libpappsomspp
Library for mass spectrometry
Loading...
Searching...
No Matches
pappso::cbor::mzcbor::MzcborSpectrumCollectionReader Class Reference

#include <mzcborspectrumcollectionreader.h>

Inheritance diagram for pappso::cbor::mzcbor::MzcborSpectrumCollectionReader:
pappso::cbor::mzcbor::MzcborReaderBase pappso::cbor::CborStreamReaderInterface

Public Member Functions

 MzcborSpectrumCollectionReader (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)
virtual ~MzcborSpectrumCollectionReader ()
void setMsRunId (const MsRunIdCstSPtr &msrun_id)
void setNativeId2SpectrumIndexMapPtr (const std::map< QString, std::size_t > *nativeId2SpectrumIndexMap)
Public Member Functions inherited from pappso::cbor::mzcbor::MzcborReaderBase
 MzcborReaderBase ()
virtual ~MzcborReaderBase ()
virtual void readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
 read mzCBOR file
virtual void readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
 read mzCBOR from any device (memory buffer or else)
virtual void close ()
 convenient function to clean pointer before leaving
bool isMzcbor () const
const QStringList & getMsrunIdList () const
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
 CborStreamReaderInterface ()
virtual ~CborStreamReaderInterface ()

Protected Member Functions

virtual void readMsrun () override
 read only the targeted msrun
void readSpectrumListAndLeave ()
 only the spectrum list of targeted msrun, then stop parsing
void readSpectrum (std::size_t index_count, bool want_binary_data)
 read each spectrum in the targeted msrun (msrunId)
std::map< QString, CvParam > readScan ()
Protected Member Functions inherited from pappso::cbor::mzcbor::MzcborReaderBase
void readRoot (pappso::UiMonitorInterface &monitor)
virtual void readReferenceableParamGroupList ()
std::map< QString, CvParam > getCvParamsMap ()
 read the array containing cvParams to give accessions and values
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool getExpectedString ()
void initCborReader (QFile *pcborfile)
void initCborReader (QIODevice *pcborfile)

Private Attributes

const MsRunReadConfig & m_msRunReadConfig
SpectrumCollectionHandlerInterface & m_SpectrumCollectionHandlerInterface
MsRunIdCstSPtr mcsp_msRunId
QString m_xmlMzMlRunId
const std::map< QString, std::size_t > * mp_nativeId2SpectrumIndexMap = nullptr

Additional Inherited Members

Protected Attributes inherited from pappso::cbor::mzcbor::MzcborReaderBase
bool m_stopParsing = false
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader * mpa_cborReader = nullptr
QString m_expectedString
QByteArray m_data

Detailed Description

Todo
write docs

Definition at line 45 of file mzcborspectrumcollectionreader.h.

Constructor & Destructor Documentation

◆ MzcborSpectrumCollectionReader()

pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::MzcborSpectrumCollectionReader ( const MsRunReadConfig & config,
SpectrumCollectionHandlerInterface & handler )

Default constructor

Definition at line 36 of file mzcborspectrumcollectionreader.cpp.

39 : m_msRunReadConfig(m_msRunReadConfig),
40 m_SpectrumCollectionHandlerInterface(m_SpectrumCollectionHandlerInterface)
41{
42}
pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_SpectrumCollectionHandlerInterface
SpectrumCollectionHandlerInterface & m_SpectrumCollectionHandlerInterface
Definition mzcborspectrumcollectionreader.h:82

References m_msRunReadConfig, and m_SpectrumCollectionHandlerInterface.

◆ ~MzcborSpectrumCollectionReader()

pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::~MzcborSpectrumCollectionReader ( )
virtual

Destructor

Definition at line 44 of file mzcborspectrumcollectionreader.cpp.

45{
46}

Member Function Documentation

◆ readMsrun()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readMsrun ( )
overrideprotectedvirtual

read only the targeted msrun

Reimplemented from pappso::cbor::mzcbor::MzcborReaderBase.

Definition at line 64 of file mzcborspectrumcollectionreader.cpp.

