pappso::MsRunReadConfig Class Reference

#include <msrunreadconfig.h>

Public Member Functions
	MsRunReadConfig ()
	MsRunReadConfig (const MsRunReadConfig &other)
	~MsRunReadConfig ()
MsRunReadConfig &	operator= (const MsRunReadConfig &other)
void	setRetentionTimeStartInSeconds (double retention_time_start_in_seconds)
double	getRetentionTimeStartInSeconds () const
void	setRetentionTimeEndInSeconds (double retention_time_end_in_seconds)
double	getRetentionTimeEndInSeconds () const
void	setMsLevels (std::vector< std::size_t > ms_levels)
const bool *	getMsLevels () const
QString	getMsLevelsAsString () const
void	setNeedPeakList (bool need_peak_list)
bool	needPeakList () const
void	setParameterValue (MsRunReadConfigParameter parameter, const QVariant &value)
const QVariant	getParameterValue (MsRunReadConfigParameter parameter) const
void	reset ()
QString	toString () const
bool	acceptMsLevel (std::size_t ms_level) const
bool	acceptRetentionTimeInSeconds (double retention_time_in_seconds) const

Private Attributes
double	m_retentionTimeStartSeconds = -1
double	m_retentionTimeEndSeconds = -1
bool	m_isPeakListNeeded = true
bool	m_msLevels [MAX_MS_LEVELS] = {false}
std::map< MsRunReadConfigParameter, QVariant >	m_paramsMap
	map containing any parameter value

Detailed Description

Definition at line 61 of file msrunreadconfig.h.

Constructor & Destructor Documentation

MsRunReadConfig() [1/2]

pappso::MsRunReadConfig::MsRunReadConfig

(

)

Definition at line 28 of file msrunreadconfig.cpp.

{
  // Set these two levels to true by default.
  m_msLevels[1] = true;
  m_msLevels[2] = true;
}

References m_msLevels.

Referenced by MsRunReadConfig(), and operator=().

MsRunReadConfig() [2/2]

pappso::MsRunReadConfig::MsRunReadConfig

(

const MsRunReadConfig &

other

)

Definition at line 35 of file msrunreadconfig.cpp.

  : m_retentionTimeStartSeconds(other.m_retentionTimeStartSeconds),
    m_retentionTimeEndSeconds(other.m_retentionTimeEndSeconds),
    m_paramsMap(other.m_paramsMap)
{
  for(std::size_t index = 0; index < MAX_MS_LEVELS; ++index)
    m_msLevels[index] = other.m_msLevels[index];
}

References MsRunReadConfig(), m_msLevels, m_paramsMap, m_retentionTimeEndSeconds, m_retentionTimeStartSeconds, and pappso::MAX_MS_LEVELS.

~MsRunReadConfig()

pappso::MsRunReadConfig::~MsRunReadConfig

(

)

Definition at line 44 of file msrunreadconfig.cpp.

{
}

Member Function Documentation

acceptMsLevel()

bool pappso::MsRunReadConfig::acceptMsLevel

(

std::size_t

ms_level

)

const

Definition at line 133 of file msrunreadconfig.cpp.

{
  if(ms_level >= MAX_MS_LEVELS)
    return false;
 
  return m_msLevels[ms_level];
}

References m_msLevels, and pappso::MAX_MS_LEVELS.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

acceptRetentionTimeInSeconds()

bool pappso::MsRunReadConfig::acceptRetentionTimeInSeconds

(

double

retention_time_in_seconds

)

const

Definition at line 142 of file msrunreadconfig.cpp.

{
  // qDebug() << "Requested retention_time_in_seconds:"
  //          << retention_time_in_seconds;
 
  // Whatever the member datum below, if it is equal to -1
  // then that means that RT is not a selection criterion.
  if(m_retentionTimeStartSeconds == -1 || m_retentionTimeEndSeconds == -1)
    {
      return true;
    }
 
  // We use inclusive RT ranges.
  if(retention_time_in_seconds >= m_retentionTimeStartSeconds)
    {
      if(retention_time_in_seconds <= m_retentionTimeEndSeconds)
        {
          return true;
        }
    }
 
  return false;
}

References m_retentionTimeEndSeconds, and m_retentionTimeStartSeconds.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

getMsLevels()

const bool * pappso::MsRunReadConfig::getMsLevels

(

void

)

const

Definition at line 112 of file msrunreadconfig.cpp.

{
  return m_msLevels;
}

References m_msLevels.

getMsLevelsAsString()

QString pappso::MsRunReadConfig::getMsLevelsAsString

(

)

const

Definition at line 118 of file msrunreadconfig.cpp.

{
  QString text = "";
 
  for(std::size_t index = 0; index < MAX_MS_LEVELS; ++index)
    {
      if(m_msLevels[index] == true)
        text += QString("%1 ").arg(index);
    }
 
  return text;
}

References m_msLevels, and pappso::MAX_MS_LEVELS.

getParameterValue()

const QVariant pappso::MsRunReadConfig::getParameterValue

(

pappso::MsRunReadConfigParameter

parameter

)

const

Definition at line 192 of file msrunreadconfig.cpp.

