#include <msrungroup.h>

Public Member Functions
	MsRunGroup (const QString &id, const std::vector< MsRunPeptideListSp > &msrun_list)
	MsRunGroup (const MsRunGroup &other)
virtual	~MsRunGroup ()
void	setIonMobilityGridSp (const std::shared_ptr< pappso::IonMobilityGrid > &ion_mobility_grid_sp)
void	align (CborOutputStream &cbor_output, const QString &align_id, pappso::UiMonitorInterface &m_uiMonitor) const
void	quantify (CborOutputStream &cbor_output, const QString &quantify_id, const QString &tmp_dir, pappso::UiMonitorInterface &m_uiMonitor, const QuantificationMethodSp &quantification_method, const std::vector< PeptideSp > &peptide_sp_list) const
void	setAlignmentMethodSp (const AlignmentMethodSp &alignment_method_sp, const QString &msrun_ref_id)
bool	contains (const MsRun *msrun_p) const
bool	hasTimsTofMobilityIndex () const
const std::shared_ptr< pappso::IonMobilityGrid > &	getIonMobilityGridSp () const
const QString &	getId () const

Private Member Functions
void	alignRetentionTimeBetweenMsRuns (CborOutputStream &cbor_output, pappso::UiMonitorInterface &m_uiMonitor) const

Private Attributes
const QString	m_id
const std::vector< MsRunPeptideListSp >	m_msRunPeptideListSpList
AlignmentMethodSp	msp_alignmentMethod
MsRunPeptideListSp	msp_msRunPeptideListAlignmentReference
bool	m_hasTimsTofMobilityIndex = false
std::shared_ptr< pappso::IonMobilityGrid >	msp_ionMobilityGrid

Detailed Description

Todo: write docs

Definition at line 47 of file msrungroup.h.

Constructor & Destructor Documentation

◆ MsRunGroup() [1/2]

pappso::masschroq::MsRunGroup::MsRunGroup	(	const QString &	id,
		const std::vector< MsRunPeptideListSp > &	msrun_list )

Default constructor

Definition at line 32 of file msrungroup.cpp.

  : m_id(id), m_msRunPeptideListSpList(msrun_list)
{
  if(m_msRunPeptideListSpList.size() > 0)
    {
      m_hasTimsTofMobilityIndex =
        m_msRunPeptideListSpList.front().get()->getMsRunSp().get()->hasTimsTofMobilityIndex();
    }
}

References m_id, and m_msRunPeptideListSpList.

◆ MsRunGroup() [2/2]

pappso::masschroq::MsRunGroup::MsRunGroup ( const MsRunGroup & other )

Copy constructor

Parameters

other TODO

Definition at line 43 of file msrungroup.cpp.

  : m_id(other.m_id), m_msRunPeptideListSpList(other.m_msRunPeptideListSpList)
{
  m_hasTimsTofMobilityIndex = other.m_hasTimsTofMobilityIndex;
}

References m_hasTimsTofMobilityIndex, m_id, and m_msRunPeptideListSpList.

◆ ~MsRunGroup()

pappso::masschroq::MsRunGroup::~MsRunGroup ( )

virtual

Destructor

Definition at line 49 of file msrungroup.cpp.

50{

51}

Member Function Documentation

◆ align()

void pappso::masschroq::MsRunGroup::align	(	CborOutputStream &	cbor_output,
		const QString &	align_id,
		pappso::UiMonitorInterface &	m_uiMonitor ) const

Definition at line 128 of file msrungroup.cpp.

