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Functions930 in github.com/RagnarGrootKoerkamp/astar-pairwise-aligner

⨍ Functions 930◇ Types & classes 197
↓ 191 callersMethodlen
(&self)
pa-base-algos/src/nw/front.rs:17
↓ 161 callersMethoditer
Iterates over all matches sorted by `LexPos(start)`.
pa-heuristic/src/prune.rs:208
↓ 108 callersMethodmap
Apply a generic function F to the instantiated heuristic.
pa-heuristic/src/cli.rs:167
↓ 104 callersMethodclone
(&self)
pa-base-algos/src/nw/bitpacking.rs:100
↓ 70 callersMethodalign
(&self, a: Seq, b: Seq)
pa-base-algos/src/nw.rs:342
↓ 70 callersMethodwith_filename
(&self, filename: &str)
pa-vis/src/visualizer.rs:578
↓ 69 callersMethodappend
Append another cigar to this one.
pa-affine-types/src/cigar.rs:168
↓ 65 callersMethodlen
(&self)
pa-heuristic/src/contour/bruteforce.rs:53
↓ 65 callersMethodpush
(&mut self, value: C)
pa-heuristic/src/split_vec.rs:85
↓ 52 callersMethodlen
(&self)
astarpa2/src/ranges.rs:27
↓ 44 callersMethodvalue
(&self)
pa-bitpacking/src/encoding.rs:20
↓ 41 callersMethodclone
(&self)
pa-heuristic/src/heuristic/csh.rs:124
↓ 40 callersMethodpush
(&mut self, p: Pos)
pa-heuristic/src/contour/bruteforce.rs:17
↓ 40 callersMethodstart
()
pa-base-algos/src/dt.rs:216
↓ 37 callersMethodend
(self, accumulator: &mut f64)
pa-heuristic/src/util.rs:29
↓ 36 callersMethodinto
(self)
pa-base-algos/src/lib.rs:168
↓ 33 callersMethodlen
(&self)
pa-heuristic/src/split_vec.rs:73
↓ 28 callersFunctionband_doubling
()
astarpa2/src/tests.rs:69
↓ 26 callersMethodget
(&self, index: usize)
pa-heuristic/src/split_vec.rs:77
↓ 25 callersMethodrange
(&self)
pa-base-algos/src/front.rs:156
↓ 25 callersFunctiontest
(cm: AffineCost<N>)
pa-base-algos/src/tests.rs:167
↓ 25 callersMethodto_string
(&self)
pa-heuristic/src/cli.rs:119
↓ 24 callersFunctionastar
Align two sequences using the given heuristic and visualizer.
astarpa/src/astar.rs:35
↓ 23 callersMethodfilter
(&mut self)
pa-heuristic/src/matches.rs:87
↓ 23 callersMethodformat_avg
( &self, align: char, width: usize, title: &str, val: T, )
astarpa/src/stats.rs:114
↓ 23 callersMethodis_empty
(&self)
pa-base-algos/src/nw/front.rs:39
↓ 20 callersMethodh
(&self)
pa-base-algos/src/lib.rs:204
↓ 20 callersFunctionslice_to_simd
(slice: &[B; L * N])
pa-bitpacking/src/simd.rs:51
↓ 20 callersMethodv_range
v_range is the vertical exclusive range of height-W blocks to compute.
astarpa2/src/ranges.rs:94
↓ 18 callersMethodlayer
(&self, layer: LayerIdx)
pa-base-algos/src/front.rs:305
↓ 18 callersMethodmake_aligner_with_visualizer
Build a type-erased aligner object from parameters. FIXME: Add costmodel support.
pa-base-algos/src/nw.rs:123
↓ 18 callersMethodtransform
TODO: Transform maps from position domain into cost domain. Contours should take a template for the type of point they deal with.
