libpappsomspp
Library for mass spectrometry
pappso::TimsMsRunReaderMs2 Class Reference

#include <timsmsrunreaderms2.h>

Inheritance diagram for pappso::TimsMsRunReaderMs2:
pappso::MsRunReader pappso::TimsMsRunReaderMs2Selected

Public Member Functions

 TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)
 
virtual ~TimsMsRunReaderMs2 ()
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index) override
 get a MassSpectrumSPtr class given its spectrum index More...
 
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 More...
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum index More...
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum More...
 
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 More...
 
virtual std::size_t spectrumListSize () const override
 get the totat number of spectrum conained in the MSrun data file More...
 
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 More...
 
void setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
 
void setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
 
void setMs2BuiltinCentroid (bool centroid)
 enable or disable simple centroid filter on raw tims data for MS2 More...
 
virtual std::vector< std::size_t > getPrecursorsIDFromMzRt (int charge, double mz_val, double rt_sec, double k0)
 Get all the precursors id which match the values. More...
 
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 More...
 
virtual bool acquireDevice () override
 acquire data back end device More...
 
virtual TimsDataSp getTimsDataSPtr ()
 give an access to the underlying raw data pointer More...
 
virtual std::vector< double > getRetentionTimeLine () override
 retention timeline get retention times along the MSrun in seconds More...
 
virtual Trace getTicChromatogram () override
 get a TIC chromatogram More...
 
- Public Member Functions inherited from pappso::MsRunReader
 MsRunReader (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. More...
 
void setMonoThread (bool is_mono_thread)
 set only one is_mono_thread to true More...
 
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 More...
 

Private Attributes

TimsDataSp msp_timsData = nullptr
 
pappso::FilterInterfaceCstSPtr msp_ms1Filter
 
pappso::FilterInterfaceCstSPtr msp_ms2Filter
 
bool m_builtinMs2Centroid = true
 enable builtin centroid on raw tims integers by default More...
 

Friends

class MsFileAccessor
 

Additional Inherited Members

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

Detailed Description

Definition at line 39 of file timsmsrunreaderms2.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2()

TimsMsRunReaderMs2::TimsMsRunReaderMs2 ( MsRunIdCstSPtr msrun_id_csp)
Todo:
write docs

Definition at line 37 of file timsmsrunreaderms2.cpp.

38  : MsRunReader(msrun_id_csp)
39 {
40  initialize();
41 }
MsRunReader(MsRunIdCstSPtr &ms_run_id)
virtual void initialize() override

References initialize().

◆ ~TimsMsRunReaderMs2()

TimsMsRunReaderMs2::~TimsMsRunReaderMs2 ( )
virtual

Definition at line 43 of file timsmsrunreaderms2.cpp.

44 {
45  if(msp_timsData != nullptr)
46  {
47  msp_timsData = nullptr;
48  }
49 }

References msp_timsData.

Member Function Documentation

◆ accept()

bool TimsMsRunReaderMs2::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::TimsMsRunReaderMs2Selected.

Definition at line 113 of file timsmsrunreaderms2.cpp.

114 {
115  qDebug() << file_name;
116  return true;
117 }

◆ acquireDevice()

bool TimsMsRunReaderMs2::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Implements pappso::MsRunReader.

Definition at line 255 of file timsmsrunreaderms2.cpp.

256 {
257  if(msp_timsData == nullptr)
258  {
259  initialize();
260  msp_timsData->setMs2BuiltinCentroid(m_builtinMs2Centroid);
261  msp_timsData->setMs1FilterCstSPtr(msp_ms1Filter);
262  msp_timsData->setMs2FilterCstSPtr(msp_ms2Filter);
263  }
264  return true;
265 }
pappso::FilterInterfaceCstSPtr msp_ms2Filter
pappso::FilterInterfaceCstSPtr msp_ms1Filter
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default

References initialize(), m_builtinMs2Centroid, msp_ms1Filter, msp_ms2Filter, and msp_timsData.

Referenced by getTicChromatogram().

◆ getPrecursorsIDFromMzRt()

std::vector< std::size_t > pappso::TimsMsRunReaderMs2::getPrecursorsIDFromMzRt ( int  charge,
double  mz_val,
double  rt_sec,
double  k0 
)
virtual

Get all the precursors id which match the values.

