[−] List of all items
Structs
- BA_SCORE_MAT
- BufWriter
- FastaRecord
- File
- HashMap
- MeaCss
- MeaSs
- Options
- Path
- PctStaProbMats
- Pool
- RIBOSUM_BA_SCORE_MAT
- RIBOSUM_BPA_SCORE_MAT
- Reader
- SPECIAL_HL_DELTA_FES
- SaScoringParams
- SeqAlign
- SsFreeEnergyMats
- SsPartFuncMats
- SsProbMats
- StaFeParams
- StaPartFuncMats
- StaPartFuncMats4Posterior
- StaProbMats
- TmpPartFuncSets
- TmpPartFuncs
- utils::BA_SCORE_MAT
- utils::FastaRecord
- utils::HashMap
- utils::Options
- utils::RIBOSUM_BA_SCORE_MAT
- utils::RIBOSUM_BPA_SCORE_MAT
- utils::SPECIAL_HL_DELTA_FES
- utils::SaScoringParams
- utils::SsFreeEnergyMats
- utils::SsPartFuncMats
- utils::SsProbMats
Traits
Functions
- consalifold
- conshomfold
- consprob
- convert
- create_dir
- from_utf8_unchecked
- get_2_loop_fe
- get_abs_diff
- get_bpp_and_unpair_prob_mats
- get_hl_fe
- get_max_bp_span
- get_seq_len_diff
- get_special_hl_fe
- get_ss_part_func_mats
- get_sta_inside_part_func_mats
- get_sta_inside_part_func_mats_4_posterior
- get_sta_prob_mats
- get_sta_prob_mats_4_posterior
- get_tmp_part_func_set_mat
- get_tmp_part_func_set_mat_4_posterior
- invert_bp
- io_algo_4_prob_mats
- is_au_or_gu
- is_canonical
- is_rna_base
- logsumexp
- max
- mccaskill_algo
- min
- multizip
- pct_of_prob_mats
- print_program_usage
- remove_small_bpps_from_bpp_mat
- scale
- sumormax
- utils::convert
- utils::from_utf8_unchecked
- utils::get_2_loop_fe
- utils::get_abs_diff
- utils::get_bpp_and_unpair_prob_mats
- utils::get_hl_fe
- utils::get_special_hl_fe
- utils::get_ss_part_func_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::multizip
- utils::print_program_usage
- utils::scale
- write_prob_mat_sets
Typedefs
- Arg
- Args
- BaScoreMat
- Base
- BasePair
- BoolsWithPosPairs
- BpaScoreMat
- CaScoreMat
- Char
- CharPair
- Col
- Cols
- DeDeltaFes
- FastaId
- FastaRecords
- FreeEnergies
- FreeEnergy
- FreeEnergy4dMat
- FreeEnergyMat
- FreeEnergyPair
- FreeEnergySetPair
- HlTmDeltaFes
- IlTmDeltaFes
- InitHlDeltaFes
- InsertScores
- LogProb
- Mea
- MeaMat
- MeaSsChar
- MeaSsStr
- Meas
- MlTmDeltaFes
- Num
- NumOfThreads
- PartFunc
- PartFunc4dMat
- PartFuncMat
- PartFuncs
- Pos
- PosMapSets
- PosMaps
- PosPair
- PosPairSeqsWithPosPairs
- PosPairs
- PosPairsWithPosPairs
- PosQuadruple
- PosSeqsWithPoss
- Poss
- Prob
- Prob1dMats
- Prob4dMat
- Prob4dMatsWithRnaIdPairs
- ProbMat
- ProbMatPair
- ProbMatSets
- ProbMats
- ProbMatsWithRnaIds
- ProbSeqPair
- ProbSetPair
- Probs
- ProbsWithPosPairs
- ProbsWithRnaIds
- RnaId
- RnaIdPair
- SaScore
- ScaleParam
- ScaleParamMat
- ScaleParams
- Seq
- SeqId
- SeqIds
- SeqPair
- SeqSlice
- SparseFreeEnergyMat
- SparsePartFuncMat
- SparseProbMat
- SparseProbMatPair
- SpecialHlDeltaFes
- SsFreeEnergyMatSetPair
- SsPair
- StaFeParamSetsWithRnaIdPairs
- StaProbMatsWithRnaIdPairs
- StackDeltaFes
- TmpPartFuncSetMat
- TmpPartFuncSetMat4El
- TmpPartFuncSetMat4Posterior
- TmpPartFuncSetMatsWithPosPairs
- TmpPartFuncSetMatsWithPosPairs4Posterior
- TmpPartFuncSetMatsWithPosQuadruples
- TmpPartFuncSetMatsWithPosQuadruples4Posterior
- utils::Args
- utils::BaScoreMat
- utils::Base
- utils::BasePair
- utils::BpaScoreMat
- utils::CaScoreMat
- utils::Char
- utils::CharPair
- utils::DeDeltaFes
- utils::FastaId
- utils::FastaRecords
- utils::FreeEnergies
- utils::FreeEnergy
- utils::FreeEnergy4dMat
- utils::FreeEnergyMat
- utils::HlTmDeltaFes
- utils::IlTmDeltaFes
- utils::InitHlDeltaFes
- utils::InsertScores
