pappso::GrpExperiment Class Reference

#include <grpexperiment.h>

Public Member Functions
GrpProteinSp &	getGrpProteinSp (const QString &acc, const QString &description)
GrpPeptideSp &	setGrpPeptide (const GrpProteinSp &proteinSp, const QString &sequence, pappso_double mass)
	GrpExperiment (GrpGroupingMonitorInterface *p_monitor)
virtual	~GrpExperiment ()
void	startGrouping ()
std::vector< GrpProteinSpConst >	getGrpProteinSpList () const
void	setRemoveNonInformativeSubgroups (bool ok)
void	addPostGroupingGrpProteinSpRemoval (GrpProteinSp sp_protein)
	protein to remove with its entire group after grouping is completed typically : to use with protein contaminants if you want to ignore any group containing one contaminant protein
void	addPreGroupingGrpProteinSpRemoval (GrpProteinSp sp_protein)
	protein peptides to remove before grouping typically : remove protein contaminants in special metaproteomics cases
std::vector< GrpGroupSpConst >	getGrpGroupSpList () const

Private Member Functions
void	addSubGroupSp (GrpMapPeptideToGroup &grp_map_peptide_to_group, GrpSubGroupSp &grpSubGroupSp) const
void	numbering ()
void	removeNonInformativeSubGroups ()

Private Attributes
GrpGroupingMonitorInterface *	mp_monitor = nullptr
bool	m_isRemoveNonInformativeSubgroups = true
std::map< QString, GrpProteinSp >	m_mapProteins
std::map< QString, std::map< unsigned long, GrpPeptideSp > >	m_mapPeptides
std::list< GrpPeptideSp >	m_grpPeptideList
std::list< GrpProteinSp >	m_grpProteinList
bool	m_isGroupingStarted = false
std::list< GrpProtein * >	m_remainingGrpProteinList
GrpPeptideSet	m_grpPostGroupingProteinListRemoval
GrpPeptideSet	m_grpPreGroupingProteinListRemoval
std::list< GrpGroupSp >	m_grpGroupSpList

Detailed Description

Definition at line 41 of file grpexperiment.h.

Constructor & Destructor Documentation

GrpExperiment()

GrpExperiment::GrpExperiment

(

GrpGroupingMonitorInterface *

p_monitor

)

Definition at line 37 of file grpexperiment.cpp.

{
  mp_monitor = p_monitor;
}

References mp_monitor.

~GrpExperiment()

GrpExperiment::~GrpExperiment ( )

virtual

Definition at line 42 of file grpexperiment.cpp.

{
}

Member Function Documentation

addPostGroupingGrpProteinSpRemoval()

void GrpExperiment::addPostGroupingGrpProteinSpRemoval

(

GrpProteinSp

sp_protein

)

protein to remove with its entire group after grouping is completed typically : to use with protein contaminants if you want to ignore any group containing one contaminant protein

Definition at line 52 of file grpexperiment.cpp.

{
  GrpPeptideSet peptide_set(sp_protein.get());
  m_grpPostGroupingProteinListRemoval.addAll(peptide_set);
}

References m_grpPostGroupingProteinListRemoval.

addPreGroupingGrpProteinSpRemoval()

void GrpExperiment::addPreGroupingGrpProteinSpRemoval

(

GrpProteinSp

sp_protein

)

protein peptides to remove before grouping typically : remove protein contaminants in special metaproteomics cases

Definition at line 60 of file grpexperiment.cpp.

{
  GrpPeptideSet peptide_set(sp_protein.get());
  m_grpPreGroupingProteinListRemoval.addAll(peptide_set);
}

References m_grpPreGroupingProteinListRemoval.

addSubGroupSp()

void GrpExperiment::addSubGroupSp ( GrpMapPeptideToGroup & grp_map_peptide_to_group, GrpSubGroupSp & grpSubGroupSp ) const

private

Definition at line 203 of file grpexperiment.cpp.

{
  qDebug() << "GrpExperiment::addSubGroupSp begin "
           << grpSubGroupSp.get()->getFirstAccession();
 
  std::list<GrpGroupSp> new_group_list;
  grp_map_peptide_to_group.getGroupList(grpSubGroupSp.get()->getPeptideSet(),
                                        new_group_list);
 
  if(new_group_list.size() == 0)
    {
      qDebug() << "GrpExperiment::addSubGroupSp create a new group";
      // create a new group
      GrpGroupSp sp_group = GrpGroup(grpSubGroupSp).makeGrpGroupSp();
      // m_grpGroupSpList.push_back(sp_group);
 
