pappso::GrpSubGroup Class Reference

#include <grpsubgroup.h>

Public Member Functions
	GrpSubGroup (GrpProtein *p_protein)
	GrpSubGroup (const GrpSubGroup &other)
bool	operator< (const GrpSubGroup &other) const
	sort subgroups between each other a subgroup containing less peptides is weaker (less) than the other
	~GrpSubGroup ()
GrpSubGroupSp	makeGrpSubGroupSp ()
const GrpPeptideSet &	getPeptideSet () const
bool	merge (GrpSubGroup *p_subgroup)
bool	includes (const GrpSubGroup *p_subgroup) const
void	numbering ()
void	setSubGroupNumber (unsigned int i)
void	setGroupNumber (unsigned int i)
const QString &	getFirstAccession () const
std::size_t	peptideListSize () const
unsigned int	maxCount () const
const QString	getGroupingId () const
unsigned int	getGroupNumber () const
unsigned int	getSubGroupNumber () const
const std::vector< GrpProtein * > &	getGrpProteinList () const

Private Attributes
std::vector< GrpProtein * >	m_grpProteinPtrList
GrpPeptideSet	m_peptidePtrList
unsigned int	m_subGroupNumber = 0
unsigned int	m_groupNumber = 0

Detailed Description

Definition at line 42 of file grpsubgroup.h.

Constructor & Destructor Documentation

GrpSubGroup() [1/2]

pappso::GrpSubGroup::GrpSubGroup

(

GrpProtein *

p_protein

)

Definition at line 36 of file grpsubgroup.cpp.

                                              : m_peptidePtrList(p_protein)
{
  m_grpProteinPtrList.push_back(p_protein);
}

References m_grpProteinPtrList, and m_peptidePtrList.

Referenced by GrpSubGroup(), includes(), merge(), and operator<().

GrpSubGroup() [2/2]

pappso::GrpSubGroup::GrpSubGroup

(

const GrpSubGroup &

other

)

Definition at line 41 of file grpsubgroup.cpp.

  : m_grpProteinPtrList(other.m_grpProteinPtrList),
    m_peptidePtrList(other.m_peptidePtrList)
{
}

References GrpSubGroup(), m_grpProteinPtrList, and m_peptidePtrList.

~GrpSubGroup()

pappso::GrpSubGroup::~GrpSubGroup

(

)

Definition at line 124 of file grpsubgroup.cpp.

{
}

Member Function Documentation

getFirstAccession()

const QString & pappso::GrpSubGroup::getFirstAccession

(

)

const

Definition at line 226 of file grpsubgroup.cpp.

{
  auto it = m_grpProteinPtrList.begin();
  if(it == m_grpProteinPtrList.end())
    {
      throw PappsoException(QObject::tr("m_grpProteinPtrList is empty"));
    }
  else
    {
      return (*it)->getAccession();
    }
}

References m_grpProteinPtrList.

Referenced by pappso::GrpExperiment::addSubGroupSp(), pappso::GrpGroup::addSubGroupSp(), pappso::GrpMapPeptideToSubGroupSet::hasSpecificPeptide(), merge(), and pappso::GrpMapPeptideToSubGroupSet::remove().

getGroupingId()

const QString pappso::GrpSubGroup::getGroupingId

(

)

const

Definition at line 63 of file grpsubgroup.cpp.

{
  if(m_groupNumber == 0)
    {
      return "";
    }
  return QString("%1.%2")
    .arg(Utils::getLexicalOrderedString(m_groupNumber))
    .arg(Utils::getLexicalOrderedString(m_subGroupNumber));
}

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

getGroupNumber()

unsigned int pappso::GrpSubGroup::getGroupNumber

(

)

const

Definition at line 48 of file grpsubgroup.cpp.

{
  return m_groupNumber;
}

References m_groupNumber.

getGrpProteinList()

const std::vector< GrpProtein * > & pappso::GrpSubGroup::getGrpProteinList

(

)

const

Definition at line 58 of file grpsubgroup.cpp.

