pappso::masschroq::MsRun Class Reference

#include <msrun.h>

Public Member Functions
	MsRun (pappso::MsRunReaderSPtr msrun_reader)
virtual	~MsRun ()
const pappso::MsRunReaderSPtr &	getMsRunReaderSPtr () const
pappso::MsRunReaderSPtr &	getMsRunReaderSPtr ()
const PrecursorSp &	getPrecursorSPtrBySpectrumIndex (std::size_t spectrum_index) const
const PrecursorSp &	getPrecursorSPtrByScanNumber (std::size_t scan_number) const
const std::vector< double > &	getRetentionTimeLine () const
bool	hasTimsTofMobilityIndex () const

Private Attributes
pappso::MsRunReaderSPtr	msp_msRunReader
std::map< std::size_t, PrecursorSp >	m_spectrumIndex2precursorMap
	new map dedicated to spectrum index to replace obsolete scan number
pappso::MsRunXicExtractorInterfaceSp	msp_msRunXicExtractorInterfaceSp
PrecursorParser *	mpa_precursorParser
std::vector< double >	m_retentionTimeLine
bool	m_hasTimsTofMobilityIndex = false

Detailed Description

@description group together an msrun reader object and list of precursors (MS1 peak chosen for fragmentation)

Definition at line 49 of file msrun.h.

Constructor & Destructor Documentation

MsRun()

pappso::masschroq::MsRun::MsRun

(

pappso::MsRunReaderSPtr

msrun_reader

)

Default constructor

Definition at line 35 of file msrun.cpp.

  : msp_msRunReader(msrun_reader)
{
 
  pappso::TimsMsRunReaderMs2 *tims2_reader =
    dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msp_msRunReader.get());
  if(tims2_reader != nullptr)
    {
      m_hasTimsTofMobilityIndex = true;
    }
 
  m_retentionTimeLine = msp_msRunReader.get()->getRetentionTimeLine();
  mpa_precursorParser = new PrecursorParser(msp_msRunReader);
 
  pappso::MsRunReadConfig config;
  config.setNeedPeakList(false);
  config.setMsLevels({2});
  qDebug();
  // msrunA01.get()->readSpectrumCollection(spectrum_list_reader);
  msp_msRunReader.get()->readSpectrumCollection2(config, *mpa_precursorParser);
}

References getRetentionTimeLine(), m_hasTimsTofMobilityIndex, m_retentionTimeLine, mpa_precursorParser, msp_msRunReader, pappso::MsRunReadConfig::setMsLevels(), and pappso::MsRunReadConfig::setNeedPeakList().

~MsRun()

pappso::masschroq::MsRun::~MsRun ( )

virtual

Destructor

Definition at line 57 of file msrun.cpp.

{
  delete mpa_precursorParser;
}

References mpa_precursorParser.

Member Function Documentation

getMsRunReaderSPtr() [1/2]

pappso::MsRunReaderSPtr & pappso::masschroq::MsRun::getMsRunReaderSPtr

(

)

Definition at line 69 of file msrun.cpp.

{
  return msp_msRunReader;
}

References msp_msRunReader.

getMsRunReaderSPtr() [2/2]

const pappso::MsRunReaderSPtr & pappso::masschroq::MsRun::getMsRunReaderSPtr

(

)

const

Definition at line 63 of file msrun.cpp.

{
  return msp_msRunReader;
}

References msp_msRunReader.

Referenced by pappso::masschroq::CborOutputStream::writeMsRun(), and pappso::masschroq::CborOutputStream::writeQrDataBlock().

getPrecursorSPtrByScanNumber()

const pappso::masschroq::PrecursorSp & pappso::masschroq::MsRun::getPrecursorSPtrByScanNumber

(

std::size_t

scan_number

)

const

Definition at line 76 of file msrun.cpp.

{
  std::size_t spectrum_index = msp_msRunReader.get()->scanNumber2SpectrumIndex(scan_number);
  return mpa_precursorParser->getPrecursorSPtrBySpectrumIndex(spectrum_index);
}

References mpa_precursorParser, and msp_msRunReader.

getPrecursorSPtrBySpectrumIndex()

const pappso::masschroq::PrecursorSp & pappso::masschroq::MsRun::getPrecursorSPtrBySpectrumIndex

(

std::size_t

spectrum_index

)

const

Definition at line 82 of file msrun.cpp.

{
  return mpa_precursorParser->getPrecursorSPtrBySpectrumIndex(spectrum_index);
}

References mpa_precursorParser.

getRetentionTimeLine()

const std::vector< double > & pappso::masschroq::MsRun::getRetentionTimeLine

(

)

const

Definition at line 88 of file msrun.cpp.

{
  return m_retentionTimeLine;
}

References m_retentionTimeLine.

Referenced by MsRun().

hasTimsTofMobilityIndex()

bool pappso::masschroq::MsRun::hasTimsTofMobilityIndex

(

)

const

Definition at line 94 of file msrun.cpp.

{
  return m_hasTimsTofMobilityIndex;
}

References m_hasTimsTofMobilityIndex.

Member Data Documentation

m_hasTimsTofMobilityIndex

bool pappso::masschroq::MsRun::m_hasTimsTofMobilityIndex = false

private

Definition at line 87 of file msrun.h.

Referenced by MsRun(), and hasTimsTofMobilityIndex().

m_retentionTimeLine

std::vector<double> pappso::masschroq::MsRun::m_retentionTimeLine

private

Definition at line 85 of file msrun.h.

Referenced by MsRun(), and getRetentionTimeLine().

m_spectrumIndex2precursorMap

std::map<std::size_t, PrecursorSp> pappso::masschroq::MsRun::m_spectrumIndex2precursorMap

private

new map dedicated to spectrum index to replace obsolete scan number

Definition at line 79 of file msrun.h.

mpa_precursorParser

PrecursorParser* pappso::masschroq::MsRun::mpa_precursorParser

private

Definition at line 83 of file msrun.h.

Referenced by MsRun(), ~MsRun(), getPrecursorSPtrByScanNumber(), and getPrecursorSPtrBySpectrumIndex().

msp_msRunReader

pappso::MsRunReaderSPtr pappso::masschroq::MsRun::msp_msRunReader

private

Definition at line 75 of file msrun.h.

Referenced by MsRun(), getMsRunReaderSPtr(), getMsRunReaderSPtr(), and getPrecursorSPtrByScanNumber().

msp_msRunXicExtractorInterfaceSp

pappso::MsRunXicExtractorInterfaceSp pappso::masschroq::MsRun::msp_msRunXicExtractorInterfaceSp

private

Definition at line 81 of file msrun.h.

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

• pappsomspp/core/masschroq/msrun.h
• pappsomspp/core/masschroq/msrun.cpp