48 [[maybe_unused]] std::size_t size)
65 unsigned int ms_level)
const
83 unsigned int ms_level,
bool want_peak_list)
115 unsigned int ms_level = qspectrum.
getMsLevel();
140 unsigned long total = 0;
173 QStringList native_id_list =
175 if(native_id_list.size() < 2)
181 std::size_t scan_number = native_id_list.back().toULong();
185 qDebug() <<
"scan number " << scan_number <<
"=>"
192 std::size_t scan_number)
const
202 QObject::tr(
"scan number %1 not found").arg(scan_number));
205 std::size_t index = it->second;
211 QObject::tr(
"scan number %1 found multiple times").arg(scan_number));
245const std::vector<double> &
278 if(spectrum_ms_level != 1)
288 using Pair = std::pair<double, double>;
289 using Map = std::map<double, double>;
290 using Iterator = Map::iterator;
299 res.first->second += sumY;
341const std::vector<QualifiedMassSpectrum> &
std::size_t getSpectrumIndex() const
const QString & getNativeId() const
const std::vector< QualifiedMassSpectrum > & getQualifiedMassSpectrumList() const
MsRunQualifiedSpectrumLoader()
virtual void spectrumListHasSize(std::size_t size) override
virtual bool needPeakList() const override
tells if we need the peak list (if we want the binary data) for each spectrum
virtual ~MsRunQualifiedSpectrumLoader()
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &qualified_mass_spectrum) override
std::vector< QualifiedMassSpectrum > m_qualifiedSpectrumList
const std::vector< double > & getRetentionTimeLine() const
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override
virtual ~MsRunReaderRetentionTimeLine()
virtual bool needPeakList() const override
tells if we need the peak list (if we want the binary data) for each spectrum
MsRunReaderRetentionTimeLine()
std::vector< double > m_retention_time_list
virtual bool needPeakList() const override
tells if we need the peak list (if we want the binary data) for each spectrum
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override
std::size_t getSpectrumIndexFromScanNumber(std::size_t scan_number) const
std::multimap< std::size_t, std::size_t > m_mmap_scan2index
virtual ~MsRunReaderScanNumberMultiMap()
MsRunReaderScanNumberMultiMap()
virtual ~MsRunReaderTicChromatogram()
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &qualified_mass_spectrum) override
MapTrace m_ticChromMapTrace
MsRunReaderTicChromatogram()
virtual bool needPeakList() const override
tells if we need the peak list (if we want the binary data) for each spectrum
Trace getTicChromatogram() const
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum) override
unsigned long getTotalCount() const
virtual void loadingEnded() override
std::vector< unsigned long > m_countMsLevelSpectrum
virtual bool needPeakList() const override
tells if we need the peak list (if we want the binary data) for each spectrum
unsigned long getMsLevelCount(unsigned int ms_level) const
Class representing a fully specified mass spectrum.
uint getMsLevel() const
Get the mass spectrum level.
pappso_double getRtInMinutes() const
Get the retention time in minutes.
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
pappso_double getRtInSeconds() const
Get the retention time in seconds.
virtual bool shouldStop()
virtual bool isReadAhead() const
tells if we want to read ahead spectrum
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
virtual void loadingEnded()
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 setReadAhead(bool is_read_ahead) final
use threads to read a spectrum by batch of batch_size
virtual void setNeedMsLevelPeakList(unsigned int ms_level, bool want_peak_list) final
tells if we need the peak list given
std::vector< bool > m_needPeakListByMsLevel
virtual void spectrumListHasSize(std::size_t size)
A simple container of DataPoint instances.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...