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

⨍ Functions 930◇ Types & classes 197
↓ 1 callersFunctionlog
(s: &str)
pa-web/src/html.rs:21
↓ 1 callersFunctionmake_aligner
Build an `AstarStatsAligner` instance from
astarpa/src/lib.rs:67
↓ 1 callersMethodmake_consistent
With local pruning, consistency can be lost. Here we ensure to add those required matches back in.
pa-heuristic/src/matches.rs:259
↓ 1 callersFunctionmake_path_heuristic_aligner
(vis: impl VisualizerT + 'static)
astarpa-next/src/bin/path_pruning.rs:25
↓ 1 callersMethodmake_visualizer
(&self)
pa-vis/src/cli.rs:88
↓ 1 callersMethodmatch_push
Extend the cigar by the given number of matches.
pa-affine-types/src/cigar.rs:149
↓ 1 callersFunctionmatch_to_arrow
(m: &Match)
pa-heuristic/src/heuristic/sh.rs:74
↓ 1 callersMethodmatches
(&self)
pa-heuristic/src/heuristic/sh.rs:162
↓ 1 callersMethodmax_score_for_match
(&self, start: Pos, end: Pos)
pa-heuristic/src/prune.rs:315
↓ 1 callersMethodmerge
(&mut self, other: Shift)
pa-heuristic/src/contour/hint_contours.rs:73
↓ 1 callersFunctionminimal_unique_matches
Determine seeds as minimal unique matches: For each seed, start from the end and keep prepending chars until the seed has at most `x` matches with cos
pa-heuristic/src/matches/suffix_array.rs:66
↓ 1 callersMethodn
(&self)
pa-heuristic/src/seeds.rs:73
↓ 1 callersMethodname
(&self)
pa-heuristic/src/heuristic/bruteforce_gcsh.rs:25
↓ 1 callersMethodnext_fixed_h
(&mut self, start: Pos, end: Pos)
pa-vis/src/visualizer.rs:240
↓ 1 callersMethodnum_dominant
(&self)
pa-heuristic/src/contour/bruteforce.rs:57
↓ 1 callersMethodone_mut
(&mut self)
pa-bitpacking/src/encoding.rs:51
↓ 1 callersMethodparent
Find the parent of `st`. NOTE: This assumes that `st.i` is in the last front, and that the front before is for `st.i-1`. `g`: distance to `st`. `block
pa-base-algos/src/nw/bitpacking.rs:915
↓ 1 callersMethodparent
(&self, st: State, _g: &mut Cost)
pa-base-algos/src/nw/affine.rs:165
↓ 1 callersMethodparent
Find the parent of `st`. NOTE: This assumes that `st.0` is in the last block, and that the block before is for `st.0-1`. `g`: distance to `st`. `block
astarpa2/src/blocks/trace.rs:145
↓ 1 callersMethodparent
(&self, q: Pos)
pa-heuristic/src/contour/bruteforce.rs:33
↓ 1 callersMethodparent_state
Trace to the direct parent of the current position. The actual sequences `a` and `b` are needed to do greedy matching in main layer states.
astarpa-next/src/compressed_history.rs:144
↓ 1 callersMethodpath_between_dc
Finds a path between two given states using divide & conquer. TODO: Improve this by skipping the overlap check when distances are already known.
pa-base-algos/src/dt.rs:783
↓ 1 callersFunctionpauseplay
()
pa-web/index.js:44
↓ 1 callersFunctionpos_to_fr
(p: Pos)
pa-base-algos/src/dt.rs:273
↓ 1 callersMethodpre_prune
(&mut self)
pa-heuristic/src/matches.rs:74
↓ 1 callersMethodpresent
(&mut self)
pa-vis/src/sdl.rs:167
↓ 1 callersMethodprune
(&mut self, pos: Pos, hint: Self::Hint)
pa-heuristic/src/heuristic/sh.rs:121
↓ 1 callersMethodpush
Add a new match. If enabled, filters for m.start <=_T end and/or local pruning. Returns whether the match was added.
