#include <timsxicextractorinterface.h>

Inheritance diagram for pappso::TimsXicExtractorInterface:

Public Member Functions
	TimsXicExtractorInterface (MsRunReaderSPtr &msrun_reader)

virtual	~TimsXicExtractorInterface ()

Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void	setXicExtractMethod (Enums::XicExtractMethod method)
	set the XIC extraction method

void	setRetentionTimeAroundTarget (double range_in_seconds)
	set the retention time range in seconds around the target rt

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

virtual void	extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
	multithreaded XIC extraction

const MsRunIdCstSPtr &	getMsRunId () const

const MsRunReaderSPtr &	getMsRunReaderSPtr () const
	get the msrunreader currently used for XIC extraction

void	setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
	filter interface to apply just after XIC extration on each trace

Protected Attributes
TimsData *	mp_timsData

Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr	msp_msrun_reader

Enums::XicExtractMethod	m_xicExtractMethod = Enums::XicExtractMethod::max

double	m_retentionTimeAroundTarget = std::numeric_limits<double>::max()

pappso::FilterInterfaceCstSPtr	mcsp_postExtractionTraceFilter = nullptr

Private Attributes
friend	TimsData

Additional Inherited Members
Protected Member Functions inherited from pappso::MsRunXicExtractorInterface
	MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
	constructor is private, use the MsRunXicExtractorFactory

	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

virtual void	protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)=0

Detailed Description

Todo: set of minimum functions to build XICs using Tims data

Definition at line 42 of file timsxicextractorinterface.h.

Constructor & Destructor Documentation

◆ TimsXicExtractorInterface()

TimsXicExtractorInterface::TimsXicExtractorInterface ( MsRunReaderSPtr & msrun_reader )

Definition at line 34 of file timsxicextractorinterface.cpp.

  : MsRunXicExtractorInterface(msrun_reader)
{
 
  pappso::TimsMsRunReaderMs2 *tims2_reader =
    dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
  if(tims2_reader != nullptr)
    {
      mp_timsData = tims2_reader->getTimsDataSPtr().get();
    }
  else
    {
      throw pappso::ExceptionNotPossible(QObject::tr(
        "error: TimsXicExtractorInterface must use a TimsMsRunReaderMs2"));
    }
}