libpappsomspp
Library for mass spectrometry
pappso::MsRunReaderScanNumberMultiMap Class Reference

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

#include <msrunreader.h>

Inheritance diagram for pappso::MsRunReaderScanNumberMultiMap:
pappso::SpectrumCollectionHandlerInterface

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 More...
 
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 More...
 
virtual void setNeedMsLevelPeakList (unsigned int ms_level, bool want_peak_list) final
 tells if we need the peak list given More...
 
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 More...
 
virtual bool isReadAhead () const
 tells if we want to read ahead spectrum More...
 

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 130 of file msrunreader.h.

Constructor & Destructor Documentation

◆ MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::MsRunReaderScanNumberMultiMap ( )

Definition at line 154 of file msrunreader.cpp.

155 {
156  // qDebug();
157 }

◆ ~MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::~MsRunReaderScanNumberMultiMap ( )
virtual

Definition at line 160 of file msrunreader.cpp.

161 {
162  // qDebug();
163 }

Member Function Documentation

◆ getSpectrumIndexFromScanNumber()

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

Definition at line 196 of file msrunreader.cpp.

198 {
199 
200  qDebug() << m_mmap_scan2index.size();
201 
202  auto it = m_mmap_scan2index.find(scan_number);
203 
204  if(it == m_mmap_scan2index.end())
205  {
206  throw ExceptionNotFound(
207  QObject::tr("scan number %1 not found").arg(scan_number));
208  }
209 
210  std::size_t index = it->second;
211 
212  it++;
213  if((it != m_mmap_scan2index.end()) && (it->first == scan_number))
214  {
215  throw PappsoException(
216  QObject::tr("scan number %1 found multiple times").arg(scan_number));
217  }
218  return index;
219 }
std::multimap< std::size_t, std::size_t > m_mmap_scan2index
Definition: msrunreader.h:134

References m_mmap_scan2index.

Referenced by pappso::MsRunReader::scanNumber2SpectrumIndex().

◆ 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 167 of file msrunreader.cpp.

168 {
169  return false;
170 }

◆ setQualifiedMassSpectrum()

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

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 173 of file msrunreader.cpp.

175 {
176  qDebug() << " " << qspectrum.getMassSpectrumId().getNativeId();
177 
178  QStringList native_id_list =
179  qspectrum.getMassSpectrumId().getNativeId().split("=");
180  if(native_id_list.size() < 2)
181  {
182  return;
183  }
184  else
185  {
186  std::size_t scan_number = native_id_list.back().toULong();
187  m_mmap_scan2index.insert(std::pair<std::size_t, std::size_t>(
188  scan_number, qspectrum.getMassSpectrumId().getSpectrumIndex()));
189 
190  qDebug() << "scan number " << scan_number << "=>"
191  << qspectrum.getMassSpectrumId().getSpectrumIndex();
192  }
193 }

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getNativeId(), pappso::MassSpectrumId::getSpectrumIndex(), and m_mmap_scan2index.

Member Data Documentation

◆ m_mmap_scan2index

std::multimap<std::size_t, std::size_t> pappso::MsRunReaderScanNumberMultiMap::m_mmap_scan2index
private

Definition at line 134 of file msrunreader.h.

Referenced by getSpectrumIndexFromScanNumber(), and setQualifiedMassSpectrum().


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