- utils::LogProb
- utils::MlTmDeltaFes
- utils::Num
- utils::PartFunc
- utils::PartFuncMat
- utils::PartFuncs
- utils::Pos
- utils::PosPair
- utils::PosQuadruple
- utils::Prob
- utils::ProbMat
- utils::ProbSeqPair
- utils::Probs
- utils::SaScore
- utils::ScaleParam
- utils::ScaleParamMat
- utils::ScaleParams
- utils::Seq
- utils::SeqSlice
- utils::SparseFreeEnergyMat
- utils::SparsePartFuncMat
- utils::SparseProbMat
- utils::SpecialHlDeltaFes
- utils::SsPair
- utils::StackDeltaFes
Constants
- A
- AA
- AC
- ACCESS_BPP_MAT_ON_2L_FILE_NAME
- ACCESS_BPP_MAT_ON_ML_FILE_NAME
- AG
- AU
- BASE_PAIRING_LEFT_BASE
- BASE_PAIRING_RIGHT_BASE
- BIG_A
- BIG_C
- BIG_G
- BIG_U
- BPP_MAT_FILE_NAME
- BPP_MAT_ON_EL_FILE_NAME
- BPP_MAT_ON_SS_FILE_NAME
- 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
- DEFAULT_MIN_BPP
- DEFAULT_OFFSET_4_MAX_GAP_NUM
- FIVE_PRIME_DE_DELTA_FES
- G
- GA
- GAP
- 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_TM_DELTA_FES
- HL_UU_OR_GA_FIRST_MISMATCH_BONUS_DELTA_FE
- IL_TM_DELTA_FES
- INIT_BL_DELTA_FES
- INIT_HL_DELTA_FES
- INIT_IL_DELTA_FES
- INIT_INSERT_SCORE
- INIT_MATCH_SCORE
- INSERT_2_MATCH_SCORE
- INSERT_EXTEND_SCORE
- INSERT_SCORES
- INSERT_SWITCH_SCORE
- INVERSE_TEMPERATURE
- K0
- KILO
- MATCH_2_INSERT_SCORE
- MATCH_2_MATCH_SCORE
- MAX_2_LOOP_LEN
- MAX_BPP_MAT_FILE_NAME
- MAX_GAP_NUM_4_IL
- MAX_LOOP_LEN_4_LOG_EXTRAPOLATION_OF_INIT_LOOP_DELTA_FE
- MAX_NINIO
- MAX_SPAN_OF_INDEX_PAIR_CLOSING_IL
- MAX_UPP_MAT_FILE_NAME
- MIN_GAP_NUM_4_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
- ML_TM_DELTA_FES
- NEG_INFINITY
- NUM_OF_BASES
- NUM_OF_SPECIAL_HLS
- NUM_OF_TRANSITS
- ONE_VS_1_IL_DELTA_FES
- ONE_VS_2_IL_DELTA_FES
- ONE_VS_MANY_IL_TM_DELTA_FES
- OTHER_IL_TM_BONUS_DELTA_FES
- PSEUDO_BASE
- SMALL_A
- SMALL_C
- SMALL_G
- SMALL_U
- STACK_DELTA_FES
- TEMPERATURE
- THREE_PRIME_DE_DELTA_FES
- TWO_VS_2_IL_DELTA_FES
- TWO_VS_3_IL_TM_BONUS_DELTA_FES
- TWO_VS_3_IL_TM_DELTA_FES
- U
- UA
- UC
- UG
- UNPAIRING_BASE
- UPP_MAT_FILE_NAME
- UPP_MAT_ON_2L_FILE_NAME
- UPP_MAT_ON_EL_FILE_NAME
- UPP_MAT_ON_HL_FILE_NAME
- UPP_MAT_ON_ML_FILE_NAME
- UU
- utils::A
- utils::AA
- utils::AC
- utils::AG
- utils::AU
- utils::BIG_A
- utils::BIG_C
- utils::BIG_G
- utils::BIG_U
- 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::FIVE_PRIME_DE_DELTA_FES
- 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_TM_DELTA_FES
- utils::HL_UU_OR_GA_FIRST_MISMATCH_BONUS_DELTA_FE
- utils::IL_TM_DELTA_FES
- utils::INIT_BL_DELTA_FES
- utils::INIT_HL_DELTA_FES
- utils::INIT_IL_DELTA_FES
- utils::INIT_INSERT_SCORE
- utils::INIT_MATCH_SCORE
- utils::INSERT_2_MATCH_SCORE
- utils::INSERT_EXTEND_SCORE
- utils::INSERT_SCORES
- utils::INSERT_SWITCH_SCORE
- utils::INVERSE_TEMPERATURE
- utils::K0
- utils::KILO
- utils::MATCH_2_INSERT_SCORE
- utils::MATCH_2_MATCH_SCORE
- 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::ML_TM_DELTA_FES
- utils::NEG_INFINITY
- utils::NUM_OF_BASES
- utils::NUM_OF_SPECIAL_HLS
- utils::NUM_OF_TRANSITS
- utils::ONE_VS_1_IL_DELTA_FES
- utils::ONE_VS_2_IL_DELTA_FES
- utils::ONE_VS_MANY_IL_TM_DELTA_FES
- utils::OTHER_IL_TM_BONUS_DELTA_FES
- utils::PSEUDO_BASE
- utils::SMALL_A
- utils::SMALL_C
- utils::SMALL_G
- utils::SMALL_U
- utils::STACK_DELTA_FES
- utils::TEMPERATURE
- utils::THREE_PRIME_DE_DELTA_FES
- utils::TWO_VS_2_IL_DELTA_FES
- utils::TWO_VS_3_IL_TM_BONUS_DELTA_FES
- utils::TWO_VS_3_IL_TM_DELTA_FES
- utils::U
- utils::UA
- utils::UC
- utils::UG
- utils::UU