pa-heuristic/src/matches.rs:205
↓ 1 callersMethodpush
(&mut self, p: Pos)
pa-heuristic/src/contour/rotate_to_front.rs:25
↓ 1 callersMethodreset
(&mut self)
astarpa2/src/blocks/trace.rs:438
↓ 1 callersFunctionresize_v_with_fixed
Resize the `v` array to the `new_j_range_rounded`. - Keep `new_front.fixed_j_range` intact. - Copy over the rest from the previous front.
pa-base-algos/src/nw/bitpacking.rs:1372
↓ 1 callersMethodsave
(&mut self, path: &Path)
pa-vis/src/sdl.rs:159
↓ 1 callersMethodsave_transparent
(&mut self, path: &Path, bg_color: Color)
pa-vis/src/sdl.rs:163
↓ 1 callersMethodscore
(&self, q: Pos)
pa-heuristic/src/contour/bruteforce.rs:100
↓ 1 callersMethodscore
(&self, q: Pos)
pa-heuristic/src/contour/rotate_to_front.rs:119
↓ 1 callersMethodscore_with_hint
(&self, q: Pos, hint: Self::Hint)
pa-heuristic/src/contour/hint_contours.rs:283
↓ 1 callersMethodseed_at_mut
(&mut self, Pos(i, _): Pos)
pa-heuristic/src/seeds.rs:101
↓ 1 callersFunctionseed_hashmap
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:77
↓ 1 callersFunctionseed_hashmap_qgrams
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:92
↓ 1 callersMethodseeds
(&self)
pa-heuristic/src/heuristic.rs:172
↓ 1 callersMethodseeds
(&self)
pa-heuristic/src/heuristic/sh.rs:166
↓ 1 callersFunctionshrink
(a: &[u8], b: &[u8], aligner: &mut dyn Aligner)
pa-bin/examples/fuzz.rs:70
↓ 1 callersFunctionslower
()
pa-web/index.js:40
↓ 1 callersFunctionsort_seeds
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:45
↓ 1 callersMethodsub_or
(&self, default: U, f: F)
pa-affine-types/src/cost_model.rs:324
↓ 1 callersFunctionsuffix_array_bio
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:53
↓ 1 callersFunctionsuffix_array_sort
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:49
↓ 1 callersFunctionsuffix_array_suffixtable
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:58
↓ 1 callersFunctionsuffix_hashmap
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:84
↓ 1 callersFunctionsuffix_hashmap_qgrams
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:99
↓ 1 callersFunctionsuffix_qgrams
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:73
↓ 1 callersFunctiontest_aligner_on_input
( a: Seq, b: Seq, aligner: &mut impl AffineAligner, cm: &AffineCost<N>, params: &str, )
pa-base-algos/src/tests.rs:11
↓ 1 callersFunctiontest_aligner_up_to
As test_aligner, but only test sequences with n <= max_n.
pa-test/src/lib.rs:113
↓ 1 callersFunctiontest_sequences
()
pa-test/src/lib.rs:7
↓ 1 callersMethodto_bruteforce_contours
(&self)
pa-heuristic/src/heuristic/csh.rs:81
↓ 1 callersMethodto_bruteforce_csh
(&self)
pa-heuristic/src/heuristic/csh.rs:72
↓ 1 callersMethodto_bruteforce_gcsh
(&self)
pa-heuristic/src/heuristic/csh.rs:63
↓ 1 callersMethodto_coords
(&self)
astarpa-next/src/compressed_history.rs:62
↓ 1 callersMethodto_pos
(&self)
pa-base-algos/src/dt.rs:240
↓ 1 callersFunctiontraceback
( states: &HashMap<DtPos, State<Hint>>, target: Pos, g: Cost, )
astarpa/src/astar_dt.rs:280
↓ 1 callersFunctiontraceback
TODO: Make this return Cigar instead.
