libpappsomspp
Library for mass spectrometry
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#include <msrunxicextractorinterface.h>
Public Member Functions | |
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 | |
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 | |
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 48 of file msrunxicextractorinterface.h.
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protected |
constructor is private, use the MsRunXicExtractorFactory
Definition at line 40 of file msrunxicextractorinterface.cpp.
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Definition at line 47 of file msrunxicextractorinterface.cpp.
References m_xicExtractMethod.
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protectedvirtual |
Definition at line 54 of file msrunxicextractorinterface.cpp.
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finalvirtual |
extract a list of XIC given a list of xic coordinates to extract
XicCoord is a vessel containing the xic to fill and coordinates of this XIC in the MS run
monitor | process monitoring |
xic_coord_list | list of xic coordinates to extract. The order of xic coordinates may change. |
Definition at line 181 of file msrunxicextractorinterface.cpp.
References postExtractionProcess(), protectedExtractXicCoordSPtrList(), pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::setTotalSteps().
Referenced by extractXicCoordSPtrListParallelized().
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finalvirtual |
multithreaded XIC extraction
divide xic_coord_list and run extractXicCoordSPtrList separated threads
monitor | process monitoring |
xic_coord_list | list of xic coordinates to extract. The order of xic coordinates may change. |
Definition at line 92 of file msrunxicextractorinterface.cpp.
References pappso::UiMonitorInterface::count(), extractXicCoordSPtrList(), pappso::res, pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::setTotalSteps().
const MsRunIdCstSPtr & pappso::MsRunXicExtractorInterface::getMsRunId | ( | ) | const |
Definition at line 72 of file msrunxicextractorinterface.cpp.
References msp_msrun_reader.
const MsRunReaderSPtr & pappso::MsRunXicExtractorInterface::getMsRunReaderSPtr | ( | ) | const |
get the msrunreader currently used for XIC extraction
Definition at line 78 of file msrunxicextractorinterface.cpp.
References msp_msrun_reader.
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protectedvirtual |
possible post extraction process, eventually trace filters
Definition at line 195 of file msrunxicextractorinterface.cpp.
References mcsp_postExtractionTraceFilter, and pappso::UiMonitorInterface::setStatus().
Referenced by extractXicCoordSPtrList().
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protectedpure virtual |
Implemented in pappso::MsRunXicExtractorDisk, pappso::MsRunXicExtractor, and pappso::TimsDirectXicExtractor.
Referenced by extractXicCoordSPtrList().
void pappso::MsRunXicExtractorInterface::setPostExtractionTraceFilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr & | filter | ) |
filter interface to apply just after XIC extration on each trace
Definition at line 84 of file msrunxicextractorinterface.cpp.
References mcsp_postExtractionTraceFilter.
void pappso::MsRunXicExtractorInterface::setRetentionTimeAroundTarget | ( | double | range_in_seconds | ) |
set the retention time range in seconds around the target rt
only the interesting part of the xic will be extracted, form the rt target
range_in_seconds | range in seconds |
Definition at line 65 of file msrunxicextractorinterface.cpp.
References m_retentionTimeAroundTarget.
void pappso::MsRunXicExtractorInterface::setXicExtractMethod | ( | XicExtractMethod | method | ) |
set the XIC extraction method
Definition at line 59 of file msrunxicextractorinterface.cpp.
References m_xicExtractMethod.
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protected |
Definition at line 127 of file msrunxicextractorinterface.h.
Referenced by pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), and setRetentionTimeAroundTarget().
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protected |
Definition at line 128 of file msrunxicextractorinterface.h.
Referenced by postExtractionProcess(), and setPostExtractionTraceFilterCstSPtr().
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protected |
Definition at line 125 of file msrunxicextractorinterface.h.
Referenced by pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk(), pappso::MsRunXicExtractorDisk::endPwizRead(), pappso::MsRunXicExtractorDiskBuffer::endPwizRead(), pappso::MsRunXicExtractor::extractOneXicCoord(), getMsRunId(), getMsRunReaderSPtr(), pappso::MsRunXicExtractor::getXicFromPwizMSDataFile(), pappso::MsRunXicExtractorDisk::prepareExtractor(), and pappso::MsRunXicExtractorDisk::serializeMsRun().