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

⨍ Functions 930◇ Types & classes 197
↓ 7 callersMethodk
(&self)
pa-heuristic/src/matches.rs:362
↓ 7 callersFunctionmake_label
(text: &str, val: impl ToString)
pa-vis/src/canvas.rs:12
↓ 7 callersMethodpush
Adds the given state with the given parent, and returns the id of the pushed state.
astarpa-next/src/compressed_history.rs:127
↓ 7 callersFunctiontest_aligner_on_input
(a: Seq, b: Seq, aligner: &mut impl Aligner, params: &str)
pa-test/src/lib.rs:65
↓ 6 callersMethodassert_rounded
(self)
astarpa2/src/ranges.rs:77
↓ 6 callersMethodback
(&self, &Pos(i, j): &Pos)
astarpa/src/alignment_graph.rs:19
↓ 6 callersMethodcost
(&self)
astarpa/src/alignment_graph.rs:48
↓ 6 callersMethoddistance
(&self, _from: Pos, _to: Pos)
pa-heuristic/src/heuristic/distances.rs:53
↓ 6 callersMethoddraw_pixel
(&self, canvas: &mut CanvasBox, pos: Pos, color: Color)
pa-vis/src/visualizer.rs:741
↓ 6 callersMethoddraw_rect
(&mut self, CPos(x, y): CPos, w: I, h: I, color: Color)
pa-vis/src/sdl.rs:116
↓ 6 callersMethodexplore
(&mut self, pos: Pos, g: Cost, f: Cost, h: Option<&H>)
pa-vis/src/visualizer.rs:139
↓ 6 callersMethodfull_range
(&self)
pa-base-algos/src/front.rs:162
↓ 6 callersMethodget
(&self, j: I)
pa-base-algos/src/nw/bitpacking.rs:207
↓ 6 callersFunctionget_matches
TODO: This should return &[I] instead.
pa-heuristic/src/matches/inexact.rs:98
↓ 6 callersMethodh_with_hint_timed
(&mut self, pos: Pos, hint: Self::Hint)
pa-heuristic/src/heuristic/sh.rs:108
↓ 6 callersFunctioninit_v_with_overlap
This prepares the `v` vector of vertical differences for a new block. It copies the overlap with the previous block, and fills the rest with +1.
astarpa2/src/blocks.rs:754
↓ 6 callersMethodis_insert
(&self)
pa-affine-types/src/cost_model.rs:20
↓ 6 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
astarpa2/src/domain.rs:77
↓ 6 callersMethodpop_last_block
Remove the last block and update the i_range.
astarpa2/src/blocks.rs:182
↓ 6 callersMethodpop_last_front
TODO: Maybe we should at some point drop the unused fronts?
pa-base-algos/src/nw/bitpacking.rs:383
↓ 6 callersFunctionrotate_left
(ph_simd: &mut [S<L>; N], mut carry: B)
pa-bitpacking/src/simd.rs:66
↓ 6 callersMethodround_out
(&self)
astarpa2/src/ranges.rs:71
↓ 6 callersMethodscore_with_hint
Hint is the total number of layers _before_ the position, since this will change less than the number of layers _after_ the position (where more pruni
pa-heuristic/src/contour/sh_contours.rs:79
↓ 6 callersMethodtrace
( &self, fronts: &Fronts<N>, from: DtState, mut to: DtState, direction
pa-base-algos/src/dt.rs:1369
↓ 6 callersMethodtransform_back
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:331
↓ 5 callersFunctionastarpa_free_cigar
(cigar: *mut u8)
astarpa-c/src/lib.rs:105
↓ 5 callersMethodb_qgrams
(&self, k: I)
pa-heuristic/src/matches/qgrams.rs:62
↓ 5 callersMethodcell_end
(&self, Pos(i, j): Pos)
pa-vis/src/visualizer.rs:734
↓ 5 callersMethodd_range
The range of diagonals to consider for the given cost `g`. Computes the minimum and maximum possible diagonal reachable for this `g`. TODO: Some of th
pa-base-algos/src/dt.rs:439
↓ 5 callersMethodexclusive_len
(&self)
pa-base-algos/src/nw/front.rs:45
↓ 5 callersMethodexclusive_len
(&self)
astarpa2/src/ranges.rs:56
↓ 5 callersMethodget
(&self, j: I)
pa-base-algos/src/nw/affine.rs:73
↓ 5 callersMethodh
(&self, pos: Pos)
pa-heuristic/src/heuristic/bruteforce_gcsh.rs:127
↓ 5 callersMethodinit_fronts
Returns None when the sequences are equal.
