pappso::ProteinPresenceAbsenceMatrix Class Reference

#include <proteinpresenceabsencematrix.h>

Public Types
enum class	ProteinPresenceAbsenceMatrixElement : std::uint8_t { absent = 0 , present = 1 }

Public Member Functions
	ProteinPresenceAbsenceMatrix ()
	ProteinPresenceAbsenceMatrix (const ProteinPresenceAbsenceMatrix &other)
virtual	~ProteinPresenceAbsenceMatrix ()
ProteinPresenceAbsenceMatrix &	operator= (const ProteinPresenceAbsenceMatrix &other)
void	fillMatrix (const pappso::ProteinIntegerCode &coded_protein, const std::vector< uint32_t > &code_list_from_spectrum)
std::vector< double >	convolution () const
	process convolution of spectrum code list along protein sequence
const boost::numeric::ublas::matrix< pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrixElement > &	getPresenceAbsenceMatrix () const

Private Member Functions
double	convolutionKernel (std::size_t position) const
double	getScore (std::size_t seq_position, std::size_t aa_fragment_size) const

Private Attributes
boost::numeric::ublas::matrix< ProteinPresenceAbsenceMatrixElement >	m_presenceAbsenceMatrix

Detailed Description

Definition at line 43 of file proteinpresenceabsencematrix.h.

Member Enumeration Documentation

ProteinPresenceAbsenceMatrixElement

enum class pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrixElement : std::uint8_t

strong

Enumerator
absent	the aa sequence code is not present
present	the aa sequence code is present

Definition at line 72 of file proteinpresenceabsencematrix.h.

  {
    absent  = 0, ///< the aa sequence code is not present
    present = 1, ///< the aa sequence code is present
  };

Constructor & Destructor Documentation

ProteinPresenceAbsenceMatrix() [1/2]

pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrix

(

)

Default constructor

Definition at line 32 of file proteinpresenceabsencematrix.cpp.

{
}

ProteinPresenceAbsenceMatrix() [2/2]

pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrix

(

const ProteinPresenceAbsenceMatrix &

other

)

copy constructor

Definition at line 41 of file proteinpresenceabsencematrix.cpp.

{
  m_presenceAbsenceMatrix = other.m_presenceAbsenceMatrix;
}

References m_presenceAbsenceMatrix.

~ProteinPresenceAbsenceMatrix()

pappso::ProteinPresenceAbsenceMatrix::~ProteinPresenceAbsenceMatrix ( )

virtual

Destructor

Definition at line 36 of file proteinpresenceabsencematrix.cpp.

{
}

Member Function Documentation

convolution()

std::vector< double > pappso::ProteinPresenceAbsenceMatrix::convolution

(

)

const

process convolution of spectrum code list along protein sequence

Definition at line 139 of file proteinpresenceabsencematrix.cpp.

{
 
  std::vector<double> convolution_score;
 
  for(std::size_t ipos = 0; ipos < m_presenceAbsenceMatrix.size1(); ipos++)
    {
      convolution_score.push_back(convolutionKernel(ipos));
    }
 
  return convolution_score;
}

References convolutionKernel(), and m_presenceAbsenceMatrix.

convolutionKernel()

double pappso::ProteinPresenceAbsenceMatrix::convolutionKernel ( std::size_t position ) const

private

Definition at line 198 of file proteinpresenceabsencematrix.cpp.

{
  double score = 0;
 
  std::size_t size_seq = m_presenceAbsenceMatrix.size1();
  // single :
  double single_score = 0;
  std::size_t endpos  = std::min(position + 5, size_seq);
  for(std::size_t ipos = position; ipos < endpos; ipos++)
    {
      single_score += getScore(ipos, 0);
    }
 
  // duo
  double duo_score = 0;
  endpos           = std::min(position + 4, size_seq);
  for(std::size_t ipos = position; ipos < endpos; ipos++)
    {
      duo_score += getScore(ipos, 1);
    }
 
 
  // trio
  double trio_score = 0;
  endpos            = std::min(position + 3, size_seq);
  for(std::size_t ipos = position; ipos < endpos; ipos++)
    {
      trio_score += getScore(ipos, 2);
    }
 
 
  // quatro
  double quatro_score = 0;
  endpos              = std::min(position + 2, size_seq);
  for(std::size_t ipos = position; ipos < endpos; ipos++)
    {
      quatro_score += getScore(ipos, 3);
    }
 
  // cinqo
  score += getScore(position, 4);
  return score * single_score * duo_score * trio_score * quatro_score;
}

References getScore(), and m_presenceAbsenceMatrix.

Referenced by convolution().

fillMatrix()

void pappso::ProteinPresenceAbsenceMatrix::fillMatrix	(	const pappso::ProteinIntegerCode &	coded_protein,
		const std::vector< uint32_t > &	code_list_from_spectrum )

Definition at line 64 of file proteinpresenceabsencematrix.cpp.

