libpappsomspp
Library for mass spectrometry
pappso::MsRunXicExtractorInterface Class Referenceabstract

#include <msrunxicextractorinterface.h>

Inheritance diagram for pappso::MsRunXicExtractorInterface:
pappso::MsRunXicExtractor pappso::TimsXicExtractorInterface pappso::MsRunXicExtractorDisk pappso::TimsDirectXicExtractor pappso::MsRunXicExtractorDiskBuffer

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)=0
 extract a list of XIC given a list of xic coordinates to extract More...
 
const MsRunIdCstSPtrgetMsRunId () const
 
const MsRunReaderSPtrgetMsRunReaderSPtr () const
 get the msrunreader currently used for XIC extraction More...
 

Protected Member Functions

 MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
 constructor is private, use the MsRunXicExtractorFactory More...
 
 MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)
 
virtual ~MsRunXicExtractorInterface ()
 

Protected Attributes

MsRunReaderSPtr msp_msrun_reader
 
XicExtractMethod m_xicExtractMethod = XicExtractMethod::max
 
double m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
 

Detailed Description

Definition at line 47 of file msrunxicextractorinterface.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorInterface() [1/2]

pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface ( MsRunReaderSPtr msrun_reader)
protected

constructor is private, use the MsRunXicExtractorFactory

Definition at line 37 of file msrunxicextractorinterface.cpp.

39  : msp_msrun_reader(msrun_reader)
40 {
41 }

◆ MsRunXicExtractorInterface() [2/2]

pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface ( const MsRunXicExtractorInterface other)
protected

Definition at line 44 of file msrunxicextractorinterface.cpp.

46  : msp_msrun_reader(other.msp_msrun_reader)
47 {
48  m_xicExtractMethod = other.m_xicExtractMethod;
49 }

References m_xicExtractMethod.

◆ ~MsRunXicExtractorInterface()

pappso::MsRunXicExtractorInterface::~MsRunXicExtractorInterface ( )
protectedvirtual

Definition at line 51 of file msrunxicextractorinterface.cpp.

52 {
53 }

Member Function Documentation

◆ extractXicCoordSPtrList()

virtual void pappso::MsRunXicExtractorInterface::extractXicCoordSPtrList ( UiMonitorInterface monitor,
std::vector< XicCoordSPtr > &  xic_coord_list 
)
pure virtual

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

Parameters
monitorprocess monitoring
xic_coord_listlist of xic coordinates to extract. The order of xic coordinates may change.

Implemented in pappso::MsRunXicExtractorDisk, pappso::MsRunXicExtractor, and pappso::TimsDirectXicExtractor.

◆ getMsRunId()

const MsRunIdCstSPtr & pappso::MsRunXicExtractorInterface::getMsRunId ( ) const

Definition at line 69 of file msrunxicextractorinterface.cpp.

70 {
71  return msp_msrun_reader.get()->getMsRunId();
72 }

References msp_msrun_reader.

◆ getMsRunReaderSPtr()

const MsRunReaderSPtr & pappso::MsRunXicExtractorInterface::getMsRunReaderSPtr ( ) const

get the msrunreader currently used for XIC extraction

Definition at line 74 of file msrunxicextractorinterface.cpp.

74  {
75  return msp_msrun_reader;
76 }

References msp_msrun_reader.

◆ setRetentionTimeAroundTarget()

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 to rt target + range in seconds by default, all the LC run time is extracted
Parameters
range_in_secondsrange in seconds

Definition at line 62 of file msrunxicextractorinterface.cpp.

64 {
65  m_retentionTimeAroundTarget = range_in_seconds;
66 }

References m_retentionTimeAroundTarget.

◆ setXicExtractMethod()

void pappso::MsRunXicExtractorInterface::setXicExtractMethod ( XicExtractMethod  method)

set the XIC extraction method

Definition at line 56 of file msrunxicextractorinterface.cpp.

57 {
58  m_xicExtractMethod = method;
59 }

References m_xicExtractMethod.

Member Data Documentation

◆ m_retentionTimeAroundTarget

double pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
protected

◆ m_xicExtractMethod

◆ msp_msrun_reader


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