libpappsomspp
Library for mass spectrometry
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#include <timsdiaslices.h>
Classes | |
struct | FrameSliceRange |
struct | MsMsWindow |
struct | MsMsWindowGroup |
struct | MsMsWindowGroupList |
Public Member Functions | |
TimsDiaSlices (QSqlQuery &query, TimsData *tims_data_origin) | |
~TimsDiaSlices () | |
const MsMsWindowGroupList & | getMsMsWindowGroupList () const |
const std::map< std::size_t, MsMsWindowGroup * > & | getMapFrame2WindowGroupPtr () const |
std::size_t | getGlobalSliceIndexBeginByFrameId (std::size_t frame_id) const |
std::size_t | getFrameIdByGlobalSliceIndex (std::size_t global_slice_id) const |
std::size_t | getTotalSlicesCount () const |
get the number of DIA MS2 slices analyzed by PASEF | |
const MsMsWindow & | getMsMsWindowByGlobalSliceIndex (std::size_t global_slice_index) const |
TimsDataFastMap & | getCombinedMs2ScansByGlobalSliceIndex (std::size_t global_slice_index) const |
void | getMs2QualifiedSpectrumByGlobalSliceIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_slice_index, bool want_binary_data) const |
void | getMs1QualifiedSpectrumByGlobalSliceIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_slice_index, bool want_binary_data, int rt_position=0) const |
get MS1 spectrum corresponding to the given slice extract MS1 mz range and mobility range corresponding to a global slice | |
std::size_t | getLastMs1FrameIdByMs2FrameId (std::size_t frame_id) const |
Private Member Functions | |
const FrameSliceRange & | getFrameSliceRangeByGlobalSliceIndex (std::size_t global_slice_index) const |
Private Attributes | |
TimsData * | mp_timsDataOrigin |
MsMsWindowGroupList | m_msMsWindowGroupList |
std::map< std::size_t, MsMsWindowGroup * > | m_mapFrame2WindowGroupPtr |
std::vector< std::size_t > | m_frameId2GlobalSliceIndexBegin |
std::vector< std::size_t > | m_ms2frameId2Ms1FrameId |
std::vector< std::size_t > | m_ms1frameIdList |
std::vector< FrameSliceRange > | m_frameSliceRangeList |
bool | m_builtinMs2Centroid = true |
enable builtin centroid on raw tims integers by default | |
std::size_t | m_totalSlicesCount |
Definition at line 36 of file timsdiaslices.h.
pappso::TimsDiaSlices::TimsDiaSlices | ( | QSqlQuery & | query, |
TimsData * | tims_data_origin | ||
) |
Default constructor
Definition at line 113 of file timsdiaslices.cpp.
References pappso::TimsDiaSlices::MsMsWindowGroupList::addInGroup(), pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDiaSlices::MsMsWindow::CollisionEnergy, pappso::TimsDiaSlices::FrameSliceRange::end_global_slice_index, pappso::TimsDiaSlices::FrameSliceRange::frame_id, pappso::TimsDiaSlices::MsMsWindowGroupList::getWindowGroupPtrByGroupId(), pappso::TimsDiaSlices::MsMsWindow::IsolationMz, pappso::TimsDiaSlices::MsMsWindow::IsolationWidth, m_frameId2GlobalSliceIndexBegin, m_frameSliceRangeList, m_mapFrame2WindowGroupPtr, m_ms1frameIdList, m_ms2frameId2Ms1FrameId, m_msMsWindowGroupList, m_totalSlicesCount, pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, and pappso::TimsDiaSlices::MsMsWindow::WindowGroup.
pappso::TimsDiaSlices::~TimsDiaSlices | ( | ) |
TimsDataFastMap & pappso::TimsDiaSlices::getCombinedMs2ScansByGlobalSliceIndex | ( | std::size_t | global_slice_index | ) | const |
Definition at line 324 of file timsdiaslices.cpp.
References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDataFastMap::clear(), pappso::TimsDiaSlices::FrameSliceRange::frame_id, getFrameSliceRangeByGlobalSliceIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsData::getTimsFrameCstSPtrCached(), m_mapFrame2WindowGroupPtr, mp_timsDataOrigin, pappso::PappsoException::qwhat(), pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, and pappso::PappsoException::what().
std::size_t pappso::TimsDiaSlices::getFrameIdByGlobalSliceIndex | ( | std::size_t | global_slice_id | ) | const |
Definition at line 264 of file timsdiaslices.cpp.
References getFrameSliceRangeByGlobalSliceIndex().
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private |
Definition at line 270 of file timsdiaslices.cpp.
References m_frameSliceRangeList, and pappso::x.
Referenced by getCombinedMs2ScansByGlobalSliceIndex(), getFrameIdByGlobalSliceIndex(), getMs1QualifiedSpectrumByGlobalSliceIndex(), getMs2QualifiedSpectrumByGlobalSliceIndex(), and getMsMsWindowByGlobalSliceIndex().
std::size_t pappso::TimsDiaSlices::getGlobalSliceIndexBeginByFrameId | ( | std::size_t | frame_id | ) | const |
Definition at line 259 of file timsdiaslices.cpp.
References m_frameId2GlobalSliceIndexBegin.
std::size_t pappso::TimsDiaSlices::getLastMs1FrameIdByMs2FrameId | ( | std::size_t | frame_id | ) | const |
Definition at line 316 of file timsdiaslices.cpp.