{
  return m_grpProteinPtrList;
}

References m_grpProteinPtrList.

getPeptideSet()

const GrpPeptideSet & pappso::GrpSubGroup::getPeptideSet

(

)

const

Definition at line 134 of file grpsubgroup.cpp.

{
  return m_peptidePtrList;
}

References m_peptidePtrList.

Referenced by pappso::GrpGroup::GrpGroup(), pappso::GrpMapPeptideToSubGroupSet::add(), pappso::GrpExperiment::addSubGroupSp(), pappso::GrpGroup::addSubGroupSp(), pappso::GrpMapPeptideToSubGroupSet::hasSpecificPeptide(), includes(), and pappso::GrpMapPeptideToSubGroupSet::remove().

getSubGroupNumber()

unsigned int pappso::GrpSubGroup::getSubGroupNumber

(

)

const

Definition at line 53 of file grpsubgroup.cpp.

{
  return m_subGroupNumber;
}

References m_subGroupNumber.

includes()

bool pappso::GrpSubGroup::includes

(

const GrpSubGroup *

p_subgroup

)

const

Definition at line 166 of file grpsubgroup.cpp.

{
  if(m_peptidePtrList.biggerAndContainsAll(p_subgroup->getPeptideSet()))
    {
      return true;
    }
  else
    {
      return false;
    }
}

References GrpSubGroup(), getPeptideSet(), and m_peptidePtrList.

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

makeGrpSubGroupSp()

GrpSubGroupSp pappso::GrpSubGroup::makeGrpSubGroupSp

(

)

Definition at line 128 of file grpsubgroup.cpp.

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

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

maxCount()

unsigned int pappso::GrpSubGroup::maxCount

(

)

const

Definition at line 74 of file grpsubgroup.cpp.

{
  unsigned int max = 0;
  for(GrpProtein *p_protein : m_grpProteinPtrList)
    {
      if(max < p_protein->getCount())
        {
          max = p_protein->getCount();
        }
    }
  return max;
}

References m_grpProteinPtrList.

Referenced by operator<().

merge()

bool pappso::GrpSubGroup::merge

(

GrpSubGroup *

p_subgroup

)

Definition at line 140 of file grpsubgroup.cpp.

{
  qDebug() << "GrpSubGroup::merge begin " << m_grpProteinPtrList.size() << " "
           << this->getFirstAccession() << " "
           << p_subgroup->getFirstAccession();
  // if (this == p_subgroup) {
  //     return true;
  //}
  if(p_subgroup->m_peptidePtrList == m_peptidePtrList)
    {
      // m_grpProteinPtrList.splice (m_grpProteinPtrList.end(),
      // p_subgroup->m_grpProteinPtrList);
      m_grpProteinPtrList.insert(m_grpProteinPtrList.end(),
                                 p_subgroup->m_grpProteinPtrList.begin(),
                                 p_subgroup->m_grpProteinPtrList.end());
      // m_grpProteinPtrList.insert (m_grpProteinPtrList.end(),
      // p_subgroup->m_grpProteinPtrList.begin(),p_subgroup->m_grpProteinPtrList.end());
      return true;
    }
  else
    {
      return false;
    }
}

References GrpSubGroup(), getFirstAccession(), m_grpProteinPtrList, and m_peptidePtrList.

numbering()

void pappso::GrpSubGroup::numbering

(

)

Definition at line 199 of file grpsubgroup.cpp.

