libpappsomspp
Library for mass spectrometry
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convert a list of mass to amino acid string codes More...
#include <aastringcodemassmatching.h>
Classes | |
struct | aaCodeAndMassRange |
Public Member Functions | |
AaStringCodeMassMatching (const AaCode &aa_code, std::size_t model_max_size, PrecisionPtr precision) | |
AaStringCodeMassMatching (const AaStringCodeMassMatching &other) | |
~AaStringCodeMassMatching () | |
PrecisionPtr | getPrecisionPtr () const |
std::vector< uint32_t > | getAaCodeFromMassList (std::vector< double > &mass_list) const |
std::vector< uint32_t > | getAaCodeFromMass (double mass) const |
get amino acid string code from a single mass delta | |
std::vector< uint32_t > | getAaCodeFromMassWearingModification (double mass, const Aa &aa, int quantifier) const |
get amino acid string code from a single mass delta wearing a specific modification | |
std::vector< uint32_t > | filterCodeList (std::vector< uint32_t > &code_list) const |
filter a list of amino acid string code find elementary amino acids (one base only) in the list and retrieve 2 or more amino acid string containing only basic aminio acid found | |
Private Attributes | |
PrecisionPtr | m_precision = nullptr |
const AaCode & | m_aaCode |
AaStringCodec | m_aaCodec |
uint32_t | m_base = 0 |
std::vector< aaCodeAndMassRange > | m_codeMassList |
convert a list of mass to amino acid string codes
Definition at line 40 of file aastringcodemassmatching.h.
AaStringCodeMassMatching::AaStringCodeMassMatching | ( | const AaCode & | aa_code, |
std::size_t | model_max_size, | ||
PrecisionPtr | precision | ||
) |
Default constructor
Definition at line 35 of file aastringcodemassmatching.cpp.
References pappso::a, pappso::b, pappso::AaStringCodeMassMatching::aaCodeAndMassRange::code, pappso::PrecisionBase::delta(), pappso::AaStringCodec::generateLlcCodeListUpToMaxPeptideSize(), pappso::AaCode::getSize(), m_aaCode, m_aaCodec, m_base, m_codeMassList, pappso::AaStringCodeMassMatching::aaCodeAndMassRange::mz, pappso::AaStringCodeMassMatching::aaCodeAndMassRange::mz_range_low, and pappso::AaStringCodeMassMatching::aaCodeAndMassRange::mz_range_up.
AaStringCodeMassMatching::AaStringCodeMassMatching | ( | const AaStringCodeMassMatching & | other | ) |
Copy constructor
other | TODO |
Definition at line 65 of file aastringcodemassmatching.cpp.
References pappso::AaCode::getSize(), m_aaCode, and m_base.
AaStringCodeMassMatching::~AaStringCodeMassMatching | ( | ) |
std::vector< uint32_t > pappso::AaStringCodeMassMatching::filterCodeList | ( | std::vector< uint32_t > & | code_list | ) | const |
filter a list of amino acid string code find elementary amino acids (one base only) in the list and retrieve 2 or more amino acid string containing only basic aminio acid found
Definition at line 210 of file aastringcodemassmatching.cpp.
std::vector< uint32_t > pappso::AaStringCodeMassMatching::getAaCodeFromMass | ( | double | mass | ) | const |
get amino acid string code from a single mass delta
mass | the mass to look for |
Definition at line 87 of file aastringcodemassmatching.cpp.
Referenced by pappso::specself::SelfSpectrumDataPoint::fillAntiSpectrumDataPoint(), and pappso::specself::SelfSpectrumDataPoint::fillSelfSpectrumDataPoint().
std::vector< uint32_t > pappso::AaStringCodeMassMatching::getAaCodeFromMassList | ( | std::vector< double > & | mass_list | ) | const |
Definition at line 176 of file aastringcodemassmatching.cpp.
std::vector< uint32_t > pappso::AaStringCodeMassMatching::getAaCodeFromMassWearingModification | ( | double | mass, |
const Aa & | aa, | ||
int | quantifier | ||
) | const |
get amino acid string code from a single mass delta wearing a specific modification
mass | the mass to look for |
aa | amino acid with modification |
quantifier | the minimum number of this aa modified required in the given aa sequence |
Definition at line 132 of file aastringcodemassmatching.cpp.
References pappso::AaBase::getLetter(), and pappso::Aa::getTotalModificationMass().
Referenced by pappso::specself::SelfSpectrumDataPoint::setVariableModification().
pappso::PrecisionPtr pappso::AaStringCodeMassMatching::getPrecisionPtr | ( | ) | const |
Definition at line 80 of file aastringcodemassmatching.cpp.
Referenced by pappso::specself::SelfSpectrumDataPoint::fillAntiSpectrumDataPoint().
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private |
Definition at line 98 of file aastringcodemassmatching.h.
Referenced by AaStringCodeMassMatching(), and AaStringCodeMassMatching().
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private |
Definition at line 100 of file aastringcodemassmatching.h.
Referenced by AaStringCodeMassMatching().
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private |
Definition at line 103 of file aastringcodemassmatching.h.
Referenced by AaStringCodeMassMatching(), and AaStringCodeMassMatching().
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private |
Definition at line 113 of file aastringcodemassmatching.h.
Referenced by AaStringCodeMassMatching().
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private |
Definition at line 97 of file aastringcodemassmatching.h.