pa-base-algos/src/dt.rs:657
↓ 5 callersMethodinto_iter
( self, )
pa-heuristic/src/split_vec.rs:28
↓ 5 callersMethodis_seed_start_or_end
(&self, pos: Pos)
pa-heuristic/src/seeds.rs:132
↓ 5 callersMethoditerate_points
(&self, mut f: F)
pa-heuristic/src/contour/bruteforce.rs:68
↓ 5 callersFunctionkey_for_sized_qgram
FIXME: Just hardcode T to u64 here. For T=u32, k can be at most 15 (or 14 with r=2).
pa-heuristic/src/matches/inexact.rs:62
↓ 5 callersMethodlast_frame
( &mut self, cigar: Option<&AffineCigar>, parent: ParentFn<'_>, h: Option<&H>,
pa-vis/src/visualizer.rs:265
↓ 5 callersFunctionmutations
TODO: Do not generate insertions at the end. (Also do not generate similar sequences by inserting elsewhere.) TODO: Move to seeds.rs.
pa-heuristic/src/matches/inexact.rs:18
↓ 5 callersMethodpop
(&mut self, other: Self)
astarpa2/src/ranges.rs:36
↓ 5 callersMethodreset
(&mut self, len: usize)
pa-web/src/interaction.rs:43
↓ 5 callersMethodset_last_block_fixed_j_range
Update the fixed range, and make sure it only grows.
astarpa2/src/blocks.rs:556
↓ 5 callersMethodset_last_front_fixed_j_range
(&mut self, fixed_j_range: Option<JRange>)
pa-base-algos/src/nw/affine.rs:282
↓ 5 callersMethodvalue_of_suffix
(&self, j: I)
pa-bitpacking/src/encoding.rs:34
↓ 4 callersMethoda_qgrams
(&self, k: I)
pa-heuristic/src/matches/qgrams.rs:45
↓ 4 callersMethoda_qgrams_rev
(&self, k: I)
pa-heuristic/src/matches/qgrams.rs:54
↓ 4 callersMethodalign_for_bounded_dist
( &self, a: Seq, b: Seq, f_max: Cost, )
pa-base-algos/src/nw.rs:353
↓ 4 callersMethodalign_for_bounded_dist
(&self, a: Seq, b: Seq, f_max: Cost)
astarpa2/src/lib.rs:186
↓ 4 callersFunctionastar_with_vis
Helper function to modify the visualizer state.
astarpa/src/astar.rs:46
↓ 4 callersMethodb_qgrams_rev
(&self, k: I)
pa-heuristic/src/matches/qgrams.rs:81
↓ 4 callersFunctionchain_score
Best score of the given `pos` by iterating over all arrows starting there, or `None` otherwise.
pa-heuristic/src/contour/hint_contours.rs:162
↓ 4 callersMethodcheck_top_bot_val
Assert that the vertical difference between the top and bottom values is correct.
astarpa2/src/block.rs:148
↓ 4 callersMethodcost_or_align
(&self, a: Seq, b: Seq, trace: bool)
astarpa2/src/lib.rs:116
↓ 4 callersFunctionfind_matches
Find all matches between `a` and `b` with the given match configuration. If `transform_filter` is true, then only matches with T(m.start) <= target ar
pa-heuristic/src/matches.rs:17
↓ 4 callersFunctionfind_matches_qgram_hash_inexact
Build a hashset of the kmers in b, and query all mutations of seeds in a. Returns the set of matches sorted by `(LexPos(start), LexPos(end), cost)`.
pa-heuristic/src/matches/inexact.rs:253
↓ 4 callersMethodformat_flt
( &self, align: char, mut width: usize, title: &str, val: T, )
astarpa/src/stats.rs:92
↓ 4 callersFunctionhash_a
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:15
↓ 4 callersMethodindex
(&self, index: usize)
astarpa2/src/blocks.rs:140
↓ 4 callersFunctioninitialize_next_v
Initialize the input vertical deltas for the given new range, by copying the overlap from the previous front. Takes `v` as a mutable reference, so mem
pa-base-algos/src/nw/bitpacking.rs:1354
↓ 4 callersMethodis_active
(&self, frame: usize, layer: usize, is_last: bool, new_layer: bool)
pa-vis/src/visualizer.rs:412
↓ 4 callersMethodis_delete
(&self)
pa-affine-types/src/cost_model.rs:26
↓ 4 callersFunctionjscol
((r, g, b, _): Color)
pa-web/src/html.rs:14
↓ 4 callersMethodlayer_mut
(&mut self, layer: LayerIdx)
pa-base-algos/src/front.rs:313
↓ 4 callersMethodmake_aligner
Build an `AstarStatsAligner` instance from
pa-base-algos/src/nw.rs:86
↓ 4 callersMethodnew
TODO: This is only used in tests.
