LocARNA-1.9.2
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calculateLCSEPM() :
LocARNA::LCSEPM
Canonical() :
LocARNA::BasePairFilter::Canonical
checkAlphabet() :
LocARNA::MultipleAlignment
clear() :
LocARNA::Alignment
,
LocARNA::SparseVector< T >
,
LocARNA::Matrix< T >
,
LocARNA::RnaStructure
,
LocARNA::SparseMatrix< T >
clear_am_to_do() :
LocARNA::EPM
cmfinder_realignment_score() :
LocARNA::MultipleAlignment
col_to_pos() :
LocARNA::MultipleAlignment::SeqEntry
column() :
LocARNA::MultipleAlignment
common_left_end_list() :
LocARNA::ArcMatches
common_right_end_list() :
LocARNA::ArcMatches
comp_E_entry() :
LocARNA::AlignerP
comp_Eprime_entry() :
LocARNA::AlignerP
comp_Erev_entry() :
LocARNA::AlignerP
comp_F_entry() :
LocARNA::AlignerP
comp_Fprime_entry() :
LocARNA::AlignerP
comp_Frev_entry() :
LocARNA::AlignerP
comp_M_entry() :
LocARNA::AlignerP
comp_Mprime_entry() :
LocARNA::AlignerP
comp_Mrev_entry() :
LocARNA::AlignerP
compute_arcmatch_probabilities() :
LocARNA::AlignerP
compute_arcmatch_score() :
LocARNA::ExactMatcher
compute_basematch_probabilities() :
LocARNA::AlignerP
compute_E_entry() :
LocARNA::AlignerN
compute_ensemble_probs() :
LocARNA::RnaEnsembleImpl
compute_F_entry() :
LocARNA::AlignerN
compute_fragment_match_prob() :
LocARNA::AlignerP
compute_IX() :
LocARNA::AlignerN
compute_M_entry() :
LocARNA::AlignerN
compute_McCaskill_alifold_matrices() :
LocARNA::RnaEnsembleImpl
compute_McCaskill_matrices() :
LocARNA::RnaEnsembleImpl
compute_Qm2() :
LocARNA::RnaEnsembleImpl
compute_Qm2_ali() :
LocARNA::RnaEnsembleImpl
ConfusionMatrix() :
LocARNA::ConfusionMatrix
consensus_cost() :
LocARNA::TraceRange
consensus_probability() :
LocARNA::RnaDataImpl
consensus_sequence() :
LocARNA::MultipleAlignment
constraints() :
LocARNA::AlignerParams
contains() :
LocARNA::RnaStructure
,
LocARNA::MultipleAlignment
count_base_pairs() :
LocARNA::ConfusionMatrix
count_common_bps() :
LocARNA::ConfusionMatrix
count_conflicting_base_pairs() :
LocARNA::ConfusionMatrix
count_potential_base_pairs() :
LocARNA::ConfusionMatrix
count_tps() :
LocARNA::ConfusionMatrix
create() :
LocARNA::AlignerN
,
LocARNA::AlignerP
,
LocARNA::Aligner
crossing() :
LocARNA::RnaStructure
current_cycles() :
LocARNA::StopWatch
current_total() :
LocARNA::StopWatch
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