libpappsomspp
Library for mass spectrometry
pappso::TimsFramesMsRunReader Class Reference

#include <timsframesmsrunreader.h>

Inheritance diagram for pappso::TimsFramesMsRunReader:
pappso::MsRunReader

Public Member Functions

 TimsFramesMsRunReader (MsRunIdCstSPtr &msrun_id_csp)
 
virtual ~TimsFramesMsRunReader ()
 
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 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 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 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...
 
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 Trace getTicChromatogram () override
 get a TIC chromatogram More...
 
virtual Trace computeTicChromatogram ()
 
- 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...
 
virtual std::vector< double > getRetentionTimeLine ()
 retention timeline get retention times along the MSrun in seconds 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
 

Friends

class MsFileAccessor
 

Additional Inherited Members

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

Detailed Description

Definition at line 43 of file timsframesmsrunreader.h.

Constructor & Destructor Documentation

◆ TimsFramesMsRunReader()

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

Definition at line 34 of file timsframesmsrunreader.cpp.

35  : MsRunReader(msrun_id_csp)
36 {
37  qDebug() << "Now initializing the TimsFramesMsRunReader.";
38 
39  initialize();
40 }
MsRunReader(MsRunIdCstSPtr &ms_run_id)
virtual void initialize() override

References initialize().

◆ ~TimsFramesMsRunReader()

TimsFramesMsRunReader::~TimsFramesMsRunReader ( )
virtual

Definition at line 42 of file timsframesmsrunreader.cpp.

43 {
44  msp_timsData = nullptr;
45 }

References msp_timsData.

Member Function Documentation

◆ accept()

bool TimsFramesMsRunReader::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.

Definition at line 62 of file timsframesmsrunreader.cpp.

63 {
64  qDebug() << file_name;
65  return true;
66 }

◆ acquireDevice()

bool TimsFramesMsRunReader::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Implements pappso::MsRunReader.

Definition at line 216 of file timsframesmsrunreader.cpp.

217 {
218  if(msp_timsData == nullptr)
219  {
220  initialize();
221  }
222  return true;
223 }

References initialize(), and msp_timsData.

Referenced by getTicChromatogram(), and getTimsDataSPtr().

◆ computeTicChromatogram()

Trace TimsFramesMsRunReader::computeTicChromatogram ( )
virtual

Definition at line 269 of file timsframesmsrunreader.cpp.

270 {
271 
272  // We want to compute the TIC chromatogram, not load the chromatogram that is
273  // located in the SQL database.
274  //
275  // For this, we need to iterated into the frames and ask for MS1 spectra only.
276  // msp_timsData has that information:
277  //
278  // std::vector<FrameIdDescr> m_frameIdDescrList;
279  //
280  // and
281 
282  // struct FrameIdDescr
283  // {
284  // std::size_t m_frameId; // frame id
285  // std::size_t m_size; // frame size (number of TOF scans in frame)
286  // std::size_t m_cumulSize; // cumulative size
287  // };
288 
289  Trace tic_chromatogram;
290 
291  const std::vector<FrameIdDescr> frame_descr_list =
292  msp_timsData->getFrameIdDescrList();
293 
294  for(FrameIdDescr frame_id_descr : frame_descr_list)
295  {
296  TimsFrameCstSPtr tims_frame_csp =
297  msp_timsData->getTimsFrameCstSPtrCached(frame_id_descr.m_frameId);
298  std::size_t scan_begin = 0;
299  std::size_t scan_end = tims_frame_csp->getTotalNumberOfScans() - 1;
300 
301  // By convention, a TIC chromatogram is only performed using MS1 spectra.
302  if(tims_frame_csp->getMsLevel() == 1)
303  {
304 
305  double rt = tims_frame_csp->getTime();
306 
307  tic_chromatogram.append(DataPoint(
308  rt,
309  tims_frame_csp->cumulateScansIntensities(scan_begin, scan_end)));
310  }
311  else
312  continue;
313  }
314 
315  return tic_chromatogram;
316 }
A simple container of DataPoint instances.
Definition: trace.h:148
size_t append(const DataPoint &data_point)
appends a datapoint and return new size
Definition: trace.cpp:583
@ rt
Retention time.
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:42

References pappso::Trace::append(), msp_timsData, and pappso::rt.