pa-heuristic/src/heuristic/csh.rs:312
↓ 17 callersMethodlast
(&self)
pa-base-algos/src/front.rs:171
↓ 17 callersMethodnew_layer
(&mut self, h: Option<&H>)
pa-vis/src/visualizer.rs:247
↓ 16 callersMethodfinish
(mut self)
pa-heuristic/src/matches.rs:300
↓ 16 callersMethodpos
(&self)
pa-vis/src/visualizer.rs:76
↓ 16 callersMethodwrite_text
(&mut self, CPos(x, y): CPos, ha: HAlign, va: VAlign, text: &str, color: Color)
pa-vis/src/sdl.rs:133
↓ 15 callersMethodlast_block
(&self)
astarpa2/src/blocks.rs:547
↓ 15 callersMethodmax
(_: Self, _: Self)
pa-heuristic/src/heuristic.rs:72
↓ 14 callersMethodcell_begin
(&self, Pos(i, j): Pos)
pa-vis/src/visualizer.rs:720
↓ 14 callersMethoddraw_line
(&mut self, p: CPos, q: CPos, color: Color)
pa-vis/src/sdl.rs:128
↓ 14 callersMethodlast_front
(&self)
pa-base-algos/src/nw/affine.rs:228
↓ 13 callersFunctionfull
()
astarpa2/src/tests.rs:20
↓ 13 callersMethodnext
(&mut self)
pa-web/src/interaction.rs:59
↓ 12 callersMethodfill_rect
(&mut self, CPos(x, y): CPos, w: I, h: I, color: Color)
pa-vis/src/sdl.rs:100
↓ 12 callersMethodpush
(&mut self, QueueElement { f, data }: QueueElement<T>)
astarpa/src/bucket_queue.rs:28
↓ 12 callersMethodreverse
Reverse the cigar string.
pa-affine-types/src/cigar.rs:163
↓ 12 callersFunctionround
(j_range: JRange)
pa-base-algos/src/nw/bitpacking.rs:216
↓ 12 callersFunctionsimd_to_slice
(simd: &[S<L>; N])
pa-bitpacking/src/simd.rs:45
↓ 12 callersFunctiontest_aligner
Test the given aligner on a large set of random sequences: - length 1 to 1000 - error rate 0.01 to 1.0 - error models: uniform, noisy insert, noisy de
pa-test/src/lib.rs:108
↓ 11 callersMethodcolor
(&self, i: usize, cnt: usize)
pa-vis/src/visualizer.rs:328
↓ 11 callersMethodcontains
(&self, j: I)
pa-base-algos/src/nw/front.rs:48
↓ 11 callersMethoddown
(self, d: i32)
pa-vis/src/canvas.rs:53
↓ 11 callersMethodis_empty
(&self)
astarpa2/src/ranges.rs:50
↓ 11 callersFunctionnw
()
astarpa2/src/tests.rs:6
↓ 11 callersMethodpeek
(&mut self)
astarpa/src/bucket_queue.rs:38
↓ 10 callersMethodbuild
( &self, a: Seq<'a>, b: Seq<'a>, v: &'a RefCell<V::Instance>, )
pa-base-algos/src/dt.rs:118
↓ 10 callersMethodcell_center
(&self, Pos(i, j): Pos)
pa-vis/src/visualizer.rs:727
↓ 10 callersFunctioncompute_block
The main function to compute the right column of a block `i_range` x `v_range`. Uses `v_range` of `v` as input vertical differences on the left and up
astarpa2/src/blocks.rs:687
↓ 10 callersFunctionget
(id: &str)
pa-web/src/wasm.rs:14
↓ 10 callersMethodget
Get the value at the given index, by counting bits from the top or bottom. For `j` outside the range, `None` is returned.
astarpa2/src/block.rs:126
↓ 10 callersMethodh
(&self)
astarpa2/src/params.rs:287
↓ 10 callersMethodp
(&self)
pa-bitpacking/src/encoding.rs:44
↓ 10 callersMethodpush
(&mut self, other: Self)
astarpa2/src/ranges.rs:31
↓ 10 callersFunctionrun
()
pa-web/src/wasm.rs:38
↓ 9 callersMethodcall
(self, h: H)
pa-base-algos/src/nw.rs:136
↓ 9 callersFunctionfr_to_coords
(d: Fr, fr: Fr)
pa-base-algos/src/dt.rs:263
↓ 9 callersMethodj_range
The range of rows `j` to consider for columns `i_range.0 .. i_range.1`, when the cost is bounded by `f_bound`. For A*, this also returns the range of
pa-base-algos/src/nw.rs:438
↓ 9 callersMethodlayer_with_hint
(&self, pos: Pos, hint: Self::Hint)
pa-heuristic/src/heuristic/sh.rs:98
↓ 9 callersMethodm
(&self)
pa-bitpacking/src/encoding.rs:48
↓ 9 callersFunctionmutations
(k: I, kmer: usize, dels: bool, subs: bool, ins: bool, dedup: bool)
pa-heuristic/benches/matches_inexact.rs:29
↓ 9 callersMethodnext_front_j_range
(&self)
pa-base-algos/src/nw/bitpacking.rs:680
↓ 9 callersMethodpotential
(&self, Pos(i, _): Pos)
pa-heuristic/src/seeds.rs:79
↓ 9 callersMethodright
(self, d: i32)
pa-vis/src/canvas.rs:45
↓ 9 callersMethodscore
The layer of position i is the largest index that has a score at least i.