Returns
list of precursors Ids

Definition at line 268 of file timsmsrunreaderms2.cpp.

272 {
273  return msp_timsData->getPrecursorsFromMzRtCharge(charge, mz_val, rt_sec, k0);
274 }

◆ getRetentionTimeLine()

std::vector< double > pappso::TimsMsRunReaderMs2::getRetentionTimeLine ( )
overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns
vector of retention times (seconds)

Reimplemented from pappso::MsRunReader.

Definition at line 312 of file timsmsrunreaderms2.cpp.

313 {
314  return msp_timsData.get()->getRetentionTimeLine();
315 }

◆ getTicChromatogram()

Trace TimsMsRunReaderMs2::getTicChromatogram ( )
overridevirtual

get a TIC chromatogram

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

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

Reimplemented from pappso::MsRunReader.

Definition at line 318 of file timsmsrunreaderms2.cpp.

319 {
320  // Use the Sqlite database to fetch the total ion current chromatogram (TIC
321  // chromatogram).
322 
323  acquireDevice();
324 
325  return msp_timsData->getTicChromatogram();
326 }
virtual bool acquireDevice() override
acquire data back end device

References acquireDevice(), and msp_timsData.

◆ getTimsDataSPtr()

pappso::TimsDataSp pappso::TimsMsRunReaderMs2::getTimsDataSPtr ( )
virtual

give an access to the underlying raw data pointer

Definition at line 277 of file timsmsrunreaderms2.cpp.

278 {
279  acquireDevice();
280  return msp_timsData;
281 }

Referenced by pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().

◆ hasScanNumbers()

bool TimsMsRunReaderMs2::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::TimsMsRunReaderMs2Selected.

Definition at line 241 of file timsmsrunreaderms2.cpp.

242 {
243  return false;
244 }

◆ initialize()

void pappso::TimsMsRunReaderMs2::initialize ( )
overrideprotectedvirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 52 of file timsmsrunreaderms2.cpp.

53 {
54  msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
55  if(msp_timsData == nullptr)
56  {
57  throw PappsoException(
58  QObject::tr("ERROR in TimsMsRunReaderMs2::initialize "
59  "msp_timsData is null for MsRunId %1")
60  .arg(mcsp_msRunId.get()->toString()));
61  }
62 }
MsRunIdCstSPtr mcsp_msRunId
Definition: msrunreader.h:298

Referenced by TimsMsRunReaderMs2(), and acquireDevice().

◆ massSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr TimsMsRunReaderMs2::massSpectrumCstSPtr ( std::size_t  spectrum_index)
overridevirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 130 of file timsmsrunreaderms2.cpp.

131 {
132  QualifiedMassSpectrum mass_spectrum =
133  qualifiedMassSpectrum(spectrum_index, true);
134  return mass_spectrum.getMassSpectrumSPtr();
135 }
Class representing a fully specified mass spectrum.
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

◆ massSpectrumSPtr()

pappso::MassSpectrumSPtr TimsMsRunReaderMs2::massSpectrumSPtr ( std::size_t  spectrum_index)
overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 121 of file timsmsrunreaderms2.cpp.

122 {
123  QualifiedMassSpectrum mass_spectrum =
124  qualifiedMassSpectrum(spectrum_index, true);
125  return mass_spectrum.getMassSpectrumSPtr();
126 }

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

pappso::XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum ( const pappso::QualifiedMassSpectrum mass_spectrum,
pappso::PrecisionPtr  precision 
) const
overridevirtual

get a xic coordinate object from a given spectrum

Implements pappso::MsRunReader.

Definition at line 303 of file timsmsrunreaderms2.cpp.

306 {
308  mass_spectrum.getMassSpectrumId().getSpectrumIndex(), precision);
309 }
std::size_t getSpectrumIndex() const
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getSpectrumIndex(), and newXicCoordSPtrFromSpectrumIndex().

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex ( std::size_t  spectrum_index,
pappso::PrecisionPtr  precision 
) const
overridevirtual

get a xic coordinate object from a given spectrum index

Implements pappso::MsRunReader.