◆ getTicChromatogram()

Trace TimsFramesMsRunReader::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.

Definition at line 257 of file timsframesmsrunreader.cpp.

258 {
259  // Use the Sqlite database to fetch the total ion current chromatogram (TIC
260  // chromatogram).
261 
262  acquireDevice();
263 
264  return msp_timsData->getTicChromatogram();
265 }
virtual bool acquireDevice() override
acquire data back end device

References acquireDevice(), and msp_timsData.

◆ getTimsDataSPtr()

TimsDataSp TimsFramesMsRunReader::getTimsDataSPtr ( )
virtual

give an access to the underlying raw data pointer

Definition at line 249 of file timsframesmsrunreader.cpp.

250 {
251  acquireDevice();
252  return msp_timsData;
253 }

References acquireDevice(), and msp_timsData.

◆ hasScanNumbers()

bool TimsFramesMsRunReader::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.

Definition at line 202 of file timsframesmsrunreader.cpp.

203 {
204  return false;
205 }

◆ initialize()

void TimsFramesMsRunReader::initialize ( )
overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 48 of file timsframesmsrunreader.cpp.

49 {
50  msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
51  if(msp_timsData == nullptr)
52  {
53  throw PappsoException(
54  QObject::tr("ERROR in TimsFramesMsRunReader::initialize "
55  "msp_timsData is null for MsRunId %1")
56  .arg(mcsp_msRunId.get()->toString()));
57  }
58 }
MsRunIdCstSPtr mcsp_msRunId
Definition: msrunreader.h:301

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

Referenced by TimsFramesMsRunReader(), and acquireDevice().

◆ massSpectrumCstSPtr()

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

Implements pappso::MsRunReader.

Definition at line 82 of file timsframesmsrunreader.cpp.

83 {
84  return msp_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index);
85 }

References msp_timsData.

◆ massSpectrumSPtr()

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

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 70 of file timsframesmsrunreader.cpp.

72 {
74  QObject::tr("Not yet implemented in TimsFramesMsRunReader %1.\n")
75  .arg(__LINE__));
76 
77  return pappso::MassSpectrumSPtr();
78 }
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

XicCoordSPtr TimsFramesMsRunReader::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 238 of file timsframesmsrunreader.cpp.

241 {
242  throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
243  .arg(__FILE__)
244  .arg(__FUNCTION__)
245  .arg(__LINE__));
246 }

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr TimsFramesMsRunReader::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 227 of file timsframesmsrunreader.cpp.

230 {
231  throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
232  .arg(__FILE__)
233  .arg(__FUNCTION__)
234  .arg(__LINE__));
235 }

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum TimsFramesMsRunReader::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 89 of file timsframesmsrunreader.cpp.

91 {
92 
93  QualifiedMassSpectrum mass_spectrum;
94 
95  msp_timsData->getQualifiedMassSpectrumByRawIndex(
96  getMsRunId(), mass_spectrum, spectrum_index, want_binary_data);
97  return mass_spectrum;
98 }
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.

References pappso::MsRunReader::getMsRunId(), and msp_timsData.

◆ readSpectrumCollection()

void TimsFramesMsRunReader::readSpectrumCollection ( SpectrumCollectionHandlerInterface handler)
overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 102 of file timsframesmsrunreader.cpp.