      grp_map_peptide_to_group.set(grpSubGroupSp.get()->getPeptideSet(),
                                   sp_group);
    }
  else
    {
      qDebug() << "GrpExperiment::addSubGroupSp fusion groupList.size() "
               << new_group_list.size();
      // fusion group and add the subgroup
      auto itGroup           = new_group_list.begin();
      GrpGroupSp p_keepGroup = *itGroup;
      qDebug() << "GrpExperiment::addSubGroupSp "
                  "p_keepGroup->addSubGroupSp(grpSubGroupSp) "
               << p_keepGroup.get();
      p_keepGroup->addSubGroupSp(grpSubGroupSp);
      grp_map_peptide_to_group.set(grpSubGroupSp.get()->getPeptideSet(),
                                   p_keepGroup);
 
      itGroup++;
      while(itGroup != new_group_list.end())
        {
          qDebug()
            << "GrpExperiment::addSubGroupSp p_keepGroup->addGroup(*itGroup) "
            << itGroup->get();
          p_keepGroup->addGroup(itGroup->get());
          grp_map_peptide_to_group.set((*itGroup)->getGrpPeptideSet(),
                                       p_keepGroup);
 
          // m_grpGroupSpList.remove_if([itGroup](GrpGroupSp & groupSp) {
          //    return (itGroup->get() == groupSp.get()) ;
          //});
          itGroup++;
        }
    }
 
  qDebug() << "GrpExperiment::addSubGroupSp end";
}

References pappso::GrpGroup::addGroup(), pappso::GrpGroup::addSubGroupSp(), pappso::GrpSubGroup::getFirstAccession(), pappso::GrpMapPeptideToGroup::getGroupList(), pappso::GrpSubGroup::getPeptideSet(), pappso::GrpGroup::makeGrpGroupSp(), and pappso::GrpMapPeptideToGroup::set().

Referenced by removeNonInformativeSubGroups(), and startGrouping().

getGrpGroupSpList()

std::vector< GrpGroupSpConst > GrpExperiment::getGrpGroupSpList

(

)

const

Definition at line 67 of file grpexperiment.cpp.

{
  std::vector<GrpGroupSpConst> grp_list;
  for(GrpGroupSp group : m_grpGroupSpList)
    {
      grp_list.push_back(group);
    }
  return grp_list;
}

References m_grpGroupSpList.

getGrpProteinSp()

GrpProteinSp & GrpExperiment::getGrpProteinSp	(	const QString &	acc,
		const QString &	description )

Definition at line 78 of file grpexperiment.cpp.

{
  GrpProtein grpProtein(accession, description);
  auto insertedPair = m_mapProteins.insert(std::pair<QString, GrpProteinSp>(
    accession, std::make_shared<GrpProtein>(grpProtein)));
  if(insertedPair.second)
    {
      m_grpProteinList.push_back(insertedPair.first->second);
      m_remainingGrpProteinList.push_back(insertedPair.first->second.get());
    }
  return (insertedPair.first->second);
}

References m_grpProteinList, m_mapProteins, and m_remainingGrpProteinList.

getGrpProteinSpList()

std::vector< GrpProteinSpConst > GrpExperiment::getGrpProteinSpList

(

)

const

Definition at line 281 of file grpexperiment.cpp.

{
  std::vector<GrpProteinSpConst> grouped_protein_list;
  if(!m_isGroupingStarted)
    {
      throw PappsoException(
        QObject::tr("unable to get grouped protein list before grouping"));
    }
  for(auto &&protein_sp : m_grpProteinList)
    {
      if(protein_sp.get()->getGroupNumber() > 0)
        {
          grouped_protein_list.push_back(protein_sp);
        }
    }
  return grouped_protein_list;
}

References m_grpProteinList, and m_isGroupingStarted.

numbering()

void GrpExperiment::numbering ( )

private

Definition at line 258 of file grpexperiment.cpp.

{
  qDebug() << "GrpExperiment::numbering begin";
  if(mp_monitor != nullptr)
    mp_monitor->startNumberingAllGroups(m_grpGroupSpList.size());
  for(auto &&group_sp : m_grpGroupSpList)
    {
      group_sp.get()->numbering();
    }
  m_grpGroupSpList.sort([](GrpGroupSp &first, GrpGroupSp &second) {
    return ((*first.get()) < (*second.get()));
  });
  unsigned int i = 1;
  for(auto &&group_sp : m_grpGroupSpList)
    {
      group_sp.get()->setGroupNumber(i);
      i++;
    }
 
  qDebug() << "GrpExperiment::numbering end";
}

References m_grpGroupSpList, and mp_monitor.

Referenced by startGrouping().

removeNonInformativeSubGroups()

void GrpExperiment::removeNonInformativeSubGroups ( )

private

Definition at line 300 of file grpexperiment.cpp.