{
 
  cbor_output.getCborStreamWriter().startMap();
  cbor_output.getCborStreamWriter().append(QLatin1String("alignment_id"));
  cbor_output.getCborStreamWriter().append(align_id);
  cbor_output.getCborStreamWriter().append(QLatin1String("group_id"));
  cbor_output.getCborStreamWriter().append(getId());
  cbor_output.getCborStreamWriter().append(QLatin1String("timestamp1"));
  cbor_output.getCborStreamWriter().append(QDateTime::currentDateTime().toString(Qt::ISODate));
 
  // std::shared_ptr<pappso::MsRunRetentionTime<QString>>
  //  retention_time_reference_sp = nullptr;
  m_uiMonitor.appendText("Starting retention time alignment");
  alignRetentionTimeBetweenMsRuns(cbor_output, m_uiMonitor);
  m_uiMonitor.appendText("retention time alignment done");
 
 
  cbor_output.getCborStreamWriter().append(QLatin1String("timestamp2"));
  cbor_output.getCborStreamWriter().append(QDateTime::currentDateTime().toString(Qt::ISODate));
  cbor_output.getCborStreamWriter().endMap();
}

References alignRetentionTimeBetweenMsRuns(), pappso::UiMonitorInterface::appendText(), pappso::masschroq::CborOutputStream::getCborStreamWriter(), and getId().

◆ alignRetentionTimeBetweenMsRuns()

void pappso::masschroq::MsRunGroup::alignRetentionTimeBetweenMsRuns	(	CborOutputStream &	cbor_output,
		pappso::UiMonitorInterface &	m_uiMonitor ) const

private

Definition at line 54 of file msrungroup.cpp.

{
  if(msp_msRunPeptideListAlignmentReference.get() == nullptr)
    {
      throw pappso::PappsoException(QObject::tr("match between run requires an MSrun reference"));
    }
  cbor_output.getCborStreamWriter().append(QLatin1String("alignment"));
  cbor_output.getCborStreamWriter().startMap();
  cbor_output.getCborStreamWriter().append(QLatin1String("msrun_ref"));
  cbor_output.getCborStreamWriter().append(msp_msRunPeptideListAlignmentReference.get()
                                             ->getMsRunSp()
                                             .get()
                                             ->getMsRunReaderSPtr()
                                             .get()
                                             ->getMsRunId()
                                             .get()
                                             ->getXmlId());
  //   "alignment": {
  //       "msrun_ref": "msruna2",
 
  for(const pappso::masschroq::MsRunPeptideListSp &msrun_peptide_list : m_msRunPeptideListSpList)
    {
      msrun_peptide_list.get()->buildMsRunRetentionTimeSpOnPeptideObservations(msp_alignmentMethod);
    }
  const pappso::MsRunRetentionTime<QString> *reference_msrun_retetiontime_p =
    msp_msRunPeptideListAlignmentReference.get()->getMsRunRetentionTimeConstPtr();
 
  cbor_output.getCborStreamWriter().append(QLatin1String("corrections"));
 
  cbor_output.getCborStreamWriter().startMap();
  // "corrections": {
  for(const pappso::masschroq::MsRunPeptideListSp &msrun_peptide_list : m_msRunPeptideListSpList)
    {
 
      if(msrun_peptide_list.get() == msp_msRunPeptideListAlignmentReference.get())
        continue;
 
 
      /*
               "msruna1": {
                   "original": [1,2,3,4.5],
                   "aligned":[1,2,3,4.5]
               },
               "msruna2": {
                   "original": [1,2,3,4.5],
                   "aligned":[1,2,3,4.5]
               }*/
      msrun_peptide_list.get()->getMsRunRetentionTimePtr()->align(*reference_msrun_retetiontime_p);
 
      pappso::Trace report_common_MS2_delta_rt =
        msrun_peptide_list.get()->getMsRunRetentionTimePtr()->getCommonDeltaRt(
          reference_msrun_retetiontime_p->getSeamarks());
 
      cbor_output.getCborStreamWriter().append(msrun_peptide_list.get()
                                                 ->getMsRunSp()
                                                 .get()
                                                 ->getMsRunReaderSPtr()
                                                 .get()
                                                 ->getMsRunId()
                                                 .get()
                                                 ->getXmlId());
      cbor_output.writeMsRunRetentionTime(report_common_MS2_delta_rt,
                                          *msrun_peptide_list.get()->getMsRunRetentionTimePtr());
    }
 
 
  cbor_output.getCborStreamWriter().endMap();
  cbor_output.getCborStreamWriter().endMap();
}

References pappso::masschroq::CborOutputStream::getCborStreamWriter(), pappso::MsRunRetentionTime< T >::getSeamarks(), m_msRunPeptideListSpList, msp_alignmentMethod, msp_msRunPeptideListAlignmentReference, and pappso::masschroq::CborOutputStream::writeMsRunRetentionTime().