{
  qDebug() << "GrpSubGroup::numbering begin";
 
  // sort proteins by accession numbers :
  // m_grpProteinPtrList.sort([](GrpProtein * first, GrpProtein * second) {
  //    return (first->getAccession() < second->getAccession()) ;
  //});
  std::sort(m_grpProteinPtrList.begin(),
            m_grpProteinPtrList.end(),
            [](GrpProtein *first, GrpProtein *second) {
              return (first->getAccession() < second->getAccession());
            });
  // list unique removes all but the first element from every consecutive group
  // of equal elements in the container
  //   m_grpProteinPtrList.unique();
 
 
  unsigned int i = 1;
  for(auto &&p_protein : m_grpProteinPtrList)
    {
      p_protein->setRank(i);
      i++;
    }
  qDebug() << "GrpSubGroup::numbering end";
}

References m_grpProteinPtrList.

operator<()

bool pappso::GrpSubGroup::operator<

(

const GrpSubGroup &

other

)

const

sort subgroups between each other a subgroup containing less peptides is weaker (less) than the other

Definition at line 86 of file grpsubgroup.cpp.

{
  if(m_peptidePtrList.size() == other.m_peptidePtrList.size())
    {
      if(maxCount() == other.maxCount())
        {
          if(m_grpProteinPtrList.size() == other.m_grpProteinPtrList.size())
            {
              // compare peptide set surface ?
              // alphabetic order taken into account
              return ((*(m_grpProteinPtrList.begin()))->getAccession() <
                      (*(other.m_grpProteinPtrList.begin()))->getAccession());
            }
          else
            {
              // if there is same peptide size evidence, then perhaps it's
              // better to consider that
              // the best group is the one that include more proteins
              return (m_grpProteinPtrList.size() >
                      other.m_grpProteinPtrList.size());
            }
        }
      else
        {
          // counts are evidences of the presence of a subgroup
          // the fewer is the count, the weaker is the subgroup
          return (maxCount() > other.maxCount());
        }
    }
  else
    {
      // peptides are evidences of the presence of a subgroup
      // the fewer is the peptide list, the weaker is the subgroup
      return (m_peptidePtrList.size() > other.m_peptidePtrList.size());
    }
}

References GrpSubGroup(), m_grpProteinPtrList, m_peptidePtrList, maxCount(), and pappso::GrpPeptideSet::size().

peptideListSize()

std::size_t pappso::GrpSubGroup::peptideListSize

(

)

const

Definition at line 240 of file grpsubgroup.cpp.

{
  return m_peptidePtrList.size();
}

References m_peptidePtrList.

setGroupNumber()

void pappso::GrpSubGroup::setGroupNumber

(

unsigned int

i

)

Definition at line 179 of file grpsubgroup.cpp.

{
  m_groupNumber = i;
  for(auto &&p_protein : m_grpProteinPtrList)
    {
      p_protein->setGroupNumber(i);
    }
}

References m_groupNumber, and m_grpProteinPtrList.

setSubGroupNumber()

void pappso::GrpSubGroup::setSubGroupNumber

(

unsigned int

i

)

Definition at line 189 of file grpsubgroup.cpp.

{
  m_subGroupNumber = i;
  for(auto &&p_protein : m_grpProteinPtrList)
    {
      p_protein->setSubGroupNumber(i);
    }
}

References m_grpProteinPtrList, and m_subGroupNumber.

Member Data Documentation

m_groupNumber

unsigned int pappso::GrpSubGroup::m_groupNumber = 0

private

Definition at line 48 of file grpsubgroup.h.

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

m_grpProteinPtrList

std::vector<GrpProtein *> pappso::GrpSubGroup::m_grpProteinPtrList

private

Definition at line 45 of file grpsubgroup.h.

Referenced by GrpSubGroup(), GrpSubGroup(), getFirstAccession(), getGrpProteinList(), maxCount(), merge(), numbering(), operator<(), setGroupNumber(), and setSubGroupNumber().

m_peptidePtrList

GrpPeptideSet pappso::GrpSubGroup::m_peptidePtrList

private

Definition at line 46 of file grpsubgroup.h.

Referenced by GrpSubGroup(), GrpSubGroup(), getPeptideSet(), includes(), merge(), operator<(), and peptideListSize().

m_subGroupNumber

unsigned int pappso::GrpSubGroup::m_subGroupNumber = 0

private

Definition at line 47 of file grpsubgroup.h.

Referenced by getGroupingId(), getSubGroupNumber(), and setSubGroupNumber().

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

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