pa-heuristic/src/contour/sh_contours.rs:63
↓ 9 callersMethodsort
(&mut self)
pa-heuristic/src/matches.rs:253
↓ 9 callersFunctionto_qgram
()
pa-heuristic/src/matches/qgrams.rs:118
↓ 8 callersFunctioncompute_columns
( params: BitFrontsTag, a: &[PA], b: &[PB], i_range: IRange, v_range: std::ops::Range<usiz
pa-base-algos/src/nw/bitpacking.rs:1281
↓ 8 callersMethodcontains
(&self, q: Pos)
pa-heuristic/src/contour/bruteforce.rs:29
↓ 8 callersMethodfixed_j_range
Compute the j_range of `front` `i` with `f(u) <= f_max`. BUG: This should take into account potential non-consistency of `h`. In particular, with inex
pa-base-algos/src/nw.rs:615
↓ 8 callersFunctionfr_to_pos
(d: Fr, fr: Fr)
pa-base-algos/src/dt.rs:268
↓ 8 callersMethodget
(&self, index: I)
pa-base-algos/src/front.rs:353
↓ 8 callersMethodindex
Get the value at the given index, by counting bits from the top or bottom. For `j` larger than the range, vertical deltas of `1` are assumed.
pa-base-algos/src/nw/bitpacking.rs:152
↓ 8 callersMethodis_enabled
(&self)
pa-heuristic/src/prune.rs:18
↓ 8 callersMethodm
(&self)
pa-base-algos/src/front.rs:250
↓ 8 callersMethodnext_block_j_range
(&self)
astarpa2/src/blocks.rs:551
↓ 8 callersMethodprune
Returns number of matches pruned by start (succeeding this pos) and by end (preceding this pos).
pa-heuristic/src/prune.rs:213
↓ 8 callersFunctiontest_aligner_on_cost_model
Test that: - the aligner gives the same cost as NW, both for `cost` and `align` members. - the `Cigar` is valid and of the correct cost.
pa-base-algos/src/tests.rs:58
↓ 7 callersMethodbuild
(&'a self, a: Seq<'a>, b: Seq<'a>)
astarpa2/src/lib.rs:81
↓ 7 callersMethodbuild
(&self)
pa-bin/src/lib.rs:26
↓ 7 callersMethoddraw
( &mut self, is_last: bool, cigar: Option<&AffineCigar>, is_new_layer: bool,
pa-vis/src/visualizer.rs:877
↓ 7 callersMethodexpand
(&mut self, pos: Pos, g: Cost, f: Cost, h: Option<&H>)
pa-vis/src/visualizer.rs:150
↓ 7 callersMethodexpand_block_simple
(&mut self, pos: Pos, size: Pos)
pa-vis/src/lib.rs:105
↓ 7 callersMethodextend
Returns true when the end is reached.
pa-base-algos/src/dt.rs:363
↓ 7 callersMethodgap_cost
(&self, s: Pos, t: Pos)
pa-affine-types/src/cost_model.rs:453
↓ 7 callersMethodget_mut
(fronts: &mut Vec<FrontElem>, g: Cost, d: I)
pa-base-algos/src/nw/bitpacking.rs:1037
↓ 7 callersMethodh_with_hint
(&self, pos: Pos, hint: Self::Hint)
pa-heuristic/src/heuristic/sh.rs:102
↓ 7 callersMethodinto
(self)
astarpa2/src/params.rs:251
↓ 7 callersMethodinto_iter
(self)
pa-affine-types/src/cigar.rs:342
↓ 7 callersMethodis_active
(&self)
pa-heuristic/src/matches.rs:69
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