[][src]Module phylofold::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_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_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
ONE_VS_MANY_IL_TM_DELTA_FES
Options

A description of the options that a program can handle.

RIBOSUM_85_60_BA_SCORE_MAT
RIBOSUM_85_60_BPA_SCORE_MAT
SPECIAL_HL_DELTA_FES
STACK_DELTA_FES
SaScoringParams
SsFreeEnergyMats
SsMaxFreeEnergyMats
SsPartFuncMats
THREE_PRIME_DE_DELTA_FES
TWO_VS_3_IL_TM_DELTA_FES

Constants

A
AA
AC
AG
AU
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
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
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

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
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_bpp_and_unpair_prob_mats
get_exp_2_loop_fe
get_exp_hl_fe
get_exp_special_hl_fe
get_hl_fe
get_max_free_energy
get_special_hl_fe
get_ss_part_func_mats
invert_bp
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.

print_program_usage
scale

Type Definitions

Args
BaScoreMat
Base
BasePair
BpaScoreMat
CaScoreMat
Char
CharPair
DeDeltaFes
FastaId
FastaRecords
FreeEnergies
FreeEnergy
FreeEnergy4dMat
FreeEnergyMat
FxHashMap

Type alias for a hashmap using the fx hash algorithm.

HlTmDeltaFes
IlTmDeltaFes
InitHlDeltaFes
LogProb
MlTmDeltaFes
Num
PartFunc
PartFuncMat
PartFuncs
Pos
PosPair
PosQuadruple
Prob
ProbMat
ProbSeqPair
Probs
SaScore
ScaleParam
ScaleParamMat
ScaleParams
Seq
SeqSlice
SparseFreeEnergyMat
SparsePartFuncMat
SparseProbMat
SpecialHlDeltaFes
SsPair
StackDeltaFes