pappso::ProteinIntegerCode Class Reference

#include <proteinintegercode.h>

Public Member Functions
	ProteinIntegerCode (ProteinSp protein, const AaStringCodec &codec, std::size_t aa_str_max_size=5)
	ProteinIntegerCode (const ProteinIntegerCode &other)
	~ProteinIntegerCode ()
const std::vector< std::uint32_t > &	getPeptideCodedFragment (std::size_t size) const
std::vector< std::pair< std::size_t, std::uint32_t > >	match (const std::vector< uint32_t > &code_list) const

Private Member Functions
std::vector< std::uint32_t >	computePeptideCodeFragments (const AaStringCodec &codec, std::size_t fragment_size) const

Private Attributes
ProteinSp	msp_protein
std::vector< std::uint8_t >	m_seqAaCode
std::vector< std::vector< std::uint32_t > >	m_peptideCodedFragments

Detailed Description

Definition at line 42 of file proteinintegercode.h.

Constructor & Destructor Documentation

ProteinIntegerCode() [1/2]

ProteinIntegerCode::ProteinIntegerCode	(	ProteinSp	protein,
		const AaStringCodec &	codec,
		std::size_t	aa_str_max_size = 5
	)

Default constructor

Definition at line 34 of file proteinintegercode.cpp.

{
  msp_protein = protein;
 
  if(aa_str_max_size > 7)
    {
      throw ExceptionOutOfRange(
        QObject::tr("aa_str_max_size exceeds max size"));
    }
 
  QString seq_str = protein.get()->getSequence();
  m_seqAaCode.clear();
 
  for(const QChar &aa_str : seq_str)
    {
      m_seqAaCode.push_back(codec.getAaCode().getAaCode(aa_str.toLatin1()));
    }
 
  for(std::size_t i = 2; i <= aa_str_max_size; i++)
    {
      m_peptideCodedFragments.push_back(computePeptideCodeFragments(codec, i));
    }
}

References computePeptideCodeFragments(), pappso::AaStringCodec::getAaCode(), pappso::AaCode::getAaCode(), m_peptideCodedFragments, m_seqAaCode, and msp_protein.

ProteinIntegerCode() [2/2]

ProteinIntegerCode::ProteinIntegerCode

(

const ProteinIntegerCode &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 60 of file proteinintegercode.cpp.

{
 
  msp_protein = other.msp_protein;
 
  m_seqAaCode             = other.m_seqAaCode;
  m_peptideCodedFragments = other.m_peptideCodedFragments;
}

References m_peptideCodedFragments, m_seqAaCode, and msp_protein.

~ProteinIntegerCode()

ProteinIntegerCode::~ProteinIntegerCode

(

)

Destructor

Definition at line 69 of file proteinintegercode.cpp.

{
}

Member Function Documentation

computePeptideCodeFragments()

std::vector< std::uint32_t > pappso::ProteinIntegerCode::computePeptideCodeFragments ( const AaStringCodec &  codec, std::size_t  fragment_size  ) const

private

Definition at line 74 of file proteinintegercode.cpp.

{
  std::vector<std::uint32_t> fragments;
 
  int max = (m_seqAaCode.size() - fragment_size);
  if(max < 0)
    return fragments;
 
  auto it = m_seqAaCode.begin();
  for(int i = 0; i <= max; i++)
    {
      fragments.push_back(codec.codeLlc(it, fragment_size));
      it++;
    }
 
  return fragments;
}

References pappso::AaStringCodec::codeLlc(), and pappso::max.

Referenced by ProteinIntegerCode().

getPeptideCodedFragment()

const std::vector< std::uint32_t > & pappso::ProteinIntegerCode::getPeptideCodedFragment

(

std::size_t

size

)

const

Definition at line 95 of file proteinintegercode.cpp.

{
  if(size < 2)
    {
 
      throw ExceptionOutOfRange(QObject::tr("size too small"));
    }
  std::size_t indice = size - 2;
  if(indice < m_peptideCodedFragments.size())
    {
      return m_peptideCodedFragments.at(indice);
    }
 
  throw ExceptionOutOfRange(QObject::tr("size too big"));
}

match()

std::vector< std::pair< std::size_t, std::uint32_t > > pappso::ProteinIntegerCode::match

(

const std::vector< uint32_t > &

code_list

)

const

Definition at line 113 of file proteinintegercode.cpp.

{
  std::vector<std::pair<std::size_t, std::uint32_t>> return_pos;
  std::vector<uint32_t> code_list = code_list_in;
 
  std::sort(code_list.begin(), code_list.end());
  auto it_end = std::unique(code_list.begin(), code_list.end());
  for(auto it_code = code_list.begin(); it_code != it_end; it_code++)
    {
 
      std::size_t size = 2;
      for(auto &liste_protein_seq_code : m_peptideCodedFragments)
        {
 
          auto it_seq_position = std::find(liste_protein_seq_code.begin(),
                                           liste_protein_seq_code.end(),
                                           *it_code);
          while(it_seq_position != liste_protein_seq_code.end())
            {
              // found
              std::size_t position =
                std::distance(liste_protein_seq_code.begin(), it_seq_position);
              return_pos.push_back({size, position});
 
              it_seq_position = std::find(
                ++it_seq_position, liste_protein_seq_code.end(), *it_code);
              qDebug();
            }
          size++;
          qDebug();
        }
      qDebug();
    }
 
  return return_pos;
}

Member Data Documentation

m_peptideCodedFragments

std::vector<std::vector<std::uint32_t> > pappso::ProteinIntegerCode::m_peptideCodedFragments

private

Definition at line 79 of file proteinintegercode.h.

Referenced by ProteinIntegerCode(), and ProteinIntegerCode().

m_seqAaCode

std::vector<std::uint8_t> pappso::ProteinIntegerCode::m_seqAaCode

private

Definition at line 78 of file proteinintegercode.h.

Referenced by ProteinIntegerCode(), and ProteinIntegerCode().

msp_protein

ProteinSp pappso::ProteinIntegerCode::msp_protein

private

Definition at line 76 of file proteinintegercode.h.

Referenced by ProteinIntegerCode(), and ProteinIntegerCode().

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

• pappsomspp/protein/proteinintegercode.h
• pappsomspp/protein/proteinintegercode.cpp