65{
66 // qDebug();
67
68 mpa_cborReader->enterContainer();
69 bool ms_run_to_read = false;
70
71 while(getExpectedString())
72 {
73 if(m_expectedString == "id")
74 {
75 getExpectedString();
76
77 if((m_expectedString == m_xmlMzMlRunId) || (m_xmlMzMlRunId.isEmpty()))
78 {
79 ms_run_to_read = true;
80 }
81 }
82 else if(m_expectedString == "spectrumList")
83 {
84 if(ms_run_to_read)
85 {
86 readSpectrumListAndLeave();
87 }
88 else
89 {
90 mpa_cborReader->next();
91 }
92 }
93 else
94 {
95 mpa_cborReader->next();
96 }
97 }
98
99 mpa_cborReader->leaveContainer();
100}
pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrumListAndLeave
void readSpectrumListAndLeave()
only the spectrum list of targeted msrun, then stop parsing
Definition mzcborspectrumcollectionreader.cpp:103

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_xmlMzMlRunId, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readSpectrumListAndLeave().

◆ readScan()

std::map< QString, pappso::cbor::mzcbor::CvParam > pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readScan ( )
protected

Definition at line 370 of file mzcborspectrumcollectionreader.cpp.

371{
372 std::map<QString, CvParam> cv_params;
373 mpa_cborReader->enterContainer();
374 while(getExpectedString())
375 {
376 qDebug() << m_expectedString;
377 if(m_expectedString == "cvParam")
378 {
379 cv_params = getCvParamsMap();
380 }
381 else
382 {
383 mpa_cborReader->next();
384 }
385 }
386 mpa_cborReader->leaveContainer();
387 return cv_params;
388}
pappso::cbor::mzcbor::MzcborReaderBase::getCvParamsMap
std::map< QString, CvParam > getCvParamsMap()
read the array containing cvParams to give accessions and values
Definition mzcborreaderbase.cpp:190

References pappso::cbor::mzcbor::MzcborReaderBase::getCvParamsMap(), pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

◆ readSpectrum()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum ( std::size_t index_count,
bool want_binary_data )
protected

read each spectrum in the targeted msrun (msrunId)

Definition at line 181 of file mzcborspectrumcollectionreader.cpp.