{
  const std::vector<std::uint8_t> &seq_aa_code = coded_protein.getSeqAaCode();
 
  m_presenceAbsenceMatrix.resize(seq_aa_code.size(), 5);
  std::vector<std::uint8_t>::const_iterator it_aa = seq_aa_code.begin();
  auto it_couple = coded_protein.getPeptideCodedFragment(2).begin();
  auto it_trio   = coded_protein.getPeptideCodedFragment(3).begin();
  auto it_quatro = coded_protein.getPeptideCodedFragment(4).begin();
  auto it_cinqo  = coded_protein.getPeptideCodedFragment(5).begin();
 
  for(std::size_t i = 0; i < seq_aa_code.size(); i++)
    {
      if(std::binary_search(
           code_list_from_spectrum.begin(), code_list_from_spectrum.end(), (std::uint32_t)(*it_aa)))
        {
          // presence
          m_presenceAbsenceMatrix(i, 0) = ProteinPresenceAbsenceMatrixElement::present;
        }
      else
        {
          m_presenceAbsenceMatrix(i, 0) = ProteinPresenceAbsenceMatrixElement::absent;
        }
      if(std::binary_search(
           code_list_from_spectrum.begin(), code_list_from_spectrum.end(), *it_couple))
        {
          // presence
          m_presenceAbsenceMatrix(i, 1) = ProteinPresenceAbsenceMatrixElement::present;
        }
      else
        {
          m_presenceAbsenceMatrix(i, 1) = ProteinPresenceAbsenceMatrixElement::absent;
        }
      if(std::binary_search(
           code_list_from_spectrum.begin(), code_list_from_spectrum.end(), *it_trio))
        {
          // presence
          m_presenceAbsenceMatrix(i, 2) = ProteinPresenceAbsenceMatrixElement::present;
        }
      else
        {
          m_presenceAbsenceMatrix(i, 2) = ProteinPresenceAbsenceMatrixElement::absent;
        }
      if(std::binary_search(
           code_list_from_spectrum.begin(), code_list_from_spectrum.end(), *it_quatro))
        {
          // presence
          m_presenceAbsenceMatrix(i, 3) = ProteinPresenceAbsenceMatrixElement::present;
        }
      else
        {
          m_presenceAbsenceMatrix(i, 3) = ProteinPresenceAbsenceMatrixElement::absent;
        }
      if(std::binary_search(
           code_list_from_spectrum.begin(), code_list_from_spectrum.end(), *it_cinqo))
        {
          // presence
          m_presenceAbsenceMatrix(i, 4) = ProteinPresenceAbsenceMatrixElement::present;
        }
      else
        {
          m_presenceAbsenceMatrix(i, 4) = ProteinPresenceAbsenceMatrixElement::absent;
        }
      it_aa++;
      it_couple++;
      it_trio++;
      it_quatro++;
      it_cinqo++;
    }
}

References absent, pappso::ProteinIntegerCode::getPeptideCodedFragment(), pappso::ProteinIntegerCode::getSeqAaCode(), m_presenceAbsenceMatrix, and present.

getPresenceAbsenceMatrix()

const boost::numeric::ublas::matrix< pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrixElement > & pappso::ProteinPresenceAbsenceMatrix::getPresenceAbsenceMatrix

(

)

const

Definition at line 58 of file proteinpresenceabsencematrix.cpp.

{
  return m_presenceAbsenceMatrix;
}

References m_presenceAbsenceMatrix.

getScore()

double pappso::ProteinPresenceAbsenceMatrix::getScore ( std::size_t seq_position, std::size_t aa_fragment_size ) const

private

Definition at line 153 of file proteinpresenceabsencematrix.cpp.

{
  if(m_presenceAbsenceMatrix(seq_position, aa_fragment_size) ==
     ProteinPresenceAbsenceMatrixElement::present)
    {
      switch(aa_fragment_size)
        {
          case 0:
            return 1;
          case 1:
            return 3;
          case 2:
            return 6;
          case 3:
            return 8;
          case 4:
            return 10;
          default:
            break;
        }
    }
  else
    {
      // absent
      switch(aa_fragment_size)
        {
          case 0:
            return 0.1;
          case 1:
            return 0.3;
          case 2:
            return 0.6;
          case 3:
            return 0.8;
          case 4:
            return 1;
          default:
            break;
        }
    }
  return 0.1;
}

References m_presenceAbsenceMatrix, and present.

Referenced by convolutionKernel().

operator=()

pappso::ProteinPresenceAbsenceMatrix & pappso::ProteinPresenceAbsenceMatrix::operator=

(

const ProteinPresenceAbsenceMatrix &

other

)

Definition at line 48 of file proteinpresenceabsencematrix.cpp.

{
  m_presenceAbsenceMatrix = other.m_presenceAbsenceMatrix;
 
  return *this;
}

References m_presenceAbsenceMatrix.

Member Data Documentation

m_presenceAbsenceMatrix

boost::numeric::ublas::matrix<ProteinPresenceAbsenceMatrixElement> pappso::ProteinPresenceAbsenceMatrix::m_presenceAbsenceMatrix

private

Definition at line 91 of file proteinpresenceabsencematrix.h.

Referenced by ProteinPresenceAbsenceMatrix(), convolution(), convolutionKernel(), fillMatrix(), getPresenceAbsenceMatrix(), getScore(), and operator=().

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

• pappsomspp/core/protein/proteinpresenceabsencematrix.h
• pappsomspp/core/protein/proteinpresenceabsencematrix.cpp