{
  auto it = m_paramsMap.find(parameter);
  if(it == m_paramsMap.end())
    {
      return QVariant();
    }
  else
    {
      return it->second;
    }
}

References m_paramsMap.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and toString().

getRetentionTimeEndInSeconds()

double pappso::MsRunReadConfig::getRetentionTimeEndInSeconds

(

)

const

Definition at line 83 of file msrunreadconfig.cpp.

{
  return m_retentionTimeEndSeconds;
}

References m_retentionTimeEndSeconds.

getRetentionTimeStartInSeconds()

double pappso::MsRunReadConfig::getRetentionTimeStartInSeconds

(

)

const

Definition at line 71 of file msrunreadconfig.cpp.

{
  return m_retentionTimeStartSeconds;
}

References m_retentionTimeStartSeconds.

needPeakList()

bool pappso::MsRunReadConfig::needPeakList

(

)

const

Definition at line 167 of file msrunreadconfig.cpp.

{
  return m_isPeakListNeeded;
}

References m_isPeakListNeeded.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

operator=()

MsRunReadConfig & pappso::MsRunReadConfig::operator=

(

const MsRunReadConfig &

other

)

Definition at line 49 of file msrunreadconfig.cpp.

{
  if(&other == this)
    return *this;
 
  m_retentionTimeStartSeconds = other.m_retentionTimeStartSeconds;
  m_retentionTimeEndSeconds   = other.m_retentionTimeEndSeconds;
  m_paramsMap                 = other.m_paramsMap;
 
  for(std::size_t index = 0; index < MAX_MS_LEVELS; ++index)
    m_msLevels[index] = other.m_msLevels[index];
 
  return *this;
}

References MsRunReadConfig(), m_msLevels, m_paramsMap, m_retentionTimeEndSeconds, m_retentionTimeStartSeconds, and pappso::MAX_MS_LEVELS.

reset()

void pappso::MsRunReadConfig::reset

(

)

Definition at line 207 of file msrunreadconfig.cpp.

{
  m_retentionTimeStartSeconds = -1;
  m_retentionTimeEndSeconds   = -1;
  m_isPeakListNeeded          = true;
 
  for(std::size_t index = 0; index < MAX_MS_LEVELS; ++index)
    {
      m_msLevels[index] = false;
    }
  // Set these two levels to true by default.
  m_msLevels[1] = true;
  m_msLevels[2] = true;
 
  m_paramsMap.clear();
}

References m_isPeakListNeeded, m_msLevels, m_paramsMap, m_retentionTimeEndSeconds, m_retentionTimeStartSeconds, and pappso::MAX_MS_LEVELS.

setMsLevels()

void pappso::MsRunReadConfig::setMsLevels

(

std::vector< std::size_t >

ms_levels

)

Definition at line 89 of file msrunreadconfig.cpp.

{
  // First reset all the levels to false, this time, since we'll fill the array
  // with explicit values.
  for(std::size_t index = 0; index < MAX_MS_LEVELS; ++index)
    m_msLevels[index] = false;
 
  // And now actually fill with true values the proper array cells.
  for(auto ms_level : ms_levels)
    {
      if(ms_level >= MAX_MS_LEVELS)
        {
          qDebug() << "The passed vector of MS levels holds a value that is "
                      "not correct:"
                   << ms_level << ": skipping it.";
 
          continue;
        }
      m_msLevels[ms_level] = true;
    }
}

References m_msLevels, and pappso::MAX_MS_LEVELS.

Referenced by pappso::masschroq::MsRun::MsRun(), pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunReader::getRetentionTimeLine(), pappso::MsRunReader::getTicChromatogram(), pappso::MzcborMsRunReader::readSpectrumCollection(), pappso::MzcborMsRunReader::readSpectrumCollectionByMsLevel(), pappso::MsRunReader::scanNumber2SpectrumIndex(), and pappso::MzxmlOutput::write().

setNeedPeakList()

void pappso::MsRunReadConfig::setNeedPeakList

(

bool

need_peak_list

)

Definition at line 173 of file msrunreadconfig.cpp.

{
  m_isPeakListNeeded = need_peak_list;
}

References m_isPeakListNeeded.

Referenced by pappso::masschroq::MsRun::MsRun(), pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunReader::getRetentionTimeLine(), pappso::MsRunReader::getTicChromatogram(), pappso::MzcborMsRunReader::readSpectrumCollection(), pappso::MzcborMsRunReader::readSpectrumCollectionByMsLevel(), pappso::MsRunReader::scanNumber2SpectrumIndex(), and pappso::MzxmlOutput::write().

setParameterValue()

void pappso::MsRunReadConfig::setParameterValue	(	pappso::MsRunReadConfigParameter	parameter,
		const QVariant &	value )

Definition at line 179 of file msrunreadconfig.cpp.

