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;
179 XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id,
189 void ms2ReaderSpectrumCollectionByMsLevel(
192 unsigned int ms_level);
200 void rawReaderSpectrumCollectionByMsLevel(
203 unsigned int ms_level);
211 std::map<quint32, quint32>
212 getRawMs2ByPrecursorId(std::size_t precursor_index);
220 std::map<quint32, quint32>
221 getRawMsBySpectrumIndex(std::size_t spectrum_index);
228 virtual std::vector<double> getRetentionTimeLine()
const;
232 SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id);
238 void setMonoThread(
bool is_mono_thread);
243 const std::pair<std::size_t, std::size_t> &scan_coordinate);
246 std::pair<std::size_t, std::size_t>
247 getScanCoordinateFromRawIndex(std::size_t spectrum_index)
const;
249 std::size_t getRawIndexFromCoordinate(std::size_t frame_id,
250 std::size_t scan_num)
const;
252 QSqlDatabase openDatabaseConnection()
const;
264 std::vector<std::size_t>
265 getMatchPrecursorIdByKo(std::vector<std::vector<double>> ids,
270 std::vector<std::size_t>
271 getClosestPrecursorIdByMz(std::vector<std::vector<double>> ids,
277 void fillFrameIdDescrList();
281 void ms2ReaderGenerateMS1MS2Spectrum(
283 std::vector<QualifiedMassSpectrum> &qualified_mass_spectrum_list,
286 unsigned int ms_level);
288 void fillSpectrumDescriptionWithSqlRecord(
SpectrumDescr &spectrum_descr,
289 QSqlQuery &qprecursor_list);
298 std::size_t m_cacheSize = 60;
307 bool m_builtinMs2Centroid =
true;
342 bool m_isMonoThread =
false;
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_mapXicCoordRecord
std::size_t m_totalNumberOfFrames
std::size_t m_totalNumberOfScans
std::deque< TimsFrameCstSPtr > m_timsFrameCache
std::vector< TimsFrameRecord > m_mapFramesRecord
std::map< int, QSqlRecord > m_mapMzCalibrationRecord
std::map< int, QSqlRecord > m_mapTimsCalibrationRecord
std::vector< std::size_t > m_someoneIsLoadingFrameId
tells if someone is loading a frame id
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 @k...
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