libpappsomspp
Library for mass spectrometry
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#include <aastringcodec.h>
Public Member Functions | |
AaStringCodec (const AaCode &aaCode) | |
AaStringCodec (const AaStringCodec &other) | |
~AaStringCodec () | |
std::size_t | getLimitMax (std::size_t size) const |
get the maximum code number for a given peptide size | |
uint32_t | code (const QString &aa_str) const |
get integer from amino acide suite string | |
uint32_t | codeLlc (const QString &aa_str) const |
get the lowest common denominator integer from amino acide suite string | |
uint32_t | codeLlc (std::vector< uint8_t >::const_iterator it_begin, std::size_t size) const |
get the lowest common denominator integer from amino acide code vector | |
QString | decode (uint32_t code) const |
double | getMass (uint32_t code) const |
std::vector< CodeToMass > | generateLlcCodeListUpToMaxPeptideSize (std::size_t size) const |
generates all possible combination of llc code mass llc : the lowest common code denominator for a given aa formula | |
std::vector< CodeToMass > | generateLlcCodeListByMaxPeptideSize (std::size_t size) const |
generates all possible combination of llc code mass llc : the lowest common code denominator for a given aa formula | |
bool | codeOnlyContains (uint32_t code, const std::vector< uint8_t > &aa_ok) const |
const AaCode & | getAaCode () const |
Private Member Functions | |
void | recGenerateModel (std::vector< CodeToMass > &glist, std::vector< uint8_t > &model, std::size_t position) const |
recursive method to generate models | |
CodeToMass | generateCodeMassFromModel (const std::vector< uint8_t > &model) const |
Private Attributes | |
uint32_t | m_base = 0 |
const AaCode & | m_aaCode |
std::vector< uint32_t > | m_units |
Definition at line 51 of file aastringcodec.h.
AaStringCodec::AaStringCodec | ( | const AaCode & | aaCode | ) |
Default constructor
Definition at line 33 of file aastringcodec.cpp.
References pappso::AaCode::getSize(), m_aaCode, m_base, and m_units.
AaStringCodec::AaStringCodec | ( | const AaStringCodec & | other | ) |
AaStringCodec::~AaStringCodec | ( | ) |
uint32_t pappso::AaStringCodec::code | ( | const QString & | aa_str | ) | const |
get integer from amino acide suite string
Definition at line 59 of file aastringcodec.cpp.
uint32_t pappso::AaStringCodec::codeLlc | ( | const QString & | aa_str | ) | const |
get the lowest common denominator integer from amino acide suite string
Definition at line 73 of file aastringcodec.cpp.
Referenced by pappso::ProteinIntegerCode::computePeptideCodeFragments().
uint32_t pappso::AaStringCodec::codeLlc | ( | std::vector< uint8_t >::const_iterator | it_begin, |
std::size_t | size | ||
) | const |
get the lowest common denominator integer from amino acide code vector
Definition at line 95 of file aastringcodec.cpp.
bool pappso::AaStringCodec::codeOnlyContains | ( | uint32_t | code, |
const std::vector< uint8_t > & | aa_ok | ||
) | const |
QString pappso::AaStringCodec::decode | ( | uint32_t | code | ) | const |
Definition at line 120 of file aastringcodec.cpp.
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private |
Definition at line 226 of file aastringcodec.cpp.
References pappso::CodeToMass::code, and pappso::CodeToMass::mass.
std::vector< CodeToMass > pappso::AaStringCodec::generateLlcCodeListByMaxPeptideSize | ( | std::size_t | size | ) | const |
generates all possible combination of llc code mass llc : the lowest common code denominator for a given aa formula
generate only for this peptide size
Definition at line 180 of file aastringcodec.cpp.
std::vector< CodeToMass > pappso::AaStringCodec::generateLlcCodeListUpToMaxPeptideSize | ( | std::size_t | size | ) | const |
generates all possible combination of llc code mass llc : the lowest common code denominator for a given aa formula
generate from peptide size =1 to peptide size
Definition at line 151 of file aastringcodec.cpp.
Referenced by pappso::AaStringCodeMassMatching::AaStringCodeMassMatching().
const pappso::AaCode & pappso::AaStringCodec::getAaCode | ( | ) | const |
Definition at line 273 of file aastringcodec.cpp.
Referenced by pappso::ProteinIntegerCode::ProteinIntegerCode().
std::size_t pappso::AaStringCodec::getLimitMax | ( | std::size_t | size | ) | const |
double pappso::AaStringCodec::getMass | ( | uint32_t | code | ) | const |
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private |
recursive method to generate models
Definition at line 198 of file aastringcodec.cpp.
References pappso::max.
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private |
Definition at line 130 of file aastringcodec.h.
Referenced by AaStringCodec().
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private |
Definition at line 129 of file aastringcodec.h.
Referenced by AaStringCodec(), and AaStringCodec().
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private |
Definition at line 131 of file aastringcodec.h.
Referenced by AaStringCodec(), and AaStringCodec().