pa-base-algos/src/nw.rs:226
↓ 4 callersMethodnew
(&self, trace: bool, a: Seq<'a>, b: Seq<'a>)
astarpa2/src/blocks.rs:111
↓ 4 callersMethodnext_front
Computes layer g from the previous ones. `ca` is the `i`th character of sequence `a`. NOTE: `next` must already have the right range set. Returns `t
pa-base-algos/src/dt.rs:568
↓ 4 callersMethodparent
( &self, fronts: &Fronts<N>, st: DtState, direction: Direction, )
pa-base-algos/src/dt.rs:1240
↓ 4 callersMethodpm
(&self)
pa-bitpacking/src/encoding.rs:40
↓ 4 callersMethodprepend
(&self, range: &SaRange, c: Base)
pa-heuristic/src/matches/suffix_array.rs:41
↓ 4 callersMethodprev
(&mut self)
pa-web/src/interaction.rs:53
↓ 4 callersMethodprune_block
Prune all matches starting in the given block. Both ranges are *inclusive*. Note that if for some `i` the `j_range` is disjoint from the previous rang
pa-heuristic/src/prune.rs:245
↓ 4 callersMethodpush_elem
(&mut self, elem: AffineCigarElem)
pa-affine-types/src/cigar.rs:137
↓ 4 callersMethodremove
(&mut self, index: usize)
pa-heuristic/src/split_vec.rs:95
↓ 4 callersMethodtarget
(&self)
astarpa/src/alignment_graph.rs:124
↓ 4 callersMethodunion
(self, other: Self)
astarpa2/src/ranges.rs:65
↓ 4 callersMethodupdate_contours
Update contours from `lowest_modified_contour` to `highest_modified_contour`. Stop when the entire contour is *left of* `_pos.0`.
pa-heuristic/src/heuristic/csh.rs:497
↓ 3 callersMethodalign
(&self, a: Seq, b: Seq)
astarpa2/src/lib.rs:175
↓ 3 callersMethodalign_affine
(&mut self, a: Seq, b: Seq)
pa-base-algos/src/nw.rs:368
↓ 3 callersFunctionastarpa
( a: *const u8, a_len: usize, b: *const u8, b_len: usize, // output parameters cigar_p
astarpa-c/src/lib.rs:58
↓ 3 callersMethodbuild
(&'a self, a: Seq<'a>, b: Seq<'a>)
pa-base-algos/src/nw.rs:252
↓ 3 callersMethodcolor_f
(&self, f: f64)
pa-vis/src/visualizer.rs:339
↓ 3 callersFunctioncompute_block_simd
( hp0: &mut S<L>, hm0: &mut S<L>, vp: &mut S<L>, vm: &mut S<L>, eq: S<L>, )
pa-bitpacking/src/myers.rs:60
↓ 3 callersMethodcost_or_align
(&self, a: Seq, b: Seq, trace: bool)
pa-base-algos/src/nw.rs:300
↓ 3 callersMethoddistance
(&self, from: Pos, to: Pos)
pa-heuristic/src/heuristic/bruteforce_gcsh.rs:52
↓ 3 callersMethoddraw_pixels
(&self, canvas: &mut CanvasBox, pos: &Vec<Pos>, color: Color)
pa-vis/src/visualizer.rs:754
↓ 3 callersFunctionexponential_search
Find the cost using exponential search based on `f`. Tries values `offset + s0 * f^i`. Worst case growth factor analysis 1, g, g^2, ... worst-case
pa-base-algos/src/lib.rs:54
↓ 3 callersFunctionfind_matches_qgramindex
( a: Seq<'a>, b: Seq<'a>, config @ MatchConfig { length, r, .. }: MatchConfig, transform_filte
pa-heuristic/src/matches/exact.rs:248
↓ 3 callersMethodfixed_j_range
Compute the j_range of `block` `i` with `f(u) <= f_max`. BUG: This should take into account potential non-consistency of `h`. In particular, with inex
astarpa2/src/domain.rs:251
↓ 3 callersMethodh
(&self, pos: Pos)
pa-heuristic/src/heuristic/csh.rs:341
↓ 3 callersMethodindex
(&self, index: I)
pa-base-algos/src/front.rs:365
↓ 3 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.
astarpa2/src/block.rs:69
↓ 3 callersMethodindex
(g: Cost, d: I)
astarpa2/src/blocks/trace.rs:258
↓ 3 callersMethodindex
(&self, index: I)
pa-heuristic/src/matches.rs:107
↓ 3 callersMethodinit
(&mut self, initial_j_range: JRange)
pa-base-algos/src/nw/affine.rs:215
↓ 3 callersMethodinit
(&mut self, mut initial_j_range: JRange)
astarpa2/src/blocks.rs:146
↓ 3 callersMethodis_match
(&self, Pos(i, j): Pos)
astarpa/src/alignment_graph.rs:129
↓ 3 callersMethodlen
(&self)
pa-heuristic/src/contour/rotate_to_front.rs:66
↓ 3 callersFunctionlookup_am_in_b_hashmap
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_inexact.rs:129
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