{
 
  auto ret = m_paramsMap.insert(std::pair<MsRunReadConfigParameter, QVariant>(parameter, value));
 
  if(ret.second == false)
    {
      ret.first->second = value;
    }
}

References m_paramsMap.

setRetentionTimeEndInSeconds()

void pappso::MsRunReadConfig::setRetentionTimeEndInSeconds

(

double

retention_time_end_in_seconds

)

Definition at line 77 of file msrunreadconfig.cpp.

{
  m_retentionTimeEndSeconds = retention_time_end_in_seconds;
}

References m_retentionTimeEndSeconds.

setRetentionTimeStartInSeconds()

void pappso::MsRunReadConfig::setRetentionTimeStartInSeconds

(

double

retention_time_start_in_seconds

)

Definition at line 65 of file msrunreadconfig.cpp.

{
  m_retentionTimeStartSeconds = retention_time_start_in_seconds;
}

References m_retentionTimeStartSeconds.

toString()

QString pappso::MsRunReadConfig::toString

(

)

const

Definition at line 225 of file msrunreadconfig.cpp.

{
  QString text = QString("MsRunReadConfig\n: RT start: %1, RT end: %2\n")
                   .arg(m_retentionTimeStartSeconds)
                   .arg(m_retentionTimeEndSeconds);
 
  text += "MS level(s): ";
 
  for(std::size_t index = 0; index < MAX_MS_LEVELS; ++index)
    {
      if(m_msLevels[index] == true)
        text += QString("%1 ").arg(index);
    }
 
  text += " \n";
 
  if(!getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexBegin).isNull())
    {
      text +=
        QString("Mobility index range: [%1-%2]\n")
          .arg(getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexBegin).toUInt())
          .arg(getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexEnd).toUInt());
    }
 
  if(!getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0Begin).isNull())
    {
      text +=
        QString("Mobility 1/K0 range: [%1-%2]\n")
          .arg(
            getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0Begin).toDouble())
          .arg(getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0End).toDouble());
    }
 
  if(!getParameterValue(MsRunReadConfigParameter::MzRangeBegin).isNull())
    {
      text += QString("m/z range: [%1-%2]\n")
                .arg(getParameterValue(MsRunReadConfigParameter::MzRangeBegin).toDouble())
                .arg(getParameterValue(MsRunReadConfigParameter::MzRangeEnd).toDouble());
    }
 
  if(!getParameterValue(MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow).isNull())
    {
      text +=
        QString("m/z merge window %1\n")
          .arg(getParameterValue(MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow).toUInt());
    }
 
  return text;
}

References getParameterValue(), m_msLevels, m_retentionTimeEndSeconds, m_retentionTimeStartSeconds, pappso::MAX_MS_LEVELS, pappso::MzRangeBegin, pappso::MzRangeEnd, pappso::TimsFrameIonMobOneOverK0Begin, pappso::TimsFrameIonMobOneOverK0End, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, and pappso::TimsFrameMzIndexMergeWindow.

Referenced by pappso::TimsMsRunReader::readSpectrumCollection2().

Member Data Documentation

m_isPeakListNeeded

bool pappso::MsRunReadConfig::m_isPeakListNeeded = true

private

Definition at line 100 of file msrunreadconfig.h.

Referenced by needPeakList(), reset(), and setNeedPeakList().

m_msLevels

bool pappso::MsRunReadConfig::m_msLevels[MAX_MS_LEVELS] = {false}

private

Definition at line 105 of file msrunreadconfig.h.

{false};

Referenced by MsRunReadConfig(), MsRunReadConfig(), acceptMsLevel(), getMsLevels(), getMsLevelsAsString(), operator=(), reset(), setMsLevels(), and toString().

m_paramsMap

std::map<MsRunReadConfigParameter, QVariant> pappso::MsRunReadConfig::m_paramsMap

private

map containing any parameter value

Definition at line 110 of file msrunreadconfig.h.

Referenced by MsRunReadConfig(), getParameterValue(), operator=(), reset(), and setParameterValue().

m_retentionTimeEndSeconds

double pappso::MsRunReadConfig::m_retentionTimeEndSeconds = -1

private

Definition at line 98 of file msrunreadconfig.h.

Referenced by MsRunReadConfig(), acceptRetentionTimeInSeconds(), getRetentionTimeEndInSeconds(), operator=(), reset(), setRetentionTimeEndInSeconds(), and toString().

m_retentionTimeStartSeconds

double pappso::MsRunReadConfig::m_retentionTimeStartSeconds = -1

private

Definition at line 97 of file msrunreadconfig.h.

Referenced by MsRunReadConfig(), acceptRetentionTimeInSeconds(), getRetentionTimeStartInSeconds(), operator=(), reset(), setRetentionTimeStartInSeconds(), and toString().

---

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

• pappsomspp/core/msrun/msrunreadconfig.h
• pappsomspp/core/msrun/msrunreadconfig.cpp