[][src]Module rnafamprob::utils

Structs

FIVE_PRIME_DE_DELTA_FES
FastaRecord
HL_TM_DELTA_FES
HashMap

A hash map implemented with quadratic probing and SIMD lookup.

IL_TM_DELTA_FES
INIT_HL_DELTA_FES
LogSsPpfMats
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
StemParams
THREE_PRIME_DE_DELTA_FES
TWO_VS_3_IL_TM_DELTA_FES

Constants

A
AA
AC
AG
AU
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
INFINITY

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

Negative infinity (-∞).

PSEUDO_BASE
SEQ_ALPHABET
TEMPERATURE
U
UA
UC
UG
UU

Functions

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_bpp_and_unpair_prob_mats
get_bpp_mat
get_hl_fe
get_log_bpp_mat
get_log_ss_ppf_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.

print_program_usage

Type Definitions

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
LogProbMat
LogProbs
MlTmDeltaFes
Num
PartitionFunc
Pos
PosPair
Prob
ProbMat
ProbSeqPair
Probs
SaScore
Seq
SeqSlice
SliceOfEpsOfTerms4LogPf
SliceOfEpsOfTerms4LogProb
SpecialHlDeltaFes
SsPair
StaFreeEnergy
StackDeltaFes