libpappsomspp
Library for mass spectrometry
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#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 |
Definition at line 43 of file proteinpresenceabsencematrix.h.
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Enumerator | |
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absent | the aa sequence code is not present |
present | the aa sequence code is present |
Definition at line 72 of file proteinpresenceabsencematrix.h.
pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrix | ( | ) |
pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrix | ( | const ProteinPresenceAbsenceMatrix & | other | ) |
copy constructor
Definition at line 41 of file proteinpresenceabsencematrix.cpp.
References m_presenceAbsenceMatrix.
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virtual |
std::vector< double > pappso::ProteinPresenceAbsenceMatrix::convolution | ( | ) | const |
process convolution of spectrum code list along protein sequence
Definition at line 155 of file proteinpresenceabsencematrix.cpp.
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private |
Definition at line 214 of file proteinpresenceabsencematrix.cpp.
void pappso::ProteinPresenceAbsenceMatrix::fillMatrix | ( | const pappso::ProteinIntegerCode & | coded_protein, |
const std::vector< uint32_t > & | code_list_from_spectrum | ||
) |
Definition at line 65 of file proteinpresenceabsencematrix.cpp.
References pappso::ProteinIntegerCode::getPeptideCodedFragment(), and pappso::ProteinIntegerCode::getSeqAaCode().
const boost::numeric::ublas::matrix< pappso::ProteinPresenceAbsenceMatrix::ProteinPresenceAbsenceMatrixElement > & pappso::ProteinPresenceAbsenceMatrix::getPresenceAbsenceMatrix | ( | ) | const |
Definition at line 59 of file proteinpresenceabsencematrix.cpp.
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private |
Definition at line 169 of file proteinpresenceabsencematrix.cpp.
pappso::ProteinPresenceAbsenceMatrix & pappso::ProteinPresenceAbsenceMatrix::operator= | ( | const ProteinPresenceAbsenceMatrix & | other | ) |
Definition at line 48 of file proteinpresenceabsencematrix.cpp.
References m_presenceAbsenceMatrix.
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private |
Definition at line 91 of file proteinpresenceabsencematrix.h.
Referenced by ProteinPresenceAbsenceMatrix(), and operator=().