Referenced by align().

◆ contains()

bool pappso::masschroq::MsRunGroup::contains ( const MsRun * msrun_p ) const

Definition at line 310 of file msrungroup.cpp.

{
  auto it = find_if(m_msRunPeptideListSpList.begin(),
                    m_msRunPeptideListSpList.end(),
                    [msrun_p](const pappso::masschroq::MsRunPeptideListSp &msrun) {
                      return (msrun.get()->getMsRunSp().get() == msrun_p);
                    });
  return (it != m_msRunPeptideListSpList.end());
}

References m_msRunPeptideListSpList.

Referenced by pappso::masschroq::Peptide::getBestIonMobilityXicCoordToExtractOverallMsRunGroup(), and pappso::masschroq::Peptide::getBestXicCoordSPtrForChargeInMsRunGroup().

◆ getId()

const QString & pappso::masschroq::MsRunGroup::getId ( ) const

Definition at line 340 of file msrungroup.cpp.

{
  return m_id;
}

References m_id.

Referenced by align(), and quantify().

◆ getIonMobilityGridSp()

const std::shared_ptr< pappso::IonMobilityGrid > & pappso::masschroq::MsRunGroup::getIonMobilityGridSp ( ) const

Definition at line 334 of file msrungroup.cpp.

{
  return msp_ionMobilityGrid;
}

References msp_ionMobilityGrid.

Referenced by pappso::masschroq::Peptide::getBestIonMobilityXicCoordToExtractOverallMsRunGroup(), pappso::masschroq::MbrPeptideMeasurements::prepareMeasurements(), and pappso::masschroq::PeptideMeasurements::prepareMeasurements().

◆ hasTimsTofMobilityIndex()

bool pappso::masschroq::MsRunGroup::hasTimsTofMobilityIndex ( ) const

Definition at line 328 of file msrungroup.cpp.

{
  return m_hasTimsTofMobilityIndex;
}

References m_hasTimsTofMobilityIndex.

◆ quantify()

void pappso::masschroq::MsRunGroup::quantify	(	CborOutputStream &	cbor_output,
		const QString &	quantify_id,
		const QString &	tmp_dir,
		pappso::UiMonitorInterface &	m_uiMonitor,
		const QuantificationMethodSp &	quantification_method,
		const std::vector< PeptideSp > &	peptide_sp_list ) const

Definition at line 155 of file msrungroup.cpp.

{
 
  bool match_between_run = quantification_method.get()->getMatchBetweenRun();
 
  cbor_output.getCborStreamWriter().startMap();
  cbor_output.getCborStreamWriter().append("quantify_id");
  cbor_output.getCborStreamWriter().append(quantify_id);
  cbor_output.getCborStreamWriter().append("group_id");
  cbor_output.getCborStreamWriter().append(getId());
  cbor_output.getCborStreamWriter().append(QLatin1String("timestamp1"));
  cbor_output.getCborStreamWriter().append(QDateTime::currentDateTime().toString(Qt::ISODate));
 
  cbor_output.getCborStreamWriter().append("first_pass");
  cbor_output.getCborStreamWriter().startMap(m_msRunPeptideListSpList.size());
 
 
  const pappso::MsRunRetentionTime<QString> *msrun_rt_reference_p = nullptr;
  if(match_between_run)
    {
 
      if(msp_msRunPeptideListAlignmentReference.get() == nullptr)
        {
          throw pappso::PappsoException(
            QObject::tr("group %1 is not aligned, match between run is not possible").arg(getId()));
        }
      msrun_rt_reference_p =
        msp_msRunPeptideListAlignmentReference.get()->getMsRunRetentionTimeConstPtr();
    }
 
 
  for(const pappso::masschroq::MsRunPeptideListSp &msrun_peptide_list : m_msRunPeptideListSpList)
    {
      msrun_peptide_list.get()->quantify(this, tmp_dir, m_uiMonitor, quantification_method);
 
