libpappsomspp
Library for mass spectrometry
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pappso::TimsMsRunReaderBase Class Reference

#include <timsmsrunreaderbase.h>

Inheritance diagram for pappso::TimsMsRunReaderBase:
pappso::MsRunReader pappso::TimsFramesMsRunReader pappso::TimsMsRunReader pappso::TimsMsRunReaderDia pappso::TimsMsRunReaderMs2 pappso::TimsMsRunReaderMs2Selected

Public Member Functions

 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 bool acquireDevice () override
 acquire data back end device
 
virtual Trace getTicChromatogram () override
 get a TIC chromatogram
 
virtual std::vector< double > getRetentionTimeLine () override
 retention timeline get retention times along the MSrun in seconds
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum index
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum
 
- Public Member Functions inherited from pappso::MsRunReader
 MsRunReader (const MsRunIdCstSPtr &ms_run_id)
 
 MsRunReader (const MsRunReader &other)
 
virtual ~MsRunReader ()
 
const MsRunIdCstSPtrgetMsRunId () const
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index)=0
 get a MassSpectrumSPtr class given its spectrum index
 
virtual MassSpectrumCstSPtr massSpectrumCstSPtr (std::size_t spectrum_index)=0
 
virtual QualifiedMassSpectrum qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const =0
 get a QualifiedMassSpectrum class given its scan number
 
virtual std::size_t spectrumListSize () const =0
 get the totat number of spectrum conained in the MSrun data file
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler)=0
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
 
virtual void readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)=0
 
virtual void readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)=0
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
 
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
 
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 Attributes

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

Friends

class MsFileAccessor
 

Detailed Description

Definition at line 37 of file timsmsrunreaderbase.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderBase() [1/2]

pappso::TimsMsRunReaderBase::TimsMsRunReaderBase ( MsRunIdCstSPtr msrun_id_csp)

Default constructor

Definition at line 36 of file timsmsrunreaderbase.cpp.

37 : MsRunReader(msrun_id_csp)
38{
39 initialize();
40}
MsRunReader(const MsRunIdCstSPtr &ms_run_id)
virtual void initialize() override

References initialize().

◆ TimsMsRunReaderBase() [2/2]

pappso::TimsMsRunReaderBase::TimsMsRunReaderBase ( const TimsMsRunReaderBase msrun_reader_base)

Definition at line 42 of file timsmsrunreaderbase.cpp.

44 : MsRunReader(msrun_reader_base.getMsRunId()),
45 msp_timsData(msrun_reader_base.msp_timsData)
46{
47 initialize();
48}

References initialize().

◆ ~TimsMsRunReaderBase()

pappso::TimsMsRunReaderBase::~TimsMsRunReaderBase ( )
virtual

Destructor

Definition at line 51 of file timsmsrunreaderbase.cpp.

52{
53
54 msp_timsData = nullptr;
55}

References msp_timsData.

Member Function Documentation

◆ accept()

bool pappso::TimsMsRunReaderBase::accept ( const QString &  file_name) const
overrideprotectedvirtual

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

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 75 of file timsmsrunreaderbase.cpp.

76{
77 qDebug() << file_name;
78 return true;
79}

◆ acquireDevice()

bool pappso::TimsMsRunReaderBase::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderDia, and pappso::TimsMsRunReaderMs2.

Definition at line 96 of file timsmsrunreaderbase.cpp.

97{
98 if(msp_timsData == nullptr)
99 {
100 initialize();
101 }
102 return true;
103}

References initialize(), and msp_timsData.

Referenced by pappso::TimsMsRunReaderDia::acquireDevice(), getTicChromatogram(), and getTimsDataSPtr().

◆ getRetentionTimeLine()

std::vector< double > pappso::TimsMsRunReaderBase::getRetentionTimeLine ( )
overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns
vector of retention times (seconds)

Reimplemented from pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 127 of file timsmsrunreaderbase.cpp.

128{
129 return msp_timsData.get()->getRetentionTimeLineInSeconds();
130}

◆ getTicChromatogram()

Trace pappso::TimsMsRunReaderBase::getTicChromatogram ( )
overridevirtual

get a TIC chromatogram

for each retention time, computes the sum of all intensities. For IM-MS, combines the mobility spectra

Note that, formally, a TIC chromatogram is computed only for MS1 spectra.

Returns
a trace (x=rt, y=intensities)

Reimplemented from pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 114 of file timsmsrunreaderbase.cpp.

115{
116 // Use the Sqlite database to fetch the total ion current chromatogram (TIC
117 // chromatogram).
118
120
121 // The time unit here is seconds, not minutes!!!
122 return msp_timsData->getTicChromatogram();
123}
virtual bool acquireDevice() override
acquire data back end device

References acquireDevice(), and msp_timsData.

◆ getTimsDataSPtr()

TimsDataSp pappso::TimsMsRunReaderBase::getTimsDataSPtr ( )
virtual

give an access to the underlying raw data pointer

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 106 of file timsmsrunreaderbase.cpp.

107{
109 return msp_timsData;
110}

References acquireDevice(), and msp_timsData.

◆ hasScanNumbers()

bool pappso::TimsMsRunReaderBase::hasScanNumbers ( ) const
overridevirtual

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

Reimplemented from pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 82 of file timsmsrunreaderbase.cpp.

83{
84 return false;
85}

◆ initialize()

void pappso::TimsMsRunReaderBase::initialize ( )
overrideprotectedvirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 58 of file timsmsrunreaderbase.cpp.

59{
60 if(msp_timsData == nullptr)
62 std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
63
64 if(msp_timsData.get() == nullptr)
65 {
66 throw PappsoException(
67 QObject::tr("ERROR in TimsMsRunReaderBase::initialize "
68 "msp_timsData is null for MsRunId %1")
69 .arg(mcsp_msRunId.get()->toString()));
70 }
71}
MsRunIdCstSPtr mcsp_msRunId

References pappso::MsRunReader::mcsp_msRunId, and msp_timsData.

Referenced by pappso::TimsMsRunReader::TimsMsRunReader(), pappso::TimsMsRunReader::TimsMsRunReader(), TimsMsRunReaderBase(), TimsMsRunReaderBase(), and acquireDevice().

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

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

get a xic coordinate object from a given spectrum

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderDia.

Definition at line 145 of file timsmsrunreaderbase.cpp.

148{
149 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
150 .arg(__FILE__)
151 .arg(__FUNCTION__)
152 .arg(__LINE__));
153}

◆ newXicCoordSPtrFromSpectrumIndex()

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

get a xic coordinate object from a given spectrum index

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderDia.

Definition at line 134 of file timsmsrunreaderbase.cpp.

137{
138 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
139 .arg(__FILE__)
140 .arg(__FUNCTION__)
141 .arg(__LINE__));
142}

◆ releaseDevice()

bool pappso::TimsMsRunReaderBase::releaseDevice ( )
overridevirtual

release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object

Returns
bool true if done

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 89 of file timsmsrunreaderbase.cpp.

90{
91 msp_timsData = nullptr;
92 return true;
93}

References msp_timsData.

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 39 of file timsmsrunreaderbase.h.

Member Data Documentation

◆ msp_timsData


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