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

⨍ Functions 930◇ Types & classes 197
↓ 2 callersMethodrotate_back
(&mut self)
pa-base-algos/src/front.rs:146
↓ 2 callersMethodsave_canvas
Saves canvas to bmp file
pa-vis/src/visualizer.rs:855
↓ 2 callersFunctionsave_transparent
(canvas: &SdlCanvas, path: &Path, bg_color: Option<Color>)
pa-vis/src/sdl.rs:58
↓ 2 callersMethodseed_at
(&self, Pos(i, _): Pos)
pa-heuristic/src/seeds.rs:92
↓ 2 callersMethodseed_ending_at
(&self, Pos(i, _): Pos)
pa-heuristic/src/seeds.rs:110
↓ 2 callersMethodshift
(&mut self, shift: Cost, below: O)
astarpa/src/bucket_queue.rs:181
↓ 2 callersMethodsize
(&self)
astarpa/src/bucket_queue.rs:78
↓ 2 callersMethodskip_prune_filter
Returns false when this match should be skipped (i.e. not pruned).
pa-heuristic/src/prune.rs:352
↓ 2 callersMethodto_base
(&self)
pa-affine-types/src/cigar.rs:43
↓ 2 callersMethodto_coords_u
(&self)
astarpa-next/src/compressed_history.rs:66
↓ 2 callersMethodto_f
(&self)
astarpa/src/alignment_graph.rs:56
↓ 2 callersMethodto_path
(&self)
pa-affine-types/src/cigar.rs:181
↓ 2 callersMethodto_pos
(self, fr: I)
astarpa/src/alignment_graph.rs:84
↓ 2 callersMethodtrace
Traceback the path from `from` to `to`. This requires `self.trace` to be `true`. In case of sparse blocks, this recomputes blocks when needed (when d
astarpa2/src/blocks/trace.rs:21
↓ 2 callersMethodupdate_layers
Update layers starting at layer `v`, continuing at least to layer `last_change`.
pa-heuristic/src/contour/hint_contours.rs:460
↓ 2 callersMethodverify
(&self, cm: &AffineCost<N>, a: Seq, b: Seq)
pa-affine-types/src/cigar.rs:265
↓ 2 callersMethodvisualize_last_frame
(&mut self, fronts: Fronts<N>, cigar: &AffineCigar)
pa-base-algos/src/dt.rs:1160
↓ 1 callersFunctionabs_diff
(i: I, j: I)
pa-heuristic/src/heuristic/distances.rs:155
↓ 1 callersMethodaffine
(&self, layer_idx: usize)
pa-base-algos/src/front.rs:268
↓ 1 callersMethodaffine_mut
(&mut self, layer_idx: usize)
pa-base-algos/src/front.rs:277
↓ 1 callersMethodalign
(&mut self, a: Seq, b: Seq)
pa-base-algos/src/dt.rs:1408
↓ 1 callersMethodalign
(&self, a: Seq, b: Seq)
astarpa/src/lib.rs:109
↓ 1 callersMethodalign_local_band_doubling
(&mut self)
pa-base-algos/src/dt.rs:972
↓ 1 callersFunctionastar_aligner
()
astarpa-next/src/bin/path_pruning.rs:21
↓ 1 callersFunctionastarpa2_full
( a: *const u8, a_len: usize, b: *const u8, b_len: usize, // output parameters cigar_p
astarpa-c/src/lib.rs:32
↓ 1 callersFunctionastarpa2_simple
( a: *const u8, a_len: usize, b: *const u8, b_len: usize, // output parameters cigar_p
astarpa-c/src/lib.rs:8
↓ 1 callersFunctionastarpa_gcsh
Align using GCSH with DT, with custom parameters. - r=1 instead of r=2 can be used when the error rate is low. - pruning by start *and* end (`Prune::B
astarpa/src/lib.rs:56
↓ 1 callersMethodbase
(&self)
pa-affine-types/src/cost_model.rs:14
↓ 1 callersMethodbinary_search_by
(&self, mut f: F)
pa-heuristic/src/split_vec.rs:107
↓ 1 callersMethodbuild_with_cost
(&self, a: Seq<'a>, b: Seq<'a>)
astarpa-next/src/path_pruning.rs:20
↓ 1 callersMethodbuild_with_filter
Matches can be filtered during construction of the contours. Used in PathHeuristic.
pa-heuristic/src/heuristic.rs:50
↓ 1 callersMethodbuild_with_filter
( &self, a: Seq<'a>, b: Seq<'a>, filter: Option<impl FnMut(&Match, Cost) -> bo
pa-heuristic/src/heuristic/csh.rs:138
↓ 1 callersMethodcheck_consistency
Check that each arrow is in the correct layer.
