libpappsomspp
Library for mass spectrometry
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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
 
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 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 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
 
virtual std::size_t spectrumListSize () const override
 get the totat number of spectrum conained in the MSrun data file
 
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 TimsDataSp getTimsDataSPtr ()
 give an access to the underlying raw data pointer
 
virtual Trace getTicChromatogram () override
 get a TIC chromatogram
 
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.
 
virtual std::vector< double > getRetentionTimeLine ()
 retention timeline get retention times along the MSrun in seconds
 
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
 

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}
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition msrunreader.h:63

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 422 of file timsframesmsrunreader.cpp.

423{
424 if(msp_timsData == nullptr)
425 {
426 initialize();
427 }
428 return true;
429}

References initialize(), and msp_timsData.

Referenced by getTicChromatogram(), and getTimsDataSPtr().

◆ computeTicChromatogram()

Trace TimsFramesMsRunReader::computeTicChromatogram ( )
virtual

Definition at line 475 of file timsframesmsrunreader.cpp.

476{
477
478 // We want to compute the TIC chromatogram, not load the chromatogram that
479 // is located in the SQL database.
480 //
481 // For this, we need to iterated into the frames and ask for MS1 spectra
482 // only. msp_timsData has that information:
483 //
484 // std::vector<FrameIdDescr> m_frameIdDescrList;
485 //
486 // and
487
488 // struct FrameIdDescr
489 // {
490 // std::size_t m_frameId; // frame id
491 // std::size_t m_size; // frame size (number of TOF scans in frame)
492 // std::size_t m_cumulSize; // cumulative size
493 // };
494
495 Trace tic_chromatogram;
496
497 const std::vector<FrameIdDescr> frame_descr_list =
498 msp_timsData->getFrameIdDescrList();
499
500 for(FrameIdDescr frame_id_descr : frame_descr_list)
501 {
502 TimsFrameCstSPtr tims_frame_csp =
503 msp_timsData->getTimsFrameCstSPtrCached(frame_id_descr.m_frameId);
504 std::size_t scan_begin = 0;
505 std::size_t scan_end = tims_frame_csp->getTotalNumberOfScans() - 1;
506
507 // By convention, a TIC chromatogram is only performed using MS1
508 // spectra.
509 if(tims_frame_csp->getMsLevel() == 1)
510 {
511
512 // Retention times are in seconds in the Bruker world.
513 double rt = tims_frame_csp->getTime();
514
515 tic_chromatogram.append(DataPoint(
516 rt,
517 tims_frame_csp->cumulateScansIntensities(scan_begin, scan_end)));
518 }
519 else
520 continue;
521 }
522
523 return tic_chromatogram;
524}
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:648
@ 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 463 of file timsframesmsrunreader.cpp.

464{
465 // Use the Sqlite database to fetch the total ion current chromatogram (TIC
466 // chromatogram).
467
469
470 return msp_timsData->getTicChromatogram();
471}
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 455 of file timsframesmsrunreader.cpp.

456{
458 return msp_timsData;
459}

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 408 of file timsframesmsrunreader.cpp.

409{
410 return false;
411}

◆ 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

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
78}
std::shared_ptr< MassSpectrum > MassSpectrumSPtr

◆ 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 444 of file timsframesmsrunreader.cpp.

447{
448 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
449 .arg(__FILE__)
450 .arg(__FUNCTION__)
451 .arg(__LINE__));
452}

◆ 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 433 of file timsframesmsrunreader.cpp.

436{
437 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
438 .arg(__FILE__)
439 .arg(__FUNCTION__)
440 .arg(__LINE__));
441}

◆ 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 qDebug() << "Reading the spectrum collection with no specific configuration.";
106 MsRunReadConfig config;
107 readSpectrumCollection2(config, handler);
108}
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override

References readSpectrumCollection2().

◆ readSpectrumCollection2()

void TimsFramesMsRunReader::readSpectrumCollection2 ( const MsRunReadConfig config,
SpectrumCollectionHandlerInterface handler 
)
overridevirtual

Implements pappso::MsRunReader.

Definition at line 112 of file timsframesmsrunreader.cpp.

