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Antonio De Lucreziis 2 months ago
parent 37cfe2eb2c
commit 69b35e6a38
15 changed files with 464 additions and 61 deletions
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157
Cargo.lock generated
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@ -237,6 +237,7 @@ name = "asd"
version = "0.1.0" version = "0.1.0"
dependencies = [ dependencies = [
"argh", "argh",
"indicatif",
] ]
[[package]] [[package]]
@ -592,6 +593,14 @@ version = "3.16.0"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c" checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c"
[[package]]
name = "by-hand"
version = "0.1.0"
dependencies = [
"indicatif",
"macroquad",
]
[[package]] [[package]]
name = "bytemuck" name = "bytemuck"
version = "1.16.0" version = "1.16.0"
@ -808,6 +817,19 @@ dependencies = [
"serde_json", "serde_json",
] ]
[[package]]
name = "console"
version = "0.15.8"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb"
dependencies = [
"encode_unicode",
"lazy_static",
"libc",
"unicode-width",
"windows-sys 0.52.0",
]
[[package]] [[package]]
name = "core-foundation" name = "core-foundation"
version = "0.9.4" version = "0.9.4"
@ -1035,6 +1057,14 @@ version = "1.2.1"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "75b325c5dbd37f80359721ad39aca5a29fb04c89279657cffdda8736d0c0b9d2" checksum = "75b325c5dbd37f80359721ad39aca5a29fb04c89279657cffdda8736d0c0b9d2"
[[package]]
name = "dual-nums"
version = "0.1.0"
dependencies = [
"nalgebra 0.33.0",
"num-dual",
]
[[package]] [[package]]
name = "ecolor" name = "ecolor"
version = "0.27.2" version = "0.27.2"
@ -1182,6 +1212,12 @@ dependencies = [
"bytemuck", "bytemuck",
] ]
[[package]]
name = "encode_unicode"
version = "0.3.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f"
[[package]] [[package]]
name = "enumflags2" name = "enumflags2"
version = "0.7.9" version = "0.7.9"
@ -1329,7 +1365,7 @@ name = "fdg"
version = "1.0.0" version = "1.0.0"
source = "git+https://github.com/grantshandy/fdg#50755f1dea20249d753600e7e7e51ca33e87b5a1" source = "git+https://github.com/grantshandy/fdg#50755f1dea20249d753600e7e7e51ca33e87b5a1"
dependencies = [ dependencies = [
"nalgebra", "nalgebra 0.32.5",
"num-traits", "num-traits",
"petgraph", "petgraph",
"rand", "rand",
@ -1344,7 +1380,7 @@ dependencies = [
"asd", "asd",
"fdg", "fdg",
"macroquad", "macroquad",
"nalgebra", "nalgebra 0.32.5",
"num-traits", "num-traits",
"petgraph", "petgraph",
"petgraph-gen", "petgraph-gen",
@ -1561,6 +1597,12 @@ version = "0.21.3"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "518faa5064866338b013ff9b2350dc318e14cc4fcd6cb8206d7e7c9886c98815" checksum = "518faa5064866338b013ff9b2350dc318e14cc4fcd6cb8206d7e7c9886c98815"
[[package]]
name = "glam"
version = "0.27.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9e05e7e6723e3455f4818c7b26e855439f7546cf617ef669d1adedb8669e5cb9"
[[package]] [[package]]
name = "glob" name = "glob"
version = "0.3.1" version = "0.3.1"
@ -1702,8 +1744,9 @@ version = "0.1.0"
dependencies = [ dependencies = [
"asd", "asd",
"fdg", "fdg",
"indicatif",
"macroquad", "macroquad",
"nalgebra", "nalgebra 0.32.5",
"num-traits", "num-traits",
"petgraph", "petgraph",
"petgraph-gen", "petgraph-gen",
@ -1719,7 +1762,7 @@ dependencies = [
"cust", "cust",
"fdg", "fdg",
"macroquad", "macroquad",
"nalgebra", "nalgebra 0.32.5",
"num-traits", "num-traits",
"petgraph", "petgraph",
"petgraph-gen", "petgraph-gen",
@ -1841,6 +1884,19 @@ dependencies = [
"hashbrown 0.14.5", "hashbrown 0.14.5",
] ]
[[package]]
name = "indicatif"
version = "0.17.8"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "763a5a8f45087d6bcea4222e7b72c291a054edf80e4ef6efd2a4979878c7bea3"
dependencies = [
"console",
"instant",
"number_prefix",
"portable-atomic",
"unicode-width",
]
[[package]] [[package]]
name = "instant" name = "instant"
version = "0.1.13" version = "0.1.13"
@ -1924,6 +1980,12 @@ version = "3.1.0"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "e2db585e1d738fc771bf08a151420d3ed193d9d895a36df7f6f8a9456b911ddc" checksum = "e2db585e1d738fc771bf08a151420d3ed193d9d895a36df7f6f8a9456b911ddc"
[[package]]
name = "lazy_static"
version = "1.5.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
[[package]] [[package]]
name = "libc" name = "libc"
version = "0.2.155" version = "0.2.155"
@ -2003,13 +2065,12 @@ checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
[[package]] [[package]]
