libpappsomspp
Library for mass spectrometry
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#include <msrunxicextractor.h>
Classes | |
struct | MsRunXicExtractorPoints |
class | MsRunXicExtractorReadPoints |
class to read retention time points of MsRun More... | |
Public Member Functions | |
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 | |
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) |
virtual void | protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override |
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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... | |
virtual void | protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)=0 |
Protected Attributes | |
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 41 of file msrunxicextractor.h.
pappso::MsRunXicExtractor::MsRunXicExtractor | ( | const MsRunXicExtractor & | other | ) |
Definition at line 67 of file msrunxicextractor.cpp.
References m_msrun_points.
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virtual |
Definition at line 62 of file msrunxicextractor.cpp.
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protected |
Definition at line 43 of file msrunxicextractor.cpp.
References pappso::a, pappso::b, m_msrun_points, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.
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private |
Definition at line 103 of file msrunxicextractor.cpp.
References pappso::FilterResampleKeepXRange::filter(), pappso::MzRange::lower(), m_msrun_points, pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::max, pappso::maxYDataPoint(), pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::sumYTrace(), pappso::MzRange::upper(), pappso::DataPoint::x, pappso::XicCoord::xicSptr, and pappso::DataPoint::y.
Referenced by protectedExtractXicCoordSPtrList().
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protectedvirtual |
Definition at line 157 of file msrunxicextractor.cpp.
References m_msrun_points, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::max, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and pappso::y.
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overrideprotectedvirtual |
Implements pappso::MsRunXicExtractorInterface.
Reimplemented in pappso::MsRunXicExtractorDisk.
Definition at line 75 of file msrunxicextractor.cpp.
References pappso::a, pappso::b, pappso::UiMonitorInterface::count(), extractOneXicCoord(), and pappso::UiMonitorInterface::shouldIstop().
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protected |
Definition at line 106 of file msrunxicextractor.h.
Referenced by MsRunXicExtractor(), extractOneXicCoord(), getXicFromPwizMSDataFile(), and pappso::MsRunXicExtractorDisk::serializeMsRun().
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private |
Definition at line 43 of file msrunxicextractor.h.