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);
112 Trace getTicChromatogram();
116 std::size_t parent_frame = 0;
117 std::size_t precursor_id = 0;
118 std::size_t scan_mobility_start = 0;
119 std::size_t scan_mobility_end = 0;
120 std::size_t ms1_index = 0;
121 std::size_t ms2_index = 0;
122 double isolationMz = 0;
123 double isolationWidth = 0;
124 float collisionEnergy = 0;
130 getQualifiedMs2MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
133 bool want_binary_data);
136 getQualifiedMs1MassSpectrumByPrecursorId(
const MsRunIdCstSPtr &msrun_id,
139 bool want_binary_data);
153 void setMs2BuiltinCentroid(
bool centroid);
159 bool getMs2BuiltinCentroid()
const;
162 std::vector<std::size_t> getTimsMS1FrameIdRange(
double rt_begin,
163 double rt_end)
const;
170 XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id,
180 void ms2ReaderSpectrumCollectionByMsLevel(
183 unsigned int ms_level);
191 void rawReaderSpectrumCollectionByMsLevel(
194 unsigned int ms_level);
202 std::map<quint32, quint32>
203 getRawMs2ByPrecursorId(std::size_t precursor_index);
211 std::map<quint32, quint32>
212 getRawMsBySpectrumIndex(std::size_t spectrum_index);
219 virtual std::vector<double> getRetentionTimeLine()
const;
223 SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id);
228 const std::pair<std::size_t, std::size_t> &scan_coordinate);
231 std::pair<std::size_t, std::size_t>
232 getScanCoordinateFromRawIndex(std::size_t spectrum_index)
const;
234 std::size_t getRawIndexFromCoordinate(std::size_t frame_id,
235 std::size_t scan_num)
const;
237 QSqlDatabase openDatabaseConnection()
const;
254 std::vector<std::size_t>
255 getMatchPrecursorIdByKo(std::vector<std::vector<double>> ids,
260 std::vector<std::size_t>
261 getClosestPrecursorIdByMz(std::vector<std::vector<double>> ids,
267 void fillFrameIdDescrList();
275 unsigned int ms_level);
277 void fillSpectrumDescriptionWithSqlRecord(
SpectrumDescr &spectrum_descr,
278 QSqlQuery &qprecursor_list);
286 std::size_t m_cacheSize = 60;
295 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
A simple container of DataPoint instances.
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