name = "macroquad" name = "macroquad"
version = "0.4.6" version = "0.4.13"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "6d983c03e9171099b2eb2067206c78cb37904ea071bb9ea4602c43ed45bb7097" checksum = "81fef16b2d4de22ac372b5d7d76273c0ead0a31f9de9bc649af8f816816db8a8"
dependencies = [ dependencies = [
"bumpalo",
"fontdue", "fontdue",
"glam 0.21.3", "glam 0.27.0",
"image", "image",
"macroquad_macro", "macroquad_macro",
"miniquad", "miniquad",
@ -2019,9 +2080,9 @@ dependencies = [
[[package]] [[package]]
name = "macroquad_macro" name = "macroquad_macro"
version = "0.1.7" version = "0.1.8"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "f5cecfede1e530599c8686f7f2d609489101d3d63741a6dc423afc997ce3fcc8" checksum = "64b1d96218903768c1ce078b657c0d5965465c95a60d2682fd97443c9d2483dd"
[[package]] [[package]]
name = "malloc_buf" name = "malloc_buf"
@ -2092,9 +2153,9 @@ dependencies = [
[[package]] [[package]]
name = "miniquad" name = "miniquad"
version = "0.4.1" version = "0.4.6"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "e17282b286b736c9ef6f79c630a5173669491a5e2f13a03fe556e59f7b577cd2" checksum = "2124e5e6bab86d96f263d78dc763c29e0da4c4f7ff0e1bb33f1d3905d1121262"
dependencies = [ dependencies = [
"libc", "libc",
"ndk-sys 0.2.2", "ndk-sys 0.2.2",
@ -2152,19 +2213,35 @@ dependencies = [
"num-traits", "num-traits",
"rand", "rand",
"rand_distr", "rand_distr",
"simba", "simba 0.8.1",
"typenum",
]
[[package]]
name = "nalgebra"
version = "0.33.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3c4b5f057b303842cf3262c27e465f4c303572e7f6b0648f60e16248ac3397f4"
dependencies = [
"approx",
"matrixmultiply",
"nalgebra-macros",
"num-complex",
"num-rational",
"num-traits",
"simba 0.9.0",
"typenum", "typenum",
] ]
[[package]] [[package]]
name = "nalgebra-macros" name = "nalgebra-macros"
version = "0.2.1" version = "0.2.2"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "91761aed67d03ad966ef783ae962ef9bbaca728d2dd7ceb7939ec110fffad998" checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
dependencies = [ dependencies = [
"proc-macro2", "proc-macro2",
"quote", "quote",
"syn 1.0.109", "syn 2.0.65",
] ]
[[package]] [[package]]
@ -2222,6 +2299,16 @@ version = "0.2.0"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "2bf50223579dc7cdcfb3bfcacf7069ff68243f8c363f62ffa99cf000a6b9c451" checksum = "2bf50223579dc7cdcfb3bfcacf7069ff68243f8c363f62ffa99cf000a6b9c451"
[[package]]
name = "num-bigint"
version = "0.4.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9"
dependencies = [
"num-integer",
"num-traits",
]
[[package]] [[package]]
name = "num-complex" name = "num-complex"
version = "0.4.6" version = "0.4.6"
@ -2231,6 +2318,18 @@ dependencies = [
"num-traits", "num-traits",
] ]
[[package]]
name = "num-dual"
version = "0.9.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d0ba622fc86ea74f6682d06848487fb7444d010726ec70addf16737c6b7f1c20"
dependencies = [
"approx",
"nalgebra 0.32.5",
"num-traits",
"simba 0.8.1",
]
[[package]] [[package]]
name = "num-integer" name = "num-integer"
version = "0.1.46" version = "0.1.46"
@ -2246,6 +2345,7 @@ version = "0.4.2"
source = "registry+https://github.com/rust-lang/crates.io-index" source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "f83d14da390562dca69fc84082e73e548e1ad308d24accdedd2720017cb37824" checksum = "f83d14da390562dca69fc84082e73e548e1ad308d24accdedd2720017cb37824"
dependencies = [ dependencies = [
"num-bigint",
"num-integer", "num-integer",
"num-traits", "num-traits",
] ]
@ -2281,6 +2381,12 @@ dependencies = [
"syn 2.0.65", "syn 2.0.65",
] ]
[[package]]
name = "number_prefix"
version = "0.4.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
[[package]] [[package]]
name = "objc" name = "objc"
version = "0.2.7" version = "0.2.7"
@ -2610,6 +2716,12 @@ dependencies = [
"windows-sys 0.52.0", "windows-sys 0.52.0",
] ]
[[package]]
name = "portable-atomic"
version = "1.9.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "cc9c68a3f6da06753e9335d63e27f6b9754dd1920d941135b7ea8224f141adb2"
[[package]] [[package]]
name = "ppv-lite86" name = "ppv-lite86"
version = "0.2.17" version = "0.2.17"
@ -2992,6 +3104,19 @@ dependencies = [
"wide", "wide",
] ]
[[package]]
name = "simba"
version = "0.9.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa"
dependencies = [
"approx",
"num-complex",
"num-traits",
"paste",
"wide",
]
[[package]] [[package]]
name = "simd-adler32" name = "simd-adler32"
version = "0.3.7" version = "0.3.7"

