pappso::IonMobilityGrid Class Reference

#include <ionmobilitygrid.h>

Public Member Functions
	IonMobilityGrid ()
virtual	~IonMobilityGrid ()
void	storeObservedIdentityBetween (const MsRunId &msrun_ida, const XicCoord *xic_coorda, const MsRunId &msrun_idb, const XicCoord *xic_coordb)
void	computeCorrections ()
pappso::XicCoordSPtr	translateXicCoordFromTo (const pappso::XicCoord &source_xic_coord, const MsRunId &source_msrunid, const MsRunId &target_msrunid) const
const std::map< QString, std::vector< qint64 > > &	getMapDiferrencesStart () const
const std::map< QString, long > &	getMapCorrectionsStart () const

Private Attributes
std::map< QString, std::vector< qint64 > >	m_mapDiferrencesStart
std::map< QString, std::vector< qint64 > >	m_mapDiferrencesStop
std::map< QString, long >	m_mapCorrectionsStart
	scan num correction on start position stored for each msrun pair
std::map< QString, long >	m_mapCorrectionsStop
	scan num correction on start position stored for each msrun pair

Detailed Description

Todo

helper to align ion mobility ranges between MS runs

Definition at line 41 of file ionmobilitygrid.h.

Constructor & Destructor Documentation

IonMobilityGrid()

IonMobilityGrid::IonMobilityGrid

(

)

Default constructor

Definition at line 37 of file ionmobilitygrid.cpp.

{
}

~IonMobilityGrid()

IonMobilityGrid::~IonMobilityGrid ( )

virtual

Destructor

Definition at line 41 of file ionmobilitygrid.cpp.

{
}

Member Function Documentation

computeCorrections()

void pappso::IonMobilityGrid::computeCorrections

(

)

Definition at line 88 of file ionmobilitygrid.cpp.

{
  for(auto pair_key_start_vector : m_mapDiferrencesStart)
    {
 
      if(pair_key_start_vector.second.size() > 5)
        {
          // median
          const auto middleItr =
            pair_key_start_vector.second.begin() + (pair_key_start_vector.second.size() / 2);
          std::nth_element(
            pair_key_start_vector.second.begin(), middleItr, pair_key_start_vector.second.end());
          m_mapCorrectionsStart[pair_key_start_vector.first] = *middleItr;
        }
      else
        {
          m_mapCorrectionsStart[pair_key_start_vector.first] = 0;
        }
    }
  m_mapDiferrencesStart.clear();
  for(auto pair_key_stop_vector : m_mapDiferrencesStop)
    {
 
      if(pair_key_stop_vector.second.size() > 5)
        {
          // median
          const auto middleItr =
            pair_key_stop_vector.second.begin() + (pair_key_stop_vector.second.size() / 2);
          std::nth_element(
            pair_key_stop_vector.second.begin(), middleItr, pair_key_stop_vector.second.end());
          m_mapCorrectionsStop[pair_key_stop_vector.first] = *middleItr;
        }
      else
        {
          m_mapCorrectionsStop[pair_key_stop_vector.first] = 0;
        }
    }
  m_mapDiferrencesStop.clear();
}

References m_mapCorrectionsStart, m_mapCorrectionsStop, m_mapDiferrencesStart, and m_mapDiferrencesStop.

getMapCorrectionsStart()

const std::map< QString, long > & pappso::IonMobilityGrid::getMapCorrectionsStart

(

)

const

Definition at line 184 of file ionmobilitygrid.cpp.

{
  return m_mapCorrectionsStart;
}

References m_mapCorrectionsStart.

getMapDiferrencesStart()

const std::map< QString, std::vector< qint64 > > & pappso::IonMobilityGrid::getMapDiferrencesStart

(

)

const

Definition at line 178 of file ionmobilitygrid.cpp.

{
  return m_mapDiferrencesStart;
}

References m_mapDiferrencesStart.

storeObservedIdentityBetween()

void pappso::IonMobilityGrid::storeObservedIdentityBetween	(	const MsRunId &	msrun_ida,
		const XicCoord *	xic_coorda,
		const MsRunId &	msrun_idb,
		const XicCoord *	xic_coordb )

Definition at line 46 of file ionmobilitygrid.cpp.