astarpa/src/astar.rs:277
↓ 1 callersMethodvalues
(&self)
astarpa/src/stats.rs:124
↓ 1 callersMethodwait
(&mut self, timeout: Duration)
pa-vis/src/sdl.rs:171
Functiona_hashmap
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:230
Functiona_hashmap_qgrams
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:248
Functiona_sort_seeds
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:203
Methodadd
(self, rhs: CPos)
pa-vis/src/canvas.rs:22
Methodadd_meeting_point
Add the given position to the optimal path for divide-and-conquer methods, and clear existing explored/expanded states.
pa-vis/src/lib.rs:94
Methodadd_meeting_point
(&mut self, pos: Pos)
pa-vis/src/visualizer.rs:257
Methodaffine
(sub: Cost, open: Cost, extend: Cost)
pa-affine-types/src/cost_model.rs:127
Methodaffine_asymmetric
( sub: Cost, ins_open: Cost, ins_extend: Cost, del_open: Cost, del_ext
pa-affine-types/src/cost_model.rs:165
Functionaho_corasick
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_old.rs:62
Methodalign_affine
(&mut self, a: Seq, b: Seq)
pa-base-algos/src/dt.rs:1464
Methodalign_for_bounded_dist
Test whether the cost is at most s. Returns None if no path was found. It may happen that a path is found, but the cost is larger than s. In this case
astarpa2/src/domain.rs:356
Methodalign_with_stats
(&mut self, a: Seq, b: Seq)
astarpa2/src/lib.rs:199
Methodastar
(h: H)
pa-base-algos/src/lib.rs:200
Methodastar
(h: H)
astarpa2/src/params.rs:283
Functionastarpa
Align using default settings: - Gap-cost chaining seed heuristic (GCSH) - with diagonal transition (DT) - inexact matches (r=2) - seed length k=15 - p
astarpa/src/lib.rs:49
Functionastarpa2_full
Align two sequences using A*PA2-full.
astarpa2/src/lib.rs:44
Functionastarpa2_nw
Align two sequences using NW with bitpacking and SIMD.
astarpa2/src/lib.rs:32
Functionastarpa2_simple
Align two sequences using A*PA2-simple.
astarpa2/src/lib.rs:38
Functionb_hashmap
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:221
Functionb_hashmap_qgrams
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:239
Functionb_qgramindex
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:212
Functionb_suffix_array
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:178
Functionb_suffix_array_2
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:186
Functionb_suffix_array_sort
(bench: &mut Bencher)
pa-heuristic/benches/matches_old.rs:194
Methodband_doubling
()
pa-base-algos/src/lib.rs:233
Methodband_doubling
()
astarpa2/src/band.rs:48
Functionband_doubling_dijkstra
()
astarpa2/src/tests.rs:49
Functionband_doubling_edlib
()
astarpa2/src/tests.rs:59
Functionband_doubling_gapgap
()
astarpa2/src/tests.rs:25
Functionbase_100
(bench: &mut Bencher)
astarpa/benches/benchmark.rs:16
Functionbase_1000
(bench: &mut Bencher)
astarpa/benches/benchmark.rs:26
Functionbase_10000
(bench: &mut Bencher)
astarpa/benches/benchmark.rs:36
Functionbase_50000_similar
(bench: &mut Bencher)
astarpa/benches/benchmark.rs:46
Functionbench
(c: &mut Criterion)
pa-bitpacking/benches/nw/main.rs:138
Functionbench
(c: &mut Criterion)
pa-heuristic/benches/qgrams.rs:6
Functionbench
(c: &mut Criterion)
pa-heuristic/benches/matches.rs:9
Functionbench_scalar
( c: &mut BenchmarkGroup<WallTime>, pa: &[P::A], pb: &[P::B], d: Cost, prefix: &str, )
pa-bitpacking/benches/nw/main.rs:13
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