88 getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index);
98 std::size_t getTotalNumberOfFrames()
const;
102 std::size_t getTotalNumberOfScans()
const;
106 std::size_t getTotalNumberOfPrecursors()
const;
112 std::vector<std::size_t> getPrecursorsFromMzRtCharge(
int charge,
117 unsigned int getMsLevelBySpectrumIndex(std::size_t spectrum_index);
119 void getQualifiedMassSpectrumByRawIndex(
const MsRunIdCstSPtr &msrun_id,
121 std::size_t spectrum_index,
122 bool want_binary_data);
124 Trace getTicChromatogram()
const;
128 std::size_t parent_frame = 0;
129 std::size_t precursor_id = 0;
130 std::size_t scan_mobility_start = 0;
131 std::size_t scan_mobility_end = 0;
132 std::size_t ms1_index = 0;
133 std::size_t ms2_index = 0;
134 double isolationMz = 0;
135 double isolationWidth = 0;
136 float collisionEnergy = 0;
142 getQualifiedMs2MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
145 bool want_binary_data);
148 getQualifiedMs1MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
151 bool want_binary_data);
165 void setMs2BuiltinCentroid(
bool centroid);
171 bool getMs2BuiltinCentroid()
const;
174 std::vector<std::size_t> getTimsMS1FrameIdRange(
double rt_begin,
175 double rt_end)
const;
191 XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id,
201 void ms2ReaderSpectrumCollectionByMsLevel(
204 unsigned int ms_level);
212 void rawReaderSpectrumCollectionByMsLevel(
215 unsigned int ms_level);
239 virtual std::vector<double> getRetentionTimeLine()
const;
243 SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id);
249 void setMonoThread(
bool is_mono_thread);
251 const std::vector<FrameIdDescr> &getFrameIdDescrList()
const;
252 const std::vector<TimsFrameRecord> &getTimsFrameRecordList()
const;
257 const std::pair<std::size_t, std::size_t> &scan_coordinate);
260 std::pair<std::size_t, std::size_t>
261 getScanCoordinateFromRawIndex(std::size_t spectrum_index)
const;
263 std::size_t getRawIndexFromCoordinate(std::size_t frame_id,
264 std::size_t scan_num)
const;
266 QSqlDatabase openDatabaseConnection()
const;
278 std::vector<std::size_t>
279 getMatchPrecursorIdByKo(std::vector<std::vector<double>> ids,
284 std::vector<std::size_t>
285 getClosestPrecursorIdByMz(std::vector<std::vector<double>> ids,
291 void fillFrameIdDescrList();
294 void ms2ReaderGenerateMS1MS2Spectrum(
296 std::vector<QualifiedMassSpectrum> &qualified_mass_spectrum_list,
299 unsigned int ms_level);
301 void fillSpectrumDescriptionWithSqlRecord(
SpectrumDescr &spectrum_descr,
302 QSqlQuery &qprecursor_list);
310 std::size_t m_cacheSize = 60;
319 bool m_builtinMs2Centroid =
true;
346 bool m_isMonoThread =
false;