libpappsomspp
Library for mass spectrometry
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replacement for std::map More...
#include <timsdatafastmap.h>
Classes | |
struct | TimsDataFastMapElement |
Public Member Functions | |
TimsDataFastMap () | |
std::size_t | accumulateIntensity (quint32 tofIndex, std::size_t intensity) |
accumulates intesity for the given tof index | |
std::size_t | readIntensity (quint32) |
reads intensity for a tof_index | |
void | downsizeMzRawMap (std::size_t mzindex_merge_window) |
downsize mz resolution to lower the number of real mz computations | |
void | builtInCentroid () |
simple filter to agregate counts on neigbhor mobility slots (+1) | |
void | removeArtefactualSpike () |
Static Public Member Functions | |
static TimsDataFastMap & | getTimsDataFastMapInstance () |
Public Attributes | |
std::vector< quint32 > | tofIndexList |
std::vector< TimsDataFastMapElement > | mapTofIndexIntensity |
Static Public Attributes | |
static std::map< QThread *, TimsDataFastMap > | m_preAllocatedFastaMapPerThread = {} |
replacement for std::map
Beware to use it carefully : clear the tofIndexList before using it
Definition at line 45 of file timsdatafastmap.h.
pappso::TimsDataFastMap::TimsDataFastMap | ( | ) |
Definition at line 53 of file timsdatafastmap.cpp.
Referenced by getTimsDataFastMapInstance().
std::size_t pappso::TimsDataFastMap::accumulateIntensity | ( | quint32 | tofIndex, |
std::size_t | intensity | ||
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accumulates intesity for the given tof index
sets the count value on the first access ( first_access is true) and add the tof index to the tofIndexList then increments it if it is called on the same tof index
Definition at line 59 of file timsdatafastmap.cpp.
References pappso::TimsDataFastMap::TimsDataFastMapElement::count, pappso::TimsDataFastMap::TimsDataFastMapElement::first_access, mapTofIndexIntensity, and tofIndexList.
Referenced by builtInCentroid(), pappso::TimsFrame::cumulateScan(), pappso::TimsFrameType1::cumulateScan(), pappso::TimsFrame::cumulateScan2(), pappso::TimsFrameType1::cumulateScan2(), and downsizeMzRawMap().
void pappso::TimsDataFastMap::builtInCentroid | ( | ) |
simple filter to agregate counts on neigbhor mobility slots (+1)
the map is modified in place
Definition at line 105 of file timsdatafastmap.cpp.
References accumulateIntensity(), readIntensity(), and tofIndexList.
Referenced by pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId().
void pappso::TimsDataFastMap::downsizeMzRawMap | ( | std::size_t | mzindex_merge_window | ) |
downsize mz resolution to lower the number of real mz computations
the map is modified in place
mzindex_merge_window | width of the mzindex window used to merge all intensities into a single point. This results in faster computing. |
Definition at line 84 of file timsdatafastmap.cpp.
References accumulateIntensity(), readIntensity(), and tofIndexList.
Referenced by pappso::TimsFrame::cumulateScansToTraceMzDownResolution(), and pappso::TimsFrame::cumulateScansToTraceMzDownResolution2().
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static |
Definition at line 40 of file timsdatafastmap.cpp.
References TimsDataFastMap(), m_preAllocatedFastaMapPerThread, and mapTofIndexIntensity.
Referenced by pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsFrame::cumulateScansToTraceMzDownResolution(), pappso::TimsFrame::cumulateScansToTraceMzDownResolution2(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsData::getRawMs2ByPrecursorId(), and pappso::TimsData::getRawMsBySpectrumIndex().
std::size_t pappso::TimsDataFastMap::readIntensity | ( | quint32 | key | ) |
reads intensity for a tof_index
reads the cumulated intensity for this tof index and replaces the first access boolean to true. => this is important to reuse the map in an other computation No need to erase the content or initialize it
Definition at line 76 of file timsdatafastmap.cpp.
References pappso::TimsDataFastMap::TimsDataFastMapElement::count, pappso::TimsDataFastMap::TimsDataFastMapElement::first_access, and mapTofIndexIntensity.
Referenced by builtInCentroid(), pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsFrame::cumulateScansToTraceMzDownResolution(), pappso::TimsFrame::cumulateScansToTraceMzDownResolution2(), downsizeMzRawMap(), and pappso::TimsFrameBase::getTraceFromCumulatedScans().
void pappso::TimsDataFastMap::removeArtefactualSpike | ( | ) |
Definition at line 163 of file timsdatafastmap.cpp.
References mapTofIndexIntensity, and tofIndexList.
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Definition at line 48 of file timsdatafastmap.h.
Referenced by getTimsDataFastMapInstance().
std::vector<TimsDataFastMapElement> pappso::TimsDataFastMap::mapTofIndexIntensity |
Definition at line 100 of file timsdatafastmap.h.
Referenced by accumulateIntensity(), getTimsDataFastMapInstance(), readIntensity(), and removeArtefactualSpike().
std::vector<quint32> pappso::TimsDataFastMap::tofIndexList |
Definition at line 98 of file timsdatafastmap.h.
Referenced by accumulateIntensity(), builtInCentroid(), pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsFrame::cumulateScansToTraceMzDownResolution(), pappso::TimsFrame::cumulateScansToTraceMzDownResolution2(), downsizeMzRawMap(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsData::getRawMs2ByPrecursorId(), pappso::TimsData::getRawMsBySpectrumIndex(), pappso::TimsFrameBase::getTraceFromCumulatedScans(), and removeArtefactualSpike().