53 std::size_t getTotalPrecursorCount()
const;
56 XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id,
62 std::size_t parent_frame = 0;
63 std::size_t precursor_id = 0;
64 std::size_t scan_mobility_start = 0;
65 std::size_t scan_mobility_end = 0;
66 std::size_t ms1_index = 0;
67 std::size_t ms2_index = 0;
68 double isolationMz = 0;
69 double isolationWidth = 0;
70 float collisionEnergy = 0;
79 getSpectrumDescrWithPrecursorId(std::size_t precursor_id)
const;
84 std::vector<TimsDdaPrecursors::SpectrumDescr>
85 getSpectrumDescrListByFrameId(std::size_t frame_id)
const;
89 void getQualifiedMs2MassSpectrumBySpectrumDescr(
93 bool want_binary_data);
97 void getQualifiedMs1MassSpectrumBySpectrumDescr(
101 bool want_binary_data);
117 void setMs2BuiltinCentroid(
bool centroid);
123 bool getMs2BuiltinCentroid()
const;
132 void ms2ReaderSpectrumCollectionByMsLevel(
135 unsigned int ms_level);
141 void setMonoThread(
bool is_mono_thread);
149 void rawReaderSpectrumCollectionByMsLevel(
152 unsigned int ms_level);
159 std::vector<std::size_t> getPrecursorsByMzRtCharge(
int charge,
165 [[deprecated(
"This function will be removed")]] std::vector<std::size_t>
166 getMatchPrecursorIdByKo(std::vector<std::vector<double>> ids,
172 [[deprecated(
"This function will be removed")]] std::vector<std::size_t>
173 getClosestPrecursorIdByMz(std::vector<std::vector<double>> ids,
185 TimsDataFastMap &getCombinedMs2ScansByPrecursorId(std::size_t precursor_id);
191 const std::pair<std::size_t, std::size_t> &scan_coordinates);
194 void ms2ReaderGenerateMS1MS2Spectrum(
196 std::vector<QualifiedMassSpectrum> &qualified_mass_spectrum_list,
199 unsigned int ms_level);
201 void fillSpectrumDescriptionWithSqlRecord(
SpectrumDescr &spectrum_descr,
202 QSqlQuery &qprecursor_list);
218 bool m_builtinMs2Centroid =
true;
220 bool m_isMonoThread =
false;