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Removed linear phylo2vec function. Streamlined tests and gave better …
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@jhellewell14
jhellewell14 committed May 1, 2024
1 parent 028f9ad commit a385523
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Showing 2 changed files with 22 additions and 108 deletions.
35 changes: 0 additions & 35 deletions src/build_tree.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -213,38 +213,3 @@ pub fn random_vector(k: usize) -> Vec<usize> {
.map(|(i, _el)| if i > 0 { rng.gen_range(0..((2 * i) - 1)) } else { 0 })
.collect()
}

pub fn phylo2vec_lin(v: Vec<usize>, permute: bool) -> Tree {
let mut tree = Tree::new(&v);
let mut sub_vec = tree.tree_vec.clone();
sub_vec.remove(0);
let k = sub_vec.len();
let mut M = Array2::<usize>::zeros((k, 3));
let mut labels_rowk: Vec<usize> = (0..=k).collect();
let mut rmk = k;

for i in 0..k {
let n = k - i - 1;
let m = sub_vec[n];

M[[i, 0]] = labels_rowk[m];
M[[i, 1]] = labels_rowk[n + 1];

rmk += 1;
labels_rowk[m] = rmk;
M[[i, 2]] = labels_rowk[m];
}

// Build tree
tree.add(M[[k - 1, 2]], None);

for i in (0..k).rev() {
tree.add(M[[i, 0]], Some(M[[i, 2]]));
tree.add(M[[i, 1]], Some(M[[i, 2]]));
}

// Does this still need to happen?
tree.max_depth = tree.max_treedepth();

tree
}
95 changes: 22 additions & 73 deletions src/tests.rs
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Original file line number Diff line number Diff line change
@@ -1,14 +1,13 @@
#[cfg(test)]
mod tests {
use crate::mutation::Mutation;
use crate::build_tree::phylo2vec_lin;
use crate::build_tree::vector_to_tree;
use crate::tree::Tree;
use crate::build_tree::newick_to_vector;
use crate::random_vector;

#[test]
fn treemake_quad() {
fn check_tree_build_manual() {
// I check that built trees have the correct parent by comparing to known parent values
let mut tree = vector_to_tree(&vec![0, 0, 0, 0]);

assert_eq!(tree.get_node(0).unwrap().parent, Some(4));
Expand Down Expand Up @@ -81,87 +80,35 @@ mod tests {
}

#[test]
fn phylo2vec_lin_same_as_vector_to_tree() {
fn update_tree() {
let mut tree_1 = vector_to_tree(&vec![0, 0, 1, 0]);

let vecs: Vec<Vec<usize>> = vec![vec![0, 0, 0, 0], vec![0, 0, 1, 0], vec![0, 0, 1, 2], vec![0, 0, 1, 1]];
let mut tree_q: Tree;
let mut tree_l: Tree;

for vec in vecs {
let v = vec.clone();
tree_q = vector_to_tree(&v);
tree_l = phylo2vec_lin(vec, false);
let tree_2 = vector_to_tree(&vec);
tree_1.update(&vec);

for i in 0..=6 {
for i in 0..=tree_1.tree_vec.len() {
assert_eq!(
tree_l.get_node(i).unwrap().parent,
tree_q.get_node(i).unwrap().parent);
tree_1.get_node(i).unwrap().parent,
tree_2.get_node(i).unwrap().parent);
assert_eq!(
tree_l.get_node(i).unwrap().index,
tree_q.get_node(i).unwrap().index
);
}
}

}

// #[test]
// fn update_tree_check() {
// let mut tree_q = vector_to_tree(vec![0, 1, 0]);
// let mut tree_l = phylo2vec_lin(vec![0, 0, 0], false);

// let vecs: Vec<Vec<usize>> = vec![vec![0, 0, 0], vec![0, 1, 0], vec![0, 1, 2], vec![0, 1, 1]];

// for vec in vecs {
// let v = vec.clone();
// tree_q = vector_to_tree(v);
// tree_l.update_quad(vec);

// for i in 0..=6 {
// assert_eq!(
// tree_l.get_node(i).unwrap().parent,
// tree_q.get_node(i).unwrap().parent);
// assert_eq!(
// tree_l.get_node(i).unwrap().index,
// tree_q.get_node(i).unwrap().index
// );
// }
// }

