Modules§
- env
- Inspection and manipulation of the process’s environment.
Macros§
- array
- Create an
Arraywith one, two or three dimensions. - azip
- Array zip macro: lock step function application across several arrays and producers.
- env
- Inspects an environment variable at compile time.
- s
- Slice argument constructor.
Structs§
- Align
- Align
Scores - Align
Sums - Alignfold
Prob Mats - Alignfold
Prob Mats Avg - Alignfold
Scores - Alignfold
Sums - Array
Base - An n-dimensional array.
- Axis
- An axis index.
- BufReader
- The
BufReader<R>struct adds buffering to any reader. - BufWriter
- Wraps a writer and buffers its output.
- Dim
- Dimension description.
- Fasta
Record - File
- An object providing access to an open file on the filesystem.
- Fold
Score Sets - Fold
Scores - Fold
Sums - HAIRPIN_
SCORES_ SPECIAL - HashMap
- A hash map implemented with quadratic probing and SIMD lookup.
- HashSet
- A hash set implemented as a
HashMapwhere the value is(). - Loop
Sums - Match
Prob Mats - NewAxis
- Token to represent a new axis in a slice description.
- 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_
PROBS_ FILE - BASEPAIR_
PROBS_ FILE2 - 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 - CONTEXT_
INDEX_ BASEPAIR - CONTEXT_
INDEX_ BULGE - CONTEXT_
INDEX_ EXTERNAL - CONTEXT_
INDEX_ HAIRPIN - CONTEXT_
INDEX_ INTERIOR - CONTEXT_
INDEX_ MULTIBRANCH - CU
- C_LOWER
- C_UPPER
- DANGLING_
SCORES_ 3PRIME - DANGLING_
SCORES_ 5PRIME - DANGLING_
SCORES_ LEFT - DANGLING_
SCORES_ RIGHT - DEFAULT_
MIN_ BASEPAIR_ PROB - DEFAULT_
MIN_ MATCH_ PROB - 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_
INSERT_ SCORE - INIT_
MATCH_ SCORE - INIT_
MULTIBRANCH_ BASE - INSER
T2MATCH_ SCORE - INSERT_
EXTEND_ SCORE - INSERT_
SCORES - INSERT_
SWITCH_ SCORE - 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 - LOOPMATCH_
PROBS_ FILE - MATC
H2INSERT_ SCORE - MATC
H2MATCH_ SCORE - MATCH_
PROBS_ FILE - MATCH_
SCORES - 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_
CONTEXTS - NUM_
SPECIAL_ HAIRPINS - NUM_
TRANSITS - PAIRMATCH_
PROBS_ FILE - PROB_
BOUND_ LOWER - PROB_
BOUND_ UPPER - PSEUDO_
BASE - README_
CONTENTS - README_
FILE - 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
- UNPAIR_
PROBS_ FILE_ BULGE - UNPAIR_
PROBS_ FILE_ EXTERNAL - UNPAIR_
PROBS_ FILE_ HAIRPIN - UNPAIR_
PROBS_ FILE_ INTERIOR - UNPAIR_
PROBS_ FILE_ MULTIBRANCH - UU
- U_LOWER
- U_UPPER
Traits§
- AsArray
- Argument conversion into an array view
- 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. - Dimension
- Array shape and index trait.
- 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
- NdFloat
- Floating-point element types
f32andf64. - 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
Readtrait allows for reading bytes from a source. - Seek
- The
Seektrait provides a cursor which can be moved within a stream of bytes. - Send
- Types that can be transferred across thread boundaries.
- Shape
Builder - A trait for
ShapeandD where D: Dimensionthat allows customizing the memory layout (strides) of an array shape. - 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§
- Dim
- Create a new dimension value.
- Ix0
- Create a zero-dimensional index
- Ix1
- Create a one-dimensional index
- Ix2
- Create a two-dimensional index
- Ix3
- Create a three-dimensional index
- Ix4
- Create a four-dimensional index
- Ix5
- Create a five-dimensional index
- Ix6
- Create a six-dimensional index
- IxDyn
- Create a dynamic-dimensional index
- align_
char2base - arr0
- Create a zero-dimensional array with the element
x. - arr1
- Create a one-dimensional array with elements from
xs. - arr2
- Create a two-dimensional array with elements from
xs. - aview0
- Create a zero-dimensional array view borrowing
x. - aview1
- Create a one-dimensional array view with elements borrowing
xs. - aview2
- Create a two-dimensional array view with elements borrowing
xs. - aview_
mut1 - Create a one-dimensional read-write array view with elements borrowing
xs. - bytes2seq
- char2base
- consprob
- consprob_
core - create_
dir - Creates a new, empty directory at the provided path
- durbin_
algo - expf
- filter_
basepair_ probs - filter_
fold_ scores - filter_
match_ probs - 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_
2loop_ sums - get_
abs_ diff - get_
accessible_ score - get_
align_ sums - get_
alignfold_ probs - get_
alignfold_ sums - get_
basepair_ probs - get_
basepair_ probs_ contra - get_
bulge_ score_ contra - get_
fold_ sums - get_
fold_ sums_ contra - get_
hairpin_ score - get_
hairpin_ score_ contra - get_
helix_ close_ score - get_
interior_ score_ contra - get_
junction_ score - get_
junction_ score_ single - get_
loop_ sums - get_
max_ basepair_ span - get_
multibranch_ close_ score - get_
sparse_ poss - get_
special_ hairpin_ score - get_
stack_ score_ contra - get_
terminal_ mismatch_ score - has_
canonical_ basepair - has_
valid_ sums - invert_
basepair - ln_
exp_ 1p - logsumexp
- matches_
augu - 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.
