libpappsomspp
Library for mass spectrometry
pappso::TimsXicExtractorInterface Class Reference

#include <timsxicextractorinterface.h>

Inheritance diagram for pappso::TimsXicExtractorInterface:
pappso::MsRunXicExtractorInterface pappso::TimsDirectXicExtractor

Public Member Functions

 TimsXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
 
virtual ~TimsXicExtractorInterface ()
 
- Public Member Functions inherited from pappso::MsRunXicExtractorInterface
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 MsRunIdCstSPtrgetMsRunId () const
 
const MsRunReaderSPtrgetMsRunReaderSPtr () 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 Attributes

TimsDatamp_timsData
 
- Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr msp_msrun_reader
 
XicExtractMethod m_xicExtractMethod = 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 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
 

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.

36  : MsRunXicExtractorInterface(msrun_reader)
37 {
38 
39  pappso::TimsMsRunReaderMs2 *tims2_reader =
40  dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
41  if(tims2_reader != nullptr)
42  {
43  mp_timsData = tims2_reader->getTimsDataSPtr().get();
44  }
45  else
46  {
47  throw pappso::ExceptionNotPossible(QObject::tr(
48  "error: TimsXicExtractorInterface must use a TimsMsRunReaderMs2"));
49  }
50 }
MsRunXicExtractorInterface(MsRunReaderSPtr &msrun_reader)
constructor is private, use the MsRunXicExtractorFactory
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer

References pappso::TimsMsRunReaderMs2::getTimsDataSPtr(), and mp_timsData.

◆ ~TimsXicExtractorInterface()

TimsXicExtractorInterface::~TimsXicExtractorInterface ( )
virtual

Definition at line 52 of file timsxicextractorinterface.cpp.

53 {
54 }

Member Data Documentation

◆ mp_timsData

TimsData* pappso::TimsXicExtractorInterface::mp_timsData
protected

Definition at line 51 of file timsxicextractorinterface.h.

Referenced by TimsXicExtractorInterface().

◆ TimsData

friend pappso::TimsXicExtractorInterface::TimsData
private

Definition at line 44 of file timsxicextractorinterface.h.


The documentation for this class was generated from the following files: