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 419 of file timsframesmsrunreader.cpp.

420{
421 if(msp_timsData == nullptr)
422 {
423 initialize();
424 }
425 return true;
426}

References initialize(), and msp_timsData.

Referenced by getTicChromatogram(), and getTimsDataSPtr().

◆ computeTicChromatogram()

Trace TimsFramesMsRunReader::computeTicChromatogram ( )
virtual

Definition at line 472 of file timsframesmsrunreader.cpp.

473{
474
475 // We want to compute the TIC chromatogram, not load the chromatogram that
476 // is located in the SQL database.
477 //
478 // For this, we need to iterated into the frames and ask for MS1 spectra
479 // only. msp_timsData has that information:
480 //
481 // std::vector<FrameIdDescr> m_frameIdDescrList;
482 //
483 // and
484
485 // struct FrameIdDescr
486 // {
487 // std::size_t m_frameId; // frame id
488 // std::size_t m_size; // frame size (number of TOF scans in frame)
489 // std::size_t m_cumulSize; // cumulative size
490 // };
491
492 Trace tic_chromatogram;
493
494 const std::vector<FrameIdDescr> frame_descr_list =
495 msp_timsData->getFrameIdDescrList();
496
497 for(FrameIdDescr frame_id_descr : frame_descr_list)
498 {
499 TimsFrameCstSPtr tims_frame_csp =
500 msp_timsData->getTimsFrameCstSPtrCached(frame_id_descr.m_frameId);
501 std::size_t scan_begin = 0;
502 std::size_t scan_end = tims_frame_csp->getTotalNumberOfScans() - 1;
503
504 // By convention, a TIC chromatogram is only performed using MS1
505 // spectra.
506 if(tims_frame_csp->getMsLevel() == 1)
507 {
508
509 // Retention times are in seconds in the Bruker world.
510 double rt = tims_frame_csp->getTime();
511
512 tic_chromatogram.append(DataPoint(
513 rt,
514 tims_frame_csp->cumulateScansIntensities(scan_begin, scan_end)));
515 }
516 else
517 continue;
518 }
519
520 return tic_chromatogram;
521}
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 460 of file timsframesmsrunreader.cpp.

461{
462 // Use the Sqlite database to fetch the total ion current chromatogram (TIC
463 // chromatogram).
464
466
467 return msp_timsData->getTicChromatogram();
468}
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 452 of file timsframesmsrunreader.cpp.

453{
455 return msp_timsData;
456}

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 405 of file timsframesmsrunreader.cpp.

406{
407 return false;
408}

◆ 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 441 of file timsframesmsrunreader.cpp.

444{
445 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
446 .arg(__FILE__)
447 .arg(__FUNCTION__)
448 .arg(__LINE__));
449}

◆ 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 430 of file timsframesmsrunreader.cpp.

433{
434 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
435 .arg(__FILE__)
436 .arg(__FUNCTION__)
437 .arg(__LINE__));
438}