114{
115 qDebug().noquote() << "20231129 Reading the spectrum collection with this "
116 "specific configuration:"
117 << config.toString();
118
119 // We want to restrict the data reading process to the configuration provided
120 // as parameter.
121 // The frame record subset will include all frames fulfiling the config
122 // requirements (retention time and ms levels)
123
124 std::vector<std::size_t> subset_of_tims_frame_ids;
125
126 // The very first sorting of frames is perfomed on the basis of the
127 // retention time range that the user might have defined. Otherwise, all the
128 // frames are deemed suitable for next processing steps.
129
130 // Then, the MS level is checked against the config provided by the user.
131 for(auto const &frame_record : msp_timsData->getTimsFrameRecordList())
132 {
133 if(frame_record.frame_id == 0)
134 continue;
135
136 if(config.acceptRetentionTimeInSeconds(frame_record.frame_time))
137 {
138 std::size_t ms_level = 2;
139 if(frame_record.msms_type == 0)
140 ms_level = 1;
141 if(config.acceptMsLevel(ms_level))
142 {
143 subset_of_tims_frame_ids.push_back(frame_record.frame_id);
144 }
145 }
146 }
147
148 // At this point, we have a subset of frame records.
149 std::size_t frames_count = subset_of_tims_frame_ids.size();
150 qDebug() << "The number of retained RT range-matching frames:"
151 << frames_count;
152
153 // Inform the handler of the spectrum list so that it can handle feedback to
154 // the user.
155 handler.spectrumListHasSize(frames_count);
156
157 // Check for ion mobility range :
158 bool asked_ion_mobility_range = false;
159 quint32 mobility_scan_num_begin = 0;
160 quint32 mobility_scan_num_end = 0;
161
162 if(!config
163 .getParameterValue(
165 .isNull())
166 {
167 asked_ion_mobility_range = true;
168
169 mobility_scan_num_begin =
170 config
173 .toUInt();
174 mobility_scan_num_end =
175 config
178 .toUInt();
179 }
180
181 // Check for m/z resolution downgrading
182 std::size_t mz_index_merge_window = 0;
183 if(!config
184 .getParameterValue(
186 .isNull())
187 {
188 mz_index_merge_window =
189 config
192 .toUInt();
193 }
194
195 // Check for m/z range selection
196 bool asked_mz_range = false;
197 double mz_range_begin = -1;
198 double mz_range_end = -1;
199
200 if(!config
201 .getParameterValue(
203 .isNull())
204 {
205 asked_mz_range = true;
206
207 mz_range_begin =
208 config
211 .toDouble();
212 mz_range_end = config
215 .toDouble();
216
217 qDebug() << "The m/z range asked is: " << mz_range_begin << "--"
218 << mz_range_end;
219 }
220
221 // Now that we have gathered all the configuration bits from the user,
222 // iterate in the vector of frames records and for each frame ask that
223 // all its scans be combined into a single mass spectrum, by taking into
224 // account the configuration bits provided by the user.
225
226 const std::vector<FrameIdDescr> &frame_id_descr_list =
227 msp_timsData->getFrameIdDescrList();
228
229 // The scan index is the index of the scan in the *whole* mass data file, it
230 // is a sequential number of scans over all the frames.
231 std::size_t scan_index = 0; // iterate in each spectrum
232
233 for(std::size_t tims_frame_id : subset_of_tims_frame_ids)
234 {
235 const FrameIdDescr &current_frame_record =
236 frame_id_descr_list[tims_frame_id];
237
238 scan_index = current_frame_record.m_cumulSize;
239 TimsFrameCstSPtr tims_frame_csp =
240 msp_timsData->getTimsFrameCstSPtrCached(tims_frame_id);
241
242 // If the user wants to select specific 1/Ko values, we need to
243 // compute the ion mobility scan value starting from that 1/Ko value in
244 // each frame.
245
246 if(!config
247 .getParameterValue(
250 .isNull())
251 {
252 asked_ion_mobility_range = true;
253
254 mobility_scan_num_begin =
255 tims_frame_csp.get()->getScanNumFromOneOverK0(
256 config
257 .getParameterValue(
260 .toDouble());
261
262 mobility_scan_num_end = tims_frame_csp.get()->getScanNumFromOneOverK0(
263 config
264 .getParameterValue(
267 .toDouble());
268 }
269
270 // Get to know the size of the frame, that is,
271 // the number of mobility scans in it.
272 quint32 mobility_scans_count = tims_frame_csp->getTotalNumberOfScans();
273
274 // Provide these two variables for the function below to fill in the
275 // values.
276 quint32 min_mz_index_out = 0;
277 quint32 max_mz_index_out = 0;
278
279 Trace spectrum;
280
281 if(config.needPeakList())
282 {
283 if(asked_ion_mobility_range)
284 {
285 if(mobility_scan_num_end > (mobility_scans_count - 1))
286 {
287 mobility_scan_num_end = mobility_scans_count - 1;
288 }
289 }
290 else
291 {
292 mobility_scan_num_begin = 0;
293 mobility_scan_num_end = mobility_scans_count - 1;
294 }
295
296 if(asked_mz_range)
297 {
298 spectrum = tims_frame_csp->cumulateScansToTraceMzDownResolution2(
299 mz_index_merge_window,
300 mz_range_begin,
301 mz_range_end,
302 mobility_scan_num_begin,
303 mobility_scan_num_end,
304 min_mz_index_out,
305 max_mz_index_out);
306 }
307 else
308 {
309 spectrum = tims_frame_csp->cumulateScansToTraceMzDownResolution(
310 mz_index_merge_window,
311 mobility_scan_num_begin,
312 mobility_scan_num_end,
313 min_mz_index_out,
314 max_mz_index_out);
315 }
316 }
317
318 // qDebug() << "Got min_mz_index_out:" << min_mz_index_out;
319 // qDebug() << "Got max_mz_index_out:" << max_mz_index_out;
320
321 // Now, with or without the peak list, we have to craft a qualified mass
322 // spectrum that will hold all the data about the data in it.
323 QualifiedMassSpectrum mass_spectrum;
324
325 MassSpectrumId spectrum_id;
326
327 spectrum_id.setSpectrumIndex(tims_frame_id);
328 spectrum_id.setMsRunId(getMsRunId());
329
330 // Can be modified to add bits that might help our case
331 spectrum_id.setNativeId(
332 QString("frame id=%1 scan index=%2 im_begin=%3 im_end=%4")
333 .arg(tims_frame_id)
334 .arg(scan_index)
335 .arg(mobility_scan_num_begin)
336 .arg(mobility_scan_num_end));
337
338 mass_spectrum.setMassSpectrumId(spectrum_id);
339
340 // We want to document the retention time!
341 mass_spectrum.setRtInSeconds(tims_frame_csp.get()->getTime());
342
343 // We do want to document the ms level of the spectrum and possibly
344 // the precursor's m/z and charge.
345 unsigned int frame_ms_level = tims_frame_csp.get()->getMsLevel();
346 mass_spectrum.setMsLevel(frame_ms_level);
347
348 // We cannot set this value because the inverse mobility (1/Ko) measured
349 // by Bruker does not correspond formally to a drift time.
350 mass_spectrum.setDtInMilliSeconds(-1);
351
352 mass_spectrum.setParameterValue(
354 (qlonglong)tims_frame_csp->getTotalNumberOfScans());
355 mass_spectrum.setParameterValue(
357 tims_frame_csp->getOneOverK0Transformation(0));
358 mass_spectrum.setParameterValue(
360 tims_frame_csp->getOneOverK0Transformation(
361 tims_frame_csp->getTotalNumberOfScans() - 1));
362
363 // qDebug() << "Setting mass spectrum parameter value mz index begin to:"
364 // << min_mz_index_out;
365 mass_spectrum.setParameterValue(
367 min_mz_index_out);
368
369 // qDebug() << "Setting mass spectrum parameter value mz index end to:"
370 // << max_mz_index_out;
371 mass_spectrum.setParameterValue(
373
374 if(config.needPeakList())
375 {
376 mass_spectrum.setEmptyMassSpectrum(false);
377
378 mass_spectrum.setMassSpectrumSPtr(
379 std::make_shared<MassSpectrum>(spectrum));
380 }
381 else
382 {
383 mass_spectrum.setEmptyMassSpectrum(true);
384 }
385
386 handler.setQualifiedMassSpectrum(mass_spectrum);
387 }
388}
void setNativeId(const QString &native_id)
void setMsRunId(MsRunIdCstSPtr other)
void setSpectrumIndex(std::size_t index)
const QVariant getParameterValue(MsRunReadConfigParameter parameter) const
bool acceptMsLevel(std::size_t ms_level) const
bool acceptRetentionTimeInSeconds(double retention_time_in_seconds) const
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 setParameterValue(QualifiedMassSpectrumParameter parameter, const QVariant &value)
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 setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
@ TimsFrameInvKoBegin
Bruker's Tims tof 1/K0 frame start range.
@ TimsFrameMzIndexBegin
Bruker's Tims tof mz index frame start range.
@ TimsFrameMzIndexEnd
Bruker's Tims tof mz index frame end range.
@ TimsFrameInvKoEnd
Bruker's Tims tof 1/K0 frame end range.
MsRunReadConfigParameter
std::size_t m_cumulSize
Definition timsdata.h:57