{
  if(msrun_ida == msrun_idb)
    return;
  QString msrun_key(QString("%1-%2").arg(msrun_ida.getXmlId()).arg(msrun_idb.getXmlId()));
 
 
  if(msrun_ida.getXmlId() > msrun_idb.getXmlId())
    {
      msrun_key = QString("%1-%2").arg(msrun_idb.getXmlId()).arg(msrun_ida.getXmlId());
      std::swap(xic_coorda, xic_coordb);
    }
 
  auto it_start = m_mapDiferrencesStart.insert({msrun_key, std::vector<qint64>()});
  const QVariant &ref_variantb =
    xic_coordb->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart);
  if(ref_variantb.isNull())
    {
      throw pappso::ExceptionNotPossible(QObject::tr(
        "XicCoordParam::TimsTofIonMobilityScanNumberStart QVariant is null for xic_coordb"));
    }
  const QVariant &ref_varianta =
    xic_coorda->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStart);
 
  if(ref_varianta.isNull())
    {
      throw pappso::ExceptionNotPossible(QObject::tr(
        "XicCoordParam::TimsTofIonMobilityScanNumberStart QVariant is null for xic_coorda"));
    }
  it_start.first->second.push_back(ref_variantb.toLongLong() - ref_varianta.toLongLong());
 
 
  auto it_stop = m_mapDiferrencesStop.insert({msrun_key, std::vector<qint64>()});
  it_stop.first->second.push_back(
    xic_coordb->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStop).toLongLong() -
    xic_coorda->getParam(XicCoordParam::TimsTofIonMobilityScanNumberStop).toLongLong());
}

References pappso::XicCoord::getParam(), pappso::MsRunId::getXmlId(), m_mapDiferrencesStart, m_mapDiferrencesStop, pappso::TimsTofIonMobilityScanNumberStart, and pappso::TimsTofIonMobilityScanNumberStop.

Referenced by pappso::masschroq::Peptide::populateIonMobilityGrid().

translateXicCoordFromTo()

pappso::XicCoordSPtr pappso::IonMobilityGrid::translateXicCoordFromTo	(	const pappso::XicCoord &	source_xic_coord,
		const MsRunId &	source_msrunid,
		const MsRunId &	target_msrunid ) const

Definition at line 129 of file ionmobilitygrid.cpp.

{
  if(m_mapCorrectionsStop.size() == 0)
    {
      return source_xic_coord.initializeAndClone();
    }
 
  bool opposed = false;
  QString msrun_key(QString("%1-%2").arg(source_msrunid.getXmlId()).arg(target_msrunid.getXmlId()));
 
 
  if(source_msrunid.getXmlId() > target_msrunid.getXmlId())
    {
      msrun_key = QString("%1-%2").arg(target_msrunid.getXmlId()).arg(source_msrunid.getXmlId());
      opposed   = true;
    }
  auto itstart   = m_mapCorrectionsStart.find(msrun_key);
  long start_dev = 0;
  if(itstart != m_mapCorrectionsStart.end())
    {
      start_dev = itstart->second;
      if(opposed)
        {
          start_dev *= -1;
        }
    }
 
  auto itstop   = m_mapCorrectionsStop.find(msrun_key);
  long stop_dev = 0;
  if(itstop != m_mapCorrectionsStop.end())
    {
      stop_dev = itstop->second;
      if(opposed)
        {
          stop_dev *= -1;
        }
    }
 
  pappso::XicCoordSPtr result_xic_coord_sp = source_xic_coord.initializeAndClone();
  XicCoordTims *tims_coord                 = static_cast<XicCoordTims *>(result_xic_coord_sp.get());
 
  tims_coord->scanNumBeginRangeCorrection(start_dev, stop_dev);
 
  return result_xic_coord_sp;
}

References pappso::MsRunId::getXmlId(), pappso::XicCoord::initializeAndClone(), m_mapCorrectionsStart, m_mapCorrectionsStop, and pappso::XicCoordTims::scanNumBeginRangeCorrection().

Referenced by pappso::masschroq::Peptide::getBestIonMobilityXicCoordToExtractOverallMsRunGroup().

Member Data Documentation

m_mapCorrectionsStart

std::map<QString, long> pappso::IonMobilityGrid::m_mapCorrectionsStart

private

scan num correction on start position stored for each msrun pair

Definition at line 76 of file ionmobilitygrid.h.

Referenced by computeCorrections(), getMapCorrectionsStart(), and translateXicCoordFromTo().

m_mapCorrectionsStop

std::map<QString, long> pappso::IonMobilityGrid::m_mapCorrectionsStop

private

scan num correction on start position stored for each msrun pair

Definition at line 81 of file ionmobilitygrid.h.

Referenced by computeCorrections(), and translateXicCoordFromTo().

m_mapDiferrencesStart

std::map<QString, std::vector<qint64> > pappso::IonMobilityGrid::m_mapDiferrencesStart

private

Definition at line 70 of file ionmobilitygrid.h.

Referenced by computeCorrections(), getMapDiferrencesStart(), and storeObservedIdentityBetween().

m_mapDiferrencesStop

std::map<QString, std::vector<qint64> > pappso::IonMobilityGrid::m_mapDiferrencesStop

private

Definition at line 71 of file ionmobilitygrid.h.

Referenced by computeCorrections(), and storeObservedIdentityBetween().

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

• pappsomspp/core/msrun/xiccoord/ionmobilitygrid.h
• pappsomspp/core/msrun/xiccoord/ionmobilitygrid.cpp