{
  qDebug() << "GrpExperiment::removeNonInformativeSubGroups begin";
  if(mp_monitor != nullptr)
    mp_monitor->startRemovingNonInformativeSubGroupsInAllGroups(
      m_grpGroupSpList.size());
 
  std::list<GrpGroupSp> old_grp_group_sp_list(m_grpGroupSpList);
  m_grpGroupSpList.clear();
  auto it_group = old_grp_group_sp_list.begin();
  while(it_group != old_grp_group_sp_list.end())
    {
      if(mp_monitor != nullptr)
        mp_monitor->removingNonInformativeSubGroupsInGroup();
      if(it_group->get()->removeNonInformativeSubGroups())
        {
          // need to regroup it
          GrpGroupSp old_group_sp = *it_group;
          GrpMapPeptideToGroup grp_map_peptide_to_group;
 
          std::list<GrpSubGroupSp> dispatch_sub_group_set =
            old_group_sp.get()->getSubGroupSpList();
          for(GrpSubGroupSp &grp_subgroup : dispatch_sub_group_set)
            {
              addSubGroupSp(grp_map_peptide_to_group, grp_subgroup);
            }
          grp_map_peptide_to_group.clear(m_grpGroupSpList);
        }
      else
        {
          qDebug() << "GrpExperiment::removeNonInformativeSubGroups  no "
                      "removeNonInformativeSubGroups";
          m_grpGroupSpList.push_back(*it_group);
        }
      it_group++;
    }
  if(mp_monitor != nullptr)
    mp_monitor->stopRemovingNonInformativeSubGroupsInAllGroups(
      m_grpGroupSpList.size());
 
  qDebug() << "GrpExperiment::removeNonInformativeSubGroups end";
}

References addSubGroupSp(), pappso::GrpMapPeptideToGroup::clear(), pappso::GrpGroup::getSubGroupSpList(), m_grpGroupSpList, and mp_monitor.

Referenced by startGrouping().

setGrpPeptide()

GrpPeptideSp & GrpExperiment::setGrpPeptide	(	const GrpProteinSp &	proteinSp,
		const QString &	sequence,
		pappso_double	mass )

Definition at line 93 of file grpexperiment.cpp.

{
  proteinSp.get()->countPlus();
  GrpPeptideSp sp_grppeptide =
    std::make_shared<GrpPeptide>(GrpPeptide(sequence, mass));
 
  auto insertedPair = m_mapPeptides.insert(
    std::pair<QString, std::map<unsigned long, GrpPeptideSp>>(
      sp_grppeptide.get()->m_sequence,
      std::map<unsigned long, GrpPeptideSp>()));
  auto secondInsertedPair =
    insertedPair.first->second.insert(std::pair<unsigned long, GrpPeptideSp>(
      (unsigned long)(mass * 100), sp_grppeptide));
  if(secondInsertedPair.second)
    {
      m_grpPeptideList.push_back(secondInsertedPair.first->second);
    }
  proteinSp.get()->push_back(secondInsertedPair.first->second.get());
  return (secondInsertedPair.first->second);
}

References pappso::GrpProtein::countPlus(), m_grpPeptideList, m_mapPeptides, pappso::GrpPeptide::m_sequence, and pappso::GrpProtein::push_back().

setRemoveNonInformativeSubgroups()

void GrpExperiment::setRemoveNonInformativeSubgroups

(

bool

ok

)

Definition at line 46 of file grpexperiment.cpp.

{
  m_isRemoveNonInformativeSubgroups = ok;
}

References m_isRemoveNonInformativeSubgroups.

startGrouping()

void GrpExperiment::startGrouping

(

)

Definition at line 117 of file grpexperiment.cpp.

{
  qDebug() << "GrpExperiment::startGrouping begin";
  if(mp_monitor != nullptr)
    mp_monitor->startGrouping(m_remainingGrpProteinList.size(),
                              m_grpPeptideList.size());
  m_isGroupingStarted = true;
  m_mapPeptides.clear();
  m_mapProteins.clear();
  qDebug() << "GrpExperiment::startGrouping sort protein list "
              "m_remainingGrpProteinList.size() "
           << m_remainingGrpProteinList.size();
  // m_remainingGrpProteinList.sort();
  // m_remainingGrpProteinList.unique();
 
  if(m_grpPreGroupingProteinListRemoval.size() > 0)
    {
      // TODO clean protein list to remove contaminant peptides before grouping
    }
 