1
Cargo.toml
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@ -5,6 +5,7 @@ edition = "2021"
[dependencies] [dependencies]
argh = "0.1.12" argh = "0.1.12"
indicatif = "0.17.8"
[workspace] [workspace]
members = ["examples/*"] members = ["examples/*"]

8
examples/by-hand/Cargo.toml
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@ -0,0 +1,8 @@
[package]
name = "by-hand"
version = "0.1.0"
edition = "2021"
[dependencies]
indicatif = "0.17.8"
macroquad = "0.4.13"

33
examples/by-hand/src/main.rs
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@ -0,0 +1,33 @@
use std::time::Instant;
use macroquad::{prelude::*, rand, ui::root_ui};
#[macroquad::main("by-hand")]
async fn main() {
println!("Hello, world!");
loop {
let start_update = Instant::now();
// update();
let update_elapsed = start_update.elapsed();
// Render
let start_render = Instant::now();
clear_background(WHITE);
// draw();
let render_elapsed = start_render.elapsed();
root_ui().label(
None,
format!("update: {:?}, render: {:?}", update_elapsed, render_elapsed).as_str(),
);
next_frame().await
}
}

8
examples/dual-nums/Cargo.toml
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@ -0,0 +1,8 @@
[package]
name = "dual-nums"
version = "0.1.0"
edition = "2021"
[dependencies]
nalgebra = "0.33.0"
num-dual = "0.9.1"

15
examples/dual-nums/src/main.rs
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@ -0,0 +1,15 @@
// use nalgebra::SVector;
// use num_dual::*;
// fn bar(x: DualSVec64<2>, y: DualSVec64<2>) -> DualSVec64<2> {
// x * x + y * y
// }
fn main() {
// // let result = bar(
// // DualSVec64::new(3.0, Derivative::some(SVector::from_vec(vec![1.0, 0.0]))),
// // DualSVec64::new(4.0, Derivative::some(SVector::from_vec(vec![0.0, 1.0]))),
// // );
// // println!("{:?}", result);
}

41
examples/fdg-example/src/stress_majorization.rs
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@ -71,26 +71,27 @@ impl<F: Field + Measure + Sum, const D: usize> StressMajorization<F, D> {
&mut self, &mut self,
graph: &mut StableGraph<(N, Point<F, D>), E>, graph: &mut StableGraph<(N, Point<F, D>), E>,
) -> F { ) -> F {
graph // graph
.node_indices() // .node_indices()
.flat_map(|v| { // .flat_map(|v| {
graph.node_indices().skip(v.index() + 1).map(move |w| { // graph.node_indices().skip(v.index() + 1).map(move |w| {
let dist = nalgebra::distance( // let dist = nalgebra::distance(
&graph.node_weight(v).unwrap().1, // &graph.node_weight(v).unwrap().1,
&graph.node_weight(w).unwrap().1, // &graph.node_weight(w).unwrap().1,
); // );
if dist != F::zero() { // if dist != F::zero() {
let dij = self.shortest_path_matrix[&v][&w]; // let dij = self.shortest_path_matrix[&v][&w];
let sp_diff = self.shortest_path_matrix[&v][&w] - dist; // let sp_diff = self.shortest_path_matrix[&v][&w] - dist;
dij.simd_sqrt().abs() * sp_diff * sp_diff // dij.simd_sqrt().abs() * sp_diff * sp_diff
} else { // } else {
F::zero() // F::zero()
} // }
}) // })
}) // })
.sum() // .sum()
F::default()
} }
} }

