[][src]Crate phyloalifold

Modules

utils

Structs

EXP_COEFFICIENT_4_NINIO
EXP_COEFFICIENT_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
EXP_COEFFICIENT_4_ALL_C_HL_DELTA_FE
EXP_COEFFICIENT_4_TERM_OF_NUM_OF_BRANCHING_HELICES_ON_INIT_ML_DELTA_FE
EXP_COEFFICIENT_4_NINIO
EXP_COEFFICIENT_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
EXP_COEFFICIENT_4_ALL_C_HL_DELTA_FE
EXP_COEFFICIENT_4_TERM_OF_NUM_OF_BRANCHING_HELICES_ON_INIT_ML_DELTA_FE
EXP_CONST_4_ALL_C_HL_DELTA_FE
EXP_CONST_4_INIT_ML_DELTA_FE
EXP_CONST_4_ALL_C_HL_DELTA_FE
EXP_CONST_4_INIT_ML_DELTA_FE
EXP_FIVE_PRIME_DE_DELTA_FES
EXP_HELIX_AU_OR_GU_END_PENALTY_DELTA_FE
EXP_HELIX_INTERMOLECULAR_INIT_DELTA_FE
EXP_HELIX_SYMMETRY_PENALTY_DELTA_FE
EXP_HL_GG_FIRST_MISMATCH_BONUS_DELTA_FE
EXP_HL_OF_3_CS_PENALTY_DELTA_FE
EXP_HL_SPECIAL_GU_CLOSURE_BONUS_DELTA_FE
EXP_HL_TM_DELTA_FES
EXP_HL_UU_OR_GA_FIRST_MISMATCH_BONUS_DELTA_FE
EXP_IL_TM_DELTA_FES
EXP_INIT_HL_DELTA_FES
EXP_MAX_NINIO
EXP_ML_TM_DELTA_FES
EXP_ONE_VS_MANY_IL_TM_DELTA_FES
EXP_RIBOSUM_85_60_BA_SCORE_MAT
EXP_RIBOSUM_85_60_BPA_SCORE_MAT
EXP_RIBOSUM_85_60_BA_SCORE_MAT
EXP_RIBOSUM_85_60_BPA_SCORE_MAT
EXP_SPECIAL_HL_DELTA_FES
EXP_STACK_DELTA_FES
EXP_THREE_PRIME_DE_DELTA_FES
EXP_TWO_VS_3_IL_TM_DELTA_FES
FIVE_PRIME_DE_DELTA_FES
FastaRecord
HL_TM_DELTA_FES
IL_TM_DELTA_FES
INIT_HL_DELTA_FES
ML_TM_DELTA_FES
MeaCss
MeaSs
ONE_VS_MANY_IL_TM_DELTA_FES
Options

A description of the options that a program can handle.

Pool

A threadpool that acts as a handle to a number of threads spawned at construction.

RIBOSUM_85_60_BA_SCORE_MAT
RIBOSUM_85_60_BPA_SCORE_MAT
RIBOSUM_85_60_BA_SCORE_MAT
RIBOSUM_85_60_BPA_SCORE_MAT
SPECIAL_HL_DELTA_FES
STACK_DELTA_FES
SaScoringParams
SeqAlign
SsFreeEnergyMats
SsMaxFreeEnergyMats
SsPartFuncMats
StaFeParams
StaInsidePartFuncMatSets
StaInsidePartFuncMats
THREE_PRIME_DE_DELTA_FES
TWO_VS_3_IL_TM_DELTA_FES
TmpStaInsidePartFuncMatSets

