31 #include <QSqlDatabase>
34 #include "../../massspectrum/qualifiedmassspectrum.h"
35 #include "../../processing/filters/filterinterface.h"
36 #include "../../msrun/xiccoord/xiccoordtims.h"
37 #include "../../msrun/msrunreader.h"
80 getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index);
90 std::size_t getTotalNumberOfScans()
const;
94 std::size_t getTotalNumberOfPrecursors()
const;
100 std::vector<std::size_t> getPrecursorsFromMzRtCharge(
int charge,
105 unsigned int getMsLevelBySpectrumIndex(std::size_t spectrum_index);
107 void getQualifiedMassSpectrumByRawIndex(
const MsRunIdCstSPtr &msrun_id,
109 std::size_t spectrum_index,
110 bool want_binary_data);
114 std::size_t parent_frame = 0;
115 std::size_t precursor_id = 0;
116 std::size_t scan_mobility_start = 0;
117 std::size_t scan_mobility_end = 0;
118 std::size_t ms1_index = 0;
119 std::size_t ms2_index = 0;
120 double isolationMz = 0;
121 double isolationWidth = 0;
122 float collisionEnergy = 0;
128 getQualifiedMs2MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
131 bool want_binary_data);
134 getQualifiedMs1MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
137 bool want_binary_data);
151 void setMs2BuiltinCentroid(
bool centroid);
157 bool getMs2BuiltinCentroid()
const;
160 std::vector<std::size_t> getTimsMS1FrameIdRange(
double rt_begin,
161 double rt_end)
const;
168 XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id,
178 void ms2ReaderSpectrumCollectionByMsLevel(
181 unsigned int ms_level);
189 void rawReaderSpectrumCollectionByMsLevel(
192 unsigned int ms_level);
200 std::map<quint32, quint32>
201 getRawMs2ByPrecursorId(std::size_t precursor_index);
209 std::map<quint32, quint32>
210 getRawMsBySpectrumIndex(std::size_t spectrum_index);
217 virtual std::vector<double> getRetentionTimeLine()
const;
221 SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id);
226 const std::pair<std::size_t, std::size_t> &scan_coordinate);
229 std::pair<std::size_t, std::size_t>
230 getScanCoordinateFromRawIndex(std::size_t spectrum_index)
const;
232 std::size_t getRawIndexFromCoordinate(std::size_t frame_id,
233 std::size_t scan_num)
const;
235 QSqlDatabase openDatabaseConnection()
const;
252 std::vector<std::size_t>
253 getMatchPrecursorIdByKo(std::vector<std::vector<double>> ids,
258 std::vector<std::size_t>
259 getClosestPrecursorIdByMz(std::vector<std::vector<double>> ids,
265 void fillFrameIdDescrList();
273 unsigned int ms_level);
275 void fillSpectrumDescriptionWithSqlRecord(
SpectrumDescr &spectrum_descr,
276 QSqlQuery &qprecursor_list);
284 std::size_t m_cacheSize = 60;
293 bool m_builtinMs2Centroid =
true;
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
std::vector< FrameIdDescr > m_frameIdDescrList
store every frame id and corresponding sizes
std::map< std::size_t, QSqlRecord > m_mapFramesRecord
std::map< std::size_t, QSqlRecord > m_mapXicCoordRecord
std::size_t m_totalNumberOfScans
std::deque< TimsFrameCstSPtr > m_timsFrameCache
std::map< int, QSqlRecord > m_mapMzCalibrationRecord
std::map< int, QSqlRecord > m_mapTimsCalibrationRecord
TimsData(const TimsData &other)
MzCalibrationStore * mpa_mzCalibrationStore
std::deque< TimsFrameBaseCstSPtr > m_timsFrameBaseCache
std::map< std::size_t, std::size_t > m_thousandIndexToFrameIdDescrListIndex
index to find quickly a frameId in the description list with the raw index of spectrum modulo 1000
std::size_t m_totalNumberOfPrecursors
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
std::vector< std::size_t > tims_frame_list
PrecursorIonData precursor_ion_data
coordinates of the XIC to extract and the resulting XIC after extraction
binary file handler of Bruker's TimsTof raw data
handle a single Bruker's TimsTof frame