1
examples/graphs-1/Cargo.toml
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@ -15,3 +15,4 @@ petgraph-gen = "0.1.3"
fdg = { git = "https://github.com/grantshandy/fdg" } fdg = { git = "https://github.com/grantshandy/fdg" }
asd = { path = "../../" } asd = { path = "../../" }
rayon = "1.10.0" rayon = "1.10.0"
indicatif = "0.17.8"

51
examples/graphs-1/src/gd.rs
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@ -0,0 +1,51 @@
use std::collections::HashMap;
struct Graph {
edges_from: Vec<u32>,
edges_to: Vec<u32>,
}
impl Graph {
fn new() -> Self {
Self {
edges_from: Vec::new(),
edges_to: Vec::new(),
}
}
fn new_with_capacity(capacity: usize) -> Self {
Self {
edges_from: Vec::with_capacity(capacity),
edges_to: Vec::with_capacity(capacity),
}
}
fn add_edge(&mut self, from: u32, to: u32) {
self.edges_from.push(from);
self.edges_to.push(to);
}
}
pub fn update(
graph: &Graph,
xs: &Vec<f32>,
ys: &Vec<f32>,
desired_distance_matrix: &HashMap<usize, HashMap<usize, f32>>,
) -> f32 {
desired_distance_matrix
.iter()
.flat_map(|(&i, targets)| {
targets
.iter()
.map(move |(&j, &target_distance)| (i, j, target_distance))
})
.map(|(i, j, target_distance)| {
let dx = xs[j] - xs[i];
let dy = ys[j] - ys[i];
let distance_sqrd = dx * dx + dy * dy;
let error = distance_sqrd - target_distance * target_distance;
error * error
})
.sum()
}

23
examples/graphs-1/src/main.rs
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@ -1,12 +1,21 @@
use std::{collections::HashMap, env, ops::AddAssign, time::Instant}; use std::{
collections::HashMap,
env,
io::{BufRead, BufReader},
ops::AddAssign,
time::Instant,
};
use asd::{gfa::Entry, parser}; use asd::{gfa::Entry, parser};
use indicatif::ProgressIterator;
use macroquad::{prelude::*, rand, ui::root_ui}; use macroquad::{prelude::*, rand, ui::root_ui};
use nalgebra::{Point2, SVector}; use nalgebra::{Point2, SVector};
use petgraph::{algo::dijkstra, graph::NodeIndex, stable_graph::StableGraph}; use petgraph::{algo::dijkstra, graph::NodeIndex, stable_graph::StableGraph};
use rayon::prelude::*; use rayon::prelude::*;
mod gd;
#[macroquad::main("graphs_1")] #[macroquad::main("graphs_1")]
async fn main() { async fn main() {
println!("Hello, world!"); println!("Hello, world!");
@ -127,8 +136,16 @@ fn load_graph() -> StableGraph<(String, Point2<f32>), ()> {
let mut graph = StableGraph::new(); let mut graph = StableGraph::new();
let file = std::fs::File::open(env::args().nth(1).expect("missing gfa file argument")).unwrap(); let filename = env::args().nth(1).expect("missing gfa file argument");
let entries = parser::parse_source(file).unwrap();
let file_lines_count = BufReader::new(std::fs::File::open(&filename).expect("file not found"))
.lines()
.progress_with(indicatif::ProgressBar::new_spinner())
.count() as u64;
let file = std::fs::File::open(filename).unwrap();
let entries = parser::parse_source(file, file_lines_count).unwrap();
let mut index_map = HashMap::new(); let mut index_map = HashMap::new();

