE__)
129 .arg(__FUNCTION__)
130 .arg(__LINE__));
131}

◆ readSpectrumCollection2()

void pappso::TimsMsRunReaderDia::readSpectrumCollection2 ( const MsRunReadConfig & config,
SpectrumCollectionHandlerInterface & handler )
overridevirtual

Implements pappso::MsRunReader.

Definition at line 134 of file timsmsrunreaderdia.cpp.

136{
137 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
138 .arg(__FILE__)
139 .arg(__FUNCTION__)
140 .arg(__LINE__));
141}

◆ readSpectrumCollectionByMsLevel()

void pappso::TimsMsRunReaderDia::readSpectrumCollectionByMsLevel ( SpectrumCollectionHandlerInterface & handler,
unsigned int ms_level )
overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

Implements pappso::MsRunReader.

Definition at line 102 of file timsmsrunreaderdia.cpp.

104{
105 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
106 .arg(__FILE__)
107 .arg(__FUNCTION__)
108 .arg(__LINE__));
109}

◆ spectrumListSize()

std::size_t pappso::TimsMsRunReaderDia::spectrumListSize ( ) const
overridevirtual

get the totat number of spectrum conained in the MSrun data file

Implements pappso::MsRunReader.

Definition at line 161 of file timsmsrunreaderdia.cpp.

162{
163
165}
std::size_t getTotalSlicesCount() const
get the number of DIA MS2 slices analyzed by PASEF

References pappso::TimsDiaSlices::getTotalSlicesCount(), and mp_timsDiaSlices.

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 46 of file timsmsrunreaderdia.h.

Member Data Documentation

◆ mp_timsDiaSlices

TimsDiaSlices* pappso::TimsMsRunReaderDia::mp_timsDiaSlices = nullptr
private

Definition at line 115 of file timsmsrunreaderdia.h.

Referenced by acquireDevice(), qualifiedMassSpectrum(), and spectrumListSize().


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