libpappsomspp
Library for mass spectrometry
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#include <proteinintegercode.h>
Public Member Functions | |
ProteinIntegerCode (ProteinSp protein, const AaStringCodec &codec, std::size_t aa_str_max_size=5) | |
ProteinIntegerCode (const ProteinIntegerCode &other) | |
virtual | ~ProteinIntegerCode () |
const std::vector< std::uint8_t > & | getSeqAaCode () const |
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 |
list of positions and matched codes along protein sequence | |
std::vector< double > | convolution (const std::vector< uint32_t > &code_list_from_spectrum) const |
process convolution of spectrum code list along protein sequence | |
pappso::ProteinSp | getProteinSp () const |
Private Member Functions | |
std::vector< std::uint32_t > | computePeptideCodeFragments (const AaStringCodec &codec, std::size_t fragment_size) const |
double | convolutionKernel (const std::vector< uint32_t > &spectrum_code_list, std::vector< std::uint8_t >::const_iterator it_aa, std::vector< std::uint32_t >::const_iterator it_couple, std::vector< std::uint32_t >::const_iterator it_trio, std::vector< std::uint32_t >::const_iterator it_quatro, std::vector< std::uint32_t >::const_iterator it_cinqo) const |
Private Attributes | |
ProteinSp | msp_protein |
std::vector< std::uint8_t > | m_seqAaCode |
std::vector< std::vector< std::uint32_t > > | m_peptideCodedFragments |
Definition at line 43 of file proteinintegercode.h.
ProteinIntegerCode::ProteinIntegerCode | ( | ProteinSp | protein, |
const AaStringCodec & | codec, | ||
std::size_t | aa_str_max_size = 5 ) |
Default constructor
Definition at line 35 of file proteinintegercode.cpp.
References computePeptideCodeFragments(), pappso::AaCode::getAaCode(), pappso::AaStringCodec::getAaCode(), pappso::Protein::getSequence(), m_peptideCodedFragments, m_seqAaCode, and msp_protein.
ProteinIntegerCode::ProteinIntegerCode | ( | const ProteinIntegerCode & | other | ) |
Copy constructor
other | TODO |
Definition at line 61 of file proteinintegercode.cpp.
References m_peptideCodedFragments, m_seqAaCode, and msp_protein.
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virtual |
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private |
Definition at line 87 of file proteinintegercode.cpp.
References pappso::AaStringCodec::codeLlc(), and pappso::max.
Referenced by ProteinIntegerCode().
std::vector< double > pappso::ProteinIntegerCode::convolution | ( | const std::vector< uint32_t > & | code_list_from_spectrum | ) | const |
process convolution of spectrum code list along protein sequence
code_list_from_spectrum | unique sorted sequence codes given by the spectrum decoder |
Definition at line 165 of file proteinintegercode.cpp.
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private |
Definition at line 195 of file proteinintegercode.cpp.
const std::vector< std::uint32_t > & pappso::ProteinIntegerCode::getPeptideCodedFragment | ( | std::size_t | size | ) | const |
Definition at line 108 of file proteinintegercode.cpp.
Referenced by pappso::ProteinPresenceAbsenceMatrix::fillMatrix().
pappso::ProteinSp pappso::ProteinIntegerCode::getProteinSp | ( | ) | const |
Definition at line 80 of file proteinintegercode.cpp.
const std::vector< std::uint8_t > & pappso::ProteinIntegerCode::getSeqAaCode | ( | ) | const |
Definition at line 74 of file proteinintegercode.cpp.
Referenced by pappso::ProteinPresenceAbsenceMatrix::fillMatrix().
std::vector< std::pair< std::size_t, std::uint32_t > > pappso::ProteinIntegerCode::match | ( | const std::vector< uint32_t > & | code_list | ) | const |
list of positions and matched codes along protein sequence
Definition at line 126 of file proteinintegercode.cpp.
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private |
Definition at line 104 of file proteinintegercode.h.
Referenced by ProteinIntegerCode(), and ProteinIntegerCode().
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private |
Definition at line 103 of file proteinintegercode.h.
Referenced by ProteinIntegerCode(), and ProteinIntegerCode().
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private |
Definition at line 101 of file proteinintegercode.h.
Referenced by ProteinIntegerCode(), and ProteinIntegerCode().