libpappsomspp
Library for mass spectrometry
pappso::MsRunSimpleStatistics Class Reference

example of interface to count MS levels of all spectrum in an MSrun More...

#include <msrunreader.h>

Inheritance diagram for pappso::MsRunSimpleStatistics:
pappso::SpectrumCollectionHandlerInterface

Public Member Functions

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...
 
virtual void loadingEnded () override
 
unsigned long getMsLevelCount (unsigned int ms_level) const
 
unsigned long getTotalCount () 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 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::vector< unsigned long > m_countMsLevelSpectrum
 

Detailed Description

example of interface to count MS levels of all spectrum in an MSrun

Definition at line 112 of file msrunreader.h.

Member Function Documentation

◆ getMsLevelCount()

unsigned long pappso::MsRunSimpleStatistics::getMsLevelCount ( unsigned int  ms_level) const

Definition at line 133 of file msrunreader.cpp.

134 {
135  if(ms_level == 0)
136  return 0;
137  if(ms_level > m_countMsLevelSpectrum.size())
138  return 0;
139  return (m_countMsLevelSpectrum[ms_level - 1]);
140 }
std::vector< unsigned long > m_countMsLevelSpectrum
Definition: msrunreader.h:116

References m_countMsLevelSpectrum.

◆ getTotalCount()

unsigned long pappso::MsRunSimpleStatistics::getTotalCount ( ) const

Definition at line 144 of file msrunreader.cpp.

145 {
146  unsigned long total = 0;
147  for(unsigned long count : m_countMsLevelSpectrum)
148  {
149  total += count;
150  }
151  return total;
152 }

References m_countMsLevelSpectrum.

◆ loadingEnded()

void pappso::MsRunSimpleStatistics::loadingEnded ( )
overridevirtual

Reimplemented from pappso::SpectrumCollectionHandlerInterface.

Definition at line 105 of file msrunreader.cpp.

106 {
107  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
108  //<< "The data loading process ended.";
109 }

◆ needPeakList()

bool pappso::MsRunSimpleStatistics::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 98 of file msrunreader.cpp.

99 {
100  return false;
101 }

◆ setQualifiedMassSpectrum()

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

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 113 of file msrunreader.cpp.

115 {
116  // The vector[0] contains the number of spectra at MS
117  // The vector[1] contains the number of spectra at MS^2
118  // The vector[2] contains the number of spectra at MS^3
119  // ...
120 
121  unsigned int ms_level = qspectrum.getMsLevel();
122  if(ms_level == 0)
123  return;
124  if(ms_level > m_countMsLevelSpectrum.size())
125  {
126  m_countMsLevelSpectrum.resize(ms_level);
127  }
128  m_countMsLevelSpectrum[ms_level - 1]++;
129 }

References pappso::QualifiedMassSpectrum::getMsLevel(), and m_countMsLevelSpectrum.

Member Data Documentation

◆ m_countMsLevelSpectrum

std::vector<unsigned long> pappso::MsRunSimpleStatistics::m_countMsLevelSpectrum
private

Definition at line 116 of file msrunreader.h.

Referenced by getMsLevelCount(), getTotalCount(), and setQualifiedMassSpectrum().


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