// }

#[test]
fn update_tree_quad_check() {
let mut tree_q = vector_to_tree(&vec![0, 0, 1, 0]);
let mut tree_l = phylo2vec_lin(vec![0, 0, 0, 0], false);

let vecs: Vec<Vec<usize>> = vec![vec![0, 0, 0, 0], vec![0, 0, 1, 0], vec![0, 0, 1, 2], vec![0, 0, 1, 1]];

for vec in vecs {
let v = vec.clone();
tree_q = vector_to_tree(&v);
tree_l.update(&vec);

for i in 0..=6 {
assert_eq!(
tree_l.get_node(i).unwrap().parent,
tree_q.get_node(i).unwrap().parent);
assert_eq!(
tree_l.get_node(i).unwrap().index,
tree_q.get_node(i).unwrap().index
tree_1.get_node(i).unwrap().index,
tree_2.get_node(i).unwrap().index
);
}
}

}

#[test]
fn likelihood_internal_consistency() {
fn likelihood_internal_consistency_check() {
let q: na::Matrix4<f64> = na::Matrix4::new(
-3.0, 1.0, 1.0, 1.0, 1.0, -3.0, 1.0, 1.0, 1.0, 1.0, -3.0, 1.0, 1.0, 1.0, 1.0, -3.0,
);

let mut tr = phylo2vec_lin(vec![0, 0, 0, 0], false);
let mut tr = vector_to_tree(&vec![0, 0, 0, 0]);

let genetic_data = vec![
vec![
Expand Down Expand Up @@ -212,32 +159,32 @@ mod tests {
}

#[test]
fn newick_test () {
let mut tr = vector_to_tree(&vec![0, 0, 0, 0]);
fn manual_parent_check () {
let tr = vector_to_tree(&vec![0, 0, 0, 0]);

// Newick string for this tree is (1,(2,(3,0)4)5)6;
// This should be the tree topology according to the ape package in R
assert_eq!(tr.get_node(4).unwrap().children, (Some(0), Some(3)));
assert_eq!(tr.get_node(5).unwrap().children, (Some(4), Some(2)));
assert_eq!(tr.get_node(6).unwrap().children, (Some(5), Some(1)));

let mut tr = vector_to_tree(&vec![0, 0, 0, 1]);
let tr = vector_to_tree(&vec![0, 0, 0, 1]);

// Newick string for this tree is ((3,1)4,(2,0)5)6;
// This should be the tree topology according to the ape package in R
assert_eq!(tr.get_node(4).unwrap().children, (Some(1), Some(3)));
assert_eq!(tr.get_node(5).unwrap().children, (Some(0), Some(2)));
assert_eq!(tr.get_node(6).unwrap().children, (Some(5), Some(4)));

let mut tr = vector_to_tree(&vec![0, 0, 1, 1]);
let tr = vector_to_tree(&vec![0, 0, 1, 1]);

// Newick string for this tree is ((2,(3,1)4)5,0)6;
// This should be the tree topology according to the ape package in R
assert_eq!(tr.get_node(4).unwrap().children, (Some(1), Some(3)));
assert_eq!(tr.get_node(5).unwrap().children, (Some(4), Some(2)));
assert_eq!(tr.get_node(6).unwrap().children, (Some(0), Some(5)));

let mut tr = vector_to_tree(&vec![0, 0, 1, 1, 3]);
let tr = vector_to_tree(&vec![0, 0, 1, 1, 3]);

// Newick string for this tree is ((2,((4,3)5,1)6)7,0)8;
// This should be the tree topology according to the ape package in R
Expand All @@ -252,11 +199,13 @@ mod tests {
}

#[test]
fn newick_conversion () {
let mut tr = vector_to_tree(&random_vector(27));
fn newick_vector_conversion_check () {
let v = random_vector(27);
let tr = vector_to_tree(&v);
let nw = tr.newick();
let n_leaves = tr.count_leaves();
let y = newick_to_vector(&nw, n_leaves);
assert_eq!(v, y);
let trstr = vector_to_tree(&y).newick();
assert_eq!(trstr, nw);
}
Expand Down

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