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pappso::specpeptidoms::SemiGlobalAlignment Member List

This is the complete list of members for pappso::specpeptidoms::SemiGlobalAlignment, including all inherited members.

checkSequenceDiversity(const QString &sequence, std::size_t window, std::size_t minimum_aa_diversity) | pappso::specpeptidoms::SemiGlobalAlignment | static
correctAlign(const SpOMSProtein &protein_subseq, const SpOMSProtein *protein_ptr, const SpOMSSpectrum &spectrum, std::vector< std::size_t > &peaks_to_remove, std::size_t offset) | pappso::specpeptidoms::SemiGlobalAlignment | private
fastAlign(const SpOMSSpectrum &spectrum, const SpOMSProtein *protein_ptr) | pappso::specpeptidoms::SemiGlobalAlignment |
getBestAlignment() const | pappso::specpeptidoms::SemiGlobalAlignment |
getInterestCells() const | pappso::specpeptidoms::SemiGlobalAlignment |
getLocationSaver() const | pappso::specpeptidoms::SemiGlobalAlignment |
getPotentialMassErrors(const pappso::AaCode &aa_code, const Alignment &alignment, const QString &protein_seq) | pappso::specpeptidoms::SemiGlobalAlignment | static
getScenario() const | pappso::specpeptidoms::SemiGlobalAlignment |
initFastAlign(const SpOMSSpectrum &spectrum) | pappso::specpeptidoms::SemiGlobalAlignment |
initpreciseAlign(const SpOMSSpectrum &spectrum, std::size_t length2) | pappso::specpeptidoms::SemiGlobalAlignment |
m_aaCode | pappso::specpeptidoms::SemiGlobalAlignment | private
m_best_alignment | pappso::specpeptidoms::SemiGlobalAlignment | private
m_best_corrected_alignment | pappso::specpeptidoms::SemiGlobalAlignment | private
m_best_post_processed_alignment | pappso::specpeptidoms::SemiGlobalAlignment | private
m_interest_cells | pappso::specpeptidoms::SemiGlobalAlignment | private
m_location_saver | pappso::specpeptidoms::SemiGlobalAlignment | private
m_precision_ptr | pappso::specpeptidoms::SemiGlobalAlignment | private
m_scenario | pappso::specpeptidoms::SemiGlobalAlignment | private
m_scorevalues | pappso::specpeptidoms::SemiGlobalAlignment | private
m_updated_cells | pappso::specpeptidoms::SemiGlobalAlignment | private
min_score | pappso::specpeptidoms::SemiGlobalAlignment | private
oneAlignStep(const pappso::specpeptidoms::SpOMSProtein &sequence, const std::size_t row_number, const std::vector< AaPosition > &aa_positions, const SpOMSSpectrum &spectrum, const bool fast_align, const pappso::specpeptidoms::SpOMSProtein *protein_ptr) | pappso::specpeptidoms::SemiGlobalAlignment |
perfectShiftPossible(const pappso::specpeptidoms::SpOMSProtein &sequence, const SpOMSSpectrum &spectrum, const std::size_t origin_row, const std::size_t current_row, const std::size_t l_peak, const std::size_t r_peak) const | pappso::specpeptidoms::SemiGlobalAlignment | private
perfectShiftPossibleEnd(const pappso::specpeptidoms::SpOMSProtein &sequence, const SpOMSSpectrum &spectrum, std::size_t end_row, std::size_t end_peak) const | pappso::specpeptidoms::SemiGlobalAlignment | private
perfectShiftPossibleFrom0(const pappso::specpeptidoms::SpOMSProtein &sequence, const SpOMSSpectrum &spectrum, const std::size_t current_row, const std::size_t r_peak) const | pappso::specpeptidoms::SemiGlobalAlignment | private
postProcessingAlign(const SpOMSSpectrum &spectrum, const SpOMSProtein *protein_ptr, std::size_t beginning, std::size_t length, const std::vector< double > &shifts) | pappso::specpeptidoms::SemiGlobalAlignment |
preciseAlign(const SpOMSSpectrum &spectrum, const SpOMSProtein *protein_ptr, const std::size_t beginning, const std::size_t length) | pappso::specpeptidoms::SemiGlobalAlignment |
saveBestAlignment(const SpOMSProtein &sequence, const SpOMSSpectrum &spectrum, std::size_t offset) | pappso::specpeptidoms::SemiGlobalAlignment | private
SemiGlobalAlignment(const ScoreValues &score_values, const pappso::PrecisionPtr precision_ptr, const AaCode &aaCode) | pappso::specpeptidoms::SemiGlobalAlignment |
updateAlignmentMatrix(const pappso::specpeptidoms::SpOMSProtein &sequence, const std::size_t row_number, const std::vector< AaPosition > &aa_positions, const SpOMSSpectrum &spectrum, const bool fast_align, const pappso::specpeptidoms::SpOMSProtein *protein_ptr) | pappso::specpeptidoms::SemiGlobalAlignment | private
~SemiGlobalAlignment() | pappso::specpeptidoms::SemiGlobalAlignment |