References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), pappso::MsRunReader::getMsRunId(), pappso::MsRunReadConfig::getParameterValue(), pappso::FrameIdDescr::m_cumulSize, msp_timsData, pappso::MsRunReadConfig::needPeakList(), pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), pappso::TimsFrameInvKoBegin, pappso::TimsFrameInvKoEnd, pappso::TimsFrameMzIndexBegin, pappso::TimsFrameMzIndexEnd, pappso::TimsFrameScansCount, pappso::TimsFramesMsRunReader_mobility_index_begin, pappso::TimsFramesMsRunReader_mobility_index_end, pappso::TimsFramesMsRunReader_mobility_one_over_k0_begin, pappso::TimsFramesMsRunReader_mobility_one_over_k0_end, pappso::TimsFramesMsRunReader_mz_begin, pappso::TimsFramesMsRunReader_mz_end, pappso::TimsFramesMsRunReader_mz_index_merge_window, and pappso::MsRunReadConfig::toString().

Referenced by readSpectrumCollection().

◆ 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 392 of file timsframesmsrunreader.cpp.

395{
396 qDebug();
397}

◆ 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 415 of file timsframesmsrunreader.cpp.

416{
417 msp_timsData = nullptr;
418 return true;
419}

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 401 of file timsframesmsrunreader.cpp.

402{
403 return msp_timsData->getTotalNumberOfScans();
404}

References msp_timsData.

Friends And Related Symbol 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: