41#include "../trace/maptrace.h"
45#include "../massspectrum/qualifiedmassspectrum.h"
46#include "../msfile/msfilereader.h"
47#include "../exportinmportconfig.h"
69 virtual bool needMsLevelPeakList(
unsigned int ms_level)
const final;
73 virtual void setNeedMsLevelPeakList(
unsigned int ms_level,
74 bool want_peak_list)
final;
75 virtual bool shouldStop();
76 virtual void loadingEnded();
77 virtual void spectrumListHasSize(std::size_t size);
83 virtual void setReadAhead(
bool is_read_ahead)
final;
87 virtual bool isReadAhead()
const;
90 bool m_isReadAhead =
false;
92 std::vector<bool> m_needPeakListByMsLevel = {
true,
121 virtual bool needPeakList()
const override;
122 virtual void loadingEnded()
override;
124 unsigned long getMsLevelCount(
unsigned int ms_level)
const;
126 unsigned long getTotalCount()
const;
142 virtual bool needPeakList()
const override;
144 std::size_t getSpectrumIndexFromScanNumber(std::size_t scan_number)
const;
160 virtual bool needPeakList()
const override;
162 const std::vector<double> &getRetentionTimeLine()
const;
173 virtual void setQualifiedMassSpectrum(
175 virtual bool needPeakList()
const override;
177 Trace getTicChromatogram()
const;
collect retention times along MS run
std::vector< double > m_retention_time_list
provides a multimap to find quickly spectrum index from scan number
std::multimap< std::size_t, std::size_t > m_mmap_scan2index
calculate a TIC chromatogram
MapTrace m_ticChromMapTrace
example of interface to count MS levels of all spectrum in an MSrun
std::vector< unsigned long > m_countMsLevelSpectrum
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
A simple container of DataPoint instances.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...