libpappsomspp
Library for mass spectrometry
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code and decode amino acid string sequence to unique integer More...
#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 |
QStringList | decode (const std::vector< uint32_t > &code_list) 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 |
tell if a code only contains a list of amino acid | |
bool | uniqueCodeContainsAminoAcid (uint32_t code, uint8_t aa_ok, int times) const |
tell if a unique code only contains one amino acid 1 or n times | |
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 |
code and decode amino acid string sequence to unique integer
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 |
tell if a code only contains a list of amino acid
code | the code to valid |
aa_ok | list of required amino acids |
Definition at line 269 of file aastringcodec.cpp.
QStringList pappso::AaStringCodec::decode | ( | const std::vector< uint32_t > & | code_list | ) | const |
Definition at line 136 of file aastringcodec.cpp.
QString pappso::AaStringCodec::decode | ( | uint32_t | code | ) | const |
Definition at line 120 of file aastringcodec.cpp.
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private |
Definition at line 238 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 192 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 163 of file aastringcodec.cpp.
Referenced by pappso::AaStringCodeMassMatching::AaStringCodeMassMatching().
const pappso::AaCode & pappso::AaStringCodec::getAaCode | ( | ) | const |
Definition at line 307 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 210 of file aastringcodec.cpp.
References pappso::max.
bool pappso::AaStringCodec::uniqueCodeContainsAminoAcid | ( | uint32_t | code, |
uint8_t | aa_ok, | ||
int | times ) const |
tell if a unique code only contains one amino acid 1 or n times
code | the code to valid |
aa_ok | the amino acid the code must contains |
times | the number of aa_ok presence in code |
Definition at line 285 of file aastringcodec.cpp.
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private |
Definition at line 147 of file aastringcodec.h.
Referenced by AaStringCodec().
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private |
Definition at line 146 of file aastringcodec.h.
Referenced by AaStringCodec(), and AaStringCodec().
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private |
Definition at line 148 of file aastringcodec.h.
Referenced by AaStringCodec(), and AaStringCodec().