pappso::GrpGroup Class Reference

#include <grpgroup.h>

Public Member Functions
	GrpGroup (const GrpGroup &grpGroupSp)
	~GrpGroup ()
bool	operator< (const GrpGroup &other) const
bool	containsAny (const GrpPeptideSet &peptideSet) const
void	addSubGroupSp (const GrpSubGroupSp &grpSubGroupSp)
void	addGroup (GrpGroup *p_group_to_add)
void	numbering ()
void	setGroupNumber (unsigned int i)
bool	removeNonInformativeSubGroups ()
const QString	getGroupingId () const
unsigned int	getGroupNumber () const
const GrpPeptideSet &	getGrpPeptideSet () const
std::vector< GrpSubGroupSpConst >	getGrpSubGroupSpList () const

Protected Member Functions
const std::list< GrpSubGroupSp > &	getSubGroupSpList () const
	GrpGroup (GrpSubGroupSp &grpSubGroupSp)
GrpGroupSp	makeGrpGroupSp ()
bool	removeFirstNonInformativeSubGroup ()
void	check () const

Private Attributes
std::list< GrpSubGroupSp >	m_subGroupList
unsigned int	m_groupNumber = 0
GrpPeptideSet	m_peptideSet
GrpMapPeptideToSubGroupSet	m_mapPeptideToSubGroupSet

Friends
class	GrpExperiment

Detailed Description

Definition at line 43 of file grpgroup.h.

Constructor & Destructor Documentation

GrpGroup() [1/2]

GrpGroup::GrpGroup ( GrpSubGroupSp & grpSubGroupSp )

protected

Definition at line 37 of file grpgroup.cpp.

{
  m_peptideSet.addAll(grpSubGroupSp.get()->getPeptideSet());
  m_subGroupList.push_back(grpSubGroupSp);
  m_mapPeptideToSubGroupSet.add(grpSubGroupSp.get());
}

References pappso::GrpSubGroup::getPeptideSet(), m_mapPeptideToSubGroupSet, m_peptideSet, and m_subGroupList.

Referenced by GrpGroup(), addGroup(), and operator<().

GrpGroup() [2/2]

GrpGroup::GrpGroup

(

const GrpGroup &

grpGroupSp

)

Definition at line 43 of file grpgroup.cpp.

  : m_subGroupList(other.m_subGroupList),
    m_peptideSet(other.m_peptideSet),
    m_mapPeptideToSubGroupSet(other.m_mapPeptideToSubGroupSet)
{
}

References GrpGroup(), m_mapPeptideToSubGroupSet, m_peptideSet, and m_subGroupList.

~GrpGroup()

GrpGroup::~GrpGroup

(

)

Definition at line 50 of file grpgroup.cpp.

{
}

Member Function Documentation

addGroup()

void GrpGroup::addGroup

(

GrpGroup *

p_group_to_add

)

Definition at line 111 of file grpgroup.cpp.

{
  if(this == p_group_to_add)
    {
      throw PappsoException(
        QObject::tr("addGroup ERROR, this == p_group_to_add"));
    }
 
  for(GrpSubGroupSp &sgToAdd : p_group_to_add->m_subGroupList)
    {
      addSubGroupSp(sgToAdd);
    }
}

References GrpGroup(), addSubGroupSp(), and m_subGroupList.

Referenced by pappso::GrpExperiment::addSubGroupSp().

addSubGroupSp()

void GrpGroup::addSubGroupSp

(

const GrpSubGroupSp &

grpSubGroupSp

)

Definition at line 150 of file grpgroup.cpp.

{
 
  qDebug() << "GrpGroup::addSubGroupSp begin "
           << grpSubGroupSp.get()->getFirstAccession();
 
 
  // look for impacted subgroups (containing peptides alsoe present in incoming
  // subgroup
  GrpSubGroupSet impacted_subgroup_list;
  m_mapPeptideToSubGroupSet.getSubGroupSet(grpSubGroupSp.get()->getPeptideSet(),
                                           impacted_subgroup_list);
  if(impacted_subgroup_list.contains(grpSubGroupSp.get()))
    {
      throw PappsoException(
        QObject::tr("addSubGroupSp ERROR, subgroup %1 is already in group")
          .arg(grpSubGroupSp.get()->getFirstAccession()));
    }
 