 
      if(match_between_run)
        {
 
 
          const pappso::MsRunRetentionTime<QString> *msrun_rt_p =
            msrun_peptide_list.get()->getMsRunRetentionTimeConstPtr();
 
 
          if((msrun_rt_reference_p == nullptr) || (msrun_rt_p == nullptr) ||
             ((!msrun_rt_p->isAligned()) && (msrun_rt_reference_p != msrun_rt_p)))
            {
              throw pappso::PappsoException(
                QObject::tr("msrun %1 is not aligned, match between run is not possible")
                  .arg(msrun_peptide_list.get()
                         ->getMsRunSp()
                         .get()
                         ->getMsRunReaderSPtr()
                         .get()
                         ->getMsRunId()
                         .get()
                         ->getXmlId()));
            }
          m_uiMonitor.appendText("Collecting peak apex");
          msrun_peptide_list.get()->collectPeptidePeakRetentionTime(msrun_rt_reference_p);
          msrun_peptide_list.get()->collectPeptideMs2RetentionTime(msrun_rt_reference_p);
        }
 
      cbor_output.writeQrDataBlock(m_uiMonitor, *msrun_peptide_list.get(), false);
 
 
      msrun_peptide_list.get()->clearMeasurements();
    }
 
  cbor_output.getCborStreamWriter().endMap();
 
  cbor_output.getCborStreamWriter().append(QLatin1String("timestamp2"));
  cbor_output.getCborStreamWriter().append(QDateTime::currentDateTime().toString(Qt::ISODate));
  if(match_between_run)
    {
      if(msrun_rt_reference_p != nullptr)
        { // second pass
 
          m_uiMonitor.appendText(
            QObject::tr("Computing consensus retention time (%1)").arg(peptide_sp_list.size()));
          for(const pappso::masschroq::PeptideSp &peptide_sp : peptide_sp_list)
            {
              peptide_sp.get()->computeConsensusRetentionTime();
            }
 
          cbor_output.getCborStreamWriter().append("second_pass");
          cbor_output.getCborStreamWriter().startMap(m_msRunPeptideListSpList.size());
          for(const pappso::masschroq::MsRunPeptideListSp &msrun_peptide_list :
              m_msRunPeptideListSpList)
            {
              const pappso::masschroq::MsRun *msrun_p =
                msrun_peptide_list.get()->getMsRunSp().get();
              std::vector<pappso::masschroq::PeptideSp> peptide_mbr_list;
              for(const pappso::masschroq::PeptideSp &peptide_sp : peptide_sp_list)
                {
                  if(!peptide_sp.get()->isObservedInMsRunSp(msrun_p))
                    {
                      peptide_mbr_list.push_back(peptide_sp);
                    }
                }
              msrun_peptide_list.get()->quantifyMatchBetweenRun(
                this, peptide_mbr_list, tmp_dir, m_uiMonitor, quantification_method);
 
 
              cbor_output.writeQrDataBlock(m_uiMonitor, *msrun_peptide_list.get(), true);
 
              msrun_peptide_list.get()->clearMeasurements();
            }
 
          cbor_output.getCborStreamWriter().endMap();
        }
    }
 
  cbor_output.getCborStreamWriter().append(QLatin1String("timestamp3"));
  cbor_output.getCborStreamWriter().append(QDateTime::currentDateTime().toString(Qt::ISODate));
  cbor_output.getCborStreamWriter().endMap();
}

References pappso::UiMonitorInterface::appendText(), pappso::masschroq::CborOutputStream::getCborStreamWriter(), getId(), pappso::masschroq::QuantificationMethod::getMatchBetweenRun(), pappso::MsRunRetentionTime< T >::isAligned(), m_msRunPeptideListSpList, msp_msRunPeptideListAlignmentReference, and pappso::masschroq::CborOutputStream::writeQrDataBlock().

◆ setAlignmentMethodSp()

void pappso::masschroq::MsRunGroup::setAlignmentMethodSp	(	const AlignmentMethodSp &	alignment_method_sp,
		const QString &	msrun_ref_id )

Definition at line 280 of file msrungroup.cpp.

