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

⨍ Functions 930◇ Types & classes 197
↓ 3 callersFunctionlookup_am_in_b_hashmap_dedup
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_inexact.rs:169
↓ 3 callersMethodmake_aligner
Convert to a typed `AstarPa2` `Aligner` instance, using a visualizer is if the `pa-vis` feature is enabled.
astarpa2/src/params.rs:132
↓ 3 callersMethodmake_aligner_with_visualizer
Convert to a typed `AstarPa2` `Aligner` instance, with a given visualizer.
astarpa2/src/params.rs:180
↓ 3 callersMethodnext_front
Computes the next front (front `i`) from the current one.
pa-base-algos/src/nw/affine.rs:139
↓ 3 callersMethodparent
The id of the parent, or `None` for the root.
astarpa-next/src/compressed_history.rs:133
↓ 3 callersMethodpos
(&self)
pa-base-algos/src/dt.rs:254
↓ 3 callersMethodpotential_distance
(&self, from: Pos, to: Pos)
pa-heuristic/src/seeds.rs:84
↓ 3 callersMethodprint_stats
(&mut self)
pa-heuristic/src/contour/hint_contours.rs:640
↓ 3 callersMethodprocess_input_pairs
Call the given function for each pair in the input.
pa-bin/src/lib.rs:69
↓ 3 callersMethodprune_end
(&self)
pa-heuristic/src/prune.rs:89
↓ 3 callersMethodprune_start
(&self)
pa-heuristic/src/prune.rs:83
↓ 3 callersMethodpush_default_front
(&mut self, range: RangeInclusive<I>)
pa-base-algos/src/front.rs:119
↓ 3 callersMethodresize_with
(&mut self, new_len: usize, f: F)
pa-heuristic/src/split_vec.rs:90
↓ 3 callersMethodround_in
(&self)
astarpa2/src/ranges.rs:74
↓ 3 callersFunctionround_inward
(j_range: JRange)
pa-base-algos/src/nw/bitpacking.rs:220
↓ 3 callersMethodscore
(&self)
pa-heuristic/src/matches.rs:64
↓ 3 callersMethodscore
The max sum of arrows starting at pos
pa-heuristic/src/contour/hint_contours.rs:258
↓ 3 callersMethodstats
(&mut self)
pa-heuristic/src/heuristic/sh.rs:157
↓ 3 callersMethodto_path_with_costs
(&self, cm: AffineCost<N>)
pa-affine-types/src/cigar.rs:185
↓ 3 callersFunctionto_point
(CPos(x, y): CPos)
pa-vis/src/sdl.rs:34
↓ 3 callersMethodtransform
(&self, pos @ Pos(i, j): Pos)
pa-heuristic/src/seeds.rs:140
↓ 3 callersMethodvalue_of_prefix
(&self, j: I)
pa-bitpacking/src/encoding.rs:26
↓ 2 callersMethodalign_for_bounded_dist
( &mut self, f_max: Option<Cost>, )
pa-base-algos/src/dt.rs:916
↓ 2 callersFunctionastar_dt
Align two sequences using the given heuristic and visualizer, using the diagonal transition (DT) optimization.
astarpa/src/astar_dt.rs:34
↓ 2 callersFunctionastarpa_gcsh
( a: *const u8, a_len: usize, b: *const u8, b_len: usize, // Parameters r: usize,
astarpa-c/src/lib.rs:73
↓ 2 callersMethodband_doubling_params
( &self, start: crate::DoublingStart, a: &[u8], b: &[u8], nw: &NWInsta
pa-base-algos/src/nw.rs:275
↓ 2 callersMethodbuild
(&self, _a: Seq, _b: Seq)
pa-vis/src/lib.rs:121
↓ 2 callersMethodbuild
(&self, a: Seq<'a>, b: Seq<'a>)
pa-heuristic/src/heuristic/bruteforce_gcsh.rs:21
↓ 2 callersFunctionchar_bicounts
(a: Seq)
pa-heuristic/src/heuristic/distances.rs:250
↓ 2 callersFunctionchar_counts
(a: Seq)
pa-heuristic/src/heuristic/distances.rs:173
↓ 2 callersMethodcheck_consistency
Returns true when the match can be pruned without causing consistency problems.
pa-heuristic/src/prune.rs:328
↓ 2 callersMethodcheck_top_bot_val
Assert that the vertical difference between the top and bottom values is correct.
pa-base-algos/src/nw/bitpacking.rs:242
↓ 2 callersMethodclone_from
(&mut self, source: &Self)
pa-base-algos/src/nw/bitpacking.rs:113
↓ 2 callersMethodcompute_next_block
TODO: Allow updating/overwriting as well.