32
src/graph.rs
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@ -6,6 +6,8 @@ use std::{
rc::Rc, rc::Rc,
}; };
use indicatif::{ProgressIterator, ProgressStyle};
#[derive(Debug)] #[derive(Debug)]
pub struct AdjacencyGraph<V> pub struct AdjacencyGraph<V>
where where
@ -152,7 +154,17 @@ where
let op = self.opposite(); let op = self.opposite();
for node in self.nodes.iter() { for node in self
.nodes
.iter()
.progress()
.with_style(
indicatif::ProgressStyle::default_bar()
.template("{prefix} {spinner} [{elapsed_precise}] [{wide_bar}] {pos}/{len}")
.unwrap(),
)
.with_prefix("computing connected components")
{
if visited.contains(node) { if visited.contains(node) {
continue; continue;
} }
@ -180,8 +192,6 @@ where
} }
} }
// println!("CC: {:?}", cc);
visited.extend(cc.iter().map(|x| x.to_owned())); visited.extend(cc.iter().map(|x| x.to_owned()));
result.push(cc.iter().map(|x| x.to_owned()).collect()); result.push(cc.iter().map(|x| x.to_owned()).collect());
} }
@ -197,26 +207,26 @@ where
continue; continue;
} }
println!("All CC: {:?}", cc); // println!("All CC: {:?}", cc);
let new_cc = Rc::new(RefCell::new(HashSet::new())); let new_cc = Rc::new(RefCell::new(HashSet::new()));
let mut stack: Vec<&V> = vec![node]; let mut stack: Vec<&V> = vec![node];
while let Some(node) = stack.pop() { while let Some(node) = stack.pop() {
println!("New CC: {:?}", new_cc.borrow()); // println!("New CC: {:?}", new_cc.borrow());
if cc.contains_key(&node) { if cc.contains_key(&node) {
// merge the two connected components and go to the next node // merge the two connected components and go to the next node
let old_cc: &Rc<RefCell<HashSet<V>>> = cc.get(&node).unwrap(); let old_cc: &Rc<RefCell<HashSet<V>>> = cc.get(&node).unwrap();
println!( // println!(
"Merging {:?} with {:?} due to link to {:?}", // "Merging {:?} with {:?} due to link to {:?}",
new_cc.borrow(), // new_cc.borrow(),
old_cc.borrow(), // old_cc.borrow(),
node // node
); // );
new_cc new_cc
.borrow_mut() .borrow_mut()

104
src/graph_2.rs
Unescape Escape View File

@ -0,0 +1,104 @@
use std::{collections::HashMap, io::Read};
use crate::{gfa::Entry, parser};
pub struct Graph {
nodes: HashMap<String, usize>,
edges_from: Vec<usize>,
edges_to: Vec<usize>,
}
#[derive(Debug)]
pub enum GraphError {
NodeNotFound(String),
}
impl Graph {
pub fn new() -> Self {
Self {
nodes: HashMap::new(),
edges_from: Vec::new(),
edges_to: Vec::new(),
}
}
pub fn add_node(&mut self, id: String) {
if self.nodes.contains_key(&id) {
return;
}
self.nodes.insert(id, self.nodes.len());
}
pub fn add_edge(&mut self, from_id: &String, to_id: &String) -> Result<(), GraphError> {
let from = self
.nodes
.get(from_id)
.ok_or(GraphError::NodeNotFound(from_id.clone()))?;
let to = self
.nodes
.get(to_id)
.ok_or(GraphError::NodeNotFound(to_id.clone()))?;
self.edges_from.push(*from);
self.edges_to.push(*to);
Ok(())
}
}
#[derive(Debug)]
pub enum LoadGraphError {
IoError(std::io::Error),
GraphError(GraphError),
}
pub fn load_graph<R: Read>(reader: R, len: u64) -> Result<Graph, LoadGraphError> {
println!("Loading graph");
let mut graph = Graph::new();
let entries = parser::parse_source(reader, len).map_err(|e| LoadGraphError::IoError(e))?;
let node_count = entries
.iter()
.filter_map(|entry| match entry {
Entry::Segment { id, .. } => Some(id),
_ => None,
})
.count();
println!("Node count: {}", node_count);
for entry in entries
.iter()
.filter(|entry| matches!(entry, Entry::Link { .. }))
{
if let Entry::Link {
from,
from_orient,
to,
to_orient,
} = entry
{
let node_from = format!("{}{}", from, from_orient);
let node_to = format!("{}{}", to, to_orient);
graph.add_node(node_from.clone());
graph.add_node(node_to.clone());
graph
.add_edge(&node_from, &node_to)
.expect("Error adding edge");
graph
.add_edge(&node_to, &node_from)
.expect("Error adding edge");
}
}
println!("Loading completed");
Ok(graph)
}