Constants

A
AA
AC
AG
AU
BASE_PAIRING_LEFT_BASE
BASE_PAIRING_RIGHT_BASE
BIG_A
BIG_C
BIG_G
BIG_U
C
CA
CC
CG
COEFFICIENT_4_NINIO
COEFFICIENT_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
COEFFICIENT_4_ALL_C_HL_DELTA_FE
COEFFICIENT_4_TERM_OF_NUM_OF_BRANCHING_HELICES_ON_INIT_ML_DELTA_FE
COEFFICIENT_4_NINIO
COEFFICIENT_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
COEFFICIENT_4_ALL_C_HL_DELTA_FE
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
CONST_4_ALL_C_HL_DELTA_FE
CONST_4_INIT_ML_DELTA_FE
CU
DEFAULT_EXTENDING_GAP_PENALTY
DEFAULT_MIN_BPP
DEFAULT_OFFSET_4_MAX_GAP_NUM
DEFAULT_OPENING_GAP_PENALTY
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_UU_OR_GA_FIRST_MISMATCH_BONUS_DELTA_FE
INVERSE_TEMPERATURE
K0
KILO
MAX_2_LOOP_LEN
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
MIN_GAP_NUM_4_IL
MIN_HL_LEN
MIN_LOOP_LEN_4_LOG_EXTRAPOLATION_OF_INIT_HL_DELTA_FE
MIN_SEQ_LENGTH_4_LOGSUMEXP_METHOD
MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL
MIN_SPAN_OF_INDEX_PAIR_CLOSING_ML
NEG_INFINITY

Negative infinity (−∞). Use f64::NEG_INFINITY instead.

NUM_OF_BASES
NUM_OF_SPECIAL_HLS
PSEUDO_BASE
SMALL_A
SMALL_C
SMALL_G
SMALL_U
TEMPERATURE
U
UA
UC
UG
UNPAIRING_BASE
UU

Functions

convert
from_utf8_unchecked

Converts a slice of bytes to a string slice without checking that the string contains valid UTF-8.

get_2_loop_fe
get_abs_diff
get_backward_tmp_sta_inside_part_func_mat_sets
get_bpp_and_unpair_prob_mats
get_exp_2_loop_fe
get_exp_hl_fe
get_exp_special_hl_fe
get_forward_tmp_sta_inside_part_func_mat_sets
get_hl_fe
get_max_bp_span
get_max_free_energy
get_seq_len_diff
get_special_hl_fe
get_ss_part_func_mats
get_sta_inside_part_func_mat_sets
get_sta_outside_part_func_4d_mat_4_bpas
invert_bp
io_algo_4_bpap_mat
is_au_or_gu
is_canonical
is_rna_base
logsumexp
max

Compares and returns the maximum of two values.

mccaskill_algo
min

Compares and returns the minimum of two values.

multizip

An iterator that generalizes .zip() and allows running multiple iterators in lockstep.

pct_of_bpp_and_upp_mat
phyloalifold
phylofold
phyloprob
print_program_usage
remove_small_bpps_from_bpp_mat
scale

Type Definitions

Arg
Args
BaScoreMat
Base
BasePair
BoolsWithPosPairs
BpaScoreMat
CaScoreMat
Char
CharPair
Col
Cols
DeDeltaFes
FastaId
FastaRecords
FreeEnergies
FreeEnergy
FreeEnergy4dMat
FreeEnergyMat
FreeEnergyPair
FxHashMap

Type alias for a hashmap using the fx hash algorithm.

HlTmDeltaFes
IlTmDeltaFes
InitHlDeltaFes
LogProb
Mea
MeaMat
MeaSsChar
MeaSsStr
Meas
MlTmDeltaFes
Num
NumOfThreads
PartFunc
PartFuncMat
PartFuncs
Pos
PosMapSets
PosMaps
PosPair
PosPairSeqsWithPosPairs
PosPairs
PosPairsWithPosPairs
PosQuadruple
PosSeqsWithPoss
Poss
Prob
Prob1dMats
Prob4dMat
Prob4dMatsWithRnaIdPairs
Prob4dMat
Prob4dMatsWithRnaIdPairs
Prob4dMat
Prob4dMatsWithRnaIdPairs
ProbMat
ProbMatPair
ProbMats
ProbMatsWithRnaIds
ProbSeqPair
Probs
ProbsWithPosPairs
ProbsWithRnaIds
RnaId
RnaIdPair
SaScore
ScaleParam
ScaleParamMat
ScaleParams
Seq
SeqId
SeqIds
SeqPair
SeqSlice
SparseFreeEnergyMat
SparsePartFuncMat
SparseProbMat
SpecialHlDeltaFes
SsFreeEnergyMatSetPair
SsPair
StaFeParamSetsWithRnaIdPairs
StackDeltaFes
TmpStaInsidePartFuncMatSetsWithPosQuadruples