pa-base-algos/src/nw/affine.rs:241
↓ 2 callersMethodcompute_next_block
The main function to compute the next block. Contains the implementation for incremental doubling (which is tedious and needs to maintain a lot of in
astarpa2/src/blocks.rs:205
↓ 2 callersMethodcontains
(&self, q: Pos)
pa-heuristic/src/contour/rotate_to_front.rs:32
↓ 2 callersMethodcost
(&self, a: Seq, b: Seq)
pa-base-algos/src/nw.rs:338
↓ 2 callersMethodcost_for_bounded_dist
The cost-only version uses linear memory. In particular, the number of fronts is max(sub, ins, del)+1.
pa-base-algos/src/dt.rs:1197
↓ 2 callersMethoddebug
( &self, pos: Pos, v: Layer, arrows: &F, )
pa-heuristic/src/contour/hint_contours.rs:92
↓ 2 callersMethoddistance
(&self, from: Pos, to: Pos)
pa-heuristic/src/heuristic/csh.rs:177
↓ 2 callersFunctiondocument
()
pa-web/src/html.rs:25
↓ 2 callersMethoddraw_point
(&mut self, p: CPos, color: Color)
pa-vis/src/sdl.rs:123
↓ 2 callersMethoddt_back
(&self, &DtPos { diagonal, g }: &DtPos)
astarpa/src/alignment_graph.rs:29
↓ 2 callersMethodexpand_block
( &mut self, pos: Pos, size: Pos, g: Cost, f: Cost, h: Option<
pa-vis/src/visualizer.rs:274
↓ 2 callersMethodextend_cost
(&self, s: Pos, t: Pos)
pa-affine-types/src/cost_model.rs:490
↓ 2 callersFunctionextend_diagonal
Given two sequences, a diagonal and point on it, expand it to a FR point. Returns the number of characters matched. NOTE: `d` and `fr` must be in Forw
pa-base-algos/src/dt.rs:280
↓ 2 callersFunctionextend_right_simd_viz
#[cfg(feature = "example")]
pa-heuristic/src/matches/prepruning.rs:65
↓ 2 callersMethodf_call
(&mut self, pos: Pos, in_bounds: bool, fixed: bool)
pa-vis/src/visualizer.rs:196
↓ 2 callersMethodfill_block
Iterate over columns `i_range` for `j_range`, storing a front per column.
pa-base-algos/src/nw/bitpacking.rs:1170
↓ 2 callersMethodfill_rects
(&mut self, rects: &[(CPos, I, I)], color: Color)
pa-vis/src/sdl.rs:107
↓ 2 callersMethodfill_with_blocks
Store a single block for each column in `i_range`.
astarpa2/src/blocks.rs:573
↓ 2 callersFunctiongen_seqs
()
pa-test/src/lib.rs:24
↓ 2 callersMethodget
(blocks: &Vec<BlockElem>, g: Cost, d: I)
astarpa2/src/blocks/trace.rs:261
↓ 2 callersMethodget_diff
Get the difference from row `j` to `j+1`.
pa-base-algos/src/nw/bitpacking.rs:257
↓ 2 callersMethodget_diff
Get the difference from row `j` to `j+1`.
astarpa2/src/block.rs:134
↓ 2 callersFunctionget_matches
TODO: This should return &[I] instead.
pa-heuristic/src/matches/exact.rs:260
↓ 2 callersMethodh
(&self, _pos: Pos)
pa-heuristic/src/heuristic.rs:185
↓ 2 callersMethodh
(&self, pos: Pos)
pa-heuristic/src/heuristic/sh.rs:88
↓ 2 callersMethodh_mut
(&mut self)
pa-base-algos/src/lib.rs:210
↓ 2 callersMethodh_mut
(&mut self)
astarpa2/src/params.rs:293
↓ 2 callersFunctionhash_a_single
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:72
↓ 2 callersFunctionhash_b
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:28
↓ 2 callersFunctionhash_b_single
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:88
↓ 2 callersFunctionhash_to_single_vec
( qgrams_hashed: impl Iterator<Item = (i32, usize)> + Clone, qgrams_lookup: impl Iterator<Item = (i32,
pa-heuristic/src/matches/exact.rs:105
↓ 2 callersFunctionhash_to_smallvec
( qgrams_hashed: impl Iterator<Item = (i32, usize)>, qgrams_lookup: impl Iterator<Item = (i32, usize)>
pa-heuristic/src/matches/exact.rs:40
↓ 2 callersMethodindex_mut
(&mut self, _index: usize)
pa-base-algos/src/nw/affine.rs:35
↓ 2 callersMethodinitial_values
Return the start value and initial increment based on DoublingStart.
