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