183{
184
185 qDebug() << index_count << " " << want_binary_data;
186 try
187 {
188 Spectrum cbor_spectrum;
189 cbor_spectrum.fromCbor(*mpa_cborReader, want_binary_data);
190 //<spectrum id="controllerType=0 controllerNumber=1 scan=1" index="0"
191 // defaultArrayLength="1552">
192
193
194 // Now, with or without the peak list, we have to craft a qualified mass
195 // spectrum that will hold all the metadata about the data potentially
196 // found in it.
197 QualifiedMassSpectrum qualified_mass_spectrum;
198
199 MassSpectrumId spectrum_id(mcsp_msRunId, cbor_spectrum.index);
200 spectrum_id.setNativeId(cbor_spectrum.id);
201
202 spectrum_id.setSpectrumIndex(cbor_spectrum.index);
203
204 qualified_mass_spectrum.setMassSpectrumId(spectrum_id);
205 qualified_mass_spectrum.setRtInSeconds(cbor_spectrum.getRtInSeconds());
206
207
208 if(cbor_spectrum.precursorList.size() > 0)
209 {
210 qualified_mass_spectrum.setPrecursorNativeId(
211 cbor_spectrum.precursorList.at(0).spectrumRef);
212 if(mp_nativeId2SpectrumIndexMap != nullptr)
213 {
214 auto it =
215 mp_nativeId2SpectrumIndexMap->find(cbor_spectrum.precursorList.at(0).spectrumRef);
216 if(it != mp_nativeId2SpectrumIndexMap->end())
217 {
218 qualified_mass_spectrum.setPrecursorSpectrumIndex(it->second);
219 }
220 }
221
222 for(auto &precursor : cbor_spectrum.precursorList)
223 {
224 PrecursorIonData ion_data;
225 ion_data.mz = precursor.isolationWindow.getTargetMz();
226 for(auto &selected_ion : precursor.selectedIonList)
227 {
228 ion_data.charge = selected_ion.getChargeState();
229
230 bool is_ok;
231 ion_data.intensity = selected_ion.getIntensity(&is_ok);
232 ion_data.mz = selected_ion.getMz();
233
234 qualified_mass_spectrum.appendPrecursorIonData(ion_data);
235 }
236 }
237 }
238
239 qDebug();
240 qualified_mass_spectrum.setMsLevel(cbor_spectrum.getMsLevel());
241
242 qDebug();
243 qualified_mass_spectrum.setEmptyMassSpectrum(!cbor_spectrum.defaultArrayLength);
244
245 if(cbor_spectrum.binaryDataArrayList.size() == 2)
246 {
247 qDebug();
248 MassSpectrumSPtr mass_spectrum_sp = std::make_shared<MassSpectrum>();
249 qDebug();
250 cbor_spectrum.decodeTrace(*(mass_spectrum_sp.get()));
251 qDebug();
252 qualified_mass_spectrum.setMassSpectrumSPtr(mass_spectrum_sp);
253 qDebug();
254 }
255
256 qDebug() << "spectrum_id.getNativeId()=" << spectrum_id.getNativeId();
257 qDebug() << "rt=" << qualified_mass_spectrum.getRtInSeconds();
258 qDebug() << "mslevel=" << qualified_mass_spectrum.getMsLevel();
259
260 if(m_msRunReadConfig.acceptMsLevel(qualified_mass_spectrum.getMsLevel()))
261 {
262 if(m_msRunReadConfig.acceptRetentionTimeInSeconds(
263 qualified_mass_spectrum.getRtInSeconds()))
264 {
265
266 if(qualified_mass_spectrum.getMassSpectrumId().getSpectrumIndex() ==
267 std::numeric_limits<std::size_t>::max())
268 {
269 throw pappso::PappsoException(
270 QObject::tr("ERROR in %1 spectrum index not initialised").arg(__FUNCTION__));
271 }
272 m_SpectrumCollectionHandlerInterface.setQualifiedMassSpectrum(
273 qualified_mass_spectrum);
274 }
275 }
276
277 /*
278 *
279 <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" />
280 <cvParam cvRef="MS" accession="MS:1000130" value="" name="positive scan" />
281 <cvParam cvRef="MS" accession="MS:1000285" value="17377980" name="total ion current" />
282 <cvParam cvRef="MS" accession="MS:1000127" value="" name="centroid spectrum" />
283 <cvParam cvRef="MS" accession="MS:1000504" value="519.138854980469" name="base peak m/z"
284 unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
285 <cvParam cvRef="MS"
286 accession="MS:1000505" value="1702482.375" name="base peak intensity"
287 unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS" /> <cvParam
288 cvRef="MS" accession="MS:1000528" value="400.153411865234" name="lowest observed m/z"
289 unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" /> <cvParam cvRef="MS"
290 accession="MS:1000527" value="1013.12335205078" name="highest observed m/z"
291 unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" /> <scanList count="1"> <cvParam
292 cvRef="MS" accession="MS:1000795" value="" name="no combination" /> <scan
293 instrumentConfigurationRef="IC1"> <cvParam cvRef="MS" accession="MS:1000016"
294 value="0.0048758833" name="scan start time" unitAccession="UO:0000031" unitName="minute"
295 unitCvRef="UO" /> <cvParam cvRef="MS" accession="MS:1000512" value="FTMS + p NSI Full lock ms
296 [400.00-1400.00]" name="filter string" /> <cvParam cvRef="MS" accession="MS:1000927"
297 value="250" name="ion injection time" unitAccession="UO:0000028" unitName="millisecond"
298 unitCvRef="UO" /> <scanWindowList count="1"> <scanWindow> <cvParam cvRef="MS"
299 accession="MS:1000501" value="400" name="scan window lower limit" unitAccession="MS:1000040"
300 unitName="m/z" unitCvRef="MS" /> <cvParam cvRef="MS" accession="MS:1000500" value="1400"
301 name="scan window upper limit" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
302 </scanWindow>
303 </scanWindowList>
304 </scan>
305 </scanList>
306 <binaryDataArrayList count="2">
307 */
308
309 // qDebug();
310 // Get the native pwiz-spectrum from the spectrum list.
311 // Note that this pointer is a shared pointer from pwiz.
312 /*
313 pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp =
314 getPwizSpectrumPtr(spectrum_list_p.get(), iter, want_binary_data);
315 // qDebug();
316
317 // Instantiate the mass spectrum id that will hold critical information
318 // like the the native id string and the spectrum index.
319
320 MassSpectrumId massSpectrumId(mcsp_msRunId, iter);
321
322 // qDebug();
323 // Get the spectrum native id as a QString to store it in the mass
324 // spectrum id class. This is will allow later to refer to the same
325 // spectrum starting back from the file.
326
327 QString native_id = QString::fromStdString(native_pwiz_spectrum_sp->id);
328 massSpectrumId.setNativeId(native_id);
329
330 // Finally, instantiate the qualified mass spectrum with its id. This
331 // function will continue performing pappso-spectrum detailed
332 // qualification.
333
334 bool ok = false;
335
336 QualifiedMassSpectrum qualified_mass_spectrum = qualifiedMassSpectrumFromPwizSpectrumPtr(
337 massSpectrumId, native_pwiz_spectrum_sp.get(), want_binary_data, ok);
338
339 if(!ok)
340 {
341 // qDebug() << "Encountered a mass spectrum for which the returned "
342 //"status is bad.";
343 continue;
344 }
345
346 // qDebug();
347 // Before handing the mass spectrum out to the m_SpectrumCollectionHandlerInterface, see if
348 // the native mass spectrum was empty or not.
349
350 // if(!native_pwiz_spectrum_sp->defaultArrayLength)
351 // qDebug() << "The mass spectrum has not defaultArrayLength";
352
353 qualified_mass_spectrum.setEmptyMassSpectrum(!native_pwiz_spectrum_sp->defaultArrayLength);
354
355 // The m_SpectrumCollectionHandlerInterface will receive the index of the mass spectrum in
356 the
357 // current run via the mass spectrum id member datum.
358
359 // qDebug();
360 */
361 }
362 catch(pappso::PappsoException &error)
363 {
364 throw pappso::PappsoException(
365 QObject::tr("ERROR reading spectrum index %1 :\%2").arg(index_count).arg(error.qwhat()));
366 }
367}
pappso::PappsoException::qwhat
virtual const QString & qwhat() const
Definition pappsoexception.h:66
pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::mp_nativeId2SpectrumIndexMap
const std::map< QString, std::size_t > * mp_nativeId2SpectrumIndexMap
Definition mzcborspectrumcollectionreader.h:86
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition massspectrum.h:53