pa-heuristic/src/contour/hint_contours.rs:136
↓ 1 callersMethodclone
(&self)
pa-heuristic/src/contour/rotate_to_front.rs:15
↓ 1 callersFunctioncomplex_ab
(scale: usize)
pa-bin/examples/local-doubling.rs:15
↓ 1 callersFunctioncompute_block_of_rows
( a: &[Bits], ap0: &[B], ap1: &[B], cbs: &[Bits; L * N], h: &mut [H], v: &mut [V; L *
pa-bitpacking/src/simd.rs:215
↓ 1 callersMethodcontains
(&self, j: I)
astarpa2/src/ranges.rs:59
↓ 1 callersMethodcontains_equal
(&self, q: Pos)
pa-heuristic/src/contour/bruteforce.rs:25
↓ 1 callersFunctiondocument
()
pa-web/src/wasm.rs:9
↓ 1 callersMethoddone
(&mut self)
pa-web/src/interaction.rs:46
↓ 1 callersMethoddraw_box
(&self, canvas: &mut CanvasBox, mut start: Pos, mut size: Pos, color: Color)
pa-vis/src/visualizer.rs:768
↓ 1 callersMethoddraw_boxes
(&self, canvas: &mut CanvasBox, boxes: &Vec<(Pos, Pos)>, color: Color)
pa-vis/src/visualizer.rs:777
↓ 1 callersMethoddraw_dt
Draw DT states to the top-right 1/3rd of the canvas.
pa-vis/src/visualizer.rs:1608
↓ 1 callersMethoddraw_f
(&mut self, cigar: Option<&AffineCigar>, h: Option<&H>)
pa-vis/src/visualizer.rs:1798
↓ 1 callersFunctiondt_parent
(states: &HashMap<DtPos, State<Hint>>, dt_pos: DtPos)
astarpa/src/astar_dt.rs:266
↓ 1 callersMethoddt_trace_block
Trace a path backwards from `st` until `i=block_start`.
pa-base-algos/src/nw/bitpacking.rs:1007
↓ 1 callersMethoddt_trace_block
Trace a path backwards from `st` until `i=block_start`.
astarpa2/src/blocks/trace.rs:231
↓ 1 callersMethodexpand_block_trace
(&mut self, pos: Pos, size: Pos)
pa-vis/src/visualizer.rs:289
↓ 1 callersMethodexpand_blocks_simple
(&mut self, poss: [Pos; 4], sizes: [Pos; 4])
pa-vis/src/lib.rs:108
↓ 1 callersMethodexpand_trace
(&mut self, pos: Pos)
pa-vis/src/visualizer.rs:178
↓ 1 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
astarpa2/src/band.rs:100
↓ 1 callersFunctionextend_left
(i: &mut i32, i0: i32, j: &mut i32, a: &[u8], b: &[u8])
pa-base-algos/src/nw/bitpacking.rs:848
↓ 1 callersFunctionextend_left
(i: &mut i32, i0: i32, j: &mut i32, a: &[u8], b: &[u8])
astarpa2/src/blocks/trace.rs:443
↓ 1 callersFunctionextend_left_simd
(i: &mut i32, i0: i32, j: &mut i32, a: &[u8], b: &[u8])
pa-base-algos/src/nw/bitpacking.rs:858
↓ 1 callersFunctionextend_left_simd
(i: &mut i32, i0: i32, j: &mut i32, a: &[u8], b: &[u8])
astarpa2/src/blocks/trace.rs:453
↓ 1 callersFunctionextend_right
Returns true when `end_i` is reached.
pa-heuristic/src/matches/prepruning.rs:25
↓ 1 callersFunctionextend_right_simd
Same as `extend` but uses SIMD. TODO: We can also try a version that does 8 chars at a time using `u64`s.
