libpappsomspp
Library for mass spectrometry
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#include <msrunxicextractordisk.h>
Public Member Functions | |
MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader) | |
MsRunXicExtractorDisk (const MsRunXicExtractorDisk &other) | |
virtual | ~MsRunXicExtractorDisk () |
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MsRunXicExtractor (const MsRunXicExtractor &other) | |
virtual | ~MsRunXicExtractor () |
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void | setXicExtractMethod (XicExtractMethod method) |
set the XIC extraction method More... | |
void | setRetentionTimeAroundTarget (double range_in_seconds) |
set the retention time range in seconds around the target rt More... | |
virtual void | extractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final |
extract a list of XIC given a list of xic coordinates to extract More... | |
virtual void | extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final |
multithreaded XIC extraction More... | |
const MsRunIdCstSPtr & | getMsRunId () const |
const MsRunReaderSPtr & | getMsRunReaderSPtr () const |
get the msrunreader currently used for XIC extraction More... | |
void | setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter) |
filter interface to apply just after XIC extration on each trace More... | |
Protected Member Functions | |
MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir) | |
virtual void | protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override |
void | prepareExtractor () |
void | serializeMsRun () |
virtual void | storeSlices (std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) |
store MassSpectrum slices (by daltons) for a given retention time More... | |
void | appendSliceOnDisk (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos) |
append a slice on disk (in a file) More... | |
std::vector< MsRunSliceSPtr > | acquireSlices (const MzRange &mz_range) |
retrieve all the slices corresponding to a given mz_range More... | |
MsRunSliceSPtr | unserializeSlice (unsigned int slice_number) |
get one slice from disk by her slice number (dalton) More... | |
virtual void | endPwizRead () |
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MsRunXicExtractor (MsRunReaderSPtr &msrun_reader) | |
virtual void | getXicFromPwizMSDataFile (std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) |
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MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader) | |
constructor is private, use the MsRunXicExtractorFactory More... | |
MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other) | |
virtual | ~MsRunXicExtractorInterface () |
virtual void | postExtractionProcess (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) |
possible post extraction process, eventually trace filters More... | |
Protected Attributes | |
QString | m_temporaryDirectory |
QTemporaryDir * | mpa_temporaryDirectory = nullptr |
std::vector< pappso::pappso_double > | m_retentionTimeList |
pappso::pappso_double | m_maxMz = 0 |
pappso::pappso_double | m_minMz = 5000 |
std::size_t | m_rtSize = 0 |
std::deque< MsRunSliceSPtr > | m_msRunSliceListCache |
QMutex | m_mutex |
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std::vector< MsRunXicExtractorPoints > | m_msrun_points |
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MsRunReaderSPtr | msp_msrun_reader |
XicExtractMethod | m_xicExtractMethod = XicExtractMethod::max |
double | m_retentionTimeAroundTarget = std::numeric_limits<double>::max() |
pappso::FilterInterfaceCstSPtr | mcsp_postExtractionTraceFilter = nullptr |
Private Member Functions | |
void | extractOneXicCoord (XicCoord &xic_coord) |
Private Attributes | |
friend | MsRunXicExtractorFactory |
Definition at line 44 of file msrunxicextractordisk.h.
pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk | ( | MsRunReaderSPtr & | msrun_reader | ) |
pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk | ( | const MsRunXicExtractorDisk & | other | ) |
Definition at line 47 of file msrunxicextractordisk.cpp.
References m_temporaryDirectory, mpa_temporaryDirectory, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.
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virtual |
Definition at line 58 of file msrunxicextractordisk.cpp.
References mpa_temporaryDirectory.
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protected |
Definition at line 39 of file msrunxicextractordisk.cpp.
References m_temporaryDirectory, and mpa_temporaryDirectory.
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protected |
retrieve all the slices corresponding to a given mz_range
mz_range | desired mz range |
Definition at line 327 of file msrunxicextractordisk.cpp.
References pappso::MzRange::lower(), m_msRunSliceListCache, m_mutex, unserializeSlice(), and pappso::MzRange::upper().
Referenced by extractOneXicCoord().
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protected |
append a slice on disk (in a file)
slice_number | the slice number == dalton integer |
spectrum | the part of the mass spectrum (mz/intensity) in the range of the slice number |
ipos | the position in the retention time vector |
Definition at line 252 of file msrunxicextractordisk.cpp.
References m_rtSize, and mpa_temporaryDirectory.
Referenced by storeSlices().
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protectedvirtual |
Reimplemented in pappso::MsRunXicExtractorDiskBuffer.
Definition at line 360 of file msrunxicextractordisk.cpp.
References pappso::MsRunXicExtractorInterface::msp_msrun_reader.
Referenced by serializeMsRun().
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private |
Definition at line 115 of file msrunxicextractordisk.cpp.
References acquireSlices(), pappso::MzRange::contains(), pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, m_retentionTimeList, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::sum, pappso::DataPoint::x, pappso::XicCoord::xicSptr, and pappso::DataPoint::y.
Referenced by protectedExtractXicCoordSPtrList().
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protected |
Definition at line 67 of file msrunxicextractordisk.cpp.
References pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::PappsoException::qwhat(), and serializeMsRun().
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overrideprotectedvirtual |
Reimplemented from pappso::MsRunXicExtractor.
Definition at line 95 of file msrunxicextractordisk.cpp.
References pappso::a, pappso::b, pappso::UiMonitorInterface::count(), and extractOneXicCoord().
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protected |
Definition at line 167 of file msrunxicextractordisk.cpp.
References endPwizRead(), m_maxMz, m_minMz, pappso::MsRunXicExtractor::m_msrun_points, m_retentionTimeList, m_rtSize, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and storeSlices().
Referenced by prepareExtractor().
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protectedvirtual |
store MassSpectrum slices (by daltons) for a given retention time
slice_vector | mass spectrum chunks (by daltons) |
ipos | the position in the retention time vector |
Reimplemented in pappso::MsRunXicExtractorDiskBuffer.
Definition at line 238 of file msrunxicextractordisk.cpp.
References appendSliceOnDisk().
Referenced by serializeMsRun().
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protected |
get one slice from disk by her slice number (dalton)
slice_number | the slice number == dalton integer |
Definition at line 286 of file msrunxicextractordisk.cpp.
References m_rtSize, mpa_temporaryDirectory, and pappso::PappsoException::qwhat().
Referenced by acquireSlices().
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protected |
Definition at line 103 of file msrunxicextractordisk.h.
Referenced by serializeMsRun().
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protected |
Definition at line 104 of file msrunxicextractordisk.h.
Referenced by serializeMsRun().
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protected |
Definition at line 108 of file msrunxicextractordisk.h.
Referenced by acquireSlices().
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Definition at line 110 of file msrunxicextractordisk.h.
Referenced by acquireSlices().
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Definition at line 101 of file msrunxicextractordisk.h.
Referenced by extractOneXicCoord(), and serializeMsRun().
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protected |
Definition at line 106 of file msrunxicextractordisk.h.
Referenced by appendSliceOnDisk(), pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk(), serializeMsRun(), and unserializeSlice().
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protected |
Definition at line 99 of file msrunxicextractordisk.h.
Referenced by MsRunXicExtractorDisk().
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protected |
Definition at line 100 of file msrunxicextractordisk.h.
Referenced by MsRunXicExtractorDisk(), ~MsRunXicExtractorDisk(), appendSliceOnDisk(), pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk(), and unserializeSlice().
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private |
Definition at line 46 of file msrunxicextractordisk.h.