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 () |
virtual XicCstSPtr | getXicCstSPtr (const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override |
get a XIC on this MsRun at the given mass range More... | |
virtual std::vector< XicCstSPtr > | getXicCstSPtrList (const std::vector< MzRange > &mz_range_list) override |
extract a list of XIC given a list of mass to extract More... | |
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MsRunXicExtractor (const MsRunXicExtractor &other) | |
virtual | ~MsRunXicExtractor () |
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void | setXicExtractMethod (XicExtractMethod method) |
set the XIC extraction method More... | |
virtual XicCstSPtr | getXicCstSPtr (const MzRange &mz_range) final |
get a XIC on this MsRun at the given mass range More... | |
const MsRunIdCstSPtr & | getMsRunId () const |
Protected Member Functions | |
MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir) | |
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 () |
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 |
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 326 of file msrunxicextractordisk.cpp.
References pappso::MzRange::lower(), m_msRunSliceListCache, m_mutex, unserializeSlice(), and pappso::MzRange::upper().
Referenced by getXicCstSPtr().
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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 251 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 359 of file msrunxicextractordisk.cpp.
Referenced by serializeMsRun().
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overridevirtual |
get a XIC on this MsRun at the given mass range
mz_range | mz range to extract |
rt_begin | begining of the XIC in seconds |
rt_end | end of the XIC in seconds |
Reimplemented from pappso::MsRunXicExtractor.
Definition at line 101 of file msrunxicextractordisk.cpp.
References acquireSlices(), pappso::MzRange::contains(), m_retentionTimeList, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::DataPoint::x, and pappso::DataPoint::y.
Referenced by getXicCstSPtrList().
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overridevirtual |
extract a list of XIC given a list of mass to extract
Reimplemented from pappso::MsRunXicExtractor.
Definition at line 153 of file msrunxicextractordisk.cpp.
References getXicCstSPtr().
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protected |
Definition at line 67 of file msrunxicextractordisk.cpp.
References pappso::b, pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::PappsoException::qwhat(), and serializeMsRun().
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protected |
Definition at line 166 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 237 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 285 of file msrunxicextractordisk.cpp.
References m_rtSize, mpa_temporaryDirectory, and pappso::PappsoException::qwhat().
Referenced by acquireSlices().
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protected |
Definition at line 102 of file msrunxicextractordisk.h.
Referenced by serializeMsRun().
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Definition at line 103 of file msrunxicextractordisk.h.
Referenced by serializeMsRun().
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Definition at line 107 of file msrunxicextractordisk.h.
Referenced by acquireSlices().
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Definition at line 109 of file msrunxicextractordisk.h.
Referenced by acquireSlices().
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Definition at line 100 of file msrunxicextractordisk.h.
Referenced by getXicCstSPtr(), and serializeMsRun().
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Definition at line 105 of file msrunxicextractordisk.h.
Referenced by appendSliceOnDisk(), pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk(), serializeMsRun(), and unserializeSlice().
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Definition at line 98 of file msrunxicextractordisk.h.
Referenced by MsRunXicExtractorDisk().
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protected |
Definition at line 99 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.