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::cbor::mzcbor::Spectrum::binaryDataArrayList, pappso::PrecursorIonData::charge, pappso::cbor::mzcbor::Spectrum::decodeTrace(), pappso::cbor::mzcbor::Spectrum::defaultArrayLength, pappso::cbor::mzcbor::Spectrum::fromCbor(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::cbor::mzcbor::Spectrum::getMsLevel(), pappso::QualifiedMassSpectrum::getMsLevel(), pappso::MassSpectrumId::getNativeId(), pappso::cbor::mzcbor::Spectrum::getRtInSeconds(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MassSpectrumId::getSpectrumIndex(), pappso::cbor::mzcbor::Spectrum::id, pappso::cbor::mzcbor::Spectrum::index, pappso::PrecursorIonData::intensity, m_msRunReadConfig, m_SpectrumCollectionHandlerInterface, mcsp_msRunId, mp_nativeId2SpectrumIndexMap, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, pappso::PrecursorIonData::mz, pappso::cbor::mzcbor::Spectrum::precursorList, pappso::PappsoException::qwhat(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), and pappso::MassSpectrumId::setSpectrumIndex().

Referenced by readSpectrumListAndLeave().

◆ readSpectrumListAndLeave()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrumListAndLeave ( )
protected

only the spectrum list of targeted msrun, then stop parsing

Definition at line 103 of file mzcborspectrumcollectionreader.cpp.

