libpappsomspp
Library for mass spectrometry
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#include <msrunxicextractordiskbuffer.h>
Public Member Functions | |
MsRunXicExtractorDiskBuffer (const MsRunXicExtractorDiskBuffer &other) | |
virtual | ~MsRunXicExtractorDiskBuffer () |
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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 | |
MsRunXicExtractorDiskBuffer (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir) | |
virtual void | storeSlices (std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) override |
store MassSpectrum slices (by daltons) for a given retention time More... | |
void | appendSliceInBuffer (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos) |
void | flushBufferOnDisk () |
virtual void | endPwizRead () override |
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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 () |
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... | |
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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 | |
std::map< unsigned int, QByteArray > | m_sliceBufferMap |
std::size_t | m_bufferSize = 0 |
std::size_t | m_bufferMaxSize = 150 |
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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 Attributes | |
friend | MsRunXicExtractorFactory |
Definition at line 43 of file msrunxicextractordiskbuffer.h.
pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer | ( | const MsRunXicExtractorDiskBuffer & | other | ) |
Definition at line 48 of file msrunxicextractordiskbuffer.cpp.
References m_sliceBufferMap.
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virtual |
Definition at line 56 of file msrunxicextractordiskbuffer.cpp.
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protected |
Definition at line 40 of file msrunxicextractordiskbuffer.cpp.
References m_sliceBufferMap.
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protected |
Definition at line 78 of file msrunxicextractordiskbuffer.cpp.
References m_sliceBufferMap, and pappso::PappsoException::qwhat().
Referenced by storeSlices().
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overrideprotectedvirtual |
Reimplemented from pappso::MsRunXicExtractorDisk.
Definition at line 206 of file msrunxicextractordiskbuffer.cpp.
References flushBufferOnDisk(), m_sliceBufferMap, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.
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protected |
Definition at line 130 of file msrunxicextractordiskbuffer.cpp.
References m_bufferSize, pappso::MsRunXicExtractorDisk::m_rtSize, m_sliceBufferMap, pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory, and pappso::PappsoException::qwhat().
Referenced by endPwizRead(), and storeSlices().
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overrideprotectedvirtual |
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 from pappso::MsRunXicExtractorDisk.
Definition at line 61 of file msrunxicextractordiskbuffer.cpp.
References appendSliceInBuffer(), flushBufferOnDisk(), m_bufferMaxSize, and m_bufferSize.
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protected |
Definition at line 69 of file msrunxicextractordiskbuffer.h.
Referenced by storeSlices().
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protected |
Definition at line 68 of file msrunxicextractordiskbuffer.h.
Referenced by flushBufferOnDisk(), and storeSlices().
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protected |
Definition at line 66 of file msrunxicextractordiskbuffer.h.
Referenced by MsRunXicExtractorDiskBuffer(), appendSliceInBuffer(), endPwizRead(), and flushBufferOnDisk().
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private |
Definition at line 45 of file msrunxicextractordiskbuffer.h.