104 {
105  // Here we want to only handle mass spectra as combined scans spectra, that
106  // is, for each frame, we want all the mobility scans to be cumulated (at the
107  // integer level, that is, without conversion of all the integers to m/z
108  // values) so as to yield a *single* mass spectrum per frame.
109 
110  // We can iterate in the vector of frames records and for each frame ask that
111  // all its scans be combined into a single mass spectrum.
112 
113  const std::vector<FrameIdDescr> frame_id_descr_list =
114  msp_timsData->getFrameIdDescrList();
115 
116  // The scan index is the index of the scan in the *whole* mass data file, it
117  // is a sequential number of scan over all the frames.
118  std::size_t scan_index = 0; // iterate in each spectrum
119 
120  // We'll need it to perform the looping in the spectrum list.
121  std::size_t frames_count = msp_timsData->getTotalNumberOfFrames();
122 
123  qDebug() << "The spectrum list has this much frames:" << frames_count;
124 
125  // Inform the handler of the spectrum list so that it can handle feedback to
126  // the user.
127  handler.spectrumListHasSize(frames_count);
128 
129  for(const FrameIdDescr &current_frame : frame_id_descr_list)
130  {
131  TimsFrameCstSPtr tims_frame =
132  msp_timsData->getTimsFrameCstSPtrCached(current_frame.m_frameId);
133 
134  // Get to know the size of the frame, that is, the number of mobility
135  // scans in it.
136 
137  quint32 scan_count = tims_frame->getTotalNumberOfScans();
138 
139  Trace spectrum = tims_frame->cumulateScanToTrace(0, scan_count - 1);
140 
141  QualifiedMassSpectrum mass_spectrum;
142 
143  MassSpectrumId spectrum_id;
144 
145  spectrum_id.setSpectrumIndex(scan_index);
146 
147  spectrum_id.setMsRunId(getMsRunId());
148 
149  // Can modify to help our case
150  spectrum_id.setNativeId(QString("frame=%1 index=%2")
151  .arg(current_frame.m_frameId)
152  .arg(scan_index));
153 
154  mass_spectrum.setMassSpectrumId(spectrum_id);
155 
156  // We want to document the retention time!
157  mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
158 
159  // We do want to document the ms level of the spectrum and possibly the
160  // precursor's m/z and charge.
161  unsigned int frame_ms_level = tims_frame.get()->getMsLevel();
162  mass_spectrum.setMsLevel(frame_ms_level);
163 
164  if(frame_ms_level > 1)
165  {
166  // FIXME
167  // We want to document the precusor's m/z, z and index.
168  }
169 
170  mass_spectrum.setDtInMilliSeconds(-1);
171 
172  mass_spectrum.setEmptyMassSpectrum(false);
173 
174  mass_spectrum.setMassSpectrumSPtr(
175  std::make_shared<MassSpectrum>(spectrum));
176 
177  handler.setQualifiedMassSpectrum(mass_spectrum);
178 
179  scan_index += scan_count;
180  }
181 }
void setNativeId(const QString &native_id)
void setMsRunId(MsRunIdCstSPtr other)
void setSpectrumIndex(std::size_t index)
void setDtInMilliSeconds(pappso_double rt)
Set the drift time in milliseconds.
void setMassSpectrumId(const MassSpectrumId &iD)
Set the MassSpectrumId.
void setMsLevel(uint ms_level)
Set the mass spectrum level.
void setMassSpectrumSPtr(MassSpectrumSPtr massSpectrum)
Set the MassSpectrumSPtr.
void setRtInSeconds(pappso_double rt)
Set the retention time in seconds.
void setEmptyMassSpectrum(bool is_empty_mass_spectrum)
virtual void spectrumListHasSize(std::size_t size)
Definition: msrunreader.cpp:53
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0

References pappso::MsRunReader::getMsRunId(), msp_timsData, pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().

◆ readSpectrumCollectionByMsLevel()

void TimsFramesMsRunReader::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 185 of file timsframesmsrunreader.cpp.

188 {
189 
190  qDebug();
191 }

◆ releaseDevice()

bool TimsFramesMsRunReader::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 209 of file timsframesmsrunreader.cpp.

210 {
211  msp_timsData = nullptr;
212  return true;
213 }

References msp_timsData.

◆ spectrumListSize()

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

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

Implements pappso::MsRunReader.

Definition at line 195 of file timsframesmsrunreader.cpp.

196 {
197  return msp_timsData->getTotalNumberOfScans();
198 }

References msp_timsData.

Friends And Related Function Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 45 of file timsframesmsrunreader.h.

Member Data Documentation

◆ msp_timsData


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