104{
105 mpa_cborReader->enterContainer();
106 // We want to iterate in the pwiz-spectrum-list and for each pwiz-spectrum
107 // create a pappso-spectrum (QualifiedMassSpectrum). Once the pappso mass
108 // spectrum has been fully qualified (that is, the member data have been
109 // set), it is transferred to the m_SpectrumCollectionHandlerInterface passed as parameter to this
110 // function for the consumer to do what it wants with it.
111
112 // Does the m_SpectrumCollectionHandlerInterface consuming the mass spectra read from file want
113 // these mass spectra to hold the binary data arrays (mz/i vectors)?
114
115 const bool want_binary_data = m_msRunReadConfig.needPeakList();
116
117
118 // qDebug();
119
120 // We'll need it to perform the looping in the spectrum list.
121 std::size_t spectrum_list_size = 0;
122
123 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
124
125 while(getExpectedString())
126 {
127
128 qDebug() << m_expectedString;
129 if(m_expectedString == "count")
130 {
131 if(mpa_cborReader->isUnsignedInteger())
132 {
133 spectrum_list_size = mpa_cborReader->toUnsignedInteger();
134 mpa_cborReader->next();
135 qDebug() << "spectrum count=" << spectrum_list_size;
136 }
137
138 // Inform the m_SpectrumCollectionHandlerInterface of the spectrum list so that it can
139 // handle feedback to the user.
140 m_SpectrumCollectionHandlerInterface.spectrumListHasSize(spectrum_list_size);
141 }
142 else if(m_expectedString == "spectrum")
143 {
144
145 mpa_cborReader->enterContainer(); // start array
146
147 std::size_t index_count = 0;
148 while(mpa_cborReader->hasNext())
149 {
150 // If the user of this reader instance wants to stop reading the
151 // spectra, then break this loop.
152 if(m_SpectrumCollectionHandlerInterface.shouldStop())
153 {
154 qDebug() << "The operation was cancelled. Breaking the loop.";
155 m_stopParsing = true;
156 return;
157 }
158
159 readSpectrum(index_count, want_binary_data);
160 index_count++;
161 }
162
163 mpa_cborReader->leaveContainer(); // stop array
164 }
165 else
166 {
167 mpa_cborReader->next();
168 }
169 }
170
171
172 qDebug() << "Loading ended";
173 m_SpectrumCollectionHandlerInterface.loadingEnded();
174
175 mpa_cborReader->leaveContainer();
176 m_stopParsing = true;
177}
pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum
void readSpectrum(std::size_t index_count, bool want_binary_data)
read each spectrum in the targeted msrun (msrunId)
Definition mzcborspectrumcollectionreader.cpp:181

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_msRunReadConfig, m_SpectrumCollectionHandlerInterface, pappso::cbor::mzcbor::MzcborReaderBase::m_stopParsing, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readSpectrum().

Referenced by readMsrun().

◆ setMsRunId()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::setMsRunId ( const MsRunIdCstSPtr & msrun_id)

Definition at line 49 of file mzcborspectrumcollectionreader.cpp.

50{
51 mcsp_msRunId = msrun_id;
52 m_xmlMzMlRunId = mcsp_msRunId.get()->getRunId();
53}

References m_xmlMzMlRunId, and mcsp_msRunId.

Referenced by pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

◆ setNativeId2SpectrumIndexMapPtr()

void pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::setNativeId2SpectrumIndexMapPtr ( const std::map< QString, std::size_t > * nativeId2SpectrumIndexMap)

Definition at line 56 of file mzcborspectrumcollectionreader.cpp.

58{
59 mp_nativeId2SpectrumIndexMap = nativeId2SpectrumIndexMap;
60}

References mp_nativeId2SpectrumIndexMap.

Referenced by pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

Member Data Documentation

◆ m_msRunReadConfig

const MsRunReadConfig& pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_msRunReadConfig
private

Definition at line 81 of file mzcborspectrumcollectionreader.h.

Referenced by MzcborSpectrumCollectionReader(), readSpectrum(), and readSpectrumListAndLeave().

◆ m_SpectrumCollectionHandlerInterface

SpectrumCollectionHandlerInterface& pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_SpectrumCollectionHandlerInterface
private

Definition at line 82 of file mzcborspectrumcollectionreader.h.

Referenced by MzcborSpectrumCollectionReader(), readSpectrum(), and readSpectrumListAndLeave().

◆ m_xmlMzMlRunId

QString pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::m_xmlMzMlRunId
private

Definition at line 84 of file mzcborspectrumcollectionreader.h.

Referenced by readMsrun(), and setMsRunId().

◆ mcsp_msRunId

MsRunIdCstSPtr pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::mcsp_msRunId
private

Definition at line 83 of file mzcborspectrumcollectionreader.h.

Referenced by readSpectrum(), and setMsRunId().

◆ mp_nativeId2SpectrumIndexMap

const std::map<QString, std::size_t>* pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::mp_nativeId2SpectrumIndexMap = nullptr
private

Definition at line 86 of file mzcborspectrumcollectionreader.h.

Referenced by readSpectrum(), and setNativeId2SpectrumIndexMapPtr().

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