astarpa2/src/band.rs:13
↓ 2 callersMethodis_empty
(&self)
astarpa/src/bucket_queue.rs:82
↓ 2 callersMethodis_score_at_least
Returns None when false, or the first layer >= v that contains the query point.
pa-heuristic/src/contour/hint_contours.rs:125
↓ 2 callersMethodis_seed_end
(&self, pos: Pos)
pa-heuristic/src/seeds.rs:127
↓ 2 callersMethodis_seed_start
(&self, pos: Pos)
pa-heuristic/src/seeds.rs:122
↓ 2 callersMethoditerate_outgoing_edges
(&self, p: Pos, mut f: F)
astarpa/src/alignment_graph.rs:151
↓ 2 callersMethodj_range_rounded
(&self)
pa-base-algos/src/nw/bitpacking.rs:143
↓ 2 callersMethodkmin
(&self)
pa-heuristic/src/matches.rs:374
↓ 2 callersFunctionlookup_a_in_bm_hashmap
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_inexact.rs:209
↓ 2 callersFunctionlookup_b_in_am_hashmap
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_inexact.rs:90
↓ 2 callersFunctionlookup_bm_in_a_hashmap
(a: Seq, b: Seq, k: I)
pa-heuristic/benches/matches_inexact.rs:242
↓ 2 callersMethodm_mut
(&mut self)
pa-base-algos/src/front.rs:259
↓ 2 callersFunctionmake_aligner_with_visualizer
Build a type-erased aligner object from parameters.
astarpa/src/lib.rs:72
↓ 2 callersFunctionmaketimer
()
pa-web/index.js:29
↓ 2 callersMethodmatches_for_start
Iterates over all matches starting in the given `pos`.
pa-heuristic/src/prune.rs:203
↓ 2 callersMethodmax_del_for_cost
(&self, s: Cost)
pa-affine-types/src/cost_model.rs:395
↓ 2 callersMethodmax_ins_for_cost
(&self, s: Cost)
pa-affine-types/src/cost_model.rs:387
↓ 2 callersMethodmut_match_end
(&mut self, m: &Match)
pa-heuristic/src/prune.rs:309
↓ 2 callersMethodmut_match_start
(&mut self, m: &Match)
pa-heuristic/src/prune.rs:303
↓ 2 callersFunctionparent
(states: &HashMap<Pos, State<Hint>>, pos: Pos, g: Cost)
astarpa/src/astar.rs:263
↓ 2 callersMethodpop
(&mut self)
astarpa/src/bucket_queue.rs:60
↓ 2 callersFunctionpreserve_for_local_pruning
Returns `false` for matches that should be removed by local pruning. After covering `i <= p` additional seeds, the cost should be less than `(i+1)*r`.
pa-heuristic/src/matches/prepruning.rs:95
↓ 2 callersMethodprint_internal
(&self, newline: bool)
astarpa/src/stats.rs:168
↓ 2 callersMethodprune_filter
(&mut self, f: &mut F)
pa-heuristic/src/contour/bruteforce.rs:41
↓ 2 callersMethodprune_match
(&mut self, m: &Match)
pa-heuristic/src/prune.rs:294
↓ 2 callersMethodprune_with_hint
(&mut self, seeds: &Seeds, a: Arrow, hint: Hint)
pa-heuristic/src/contour/sh_contours.rs:118
↓ 2 callersMethodpush_op
(&mut self, op: AffineCigarOp)
pa-affine-types/src/cigar.rs:126
↓ 2 callersFunctionqgram_index
A qgram index first stores the count per kmer in a list of size 4^k. If 4^k is more than the size of the input (typically the case for us), this is sl
pa-heuristic/src/matches/exact.rs:195
↓ 2 callersMethodreset
Resize the current front for the given range, reusing the buffer sizes.
pa-base-algos/src/front.rs:222
↓ 2 callersMethodreset
(&mut self)
pa-base-algos/src/nw/bitpacking.rs:843
↓ 2 callersMethodreuse_next_block
(&mut self, i_range: IRange, j_range: JRange)
pa-base-algos/src/nw/bitpacking.rs:389
↓ 2 callersMethodreuse_next_block
The next block can be reused from an earlier iteration. Simply increment the last_block_idx, update the i_range, and check that the reused block indee
astarpa2/src/blocks.rs:190
↓ 2 callersMethodroot_potential
(&self)
pa-heuristic/src/heuristic/sh.rs:115
↓ 2 callersMethodrotate
(&mut self, range: RangeInclusive<I>)
pa-base-algos/src/front.rs:134
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