  // look for impacted subgroup equal to incoming subgroup and merge it and exit
  qDebug() << "GrpGroup::addSubGroupSp look for impacted subgroup equal to "
              "incoming subgroup and merge it and exit";
  auto it_impacted_sg     = impacted_subgroup_list.m_grpSubGroupPtrList.begin();
  auto it_impacted_sg_end = impacted_subgroup_list.m_grpSubGroupPtrList.end();
  while(it_impacted_sg != it_impacted_sg_end)
    {
 
      if((*it_impacted_sg)->merge(grpSubGroupSp.get()))
        {
          qDebug() << "GrpGroup::addSubGroupSp merge";
          return;
        }
      it_impacted_sg++;
    }
 
  // look for impacted subgroup including totally the incoming subgroup and exit
  qDebug() << "GrpGroup::addSubGroupSp look for impacted subgroup including "
              "totally the incoming subgroup and exit";
  it_impacted_sg = impacted_subgroup_list.m_grpSubGroupPtrList.begin();
  while(it_impacted_sg != it_impacted_sg_end)
    {
      if((*it_impacted_sg)->includes(grpSubGroupSp.get()))
        {
          qDebug() << "GrpGroup::addSubGroupSp includes";
          return;
        }
      it_impacted_sg++;
    }
 
  // look for impacted subgroup totally included in incoming subgroup and remove
  // it
  qDebug() << "GrpGroup::addSubGroupSp look for impacted subgroup totally "
              "included in incoming subgroup and remove it";
  it_impacted_sg = impacted_subgroup_list.m_grpSubGroupPtrList.begin();
  while(it_impacted_sg != it_impacted_sg_end)
    {
      if(grpSubGroupSp.get()->includes((*it_impacted_sg)))
        {
          // this->removeSubGroup(*it_impacted_sg);
          // it_impacted_sg = impacted_subgroup_list.erase(it_impacted_sg);
          GrpSubGroup *sg_to_remove = *it_impacted_sg;
          it_impacted_sg = impacted_subgroup_list.erase(it_impacted_sg);
          m_mapPeptideToSubGroupSet.remove(sg_to_remove);
          m_subGroupList.remove_if([sg_to_remove](GrpSubGroupSp &sub_groupSp) {
            return (sg_to_remove == sub_groupSp.get());
          });
          // m_mapPeptideToSubGroupSet.check(m_subGroupList);
        }
      else
        {
          it_impacted_sg++;
        }
    }
  qDebug()
    << "GrpGroup::addSubGroupSp finally add the new subgroup to current group";
 
  // finally add the new subgroup to current group
  m_subGroupList.push_back(grpSubGroupSp);
  m_mapPeptideToSubGroupSet.add(grpSubGroupSp.get());
  m_peptideSet.addAll(grpSubGroupSp.get()->getPeptideSet());
 
 
  // check();
  // m_mapPeptideToSubGroupSet.check(m_subGroupList);
 
  qDebug() << "GrpGroup::addSubGroupSp end";
}

References pappso::GrpSubGroupSet::contains(), pappso::GrpSubGroupSet::erase(), pappso::GrpSubGroup::getFirstAccession(), pappso::GrpSubGroup::getPeptideSet(), pappso::GrpSubGroup::includes(), pappso::GrpSubGroupSet::m_grpSubGroupPtrList, m_mapPeptideToSubGroupSet, m_peptideSet, and m_subGroupList.

Referenced by addGroup(), and pappso::GrpExperiment::addSubGroupSp().

check()

void GrpGroup::check ( ) const

protected

Definition at line 126 of file grpgroup.cpp.

{
  qDebug() << "GrpGroup::check begin ";
  GrpSubGroupSet impacted_subgroup_list;
  m_mapPeptideToSubGroupSet.getSubGroupSet(this->m_peptideSet,
                                           impacted_subgroup_list);
 
  // if (impacted_subgroup_list.size() != this->m_subGroupList.size()) {
  qDebug() << "GrpGroup::check impacted_subgroup_list.size() != "
              "this->m_subGroupList.size()";
  qDebug() << impacted_subgroup_list.printInfos();
 
  for(auto sg : m_subGroupList)
    {
      qDebug() << sg->getFirstAccession() << " " << sg.get();
    }
  //}
  qDebug() << m_mapPeptideToSubGroupSet.printInfos();
  qDebug() << m_peptideSet.printInfos();
  qDebug() << "GrpGroup::check end ";
}

References m_mapPeptideToSubGroupSet, m_peptideSet, m_subGroupList, and pappso::GrpSubGroupSet::printInfos().

containsAny()

bool GrpGroup::containsAny

(

const GrpPeptideSet &

peptideSet

)

const

Definition at line 104 of file grpgroup.cpp.

