List of all items
Structs
- FIVE_PRIME_DE_DELTA_FES
- FastaRecord
- HL_TM_DELTA_FES
- HashMap
- IL_TM_DELTA_FES
- INIT_HL_DELTA_FES
- LogProbMatPairOnSta
- LogSsPpfMats
- LogStaPpfMatSets
- LogStaPpfMats
- ML_TM_DELTA_FES
- MeaSs
- ONE_VS_MANY_IL_TM_DELTA_FES
- Options
- ProbMatPairOnSta
- RIBOSUM_85_60_BA_SCORE_MAT
- RIBOSUM_85_60_BPA_SCORE_MAT
- SPECIAL_HL_DELTA_FES
- STACK_DELTA_FES
- SaScoringParams
- StaFeParams
- StemParams
- THREE_PRIME_DE_DELTA_FES
- TWO_VS_3_IL_TM_DELTA_FES
- utils::FIVE_PRIME_DE_DELTA_FES
- utils::FastaRecord
- utils::HL_TM_DELTA_FES
- utils::HashMap
- utils::IL_TM_DELTA_FES
- utils::INIT_HL_DELTA_FES
- utils::LogSsPpfMats
- utils::ML_TM_DELTA_FES
- utils::ONE_VS_MANY_IL_TM_DELTA_FES
- utils::Options
- utils::RIBOSUM_85_60_BA_SCORE_MAT
- utils::RIBOSUM_85_60_BPA_SCORE_MAT
- utils::SPECIAL_HL_DELTA_FES
- utils::STACK_DELTA_FES
- utils::SaScoringParams
- utils::StemParams
- utils::THREE_PRIME_DE_DELTA_FES
- utils::TWO_VS_3_IL_TM_DELTA_FES
Functions
- from_utf8_unchecked
- get_2_loop_fe
- get_bpp_mat
- get_bpp_mat_and_nbpps
- get_hl_fe
- get_log_bpp_mat
- get_log_ss_ppf_mats
- get_log_sta_ppf_4d_mats
- get_prob_mat_pairs_on_sta_with_rna_id_pairs
- get_seq_len_diff
- invert_bp
- io_algo_4_log_prob_mat_pair_on_rna_sta
- io_algo_4_prob_mat_pair_on_rna_sta
- is_au_or_gu
- is_canonical
- is_rna_base
- logsumexp
- max
- mccaskill_algo
- min
- neofold
- pct_of_bpp_and_upp_mat
- print_program_usage
- prob_cons_transformation_of_log_prob_mat_pair_on_sta
- remove_small_bpps_from_bpp_mat
- remove_zeros_from_bpp_mat
- utils::from_utf8_unchecked
- utils::get_2_loop_fe
- utils::get_bpp_mat
- utils::get_bpp_mat_and_nbpps
- utils::get_hl_fe
- utils::get_log_bpp_mat
- utils::get_log_ss_ppf_mats
- utils::invert_bp
- utils::is_au_or_gu
- utils::is_canonical
- utils::is_rna_base
- utils::logsumexp
- utils::max
- utils::mccaskill_algo
- utils::min
- utils::print_program_usage
Type Aliases
- Args
- BaScoreMat
- Base
- BasePair
- BaseQuadruple
- BpaScoreMat
- CaScoreMat
- Char
- CharPair
- DeDeltaFes
- Energy
- EpsOfTerms4LogPf
- EpsOfTerms4LogProb
- ExpPartOfTerm4LogPf
- ExpPartOfTerm4LogProb
- FastaId
- FastaRecords
- FreeEnergy
- Hasher
- HlTmDeltaFes
- IlTmDeltaFes
- InitHlDeltaFes
- LogPartialPfs
- LogPf
- LogPpfMat
- LogProb
- LogProb3dMat
- LogProb4dMat
- LogProbMat
- LogProbMatPairsOnStaWithRnaIdPairs
- LogProbMats
- LogProbSeqs
- LogProbs
- Mea
- MeaMat
- MeaSsChar
- MeaSsStr
- Meas
- MlTmDeltaFes
- Num
- PartitionFunc
- Pos
- PosPair
- PosPairSeqsWithPosPairs
- PosPairs
- PosQuadruple
- PosSeqsWithPoss
- PosTriple
- Poss
- Prob
- Prob1dMat
- Prob3dMat
- Prob4dMat
- ProbMat
- ProbMats
- ProbSeqPair
- Probs
- RnaId
- RnaIdPair
- SaScore
- Seq
- SeqPair
- SeqSlice
- SliceOfEpsOfTerms4LogPf
- SliceOfEpsOfTerms4LogProb
- SparseLogProbMat
- SparseProbMat
- SpecialHlDeltaFes
- SsPair
- StaFeParamSetsWithRnaIdPairs
- StaFreeEnergy
- StackDeltaFes
- utils::Args
- utils::BaScoreMat
- utils::Base
- utils::BasePair
- utils::BaseQuadruple
- utils::BpaScoreMat
- utils::CaScoreMat
- utils::Char
- utils::CharPair
- utils::DeDeltaFes
- utils::Energy
- utils::EpsOfTerms4LogPf
- utils::EpsOfTerms4LogProb