Definition at line 285 of file timsmsrunreaderms2.cpp.

287 {
288  XicCoordTimsSPtr xic_coord = std::make_shared<XicCoordTims>();
289  std::size_t precursor_index = (spectrum_index / 2) + 1;
290  auto xic = this->msp_timsData.get()->getXicCoordTimsFromPrecursorId(
291  precursor_index, precision);
292 
293  xic_coord.get()->mzRange = xic.mzRange;
294  xic_coord.get()->rtTarget = xic.rtTarget;
295  xic_coord.get()->scanNumBegin = xic.scanNumBegin;
296  xic_coord.get()->scanNumEnd = xic.scanNumEnd;
297 
298 
299  return xic_coord;
300 }
std::shared_ptr< XicCoordTims > XicCoordTimsSPtr
Definition: xiccoordtims.h:38

References msp_timsData.

Referenced by newXicCoordSPtrFromQualifiedMassSpectrum().

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum TimsMsRunReaderMs2::qualifiedMassSpectrum ( std::size_t  spectrum_index,
bool  want_binary_data = true 
) const
overridevirtual

get a QualifiedMassSpectrum class given its scan number

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 139 of file timsmsrunreaderms2.cpp.

141 {
142 
143  std::size_t precursor_index = (spectrum_index / 2) + 1;
144  TimsData::SpectrumDescr spectrum_descr;
145  try
146  {
147  spectrum_descr =
148  msp_timsData.get()->getSpectrumDescrWithPrecursorId(precursor_index);
149  }
150  catch(ExceptionNotFound &error)
151  {
152  throw ExceptionNotFound(
153  QObject::tr("spectrum_index %1 NOT FOUND in file %2 : %3")
154  .arg(spectrum_index)
155  .arg(getMsRunId().get()->getFileName())
156  .arg(error.qwhat()));
157  }
158 
159  if(spectrum_index % 2 == 0)
160  {
161  qDebug() << "MS1 spectrum precursor_index=" << precursor_index;
162  // this is an MS1 spectrum
163  QualifiedMassSpectrum mass_spectrum_ms1;
164  msp_timsData->getQualifiedMs1MassSpectrumByPrecursorId(
165  getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
166  qDebug(); // << mass_spectrum_ms1.toString();
167 
168  // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
169  return mass_spectrum_ms1;
170  }
171  else
172  {
173  qDebug() << "MS2 spectrum precursor_index=" << precursor_index;
174  QualifiedMassSpectrum mass_spectrum_ms2;
175  if(spectrum_descr.ms2_index != spectrum_index)
176  {
177  qDebug();
178  throw PappsoException(
179  QObject::tr("ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != "
180  "spectrum_index(%5)")
181  .arg(__FILE__)
182  .arg(__FUNCTION__)
183  .arg(__LINE__)
184  .arg(spectrum_descr.ms2_index)
185  .arg(spectrum_index));
186  }
187 
188  msp_timsData->getQualifiedMs2MassSpectrumByPrecursorId(
189  getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
190  qDebug(); // << mass_spectrum_ms2.toString();
191 
192  // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
193  return mass_spectrum_ms2;
194  }
195 }
const MsRunIdCstSPtr & getMsRunId() const
virtual const QString & qwhat() const

References pappso::MsRunReader::getMsRunId(), pappso::TimsData::SpectrumDescr::ms2_index, msp_timsData, and pappso::PappsoException::qwhat().

Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().

◆ readSpectrumCollection()

void TimsMsRunReaderMs2::readSpectrumCollection ( SpectrumCollectionHandlerInterface handler)
overridevirtual

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

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 199 of file timsmsrunreaderms2.cpp.

201 {
203 }
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

References readSpectrumCollectionByMsLevel().

◆ readSpectrumCollectionByMsLevel()

void TimsMsRunReaderMs2::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 206 of file timsmsrunreaderms2.cpp.

