libpappsomspp
Library for mass spectrometry
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#include <timsdirectxicextractor.h>
Public Member Functions | |
TimsDirectXicExtractor (MsRunReaderSPtr &msrun_reader) | |
virtual | ~TimsDirectXicExtractor () |
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TimsXicExtractorInterface (MsRunReaderSPtr &msrun_reader) | |
virtual | ~TimsXicExtractorInterface () |
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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 | |
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 |
Additional Inherited Members | |
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TimsData * | mp_timsData |
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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 |
Definition at line 36 of file timsdirectxicextractor.h.
TimsDirectXicExtractor::TimsDirectXicExtractor | ( | MsRunReaderSPtr & | msrun_reader | ) |
Default constructor
Definition at line 35 of file timsdirectxicextractor.cpp.
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virtual |
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overrideprotectedvirtual |
Implements pappso::MsRunXicExtractorInterface.
Definition at line 46 of file timsdirectxicextractor.cpp.
References pappso::UiMonitorInterface::count(), pappso::UiMonitorInterface::setStatus(), pappso::UiMonitorInterface::setTotalSteps(), and pappso::UiMonitorInterface::shouldIstop().