From 4a8edd5864bbbc94b77821ca40edab20adcd2eeb Mon Sep 17 00:00:00 2001
From: Joel Hellewell <joel@ebi.ac.uk>
Date: Thu, 2 May 2024 09:41:58 +0100
Subject: [PATCH] Fix tests

---
 src/lib.rs         | 23 -----------------------
 src/likelihoods.rs |  8 ++++----
 2 files changed, 4 insertions(+), 27 deletions(-)

diff --git a/src/lib.rs b/src/lib.rs
index ea08062..aa91649 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -13,8 +13,6 @@ use crate::tree::Tree;
 extern crate nalgebra as na;
 pub mod cli;
 use crate::cli::*;
-use crate::mutation::{to_mutation, Mutation};
-use logaddexp::{LogAddExp, LogSumExp};
 
 pub fn main() {
     let args = cli_args(); 
@@ -29,27 +27,6 @@ pub fn main() {
            1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0, -1.0,
     );
 
-    let mut m1: Mutation = Mutation(0.25, 0.1, 0.5, 0.15);
-    let p1 = na::Matrix::exp(&(q * 1.0));
-
-    let mut outmut: Mutation = Mutation(0.0, 0.0, 0.0, 0.0);
-    println!("{:?}", m1);
-
-    for i in 0..=3 {
-        if let Some(mut val) = outmut.get_mut(i) {
-            *val = p1.row(i).iter().zip(m1.iter()).map(|(a, b)| a.ln() + b).reduce(|a, b| a.ln_add_exp(b)).unwrap();
-        }
-    }
-
-    println!("{:?}", outmut);
-
-
-    // for 
-
-    // let y1: Mutation = to_mutation((0..=3).into_iter().map(|ind| {
-    //     hi: Option<f64> = p1.row(ind).iter().zip(m1.iter()).map(|(a, b)| a.ln() + b).reduce(|a, b| a.ln_add_exp(b));
-    //     }).collect());
-
     let mut tr = vector_to_tree(&random_vector(27));
 
     // let end = Instant::now();
diff --git a/src/likelihoods.rs b/src/likelihoods.rs
index 6a3fea7..7943a5f 100644
--- a/src/likelihoods.rs
+++ b/src/likelihoods.rs
@@ -46,10 +46,10 @@ pub fn calculate_likelihood(
 }
 
 // LogSumExp function
-pub fn logse(x: Vec<f64>) -> f64 {
-    let xstar = x.iter().max_by(|x, y| x.total_cmp(y)).unwrap();
-    xstar + x.iter().fold(0.0,|acc, el| acc + f64::exp(el - xstar)).ln()
-}
+// pub fn logse(x: Vec<f64>) -> f64 {
+//     let xstar = x.iter().max_by(|x, y| x.total_cmp(y)).unwrap();
+//     xstar + x.iter().fold(0.0,|acc, el| acc + f64::exp(el - xstar)).ln()
+// }
 
 // LogSumExp function that includes base frequency values for final likelihood calculation
 pub fn base_freq_logse(muta: &Mutation, bf: [f64; 4]) -> f64 {