libpappsomspp
Library for mass spectrometry
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pappso::MsRunReaderScanNumberMultiMap Class Reference

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

#include <spectrumcollectionhandlerinterface.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
 
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.

150{
151 // qDebug();
152}

◆ ~MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::~MsRunReaderScanNumberMultiMap ( )
virtual

Definition at line 155 of file spectrumcollectionhandlerinterface.cpp.

156{
157 // qDebug();
158}

Member Function Documentation

◆ getSpectrumIndexFromScanNumber()

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

Definition at line 191 of file spectrumcollectionhandlerinterface.cpp.

193{
194
195 qDebug() << m_mmap_scan2index.size();
196
197 auto it = m_mmap_scan2index.find(scan_number);
198
199 if(it == m_mmap_scan2index.end())
200 {
201 throw ExceptionNotFound(
202 QObject::tr("scan number %1 not found").arg(scan_number));
203 }
204
205 std::size_t index = it->second;
206
207 it++;
208 if((it != m_mmap_scan2index.end()) && (it->first == scan_number))
209 {
210 throw PappsoException(
211 QObject::tr("scan number %1 found multiple times").arg(scan_number));
212 }
213 return index;
214}
std::multimap< std::size_t, std::size_t > m_mmap_scan2index

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 162 of file spectrumcollectionhandlerinterface.cpp.

163{
164 return false;
165}

◆ setQualifiedMassSpectrum()

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

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 168 of file spectrumcollectionhandlerinterface.cpp.

170{
171 qDebug() << " " << qspectrum.getMassSpectrumId().getNativeId();
172
173 QStringList native_id_list =
174 qspectrum.getMassSpectrumId().getNativeId().split("=");
175 if(native_id_list.size() < 2)
176 {
177 return;
178 }
179 else
180 {
181 std::size_t scan_number = native_id_list.back().toULong();
182 m_mmap_scan2index.insert(std::pair<std::size_t, std::size_t>(
183 scan_number, qspectrum.getMassSpectrumId().getSpectrumIndex()));
184
185 qDebug() << "scan number " << scan_number << "=>"
186 << qspectrum.getMassSpectrumId().getSpectrumIndex();
187 }
188}

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

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