Crate consalifold[][src]

Modules

utils

Macros

Hash

Derive macro generating an impl of the trait Hash.

Ord

Derive macro generating an impl of the trait Ord.

env

Inspects an environment variable at compile time.

Structs

BA_SCORE_MAT
BufReader

The BufReader<R> struct adds buffering to any reader.

BufWriter

Wraps a writer and buffers its output.

FastaRecord
File

A reference to an open file on the filesystem.

HashMap

A hash map implemented with quadratic probing and SIMD lookup.

HashSet

A hash set implemented as a HashMap where the value is ().

MeaCss
Options

A description of the options that a program can handle.

Path

A slice of a path (akin to str).

PctStaProbMats
Pool

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

RIBOSUM_BA_SCORE_MAT
RIBOSUM_BPA_SCORE_MAT
Reader

A FASTA reader.

SPECIAL_HL_DELTA_FES
SaScoringParams
SeqAlign
SsFreeEnergyMats
SsPartFuncMats
SsPartFuncMatsContra
StaFeParams
StaPartFuncMats
StaProbMats
TmpPartFuncSets
TmpPartFuncs

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_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_INIT_ML_DELTA_FE
CONTRA_BASE_PAIR_FES
CONTRA_BL_0X1_FES
CONTRA_BL_LENGTH_FES
CONTRA_BL_LENGTH_FES_AT_LEAST
CONTRA_EL_PAIRED_FE
CONTRA_EL_UNPAIRED_FE
CONTRA_HELIX_CLOSING_FES
CONTRA_HL_LENGTH_FES
CONTRA_HL_LENGTH_FES_AT_LEAST
CONTRA_IL_1X1_FES
CONTRA_IL_ASYMM_LENGTH_FES
CONTRA_IL_ASYMM_LENGTH_FES_AT_LEAST
CONTRA_IL_EXPLICIT_FES
CONTRA_IL_LENGTH_FES
CONTRA_IL_LENGTH_FES_AT_LEAST
CONTRA_IL_SYMM_LENGTH_FES
CONTRA_IL_SYMM_LENGTH_FES_AT_LEAST
CONTRA_LEFT_DANGLE_FES
CONTRA_MAX_IL_EXPLICIT_LEN
CONTRA_MAX_LOOP_LEN
CONTRA_ML_BASE_FE
CONTRA_ML_PAIRED_FE
CONTRA_ML_UNPAIRED_FE
CONTRA_RIGHT_DANGLE_FES
CONTRA_STACK_FES
CONTRA_TERMINAL_MISMATCH_FES
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
HL_TM_DELTA_FES
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
LOGSUMEXP_THRES_UPPER
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_INF
NEG_INFINITYDeprecation planned

Negative infinity (−∞). Use f32::NEG_INFINITY instead.

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

Traits

Bounded

Numbers which have upper and lower bounds

BufRead

A BufRead is a type of Reader which has an internal buffer, allowing it to perform extra ways of reading.

Display

Format trait for an empty format, {}.

FromPrimitive

A generic trait for converting a number to a value.

Hash

A hashable type.

Integer
One

Defines a multiplicative identity element for Self.

Ord

Trait for types that form a total order.

PrimInt

Generic trait for primitive integers.

Read

The Read trait allows for reading bytes from a source.

Seek

The Seek trait provides a cursor which can be moved within a stream of bytes.

Send

Types that can be transferred across thread boundaries.

Sync

Types for which it is safe to share references between threads.

ToPrimitive

A generic trait for converting a value to a number.

Unsigned

A trait for values which cannot be negative

Write

A trait for objects which are byte-oriented sinks.

Zero

Defines an additive identity element for Self.

Functions

consalifold
consprob
convert
convert_char
convert_sa_char
create_dir

Creates a new, empty directory at the provided path

expf
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_2_loop_fe_contra
get_abs_diff
get_bl_fe_contra
get_contra_helix_closing_fe
get_contra_junction_fe_multi
get_contra_junction_fe_single
get_contra_terminal_mismatch_fe
get_hl_fe
get_hl_fe_contra
get_il_fe_contra
get_max_bp_span
get_ml_closing_basepairing_fe
get_ml_or_el_accessible_basepairing_fe
get_seq_len_diff
get_sparse_pos_sets
get_special_hl_fe
get_ss_part_func_mats
get_ss_part_func_mats_contra
get_sta_inside_part_func_mats
get_sta_prob_mats
get_stack_fe_contra
get_tmp_part_func_set_mat
invert_bp
io_algo_4_prob_mats
is_au_or_gu
is_canonical
is_rna_base
ln_exp_1p
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_prob_mats
print_program_usage
range

Returns an iterator over the given range [start, stop) (that is, starting at start (inclusive), and ending at stop (exclusive)).

range_inclusive

Return an iterator over the range [start, stop]

read_sa_from_clustal_file
remove_small_bpps_from_bpp_mat
revert_char
scale
sparsify
write_prob_mat_sets

Type Definitions

Arg
Args
BaScoreMat
Base
BasePair
BoolsWithPosPairs
BpaScoreMat
CaScoreMat
Char
CharPair
Col
Cols
ContraBasePairFes
ContraBl0x1Fes
ContraBlLengthFes
ContraDangleFes
ContraHelixClosingFes
ContraHlLengthFes
ContraIl1x1Fes
ContraIlAsymmLengthFes
ContraIlExplicitFes
ContraIlLengthFes
ContraIlSymmLengthFes
ContraStackFes
ContraTerminalMismatchFes
DeDeltaFes
FastaId
FastaRecords
FreeEnergies
FreeEnergy
FreeEnergy4dMat
FreeEnergyMat
FreeEnergyPair
FreeEnergySetPair
HlTmDeltaFes
IlTmBonusDeltaFes
IlTmDeltaFes
InitBlDeltaFes
InitHlDeltaFes
InitIlDeltaFes
InsertScores
LogProb
Mea
MeaSsChar
MeaSsStr
MlTmDeltaFes
Num
NumOfThreads
OneVs1IlDeltaFes
OneVs2Il
OneVs2IlDeltaFes
PartFunc
PartFunc4dMat
PartFuncMat
PartFuncs
Pos
PosMapSets
PosMaps
PosPair
PosPairMat
PosPairMatSet
PosPairs
PosPairsWithPosPairs
PosQuadruple
PosQuadrupleMat
Poss
Prob
Prob1dMats
Prob4dMat
Prob4dMatsWithRnaIdPairs
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
TmpPartFuncSetMatsWithPosPairs
TwoVs2Il
TwoVs2IlDeltaFes