Modules§
- env
- Inspection and manipulation of the process’s environment.
Macros§
- env
- Inspects an environment variable at compile time.
Structs§
- Align
- BufReader
- The
BufReader<R>struct adds buffering to any reader. - BufWriter
- Wraps a writer and buffers its output.
- Fasta
Record - File
- An object providing access to an open file on the filesystem.
- Fold
Score Sets - HAIRPIN_
SCORES_ SPECIAL - HashMap
- A hash map implemented with quadratic probing and SIMD lookup.
- Options
- A description of the options that a program can handle.
- Path
- A slice of a path (akin to
str). - Pool
- A threadpool that acts as a handle to a number of threads spawned at construction.
- Reader
- A FASTA reader.
Constants§
- A
- AA
- AC
- AG
- AU
- A_LOWER
- A_UPPER
- BASEPAIR_
LEFT - BASEPAIR_
RIGHT - BASEPAIR_
SCORES - BULGE_
SCORES_ 0X1 - BULGE_
SCORES_ INIT - BULGE_
SCORES_ LEN - BULGE_
SCORES_ LEN_ ATLEAST - C
- CA
- CC
- CG
- COEFF_
HAIRPIN_ LEN_ EXTRAPOLATION - COEFF_
NUM_ BRANCHES - CU
- C_LOWER
- C_UPPER
- DANGLING_
SCORES_ 3PRIME - DANGLING_
SCORES_ 5PRIME - DANGLING_
SCORES_ LEFT - DANGLING_
SCORES_ RIGHT - EPSILON
- EXAMPLE_
FASTA_ FILE_ PATH - EXTERNAL_
SCORE_ BASEPAIR - EXTERNAL_
SCORE_ UNPAIR - G
- GA
- GAS_
CONST - GC
- GG
- GU
- G_LOWER
- G_UPPER
- HAIRPIN_
SCORES_ INIT - HAIRPIN_
SCORES_ LEN - HAIRPIN_
SCORES_ LEN_ ATLEAST - HELIX_
AUGU_ END_ PENALTY - HELIX_
CLOSE_ SCORES - INIT_
MULTIBRANCH_ BASE - INTERIOR_
SCORES_ 1X1 - INTERIOR_
SCORES_ 1X2 - INTERIOR_
SCORES_ 1X1_ CONTRA - INTERIOR_
SCORES_ 2X2 - INTERIOR_
SCORES_ ASYMMETRIC - INTERIOR_
SCORES_ ASYMMETRIC_ ATLEAST - INTERIOR_
SCORES_ EXPLICIT - INTERIOR_
SCORES_ INIT - INTERIOR_
SCORES_ LEN - INTERIOR_
SCORES_ LEN_ ATLEAST - INTERIOR_
SCORES_ SYMMETRIC - INTERIOR_
SCORES_ SYMMETRIC_ ATLEAST - INVERSE_
TEMPERATURE - K0
- KILO
- LOGSUMEXP_
THRESHOLD_ UPPER - MAX_
2LOOP_ LEN - MAX_
HAIRPIN_ LEN_ EXTRAPOLATION - MAX_
INTERIOR_ ASYMMETRIC - MAX_
INTERIOR_ EXPLICIT - MAX_
INTERIOR_ SYMMETRIC - MAX_
LOOP_ LEN - MIN_
HAIRPIN_ LEN - MIN_
HAIRPIN_ LEN_ EXTRAPOLATION - MIN_
SPAN_ HAIRPIN_ CLOSE - MULTIBRANCH_
SCORE_ BASE - MULTIBRANCH_
SCORE_ BASEPAIR - MULTIBRANCH_
SCORE_ UNPAIR - NEG_INF
- NEG_
INFINITY Deprecation planned - Negative infinity (−∞).
Use
f32::NEG_INFINITYinstead. - NINIO_
COEFF - NINIO_
MAX - NUM_
BASES - NUM_
SPECIAL_ HAIRPINS - NUM_
TRANSITS - PROB_
BOUND_ LOWER - PROB_
BOUND_ UPPER - PSEUDO_
BASE - STACK_
SCORES - STACK_
SCORES_ CONTRA - TEMPERATURE
- TERMINAL_
MISMATCH_ SCORES_ 1XMANY - TERMINAL_
MISMATCH_ SCORES_ 2X3 - TERMINAL_
MISMATCH_ SCORES_ CONTRA - TERMINAL_
MISMATCH_ SCORES_ HAIRPIN - TERMINAL_
MISMATCH_ SCORES_ INTERIOR - TERMINAL_
MISMATCH_ SCORES_ MULTIBRANCH - U
- UA
- UC
- UG
- UNPAIR
- UU
- U_LOWER
- U_UPPER
Traits§
- Bounded
- Numbers which have upper and lower bounds
- BufRead
- A
BufReadis a type ofReader which has an internal buffer, allowing it to perform extra ways of reading. - Display
- Format trait for an empty format,
{}. - From
Primitive - A generic trait for converting a number to a value.
- Hash
- A hashable type.
- Hash
Index - Integer
- One
- Defines a multiplicative identity element for
Self. - PrimInt
- Generic trait for primitive integers.
- Read
- The
Readtrait allows for reading bytes from a source. - Seek
- The
Seektrait provides a cursor which can be moved within a stream of bytes. - 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§
- align_
char2base - bytes2seq
- char2base
- 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_
2loop_ score - get_
2loop_ score_ contra - get_
abs_ diff - get_
accessible_ score - get_
bulge_ score_ contra - get_
hairpin_ score - get_
hairpin_ score_ contra - get_
helix_ close_ score - get_
interior_ score_ contra - get_
junction_ score - get_
junction_ score_ single - get_
multibranch_ close_ score - get_
special_ hairpin_ score - get_
stack_ score_ contra - get_
terminal_ mismatch_ score - has_
canonical_ basepair - invert_
basepair - ln_
exp_ 1p - logsumexp
- matches_
augu - max
- Compares and returns the maximum of two values.
- 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 - 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_
align_ clustal - read_
align_ fasta - read_
align_ stockholm - scale
Type Aliases§
- Args
- Base
- Basepair
- Basepair
Scores - Bulge
Scores0x1 - Bulge
Scores Init - Bulge
Scores Len - Char
- Col
- Cols
- Dangling
Scores - FastaId
- Fasta
Records - Fold
Char - FoldStr
- Hairpin
Scores Init - Hairpin
Scores Len - Hairpin
Scores Special - Helix
Close Scores - Insert
Scores - Interior1x2
- Interior2x2
- Interior
Scores1x1 - Interior
Scores1x2 - Interior
Scores1x1 Contra - Interior
Scores2x2 - Interior
Scores Asymmetric - Interior
Scores Bonus - Interior
Scores Explicit - Interior
Scores Init - Interior
Scores Len - Interior
Scores Symmetric - Match
Scores - NumThreads
- Pos
- PosMap
Sets - PosMaps
- PosPair
- PosPairs
- PosQuad
- Prob
- ProbMat
- Prob
Mats Hashed Ids - Probs
- RnaId
- RnaId
Pair - Score
- Seq
- SeqId
- SeqIds
- SeqPair
- SeqSlice
- Sparse
Prob Mat - Sparse
SumMat - Stack
Scores - Sum
- Sum4d
Mat - SumMat
- Sums
- Terminal
Mismatch Scores
Derive Macros§
- Hash
- Derive macro generating an impl of the trait
Hash.