{
 
  return m_peptideSet.containsAny(peptideSet);
}

References m_peptideSet.

Referenced by ContainsAny::operator()(), and pappso::GrpExperiment::startGrouping().

getGroupingId()

const QString GrpGroup::getGroupingId

(

)

const

Definition at line 82 of file grpgroup.cpp.

{
  if(m_groupNumber == 0)
    {
      return "";
    }
  return QString("%1").arg(Utils::getLexicalOrderedString(m_groupNumber));
}

References pappso::Utils::getLexicalOrderedString(), and m_groupNumber.

getGroupNumber()

unsigned int GrpGroup::getGroupNumber

(

)

const

Definition at line 77 of file grpgroup.cpp.

{
  return m_groupNumber;
}

References m_groupNumber.

getGrpPeptideSet()

const GrpPeptideSet & GrpGroup::getGrpPeptideSet

(

)

const

Definition at line 72 of file grpgroup.cpp.

{
  return m_peptideSet;
}

References m_peptideSet.

getGrpSubGroupSpList()

std::vector< GrpSubGroupSpConst > GrpGroup::getGrpSubGroupSpList

(

)

const

Definition at line 55 of file grpgroup.cpp.

{
  std::vector<GrpSubGroupSpConst> subgroup_list;
  for(GrpSubGroupSp subgroup : m_subGroupList)
    {
      subgroup_list.push_back(subgroup);
    }
  return subgroup_list;
};

References m_subGroupList.

getSubGroupSpList()

const std::list< GrpSubGroupSp > & GrpGroup::getSubGroupSpList ( ) const

protected

Definition at line 66 of file grpgroup.cpp.

{
  return m_subGroupList;
}

References m_subGroupList.

Referenced by pappso::GrpExperiment::removeNonInformativeSubGroups().

makeGrpGroupSp()

GrpGroupSp GrpGroup::makeGrpGroupSp ( )

protected

Definition at line 98 of file grpgroup.cpp.

{
  return std::make_shared<GrpGroup>(*this);
}

Referenced by pappso::GrpExperiment::addSubGroupSp().

numbering()

void GrpGroup::numbering

(

)

Definition at line 254 of file grpgroup.cpp.

{
  qDebug() << "GrpGroup::numbering begin";
 
  for(auto &&sub_group_sp : m_subGroupList)
    {
      sub_group_sp.get()->numbering();
    }
  m_subGroupList.sort([](GrpSubGroupSp &first, GrpSubGroupSp &second) {
    return ((*first.get()) < (*second.get()));
  });
  unsigned int i = 1;
  for(auto &&sub_group_sp : m_subGroupList)
    {
      sub_group_sp.get()->setSubGroupNumber(i);
      i++;
    }
 
  m_peptideSet.numbering();
  qDebug() << "GrpGroup::numbering end";
}

References m_peptideSet, and m_subGroupList.

operator<()

bool GrpGroup::operator<

(

const GrpGroup &

other

)

const

Definition at line 90 of file grpgroup.cpp.

{
  return ((*(m_subGroupList.begin()->get())) <
          (*(other.m_subGroupList.begin()->get())));
}

References GrpGroup(), and m_subGroupList.

removeFirstNonInformativeSubGroup()

bool GrpGroup::removeFirstNonInformativeSubGroup ( )

protected

Definition at line 278 of file grpgroup.cpp.