208 {
209  qDebug() << " ms_level=" << ms_level;
210  // We'll need it to perform the looping in the spectrum list.
211  std::size_t spectrum_list_size = spectrumListSize();
212 
213  // qDebug() << "The spectrum list has size:" << spectrum_list_size;
214 
215  // Inform the handler of the spectrum list so that it can handle feedback to
216  // the user.
217  handler.spectrumListHasSize(spectrum_list_size);
218 
219 
220  msp_timsData.get()->setMonoThread(isMonoThread());
221 
222  msp_timsData.get()->ms2ReaderSpectrumCollectionByMsLevel(
223  getMsRunId(), handler, ms_level);
224  // Now let the loading handler know that the loading of the data has ended.
225  // The handler might need this "signal" to perform additional tasks or to
226  // cleanup cruft.
227 
228  // qDebug() << "Loading ended";
229  handler.loadingEnded();
230 }
bool isMonoThread() const
virtual void spectrumListHasSize(std::size_t size)
Definition: msrunreader.cpp:53
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file

References pappso::MsRunReader::getMsRunId(), pappso::MsRunReader::isMonoThread(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), msp_timsData, pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().

Referenced by readSpectrumCollection().

◆ releaseDevice()

bool TimsMsRunReaderMs2::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.

Definition at line 248 of file timsmsrunreaderms2.cpp.

249 {
250  msp_timsData = nullptr;
251  return true;
252 }

References msp_timsData.

◆ setMs1FilterCstSPtr()

void TimsMsRunReaderMs2::setMs1FilterCstSPtr ( pappso::FilterInterfaceCstSPtr  filter)

Definition at line 97 of file timsmsrunreaderms2.cpp.

98 {
99  msp_ms1Filter = filter;
100  if(msp_timsData != nullptr)
101  {
102  msp_timsData->setMs1FilterCstSPtr(filter);
103  }
104  else
105  {
106  throw PappsoException(
107  QObject::tr("ERROR in TimsMsRunReaderMs2::setMs1FilterCstSPtr "
108  "msp_timsData is null"));
109  }
110 }

References msp_ms1Filter, and msp_timsData.

◆ setMs2BuiltinCentroid()

void TimsMsRunReaderMs2::setMs2BuiltinCentroid ( bool  centroid)

enable or disable simple centroid filter on raw tims data for MS2

Definition at line 65 of file timsmsrunreaderms2.cpp.

66 {
67  m_builtinMs2Centroid = centroid;
68  if(msp_timsData != nullptr)
69  {
70  msp_timsData->setMs2BuiltinCentroid(m_builtinMs2Centroid);
71  }
72  else
73  {
74  throw PappsoException(
75  QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2BuiltinCentroid "
76  "msp_timsData is null"));
77  }
78 }

References m_builtinMs2Centroid, and msp_timsData.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ setMs2FilterCstSPtr()

void TimsMsRunReaderMs2::setMs2FilterCstSPtr ( pappso::FilterInterfaceCstSPtr  filter)

Definition at line 81 of file timsmsrunreaderms2.cpp.

82 {
83  msp_ms2Filter = filter;
84  if(msp_timsData != nullptr)
85  {
86  msp_timsData->setMs2FilterCstSPtr(msp_ms2Filter);
87  }
88  else
89  {
90  throw PappsoException(
91  QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2FilterCstSPtr "
92  "msp_timsData is null"));
93  }
94 }

References msp_ms2Filter, and msp_timsData.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ spectrumListSize()

std::size_t TimsMsRunReaderMs2::spectrumListSize ( ) const
overridevirtual

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

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 234 of file timsmsrunreaderms2.cpp.

235 {
236  return (msp_timsData->getTotalNumberOfPrecursors() * 2);
237 }

References msp_timsData.

Referenced by readSpectrumCollectionByMsLevel().

Friends And Related Function Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 41 of file timsmsrunreaderms2.h.

Member Data Documentation

◆ m_builtinMs2Centroid

bool pappso::TimsMsRunReaderMs2::m_builtinMs2Centroid = true
private

enable builtin centroid on raw tims integers by default

Definition at line 120 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2BuiltinCentroid().

◆ msp_ms1Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms1Filter
private

Definition at line 116 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs1FilterCstSPtr().

◆ msp_ms2Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms2Filter
private

Definition at line 117 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2FilterCstSPtr().

◆ msp_timsData


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