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

⨍ Functions 930◇ Types & classes 197
Functionbench_simd
( c: &mut BenchmarkGroup<WallTime>, pa: &[Bits], pb: &[Bits], d: Cost, prefix: &str, )
pa-bitpacking/benches/nw/main.rs:92
Methodboth
()
pa-heuristic/src/prune.rs:70
Methodbuild
(&self, a: Seq<'a>, b: Seq<'a>)
astarpa-next/src/path_pruning.rs:67
Methodbuild
(&self, a: Seq, b: Seq)
pa-vis/src/visualizer.rs:595
Methodbuild
(a: Seq, b: Seq)
pa-bitpacking/src/profile.rs:29
Methodbuild
(&self, a: Seq<'a>, b: Seq<'a>)
pa-heuristic/src/heuristic.rs:44
Methodbuild
(&self, a: Seq<'a>, b: Seq<'a>)
pa-heuristic/src/heuristic/sh.rs:25
Methodbuild
(&self, _a: Seq<'a>, _b: Seq<'a>)
pa-heuristic/src/heuristic/distances.rs:34
Methodbuild
(&self, a: Seq<'a>, b: Seq<'a>)
pa-heuristic/src/heuristic/wrappers.rs:27
Methodbuild_from_factory
(&self, _a: Seq, _b: Seq)
pa-vis/src/lib.rs:125
Methodbuild_from_factory
(&self, a: Seq, b: Seq)
pa-vis/src/visualizer.rs:603
Methodcall
(self, h: H)
astarpa-next/src/bin/path_pruning.rs:35
Methodcall
(self, h: H)
astarpa2/src/params.rs:192
Methodcall
(self, h: H)
astarpa/src/lib.rs:83
Methodchar_to_bits
(c: u8)
pa-heuristic/src/matches/qgrams.rs:30
Functioncli_test
()
astarpa-next/src/bin/path_pruning.rs:78
Functioncli_test
()
pa-bin/src/main.rs:42
Methodcm
(&self)
pa-base-algos/src/nw/bitpacking.rs:668
Methodcm
(&self)
pa-base-algos/src/nw/affine.rs:232
Functioncol
Compute a rectangle column by column.
pa-bitpacking/src/scalar.rs:9
Functioncol_local_h
Compute a rectangle column by column, assuming horizontal input deltas of 1. Slightly faster than `col_with_h` below because `h` can be local.
pa-bitpacking/src/scalar.rs:23
Functioncols_ld
Do N columns at a time.
pa-bitpacking/src/scalar.rs:153
Functioncols_ld_local_h
Do N columns at a time.
pa-bitpacking/src/scalar.rs:255
Functioncols_ru
Do N columns at a time.
pa-bitpacking/src/scalar.rs:102
Functioncols_ru_local_h
Do N columns at a time.
pa-bitpacking/src/scalar.rs:202
Functioncompute
Compute bottom and right output differences of a rectangular block of values. Inputs: `a`: horizontal sequence `b`: vertical sequence `h`: horizontal
pa-bitpacking/src/simd.rs:85
Functioncompute
If `exact_end` is false, padding rows may be added at the end to speed things up. This means `h` will have a meaningless value at the end that does no
pa-bitpacking/src/simd/scatter_profile.rs:6
Functioncompute_block
(h0: &mut H, v: &mut V, ca: &P::A, cb: &P::B)
pa-bitpacking/src/myers.rs:26
Functioncompute_block_of_rows
( a: &[CC], cbs: &[[B; 4]; L * N], h: &mut [H], v: &mut [V; L * N], values: &mut [Vec<V>],
pa-bitpacking/src/simd/scatter_profile.rs:169
Methodcompute_next_block
( &mut self, i_range: IRange, mut j_range: JRange, viz: &mut impl VisualizerIn
pa-base-algos/src/nw/bitpacking.rs:400
Methodconsecutive
(self, other: Self)
astarpa2/src/ranges.rs:44
Methodcontains_equal
(&self, q: Pos)
pa-heuristic/src/contour/rotate_to_front.rs:28
Methodcontains_range
(&self, other: Self)
astarpa2/src/ranges.rs:62
Methodcost
(&mut self, a: Seq, b: Seq)
pa-base-algos/src/dt.rs:1393
Methodcost
(&self, a: Seq, b: Seq)
astarpa2/src/lib.rs:171
Methodcost_for_bounded_dist
(&self, a: Seq, b: Seq, f_max: Cost)
pa-base-algos/src/nw.rs:347
Methodcost_for_bounded_dist
(&self, a: Seq, b: Seq, f_max: Cost)
astarpa2/src/lib.rs:180
Methodcount_match
(&self, Pos(i, j): Pos)
astarpa/src/alignment_graph.rs:140
Functioncsh_dt_inconsistent_greedy
()
astarpa/src/tests.rs:156
Methoddefault
()
pa-base-algos/src/nw.rs:40
Methoddefault
()
pa-base-algos/src/lib.rs:162
Methoddefault
()
pa-base-algos/src/front.rs:185
Methoddefault
()
pa-base-algos/src/nw/bitpacking.rs:40
Methoddefault
()
pa-base-algos/src/nw/affine.rs:52
Methoddefault
()
astarpa2/src/params.rs:245
Methoddefault
()
astarpa2/src/band.rs:57
Methoddefault
()
astarpa2/src/blocks.rs:63
Methoddefault
()
astarpa2/src/block.rs:34
Methoddefault
()
astarpa2/src/blocks/trace.rs:429
Methoddefault
()
pa-web/src/interaction.rs:24
Methoddefault
()
pa-vis/src/visualizer.rs:586
Methoddefault
()
pa-heuristic/src/prune.rs:46
Methoddefault
()
pa-heuristic/src/matches.rs:426
Methoddefault
()
pa-heuristic/src/cli.rs:101
Methoddefault
()
pa-heuristic/src/contour/hint_contours.rs:58
Methoddefault
()
astarpa/src/astar_dt.rs:19
Methoddefault
()
astarpa/src/bucket_queue.rs:88
Methoddefault
()
astarpa/src/astar.rs:20
Functiondefault_local_prune
()
pa-heuristic/src/cli.rs:39
Functiondefault_match_cost
()
pa-heuristic/src/cli.rs:33
Functiondefault_prune
()
pa-heuristic/src/cli.rs:42
Functiondefault_seed_length
()
pa-heuristic/src/cli.rs:36
Methoddel_or
(&self, default: U, f: F)
pa-affine-types/src/cost_model.rs:352
Methodderef
(&self)
astarpa2/src/ranges.rs:114
Functiondiag_ld
Diagonal by diagonal, where each diag goes left-down. Same as previous, but inner loop is reversed.