◆ 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() << "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
218 // Now that we have gathered all the configuration bits from the user,
219 // iterate in the vector of frames records and for each frame ask that
220 // all its scans be combined into a single mass spectrum, by taking into
221 // account the configuration bits provided by the user.
222
223 const std::vector<FrameIdDescr> &frame_id_descr_list =
224 msp_timsData->getFrameIdDescrList();
225
226 // The scan index is the index of the scan in the *whole* mass data file, it
227 // is a sequential number of scans over all the frames.
228 std::size_t scan_index = 0; // iterate in each spectrum
229
230 for(std::size_t tims_frame_id : subset_of_tims_frame_ids)
231 {
232 const FrameIdDescr &current_frame_record =
233 frame_id_descr_list[tims_frame_id];
234
235 scan_index = current_frame_record.m_cumulSize;
236 TimsFrameCstSPtr tims_frame_csp =
237 msp_timsData->getTimsFrameCstSPtrCached(tims_frame_id);
238
239 // If the user wants to select specific 1/Ko values, we need to
240 // compute the ion mobility scan value starting from that 1/Ko value in
241 // each frame.
242
243 if(!config
244 .getParameterValue(
247 .isNull())
248 {
249 asked_ion_mobility_range = true;
250
251 mobility_scan_num_begin =
252 tims_frame_csp.get()->getScanNumFromOneOverK0(
253 config
254 .getParameterValue(
257 .toDouble());
258
259 mobility_scan_num_end = tims_frame_csp.get()->getScanNumFromOneOverK0(
260 config
261 .getParameterValue(
264 .toDouble());
265 }
266
267 // Get to know the size of the frame, that is,
268 // the number of mobility scans in it.
269 quint32 mobility_scans_count = tims_frame_csp->getTotalNumberOfScans();
270
271 // Provide these two variables for the function below to fill in the
272 // values.
273 quint32 min_mz_index_out = 0;
274 quint32 max_mz_index_out = 0;
275
276 Trace spectrum;
277
278 if(config.needPeakList())
279 {
280 if(asked_ion_mobility_range)
281 {
282 if(mobility_scan_num_end > (mobility_scans_count - 1))
283 mobility_scan_num_end = mobility_scans_count - 1;
284
285 if(asked_mz_range)
286 spectrum = tims_frame_csp->cumulateScanToTraceMzDownResolution2(
287 mz_index_merge_window,
288 mz_range_begin,
289 mz_range_end,
290 mobility_scan_num_begin,
291 mobility_scan_num_end,
292 min_mz_index_out,
293 max_mz_index_out);
294 else
295 spectrum = tims_frame_csp->cumulateScanToTraceMzDownResolution(
296 mz_index_merge_window,
297 mobility_scan_num_begin,
298 mobility_scan_num_end,
299 min_mz_index_out,
300 max_mz_index_out);
301 }
302 else
303 {
304 mobility_scan_num_end = mobility_scans_count - 1;
305
306 spectrum = tims_frame_csp->cumulateScanToTraceMzDownResolution(
307 mz_index_merge_window,
308 0,
309 mobility_scan_num_end,
310 min_mz_index_out,
311 max_mz_index_out);
312 }
313 }
314
315 // qDebug() << "Got min_mz_index_out:" << min_mz_index_out;
316 // qDebug() << "Got max_mz_index_out:" << max_mz_index_out;
317
318 // Now, with or without the peak list, we have to craft a qualified mass
319 // spectrum that will hold all the data about the data in it.
320 QualifiedMassSpectrum mass_spectrum;
321
322 MassSpectrumId spectrum_id;
323
324 spectrum_id.setSpectrumIndex(tims_frame_id);
325 spectrum_id.setMsRunId(getMsRunId());
326
327 // Can be modified to add bits that might help our case
328 spectrum_id.setNativeId(
329 QString("frame id=%1 scan index=%2 im_begin=%3 im_end=%4")
330 .arg(tims_frame_id)
331 .arg(scan_index)
332 .arg(mobility_scan_num_begin)
333 .arg(mobility_scan_num_end));
334
335 mass_spectrum.setMassSpectrumId(spectrum_id);
336
337 // We want to document the retention time!
338 mass_spectrum.setRtInSeconds(tims_frame_csp.get()->getTime());
339
340 // We do want to document the ms level of the spectrum and possibly
341 // the precursor's m/z and charge.
342 unsigned int frame_ms_level = tims_frame_csp.get()->getMsLevel();
343 mass_spectrum.setMsLevel(frame_ms_level);
344
345 // We cannot set this value because the inverse mobility (1/Ko) measured
346 // by Bruker does not correspond formally to a drift time.
347 mass_spectrum.setDtInMilliSeconds(-1);
348
349 mass_spectrum.setParameterValue(
351 (qlonglong)tims_frame_csp->getTotalNumberOfScans());
352 mass_spectrum.setParameterValue(
354 tims_frame_csp->getOneOverK0Transformation(0));
355 mass_spectrum.setParameterValue(
357 tims_frame_csp->getOneOverK0Transformation(
358 tims_frame_csp->getTotalNumberOfScans() - 1));
359
360 // qDebug() << "Setting mass spectrum parameter value mz index begin to:"
361 // << min_mz_index_out;
362 mass_spectrum.setParameterValue(
364 min_mz_index_out);
365
366 // qDebug() << "Setting mass spectrum parameter value mz index end to:"
367 // << max_mz_index_out;
368 mass_spectrum.setParameterValue(
370
371 if(config.needPeakList())
372 {
373 mass_spectrum.setEmptyMassSpectrum(false);
374
375 mass_spectrum.setMassSpectrumSPtr(
376 std::make_shared<MassSpectrum>(spectrum));
377 }
378 else
379 {
380 mass_spectrum.setEmptyMassSpectrum(true);
381 }
382
383 handler.setQualifiedMassSpectrum(mass_spectrum);
384 }
385}
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 389 of file timsframesmsrunreader.cpp.

392{
393 qDebug();
394}

◆ 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 412 of file timsframesmsrunreader.cpp.

413{
414 msp_timsData = nullptr;
415 return true;
416}

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 398 of file timsframesmsrunreader.cpp.

399{
400 return msp_timsData->getTotalNumberOfScans();
401}

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: