provides a multimap to find quickly spectrum index from scan number More...

#include <spectrumcollectionhandlerinterface.h>

Inheritance diagram for pappso::MsRunReaderScanNumberMultiMap:

Public Member Functions
	MsRunReaderScanNumberMultiMap ()

virtual	~MsRunReaderScanNumberMultiMap ()

virtual void	setQualifiedMassSpectrum (const QualifiedMassSpectrum &spectrum) override

virtual bool	needPeakList () const override
	tells if we need the peak list (if we want the binary data) for each spectrum

std::size_t	getSpectrumIndexFromScanNumber (std::size_t scan_number) const

Public Member Functions inherited from pappso::SpectrumCollectionHandlerInterface
virtual bool	needMsLevelPeakList (unsigned int ms_level) const final
	tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level

virtual void	setNeedMsLevelPeakList (unsigned int ms_level, bool want_peak_list) final
	tells if we need the peak list given

virtual bool	shouldStop ()

virtual void	loadingEnded ()

virtual void	spectrumListHasSize (std::size_t size)

virtual void	setReadAhead (bool is_read_ahead) final
	use threads to read a spectrum by batch of batch_size

virtual bool	isReadAhead () const
	tells if we want to read ahead spectrum

Private Attributes
std::multimap< std::size_t, std::size_t >	m_mmap_scan2index

Detailed Description

provides a multimap to find quickly spectrum index from scan number

Definition at line 131 of file spectrumcollectionhandlerinterface.h.

Constructor & Destructor Documentation

◆ MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::MsRunReaderScanNumberMultiMap ( )

Definition at line 149 of file spectrumcollectionhandlerinterface.cpp.

{
  // qDebug();
}

◆ ~MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::~MsRunReaderScanNumberMultiMap ( )

virtual

Definition at line 155 of file spectrumcollectionhandlerinterface.cpp.

{
  // qDebug();
}

Member Function Documentation

◆ getSpectrumIndexFromScanNumber()

std::size_t pappso::MsRunReaderScanNumberMultiMap::getSpectrumIndexFromScanNumber ( std::size_t scan_number ) const

Definition at line 191 of file spectrumcollectionhandlerinterface.cpp.

{
 
  qDebug() << m_mmap_scan2index.size();
 
  auto it = m_mmap_scan2index.find(scan_number);
 
  if(it == m_mmap_scan2index.end())
    {
      throw ExceptionNotFound(
        QObject::tr("scan number %1 not found").arg(scan_number));
    }
 
  std::size_t index = it->second;
 
  it++;
  if((it != m_mmap_scan2index.end()) && (it->first == scan_number))
    {
      throw PappsoException(
        QObject::tr("scan number %1 found multiple times").arg(scan_number));
    }
  return index;
}

References m_mmap_scan2index.

◆ needPeakList()

bool pappso::MsRunReaderScanNumberMultiMap::needPeakList ( ) const

overridevirtual

tells if we need the peak list (if we want the binary data) for each spectrum

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 162 of file spectrumcollectionhandlerinterface.cpp.

{
  return false;
}

◆ setQualifiedMassSpectrum()

void pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum ( const QualifiedMassSpectrum & spectrum )

overridevirtual

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 168 of file spectrumcollectionhandlerinterface.cpp.

{
  qDebug() << " " << qspectrum.getMassSpectrumId().getNativeId();
 
  QStringList native_id_list =
    qspectrum.getMassSpectrumId().getNativeId().split("=");
  if(native_id_list.size() < 2)
    {
      return;
    }
  else
    {
      std::size_t scan_number = native_id_list.back().toULong();
      m_mmap_scan2index.insert(std::pair<std::size_t, std::size_t>(
        scan_number, qspectrum.getMassSpectrumId().getSpectrumIndex()));
 
      qDebug() << "scan number " << scan_number << "=>"
               << qspectrum.getMassSpectrumId().getSpectrumIndex();
    }
}