- utils::ExpPartOfTerm4LogPf
- utils::ExpPartOfTerm4LogProb
- utils::FastaId
- utils::FastaRecords
- utils::FreeEnergy
- utils::Hasher
- utils::HlTmDeltaFes
- utils::IlTmDeltaFes
- utils::InitHlDeltaFes
- utils::LogPartialPfs
- utils::LogPf
- utils::LogPpfMat
- utils::LogProb
- utils::LogProbMat
- utils::LogProbs
- utils::MlTmDeltaFes
- utils::Num
- utils::PartitionFunc
- utils::Pos
- utils::PosPair
- utils::Prob
- utils::ProbMat
- utils::ProbSeqPair
- utils::Probs
- utils::SaScore
- utils::Seq
- utils::SeqSlice
- utils::SliceOfEpsOfTerms4LogPf
- utils::SliceOfEpsOfTerms4LogProb
- utils::SpecialHlDeltaFes
- utils::SsPair
- utils::StaFreeEnergy
- utils::StackDeltaFes
Constants
- A
- AA
- AC
- AG
- AU
- BASE_PAIRING_LEFT_BASE
- BASE_PAIRING_RIGHT_BASE
- C
- CA
- CC
- CG
- COEFFICIENT_4_ALL_C_HL_DELTA_FE
- COEFFICIENT_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
- COEFFICIENT_4_NINIO
- COEFFICIENT_4_TERM_OF_NUM_OF_BRANCHING_HELICES_ON_INIT_ML_DELTA_FE
- CONST_4_ALL_C_HL_DELTA_FE
- CONST_4_INIT_ML_DELTA_FE
- CU
- G
- GA
- GAS_CONST
- GC
- GG
- GU
- HELIX_AU_OR_GU_END_PENALTY_DELTA_FE
- HELIX_INTERMOLECULAR_INIT_DELTA_FE
- HELIX_SYMMETRY_PENALTY_DELTA_FE
- HL_GG_FIRST_MISMATCH_BONUS_DELTA_FE
- HL_OF_3_CS_PENALTY_DELTA_FE
- HL_SPECIAL_GU_CLOSURE_BONUS_DELTA_FE
- HL_UU_OR_GA_FIRST_MISMATCH_BONUS_DELTA_FE
- INFINITY
- INVERSE_TEMPERATURE
- K0
- KILO
- MAX_2_LOOP_LEN
- MAX_LOOP_LEN_4_LOG_EXTRAPOLATION_OF_INIT_LOOP_DELTA_FE
- MAX_NINIO
- MAX_SPAN_OF_INDEX_PAIR_CLOSING_IL
- MIN_HL_LEN
- MIN_LOOP_LEN_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
- MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL
- MIN_SPAN_OF_INDEX_PAIR_CLOSING_ML
- NEG_INFINITY
- PSEUDO_BASE
- SEQ_ALPHABET
- TEMPERATURE
- U
- UA
- UC
- UG
- UNPAIRING_BASE
- UU
- utils::A
- utils::AA
- utils::AC
- utils::AG
- utils::AU
- utils::C
- utils::CA
- utils::CC
- utils::CG
- utils::COEFFICIENT_4_ALL_C_HL_DELTA_FE
- utils::COEFFICIENT_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
- utils::COEFFICIENT_4_NINIO
- utils::COEFFICIENT_4_TERM_OF_NUM_OF_BRANCHING_HELICES_ON_INIT_ML_DELTA_FE
- utils::CONST_4_ALL_C_HL_DELTA_FE
- utils::CONST_4_INIT_ML_DELTA_FE
- utils::CU
- utils::G
- utils::GA
- utils::GAS_CONST
- utils::GC
- utils::GG
- utils::GU
- utils::HELIX_AU_OR_GU_END_PENALTY_DELTA_FE
- utils::HELIX_INTERMOLECULAR_INIT_DELTA_FE
- utils::HELIX_SYMMETRY_PENALTY_DELTA_FE
- utils::HL_GG_FIRST_MISMATCH_BONUS_DELTA_FE
- utils::HL_OF_3_CS_PENALTY_DELTA_FE
- utils::HL_SPECIAL_GU_CLOSURE_BONUS_DELTA_FE
- utils::HL_UU_OR_GA_FIRST_MISMATCH_BONUS_DELTA_FE
- utils::INFINITY
- utils::INVERSE_TEMPERATURE
- utils::K0
- utils::KILO
- utils::MAX_2_LOOP_LEN
- utils::MAX_LOOP_LEN_4_LOG_EXTRAPOLATION_OF_INIT_LOOP_DELTA_FE
- utils::MAX_NINIO
- utils::MAX_SPAN_OF_INDEX_PAIR_CLOSING_IL
- utils::MIN_HL_LEN
- utils::MIN_LOOP_LEN_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
- utils::MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL
- utils::MIN_SPAN_OF_INDEX_PAIR_CLOSING_ML
- utils::NEG_INFINITY
- utils::PSEUDO_BASE
- utils::SEQ_ALPHABET
- utils::TEMPERATURE
- utils::U
- utils::UA
- utils::UC
- utils::UG
- utils::UU