pa-heuristic/src/matches/prepruning.rs:35
↓ 1 callersMethodextend_trace
(&mut self, pos: Pos)
pa-vis/src/visualizer.rs:184
↓ 1 callersFunctionfaster
()
pa-web/index.js:36
↓ 1 callersFunctionfill_block_of_rows
( a: &[Bits], ap0: &[B], ap1: &[B], cbs: &[Bits; L * N], h: &mut [H], v: &mut [V; L *
pa-bitpacking/src/simd.rs:434
↓ 1 callersFunctionfind_matches_qgramindex
( a: Seq<'a>, b: Seq<'a>, config @ MatchConfig { length, r, .. }: MatchConfig, transform_filte
pa-heuristic/src/matches/inexact.rs:86
↓ 1 callersMethodfixed_h
(&mut self, start: Pos, end: Pos)
pa-vis/src/visualizer.rs:222
↓ 1 callersMethodfixed_length_seeds
(&self, k: I, r: MatchCost)
pa-heuristic/src/matches/qgrams.rs:99
↓ 1 callersMethodfor_del
(&self, mut f: impl FnMut(Cost, Cost))
pa-affine-types/src/cost_model.rs:374
↓ 1 callersMethodfor_ins
(&self, mut f: impl FnMut(Cost, Cost))
pa-affine-types/src/cost_model.rs:361
↓ 1 callersMethodformat_raw
( &self, align: char, width: usize, title: &str, val: T, )
astarpa/src/stats.rs:78
↓ 1 callersMethodfronts_overlap
( &self, forward: &Fronts<N>, backward: &Fronts<N>, )
pa-base-algos/src/dt.rs:699
↓ 1 callersMethodfull_range
(&self)
pa-heuristic/src/matches/suffix_array.rs:38
↓ 1 callersFunctionfuzz
(aligner: &mut dyn Aligner)
pa-bin/examples/fuzz.rs:44
↓ 1 callersMethodget
Get the stored state for an id.
astarpa-next/src/compressed_history.rs:138
↓ 1 callersMethodget
(&self)
pa-web/src/interaction.rs:78
↓ 1 callersMethodget_mut
(blocks: &mut Vec<BlockElem>, g: Cost, d: I)
astarpa2/src/blocks/trace.rs:264
↓ 1 callersMethodh
(&self, pos: Pos)
pa-heuristic/src/heuristic/wrappers.rs:40
↓ 1 callersMethodh_call
(&mut self, pos: Pos)
pa-vis/src/visualizer.rs:190
↓ 1 callersMethodh_with_hint
(&self, pos: Pos, _hint: Self::Hint)
pa-heuristic/src/heuristic.rs:124
↓ 1 callersMethodh_with_hint
(&self, pos: Pos, hint: Self::Hint)
pa-heuristic/src/heuristic/csh.rs:367
↓ 1 callersMethodh_with_parent
(&self, pos: Pos)
pa-heuristic/src/heuristic/csh.rs:360
↓ 1 callersFunctionhash_a_qgram_index
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:160
↓ 1 callersFunctionhash_a_sliding_window
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:356
↓ 1 callersFunctionhash_b_qgram_index
Build a hashset of the seeds in a, and query all kmers in b.
pa-heuristic/src/matches/exact.rs:176
↓ 1 callersMethodidx_to_pos
(&self, idx: usize)
pa-bitpacking/src/search.rs:113
↓ 1 callersMethodindex
(&self, _index: usize)
pa-base-algos/src/nw/affine.rs:43
↓ 1 callersMethodindex_mut
(&mut self, index: I)
pa-base-algos/src/front.rs:389
↓ 1 callersMethodindex_mut
(&mut self, index: I)
pa-heuristic/src/matches.rs:113
↓ 1 callersFunctioninit_v_with_overlap_preserve_fixed
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. Unl
astarpa2/src/blocks.rs:775
↓ 1 callersMethodintersection
(self, other: Self)
astarpa2/src/ranges.rs:68
↓ 1 callersMethodinto
(self)
pa-affine-types/src/cigar.rs:84
↓ 1 callersMethodis_dominant
(&self, q: Pos)
pa-heuristic/src/contour/bruteforce.rs:37
↓ 1 callersMethodis_dominant
(&self, q: Pos)
pa-heuristic/src/contour/rotate_to_front.rs:50
↓ 1 callersMethodis_done
(&mut self)
pa-web/src/interaction.rs:49
↓ 1 callersMethodis_root
(&self)
pa-base-algos/src/dt.rs:246
↓ 1 callersMethodj_range
(&self)
pa-base-algos/src/nw/affine.rs:62
↓ 1 callersFunctionjsstr
(s: &str)
pa-web/src/wasm.rs:21
↓ 1 callersFunctionjsstr
(s: &str)
pa-web/src/html.rs:17
↓ 1 callersMethodkmax
(&self)
pa-heuristic/src/matches.rs:368
↓ 1 callersMethodlayer
The internal contour value at the given position, if available.
pa-heuristic/src/heuristic.rs:110
↓ 1 callersFunctionlinear_search
( s0: Cost, delta: Cost, mut f: impl FnMut(Cost) -> Option<(Cost, T)>, )
pa-base-algos/src/lib.rs:97
↓ 1 callersFunctionlinear_search
( s0: Cost, delta: Cost, mut f: impl FnMut(Cost) -> Option<(Cost, T)>, )
astarpa2/src/band.rs:143
↓ 1 callersMethodlocal_doubling
(&mut self)
pa-base-algos/src/nw.rs:825
↓ 1 callersMethodlocal_doubling
(&mut self)
astarpa2/src/domain/local_doubling.rs:4
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