- pair_
probs2avg_ probs - 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
- write_
alignfold_ prob_ mats - write_
readme
Type Aliases§
- Alignfold
Probs Hashed Ids - ArcArray
- An array where the data has shared ownership and is copy on write.
- Arg
- Args
- Array
- An array that owns its data uniquely.
- Array0
- zero-dimensional array
- Array1
- one-dimensional array
- Array2
- two-dimensional array
- Array3
- three-dimensional array
- Array4
- four-dimensional array
- Array5
- five-dimensional array
- Array6
- six-dimensional array
- ArrayD
- dynamic-dimensional array
- Array
View - A read-only array view.
- Array
View0 - zero-dimensional array view
- Array
View1 - one-dimensional array view
- Array
View2 - two-dimensional array view
- Array
View3 - three-dimensional array view
- Array
View4 - four-dimensional array view
- Array
View5 - five-dimensional array view
- Array
View6 - six-dimensional array view
- Array
ViewD - dynamic-dimensional array view
- Array
View Mut - A read-write array view.
- Array
View Mut0 - zero-dimensional read-write array view
- Array
View Mut1 - one-dimensional read-write array view
- Array
View Mut2 - two-dimensional read-write array view
- Array
View Mut3 - three-dimensional read-write array view
- Array
View Mut4 - four-dimensional read-write array view
- Array
View Mut5 - five-dimensional read-write array view
- Array
View Mut6 - six-dimensional read-write array view
- Array
View MutD - dynamic-dimensional read-write array view
- Base
- Basepair
- Basepair
Scores - Bools
Hashed Poss - Bulge
Scores0x1 - Bulge
Scores Init - Bulge
Scores Len - Char
- Col
- Cols
- Context
Prof - Context
Prof SetPair - Context
Profs - CowArray
- An array with copy-on-write behavior.
- Dangling
Scores - FastaId
- Fasta
Records - Fold
Char - Fold
Score SetPair - FoldStr
- Hairpin
Scores Init - Hairpin
Scores Len - Hairpin
Scores Special - Helix
Close Scores - Inputs2loop
Sums Getter - Inputs
Alignfold Probs Getter - Inputs
Consprob Core - Inputs
Inside Sums Getter - Inputs
Loop Sums Getter - 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 - Ix0
- zero-dimensionial
- Ix1
- one-dimensional
- Ix2
- two-dimensional
- Ix3
- three-dimensional
- Ix4
- four-dimensional
- Ix5
- five-dimensional
- Ix6
- six-dimensional
- IxDyn
- dynamic-dimensional
- Loop
Sums Hashed Poss - Loop
Sums Mat - Match
Probs Hashed Ids - Match
Scores - NumThreads
- Outputs
Sparse Poss Getter - Param
Sets Hashed Ids - Pos
- PosMap
Sets - PosMaps
- PosPair
- PosPair
Mat - PosPair
MatSet - PosPairs
- PosPairs
Hashed Poss - PosQuad
- PosQuad
Mat - PosQuads
Hashed Lens - Poss
- Prob
- Prob1d
Mats - ProbMat
- Prob
Mat4d - Prob
MatPair - Prob
MatSets Avg - Prob
Mats - Prob
Mats Hashed Ids - Probs
- Probs4d
Hashed Ids - RawArray
View - A read-only array view without a lifetime.
- RawArray
View Mut - A mutable array view without a lifetime.
- RnaId
- RnaId
Pair - Score
- Score
Mat - Score
Mat4d - Score
Pair - Seq
- SeqId
- SeqIds
- SeqPair
- SeqSlice
- SeqSlices
- Sparse
PosSets - Sparse
Poss - Sparse
Prob Mat - Sparse
Prob MatPair - Sparse
Probs Hashed Ids - Sparse
Score Mat - Sparse
SumMat - Stack
Scores - Sum
- Sum4d
Mat - SumMat
- SumMat4d
- Sums
- Terminal
Mismatch Scores