1
src/lib.rs
Unescape Escape View File

@ -1,3 +1,4 @@
pub mod gfa; pub mod gfa;
pub mod graph; pub mod graph;
pub mod graph_2;
pub mod parser; pub mod parser;

18
src/main.rs
Unescape Escape View File

@ -1,8 +1,12 @@
use std::collections::HashMap; use std::{
collections::HashMap,
io::{BufRead, BufReader},
};
use argh::FromArgs; use argh::FromArgs;
use gfa::{Entry, Orientation}; use gfa::{Entry, Orientation};
use graph::AdjacencyGraph; use graph::AdjacencyGraph;
use indicatif::ProgressIterator;
mod gfa; mod gfa;
mod graph; mod graph;
@ -35,15 +39,21 @@ fn main() -> std::io::Result<()> {
match opts.nested { match opts.nested {
MySubCommandEnum::Show(show) => { MySubCommandEnum::Show(show) => {
let file_lines_count = BufReader::new(std::fs::File::open(&show.input)?)
.lines()
.progress_with(indicatif::ProgressBar::new_spinner().with_message("counting lines"))
.count() as u64;
let file = std::fs::File::open(show.input)?; let file = std::fs::File::open(show.input)?;
let entries = parser::parse_source(file)?;
let entries = parser::parse_source(file, file_lines_count)?;
println!("Number of entries: {}", entries.len());
let mut sequence_map = HashMap::new(); let mut sequence_map = HashMap::new();
let mut graph: AdjacencyGraph<(String, Orientation)> = AdjacencyGraph::new(); let mut graph: AdjacencyGraph<(String, Orientation)> = AdjacencyGraph::new();
for entry in entries { for entry in entries {
println!("{:?}", entry);
match entry { match entry {
Entry::Segment { id, sequence } => { Entry::Segment { id, sequence } => {
sequence_map.insert(id.clone(), sequence); sequence_map.insert(id.clone(), sequence);

32
src/parser.rs
Unescape Escape View File

@ -1,8 +1,12 @@
use std::{ use std::{
io::{self, BufRead, BufReader, Read}, io::{self, BufRead, BufReader, Read},
str::FromStr, str::FromStr,
thread,
time::Duration,
}; };
use indicatif::ProgressIterator;
use crate::gfa::{Entry, Orientation}; use crate::gfa::{Entry, Orientation};
fn parse_orientation(s: &str) -> Orientation { fn parse_orientation(s: &str) -> Orientation {
@ -122,9 +126,20 @@ fn parse_walk(line: &str) -> Entry {
} }
} }
pub fn parse_source<R: Read>(reader: R) -> io::Result<Vec<Entry>> { pub fn parse_source<R: Read>(reader: R, line_count: u64) -> io::Result<Vec<Entry>> {
let mut entries = Vec::new(); let mut entries = Vec::new();
for line in BufReader::new(reader).lines() { let mut skipped = Vec::new();
for line in BufReader::new(reader)
.lines()
.progress_count(line_count)
.with_style(
indicatif::ProgressStyle::default_bar()
.template("{prefix} {spinner} [{elapsed_precise}] [{wide_bar}] {pos}/{len}")
.unwrap(),
)
.with_prefix("parsing source file")
{
let line = line?; let line = line?;
let line = line.trim(); let line = line.trim();
@ -132,22 +147,25 @@ pub fn parse_source<R: Read>(reader: R) -> io::Result<Vec<Entry>> {
continue; continue;
} }
// println!("Parsing: {}", line);
let first_char = line.chars().next().unwrap(); let first_char = line.chars().next().unwrap();
let entry = match first_char { let entry = match first_char {
'H' => parse_header(line), 'H' => parse_header(line),
'S' => parse_segment(line), 'S' => parse_segment(line),
'L' => parse_link(line), 'L' => parse_link(line),
'P' => parse_path(line), // 'P' => parse_path(line),
'W' => parse_walk(line), // 'W' => parse_walk(line),
_ => { _ => {
eprintln!("Unknown line type: {}", line); skipped.push(line.chars().next().expect("got empty line"));
continue; continue;
} }
}; };
entries.push(entry); entries.push(entry);
} }
for s in skipped {
eprintln!("skipped line type: {}", s);
}
Ok(entries) Ok(entries)
} }

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