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 More...
	~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 61 of file grpsubgroup.h.

Constructor & Destructor Documentation

GrpSubGroup() [1/2]

pappso::GrpSubGroup::GrpSubGroup

(

GrpProtein *

p_protein

)

Definition at line 55 of file grpsubgroup.cpp.

{

GrpSubGroup() [2/2]

pappso::GrpSubGroup::GrpSubGroup

(

const GrpSubGroup &

other

)

Definition at line 60 of file grpsubgroup.cpp.

{

~GrpSubGroup()

pappso::GrpSubGroup::~GrpSubGroup

(

)

Definition at line 143 of file grpsubgroup.cpp.

    {

Member Function Documentation

getFirstAccession()

const QString & pappso::GrpSubGroup::getFirstAccession

(

)

const

Definition at line 245 of file grpsubgroup.cpp.

getGroupingId()

const QString pappso::GrpSubGroup::getGroupingId

(

)

const

Definition at line 82 of file grpsubgroup.cpp.

{
  if(m_peptidePtrList.size() == other.m_peptidePtrList.size())
    {
      if(maxCount() == other.maxCount())

getGroupNumber()

unsigned int pappso::GrpSubGroup::getGroupNumber

(

)

const

Definition at line 67 of file grpsubgroup.cpp.

getGrpProteinList()

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

(

)

const

Definition at line 77 of file grpsubgroup.cpp.

                            : m_grpProteinPtrList)
    {
      if(max < p_protein->getCount())
        {

References pappso::max.

getPeptideSet()

const GrpPeptideSet & pappso::GrpSubGroup::getPeptideSet

(

)

const

Definition at line 153 of file grpsubgroup.cpp.

    {

getSubGroupNumber()

unsigned int pappso::GrpSubGroup::getSubGroupNumber

(

)

const

Definition at line 72 of file grpsubgroup.cpp.

{

includes()

bool pappso::GrpSubGroup::includes

(

const GrpSubGroup *

p_subgroup

)

const

Definition at line 185 of file grpsubgroup.cpp.

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

makeGrpSubGroupSp()

GrpSubGroupSp pappso::GrpSubGroup::makeGrpSubGroupSp

(

)

Definition at line 147 of file grpsubgroup.cpp.

    {
      // m_grpProteinPtrList.splice (m_grpProteinPtrList.end(),

References m_grpProteinPtrList.

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

maxCount()

unsigned int pappso::GrpSubGroup::maxCount

(

)

const

Definition at line 93 of file grpsubgroup.cpp.

            {
              // 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

References m_grpProteinPtrList.

merge()

bool pappso::GrpSubGroup::merge

(

GrpSubGroup *

p_subgroup

)

Definition at line 159 of file grpsubgroup.cpp.

    {
      return false;
    }
}
 
bool
GrpSubGroup::includes(const GrpSubGroup *p_subgroup) const
{
  if(m_peptidePtrList.biggerAndContainsAll(p_subgroup->getPeptideSet()))
    {
      return true;
    }
  else
    {
      return false;
    }
}
 
void
GrpSubGroup::setGroupNumber(unsigned int i)
{
  m_groupNumber = i;
  for(auto &&p_protein : m_grpProteinPtrList)

numbering()

void pappso::GrpSubGroup::numbering

(

)

Definition at line 218 of file grpsubgroup.cpp.

                       : m_grpProteinPtrList)
    {
      p_protein->setRank(i);
      i++;
    }
  qDebug() << "GrpSubGroup::numbering end";
}
const QString &
GrpSubGroup::getFirstAccession() const
{
  auto it = m_grpProteinPtrList.begin();
  if(it == m_grpProteinPtrList.end())
    {
      throw PappsoException(QObject::tr("m_grpProteinPtrList is empty"));
    }
  else
    {
      return (*it)->getAccession();
    }
}
 
std::size_t
GrpSubGroup::peptideListSize() const
{
  return m_peptidePtrList.size();
}

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 106 of file grpsubgroup.cpp.

        {
          // 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());
    }
}
 
GrpSubGroup::~GrpSubGroup()
{
}
GrpSubGroupSp
GrpSubGroup::makeGrpSubGroupSp()
{
  return std::make_shared<GrpSubGroup>(*this);
}
 
const GrpPeptideSet &
GrpSubGroup::getPeptideSet() const
{
  return m_peptidePtrList;
}
 
bool
GrpSubGroup::merge(GrpSubGroup *p_subgroup)
{

peptideListSize()

std::size_t pappso::GrpSubGroup::peptideListSize

(

)

const

Definition at line 259 of file grpsubgroup.cpp.

setGroupNumber()

void pappso::GrpSubGroup::setGroupNumber

(

unsigned int

i

)

Definition at line 198 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()) ;

References m_grpProteinPtrList.

setSubGroupNumber()

void pappso::GrpSubGroup::setSubGroupNumber

(

unsigned int

i

)

Definition at line 208 of file grpsubgroup.cpp.

                                                      {
              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();
 

References pappso::GrpProtein::getAccession().

Member Data Documentation

m_groupNumber

unsigned int pappso::GrpSubGroup::m_groupNumber = 0

private

Definition at line 67 of file grpsubgroup.h.

m_grpProteinPtrList

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

private

Definition at line 64 of file grpsubgroup.h.

Referenced by makeGrpSubGroupSp(), maxCount(), and setGroupNumber().

m_peptidePtrList

GrpPeptideSet pappso::GrpSubGroup::m_peptidePtrList

private

Definition at line 65 of file grpsubgroup.h.

m_subGroupNumber

unsigned int pappso::GrpSubGroup::m_subGroupNumber = 0

private

Definition at line 66 of file grpsubgroup.h.

---

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

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