pa-bitpacking/src/scalar.rs:79
Functiondiag_ru
Diagonal by diagonal, where each diag goes right-up. diagonal number d: 1 2 3 .. n 2 3 4 .. n+1 3 4 5 .. n+2 ... m m+1 m+2 .. m+n-1
pa-bitpacking/src/scalar.rs:55
Methoddijkstra
()
pa-base-algos/src/lib.rs:188
Methoddijkstra
()
astarpa2/src/params.rs:271
Methoddisabled
()
pa-heuristic/src/prune.rs:58
Methoddist_gap
()
pa-base-algos/src/lib.rs:194
Methoddist_gap
()
astarpa2/src/params.rs:277
Methoddiv
(self, rhs: i32)
pa-vis/src/canvas.rs:36
Methoddouble_affine
( sub: Cost, open: Cost, extend: Cost, open2: Cost, extend2: Cost,
pa-affine-types/src/cost_model.rs:192
Methoddraw_diag_line
TODO: Does this work with html canvas? maybe there is a simpler API there.
pa-vis/src/visualizer.rs:790
Methoddraw_line
(&mut self, p: CPos, q: CPos, color: Color)
pa-web/src/html.rs:64
Methoddraw_point
(&mut self, p: CPos, color: Color)
pa-vis/src/canvas.rs:103
Methoddraw_rect
(&mut self, CPos(x, y): CPos, w: I, h: I, color: canvas::Color)
pa-web/src/html.rs:57
Methoddraw_thick_line_horizontal
( canvas: &mut CanvasBox, from: CPos, to: CPos, width: i32, margin: i3
pa-vis/src/visualizer.rs:837
Methoddrop
(&mut self)
pa-base-algos/src/nw.rs:408
Methoddrop
(&mut self)
pa-base-algos/src/nw/bitpacking.rs:304
Methoddrop
(&mut self)
pa-heuristic/src/heuristic/csh.rs:191
Functiondt_trace
()
pa-base-algos/src/nw.rs:1144
Functiondt_trace
()
astarpa2/src/tests.rs:92
Functiondt_trace_gapgap
()
astarpa2/src/tests.rs:35
Methodeach
(each: usize, cnt: &mut usize)
pa-heuristic/src/util.rs:16
Methodend
(&self)
pa-heuristic/src/prune.rs:30
Methodeq
(ca: &Self::A, cb: &Self::B)
pa-bitpacking/src/profile.rs:68
Methodeq_simd
(ca: (&S<L>, &S<L>), cb: (&S<L>, &S<L>))
pa-bitpacking/src/profile.rs:150
Methodequal_to_bruteforce_contours
(&self)
pa-heuristic/src/heuristic/csh.rs:104
Methodequal_to_bruteforce_csh
(&self)
pa-heuristic/src/heuristic/csh.rs:97
Methodequal_to_bruteforce_gcsh
(&self)
pa-heuristic/src/heuristic/csh.rs:90
Methodexact
(k: I)
pa-heuristic/src/matches.rs:409
Functionexact_hash
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:149
Functionexact_matches
Some options for finding all matches between a[i*k, (i+1)*k) and b: - qgramindex on b, query all seeds - qgramindex on a, query all b - suffixarray on
pa-heuristic/benches/matches_old.rs:44
Functionexact_noprune
()
astarpa/src/tests.rs:88
Functionexact_noprune_dt
()
astarpa/src/tests.rs:96
Functionexact_qgramindex
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:143
Methodexpand
( &mut self, _pos: Pos, _g: Cost, _f: Cost, _h: Option<&HI>, )
pa-vis/src/lib.rs:42
Methodexpand_block
( &mut self, _pos: Pos, _size: Pos, _g: Cost, _f: Cost, _h: Op
pa-vis/src/lib.rs:62
Methodexpand_block_trace
(&mut self, _pos: Pos, _size: Pos)
pa-vis/src/lib.rs:71
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