{
  qDebug() << "GrpGroup::removeFirstNonInformativeSubGroup begin";
  std::list<GrpSubGroup *> subgroup_list_to_remove;
 
  for(auto &&sub_group_sp : m_subGroupList)
    {
      if(m_mapPeptideToSubGroupSet.hasSpecificPeptide(sub_group_sp.get()))
        {
        }
      else
        {
          subgroup_list_to_remove.push_back(sub_group_sp.get());
        }
    }
  if(subgroup_list_to_remove.size() == 0)
    {
      qDebug() << "GrpGroup::removeFirstNonInformativeSubGroup end false";
      return false;
    }
 
  // sort subgroup to remove
  subgroup_list_to_remove.sort([](GrpSubGroup *first, GrpSubGroup *second) {
    return ((*first) < (*second));
  });
 
  // remove the last one
  qDebug() << "GrpGroup::removeFirstNonInformativeSubGroup "
              "subgroup_list_to_remove.front()->peptideListSize() "
           << subgroup_list_to_remove.front()->peptideListSize();
  qDebug() << "GrpGroup::removeFirstNonInformativeSubGroup "
              "subgroup_list_to_remove.back()->peptideListSize() "
           << subgroup_list_to_remove.back()->peptideListSize();
 
  // the first subgroup is weaker (less peptides or less protein than others)
  GrpSubGroup *sg_to_remove = subgroup_list_to_remove.front();
  m_mapPeptideToSubGroupSet.remove(sg_to_remove);
  qDebug()
    << "GrpGroup::removeFirstNonInformativeSubGroup m_subGroupList.size() "
    << m_subGroupList.size();
  m_subGroupList.remove_if([sg_to_remove](GrpSubGroupSp &sub_groupSp) {
    return (sg_to_remove == sub_groupSp.get());
  });
  qDebug() << "GrpGroup::removeFirstNonInformativeSubGroup after remove if "
              "m_subGroupList.size() "
           << m_subGroupList.size();
  qDebug() << "GrpGroup::removeFirstNonInformativeSubGroup end true";
  return true;
}

References m_mapPeptideToSubGroupSet, and m_subGroupList.

Referenced by removeNonInformativeSubGroups().

removeNonInformativeSubGroups()

bool GrpGroup::removeNonInformativeSubGroups

(

)

Definition at line 329 of file grpgroup.cpp.

{
  qDebug() << "GrpGroup::removeNonInformativeSubGroups begin";
  if(removeFirstNonInformativeSubGroup())
    {
      while(removeFirstNonInformativeSubGroup())
        {
          qDebug() << "GrpGroup::removeNonInformativeSubGroups while";
        }
    }
  else
    {
      return false;
    }
  return true;
}

References removeFirstNonInformativeSubGroup().

setGroupNumber()

void GrpGroup::setGroupNumber

(

unsigned int

i

)

Definition at line 240 of file grpgroup.cpp.

{
  qDebug() << "GrpGroup::setGroupNumber begin";
  m_groupNumber = i;
  for(auto &&sub_group_sp : m_subGroupList)
    {
      sub_group_sp->setGroupNumber(i);
    }
  m_peptideSet.setGroupNumber(i);
  qDebug() << "GrpGroup::setGroupNumber end";
}

References m_groupNumber, m_peptideSet, and m_subGroupList.

Friends And Related Symbol Documentation

GrpExperiment

friend class GrpExperiment

friend

Definition at line 45 of file grpgroup.h.

References GrpExperiment.

Referenced by GrpExperiment.

Member Data Documentation

m_groupNumber

unsigned int pappso::GrpGroup::m_groupNumber = 0

private

Definition at line 49 of file grpgroup.h.

Referenced by getGroupingId(), getGroupNumber(), and setGroupNumber().

m_mapPeptideToSubGroupSet

GrpMapPeptideToSubGroupSet pappso::GrpGroup::m_mapPeptideToSubGroupSet

private

Definition at line 52 of file grpgroup.h.

Referenced by GrpGroup(), GrpGroup(), addSubGroupSp(), check(), and removeFirstNonInformativeSubGroup().

m_peptideSet

GrpPeptideSet pappso::GrpGroup::m_peptideSet

private

Definition at line 50 of file grpgroup.h.

Referenced by GrpGroup(), GrpGroup(), addSubGroupSp(), check(), containsAny(), getGrpPeptideSet(), numbering(), and setGroupNumber().

m_subGroupList

std::list<GrpSubGroupSp> pappso::GrpGroup::m_subGroupList

private

Definition at line 48 of file grpgroup.h.

Referenced by GrpGroup(), GrpGroup(), addGroup(), addSubGroupSp(), check(), getGrpSubGroupSpList(), getSubGroupSpList(), numbering(), operator<(), removeFirstNonInformativeSubGroup(), and setGroupNumber().

---

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

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