 
  GrpMapPeptideToGroup grp_map_peptide_to_group;
  qDebug() << "GrpExperiment::startGrouping grouping begin";
  for(auto p_grpProtein : m_remainingGrpProteinList)
    {
      p_grpProtein->strip();
      if(p_grpProtein->m_count == 0)
        {
          // no peptides : do not group this protein
        }
      else
        {
          GrpSubGroupSp grpSubGroupSp =
            GrpSubGroup(p_grpProtein).makeGrpSubGroupSp();
 
          if(mp_monitor != nullptr)
            mp_monitor->groupingProtein();
          this->addSubGroupSp(grp_map_peptide_to_group, grpSubGroupSp);
        }
    }
  grp_map_peptide_to_group.clear(m_grpGroupSpList);
  qDebug() << "GrpExperiment::startGrouping grouping end";
 
  qDebug() << "GrpExperiment::startGrouping grouping  m_grpGroupSpList.size() "
           << m_grpGroupSpList.size();
 
  if(m_isRemoveNonInformativeSubgroups)
    {
      this->removeNonInformativeSubGroups();
    }
 
  // post grouping protein group removal
  // remove any group containing contaminants
  m_grpGroupSpList.remove_if([this](GrpGroupSp &groupSp) {
    return (
      groupSp.get()->containsAny(this->m_grpPostGroupingProteinListRemoval));
  });
 
 
  numbering();
  if(mp_monitor != nullptr)
    mp_monitor->stopGrouping();
  // GrpGroup(this, *m_remainingGrpProteinList.begin());
  qDebug() << "GrpExperiment::startGrouping end";
}

References addSubGroupSp(), pappso::GrpMapPeptideToGroup::clear(), pappso::GrpGroup::containsAny(), m_grpGroupSpList, m_grpPeptideList, m_grpPreGroupingProteinListRemoval, m_isGroupingStarted, m_isRemoveNonInformativeSubgroups, m_mapPeptides, m_mapProteins, m_remainingGrpProteinList, pappso::GrpSubGroup::makeGrpSubGroupSp(), mp_monitor, numbering(), and removeNonInformativeSubGroups().

Member Data Documentation

m_grpGroupSpList

std::list<GrpGroupSp> pappso::GrpExperiment::m_grpGroupSpList

private

Definition at line 58 of file grpexperiment.h.

Referenced by getGrpGroupSpList(), numbering(), removeNonInformativeSubGroups(), and startGrouping().

m_grpPeptideList

std::list<GrpPeptideSp> pappso::GrpExperiment::m_grpPeptideList

private

Definition at line 49 of file grpexperiment.h.

Referenced by setGrpPeptide(), and startGrouping().

m_grpPostGroupingProteinListRemoval

GrpPeptideSet pappso::GrpExperiment::m_grpPostGroupingProteinListRemoval

private

Definition at line 54 of file grpexperiment.h.

Referenced by addPostGroupingGrpProteinSpRemoval().

m_grpPreGroupingProteinListRemoval

GrpPeptideSet pappso::GrpExperiment::m_grpPreGroupingProteinListRemoval

private

Definition at line 56 of file grpexperiment.h.

Referenced by addPreGroupingGrpProteinSpRemoval(), and startGrouping().

m_grpProteinList

std::list<GrpProteinSp> pappso::GrpExperiment::m_grpProteinList

private

Definition at line 50 of file grpexperiment.h.

Referenced by getGrpProteinSp(), and getGrpProteinSpList().

m_isGroupingStarted

bool pappso::GrpExperiment::m_isGroupingStarted = false

private

Definition at line 51 of file grpexperiment.h.

Referenced by getGrpProteinSpList(), and startGrouping().

m_isRemoveNonInformativeSubgroups

bool pappso::GrpExperiment::m_isRemoveNonInformativeSubgroups = true

private

Definition at line 45 of file grpexperiment.h.

Referenced by setRemoveNonInformativeSubgroups(), and startGrouping().

m_mapPeptides

std::map<QString, std::map<unsigned long, GrpPeptideSp> > pappso::GrpExperiment::m_mapPeptides

private

Definition at line 47 of file grpexperiment.h.

Referenced by setGrpPeptide(), and startGrouping().

m_mapProteins

std::map<QString, GrpProteinSp> pappso::GrpExperiment::m_mapProteins

private

Definition at line 46 of file grpexperiment.h.

Referenced by getGrpProteinSp(), and startGrouping().

m_remainingGrpProteinList

std::list<GrpProtein *> pappso::GrpExperiment::m_remainingGrpProteinList

private

Definition at line 52 of file grpexperiment.h.

Referenced by getGrpProteinSp(), and startGrouping().

mp_monitor

GrpGroupingMonitorInterface* pappso::GrpExperiment::mp_monitor = nullptr

private

Definition at line 44 of file grpexperiment.h.

Referenced by GrpExperiment(), numbering(), removeNonInformativeSubGroups(), and startGrouping().

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

• pappsomspp/core/grouping/grpexperiment.h
• pappsomspp/core/grouping/grpexperiment.cpp