Added Tree method to get all branch lengths in an nalgebra Vector so …

…that it can be used with an optimiser

src/lib.rs

@@ -23,26 +23,6 @@ pub fn main() {
     let args = cli_args();
     let start = Instant::now();
 
-    // Trees initialise with a default rate matrix equal to this
-    // let q: na::Matrix4<f64> = na::Matrix4::new(
-    //     -1.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     -1.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     -1.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     1.0 / 3.0,
-    //     -1.0,
-    // );
-
     // let mut tr = vector_to_tree(&random_vector(4));
     // tr.add_genetic_data(&String::from("/Users/joel/Downloads/listeria0.aln"));
     let mut tr = vector_to_tree(&random_vector(27), &GTR::default());
@@ -55,7 +35,7 @@ pub fn main() {
 
     if !args.no_optimise {
         let start = Instant::now();
-        tr.hillclimb(5);
+        tr.hillclimb(1);
         let end = Instant::now();
 
         eprintln!("Done in {}s", end.duration_since(start).as_secs());

src/tree.rs

@@ -124,6 +124,11 @@ impl<T: RateMatrix> Tree<T> {
         self.get_node(index).unwrap().branch_length
     }
 
+    pub fn get_branchlengths(&self) -> nalgebra::Vector1<f64> {
+        let out: Vec<f64> = self.nodes.iter().map(|node| node.branch_length).collect();
+        nalgebra::Vector1::from_vec(out)
+    }
+
     // Find maximum node depth
     pub fn max_treedepth(&self) -> usize {
         self.nodes.iter().map(|node| node.depth).max().unwrap_or(0)

src/tree_iterators.rs

@@ -1,3 +1,5 @@
+use std::thread::current;
+
 use clap::builder::NonEmptyStringValueParser;
 use ndarray::AssignElem;
 
@@ -108,29 +110,28 @@ impl<'a, T: RateMatrix> Tree<T> {
 
 // Changes iterator
 // #[derive(Debug)]
-// pub struct ChangeOrder {
-//     nodevec: Option<Vec<usize>>,
+// pub struct ChangeOrder<'a, T: RateMatrix> {
+//     tree: &'a mut Tree<T>,
+//     current_vec: Vec<usize>,
 // }
 
-// impl Iterator for ChangeOrder {
+// impl<'a, T: RateMatrix> Iterator for ChangeOrder<'a, T> {
 //     type Item = &'a Node;
-// Will changes be faster and easier using
-// Vec<Option<Vec<usize>>> ?
-// fn next(&mut self) -> Option<Self::Item> {
-//     if self.tree.changes.is_empty() {
-//         return None;
-//     }
-
-//     while !self.tree.changes.contains_key(&self.depth) {
-//         self.depth -= 1;
+//     fn next(&mut self) -> Option<Self::Item> {
+//         if self.tree.changes.is_empty() {
+//             return None
+//         } else if self.current_vec.is_empty() {
+//             let k = *self.tree.changes.keys().max().unwrap();
+//             self.current_vec = self.tree.changes.remove(&k).unwrap();
+//             let x = self.current_vec.pop().unwrap();
+//             let n: &'a Node = self.tree.get_node(x)?;
+//             return Some(n)
+//         } else {
+//             let x = self.current_vec.pop().unwrap();
+//             let n: Self::Item = self.tree.get_node(x)?;
+//             return Some(n)
+//         };
 //     }
-
-//     let x = self.tree.changes.remove(&self.depth).unwrap();
-//     let ni = x.pop();
-//     self.tree.changes.insert(self.depth, x);
-
-//     next_node
-// }
 // }
 
 // impl<'a> Tree {