References m_ms2frameId2Ms1FrameId.
Referenced by getMs1QualifiedSpectrumByGlobalSliceIndex().
const std::map< std::size_t, TimsDiaSlices::MsMsWindowGroup * > & pappso::TimsDiaSlices::getMapFrame2WindowGroupPtr | ( | ) | const |
Definition at line 248 of file timsdiaslices.cpp.
References m_mapFrame2WindowGroupPtr.
void pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
std::size_t | global_slice_index, | ||
bool | want_binary_data, | ||
int | rt_position = 0 |
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) | const |
get MS1 spectrum corresponding to the given slice extract MS1 mz range and mobility range corresponding to a global slice
msrun_id | |
mass_spectrum | |
global_slice_index | |
want_binary_data | |
rt_position | relative MS1 frame retention time : 0 latest MS1 frame, +1 next MS1 frame, -1 previous MS1 frame |
Definition at line 523 of file timsdiaslices.cpp.
References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDataFastMap::builtInCentroid(), pappso::TimsDataFastMap::clear(), pappso::TimsDiaSlices::FrameSliceRange::frame_id, getFrameSliceRangeByGlobalSliceIndex(), getLastMs1FrameIdByMs2FrameId(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsData::getTimsFrameBaseCstSPtrCached(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::TimsDiaSlices::MsMsWindow::IsolationMz, pappso::TimsDiaSlices::MsMsWindow::IsolationWidth, m_builtinMs2Centroid, m_mapFrame2WindowGroupPtr, m_ms1frameIdList, mp_timsDataOrigin, pappso::mz, pappso::PappsoException::qwhat(), pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsDiaSlices::MsMsWindow::SliceIndex, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, pappso::PappsoException::what(), and pappso::TimsDiaSlices::MsMsWindow::WindowGroup.
void pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
std::size_t | global_slice_index, | ||
bool | want_binary_data | ||
) | const |
Definition at line 367 of file timsdiaslices.cpp.
References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDataFastMap::builtInCentroid(), pappso::TimsDataFastMap::clear(), pappso::CollisionEnergy, pappso::TimsDiaSlices::MsMsWindow::CollisionEnergy, pappso::TimsDiaSlices::FrameSliceRange::frame_id, getFrameSliceRangeByGlobalSliceIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsData::getTimsFrameBaseCstSPtrCached(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::IsolationMz, pappso::TimsDiaSlices::MsMsWindow::IsolationMz, pappso::IsolationMzWidth, pappso::TimsDiaSlices::MsMsWindow::IsolationWidth, m_builtinMs2Centroid, m_mapFrame2WindowGroupPtr, m_ms2frameId2Ms1FrameId, mp_timsDataOrigin, pappso::PappsoException::qwhat(), pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsDiaSlices::MsMsWindow::SliceIndex, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, pappso::PappsoException::what(), and pappso::TimsDiaSlices::MsMsWindow::WindowGroup.
Referenced by pappso::TimsMsRunReaderDia::qualifiedMassSpectrum().
const TimsDiaSlices::MsMsWindow & pappso::TimsDiaSlices::getMsMsWindowByGlobalSliceIndex | ( | std::size_t | global_slice_index | ) | const |
Definition at line 301 of file timsdiaslices.cpp.
References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDiaSlices::FrameSliceRange::frame_id, getFrameSliceRangeByGlobalSliceIndex(), and m_mapFrame2WindowGroupPtr.
const TimsDiaSlices::MsMsWindowGroupList & pappso::TimsDiaSlices::getMsMsWindowGroupList | ( | ) | const |
Definition at line 253 of file timsdiaslices.cpp.
References m_msMsWindowGroupList.
std::size_t pappso::TimsDiaSlices::getTotalSlicesCount | ( | ) | const |
get the number of DIA MS2 slices analyzed by PASEF
Definition at line 295 of file timsdiaslices.cpp.
References m_totalSlicesCount.
Referenced by pappso::TimsMsRunReaderDia::spectrumListSize().
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enable builtin centroid on raw tims integers by default
Definition at line 148 of file timsdiaslices.h.
Referenced by getMs1QualifiedSpectrumByGlobalSliceIndex(), and getMs2QualifiedSpectrumByGlobalSliceIndex().
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Definition at line 141 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), and getGlobalSliceIndexBeginByFrameId().
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Definition at line 144 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), and getFrameSliceRangeByGlobalSliceIndex().
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Definition at line 140 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), getCombinedMs2ScansByGlobalSliceIndex(), getMapFrame2WindowGroupPtr(), getMs1QualifiedSpectrumByGlobalSliceIndex(), getMs2QualifiedSpectrumByGlobalSliceIndex(), and getMsMsWindowByGlobalSliceIndex().
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Definition at line 143 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), and getMs1QualifiedSpectrumByGlobalSliceIndex().
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Definition at line 142 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), getLastMs1FrameIdByMs2FrameId(), and getMs2QualifiedSpectrumByGlobalSliceIndex().
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Definition at line 139 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), and getMsMsWindowGroupList().
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Definition at line 150 of file timsdiaslices.h.
Referenced by TimsDiaSlices(), and getTotalSlicesCount().
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Definition at line 138 of file timsdiaslices.h.
Referenced by getCombinedMs2ScansByGlobalSliceIndex(), getMs1QualifiedSpectrumByGlobalSliceIndex(), and getMs2QualifiedSpectrumByGlobalSliceIndex().