{
  auto it = find_if(m_msRunPeptideListSpList.begin(),
                    m_msRunPeptideListSpList.end(),
                    [msrun_ref_id](const pappso::masschroq::MsRunPeptideListSp &msrun) {
                      if(msrun.get()
                           ->getMsRunSp()
                           .get()
                           ->getMsRunReaderSPtr()
                           .get()
                           ->getMsRunId()
                           .get()
                           ->getXmlId() == msrun_ref_id)
                        return true;
                      return false;
                    });
  if(it != m_msRunPeptideListSpList.end())
    {
      msp_alignmentMethod                    = alignment_method_sp;
      msp_msRunPeptideListAlignmentReference = *it;
    }
  else
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("msrun_id %1 not found in group %2").arg(msrun_ref_id).arg(m_id));
    }
}

References m_id, m_msRunPeptideListSpList, msp_alignmentMethod, and msp_msRunPeptideListAlignmentReference.

◆ setIonMobilityGridSp()

void pappso::masschroq::MsRunGroup::setIonMobilityGridSp ( const std::shared_ptr< pappso::IonMobilityGrid > & ion_mobility_grid_sp )

Definition at line 321 of file msrungroup.cpp.

{
  msp_ionMobilityGrid = ion_mobility_grid_sp;
}

References msp_ionMobilityGrid.

Member Data Documentation

◆ m_hasTimsTofMobilityIndex

bool pappso::masschroq::MsRunGroup::m_hasTimsTofMobilityIndex = false

private

Definition at line 102 of file msrungroup.h.

Referenced by MsRunGroup(), and hasTimsTofMobilityIndex().

◆ m_id

const QString pappso::masschroq::MsRunGroup::m_id

private

Definition at line 98 of file msrungroup.h.

Referenced by MsRunGroup(), MsRunGroup(), getId(), and setAlignmentMethodSp().

◆ m_msRunPeptideListSpList

const std::vector<MsRunPeptideListSp> pappso::masschroq::MsRunGroup::m_msRunPeptideListSpList

private

Definition at line 99 of file msrungroup.h.

Referenced by MsRunGroup(), MsRunGroup(), alignRetentionTimeBetweenMsRuns(), contains(), quantify(), and setAlignmentMethodSp().

◆ msp_alignmentMethod

AlignmentMethodSp pappso::masschroq::MsRunGroup::msp_alignmentMethod

private

Definition at line 100 of file msrungroup.h.

Referenced by alignRetentionTimeBetweenMsRuns(), and setAlignmentMethodSp().

◆ msp_ionMobilityGrid

std::shared_ptr<pappso::IonMobilityGrid> pappso::masschroq::MsRunGroup::msp_ionMobilityGrid

private

Definition at line 103 of file msrungroup.h.

Referenced by getIonMobilityGridSp(), and setIonMobilityGridSp().

◆ msp_msRunPeptideListAlignmentReference

MsRunPeptideListSp pappso::masschroq::MsRunGroup::msp_msRunPeptideListAlignmentReference

private

Definition at line 101 of file msrungroup.h.

Referenced by alignRetentionTimeBetweenMsRuns(), quantify(), and setAlignmentMethodSp().

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

pappsomspp/core/masschroq/msrungroup.h
pappsomspp/core/masschroq/msrungroup.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MsRunGroup() [1/2]

◆ MsRunGroup() [2/2]

◆ ~MsRunGroup()

Member Function Documentation

◆ align()

◆ alignRetentionTimeBetweenMsRuns()

◆ contains()

◆ getId()

◆ getIonMobilityGridSp()

◆ hasTimsTofMobilityIndex()

◆ quantify()

◆ setAlignmentMethodSp()

◆ setIonMobilityGridSp()

Member Data Documentation

◆ m_hasTimsTofMobilityIndex

◆ m_id

◆ m_msRunPeptideListSpList

◆ msp_alignmentMethod

◆ msp_ionMobilityGrid

◆ msp_msRunPeptideListAlignmentReference