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();
}

getMapCorrectionsStart()

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

(

)

const

Definition at line 184 of file ionmobilitygrid.cpp.

{
  return 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;
}

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(), 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(), 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.

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.

m_mapDiferrencesStart

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

private

Definition at line 70 of file ionmobilitygrid.h.

m_mapDiferrencesStop

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

private

Definition at line 71 of file ionmobilitygrid.h.

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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