libpappsomspp
Library for mass spectrometry
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#include <xtandemhyperscorebis.h>
Public Member Functions | |
XtandemHyperscoreBis (bool refine_spectrum_synthesis, PrecisionPtr precision, const std::vector< PeptideIon > &ion_list) | |
~XtandemHyperscoreBis () | |
pappso_double | getHyperscore () const |
unsigned int | getMatchedIons (PeptideIon ion_type) const |
void | reset () |
bool | computeXtandemHyperscore (const MassSpectrum &spectrum, const Peptide &peptide, unsigned int parent_charge) |
unsigned int | getTotalMatchedIons () const |
Private Types | |
using | AaFactorMap = std::map< char, pappso_double > |
Private Member Functions | |
unsigned int | getXtandemPredictedIonIntensityFactor (const QString &sequence, PeptideIon ion_type, unsigned int size) const |
Private Attributes | |
bool | m_isRefineSpectrumSynthesis |
PrecisionPtr | mp_precision |
std::vector< PeptideIon > | m_ionList |
unsigned int | m_totalMatchedIons = 0 |
unsigned int | m_ionCount [PEPTIDE_ION_TYPE_COUNT] = {0} |
pappso_double | m_protoHyperscore |
Static Private Attributes | |
static AaFactorMap | m_aaIonFactorY |
static AaFactorMap | m_aaIonFactorBb |
Definition at line 40 of file xtandemhyperscorebis.h.
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private |
Definition at line 42 of file xtandemhyperscorebis.h.
XtandemHyperscoreBis::XtandemHyperscoreBis | ( | bool | refine_spectrum_synthesis, |
PrecisionPtr | precision, | ||
const std::vector< PeptideIon > & | ion_list | ||
) |
Definition at line 50 of file xtandemhyperscorebis.cpp.
References m_ionList, m_isRefineSpectrumSynthesis, m_totalMatchedIons, and mp_precision.
XtandemHyperscoreBis::~XtandemHyperscoreBis | ( | ) |
Definition at line 62 of file xtandemhyperscorebis.cpp.
bool XtandemHyperscoreBis::computeXtandemHyperscore | ( | const MassSpectrum & | spectrum, |
const Peptide & | peptide, | ||
unsigned int | parent_charge | ||
) |
Definition at line 85 of file xtandemhyperscorebis.cpp.
References pappso::factorial(), pappso::full, pappso::Peptide::getSequence(), getXtandemPredictedIonIntensityFactor(), m_ionCount, m_ionList, m_protoHyperscore, m_totalMatchedIons, mp_precision, pappso::PeptideRawFragmentMasses::pushBackMatchSpectrum(), and pappso::PappsoException::qwhat().
pappso_double XtandemHyperscoreBis::getHyperscore | ( | ) | const |
Definition at line 269 of file xtandemhyperscorebis.cpp.
References pappso::log10, m_protoHyperscore, and pappso::PappsoException::qwhat().
unsigned int XtandemHyperscoreBis::getMatchedIons | ( | PeptideIon | ion_type | ) | const |
Definition at line 67 of file xtandemhyperscorebis.cpp.
References m_ionCount.
unsigned int XtandemHyperscoreBis::getTotalMatchedIons | ( | ) | const |
Definition at line 263 of file xtandemhyperscorebis.cpp.
References m_totalMatchedIons.
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private |
Definition at line 208 of file xtandemhyperscorebis.cpp.
References m_aaIonFactorBb, m_aaIonFactorY, m_isRefineSpectrumSynthesis, and pappso::peptideIonIsNter().
Referenced by computeXtandemHyperscore().
void XtandemHyperscoreBis::reset | ( | ) |
Definition at line 74 of file xtandemhyperscorebis.cpp.
References m_ionCount, m_protoHyperscore, m_totalMatchedIons, and PEPTIDE_ION_TYPE_COUNT.
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staticprivate |
Definition at line 59 of file xtandemhyperscorebis.h.
Referenced by getXtandemPredictedIonIntensityFactor().
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staticprivate |
Definition at line 58 of file xtandemhyperscorebis.h.
Referenced by getXtandemPredictedIonIntensityFactor().
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private |
Definition at line 53 of file xtandemhyperscorebis.h.
Referenced by computeXtandemHyperscore(), getMatchedIons(), and reset().
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Definition at line 50 of file xtandemhyperscorebis.h.
Referenced by XtandemHyperscoreBis(), and computeXtandemHyperscore().
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private |
Definition at line 48 of file xtandemhyperscorebis.h.
Referenced by XtandemHyperscoreBis(), and getXtandemPredictedIonIntensityFactor().
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private |
Definition at line 56 of file xtandemhyperscorebis.h.
Referenced by computeXtandemHyperscore(), getHyperscore(), and reset().
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private |
Definition at line 52 of file xtandemhyperscorebis.h.
Referenced by XtandemHyperscoreBis(), computeXtandemHyperscore(), getTotalMatchedIons(), and reset().
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private |
Definition at line 49 of file xtandemhyperscorebis.h.
Referenced by XtandemHyperscoreBis(), and computeXtandemHyperscore().