linking newick to vector C++ code

src/dspsa.rs

@@ -73,8 +73,7 @@ impl Tree {
             println!("Tree log likelihood: {}", self.get_tree_likelihood());
             // Generate peturbation vector
             delta = peturbation_vec(n);
-            // println!("Peturbation vector: {:?}", delta);
-
+
             // Generate pi vector
             pivec = piv(&theta);
             // println!("Pi vector: {:?}", pivec);

src/lib.rs

@@ -31,29 +31,31 @@ pub fn main() {
 
     let start = Instant::now();
 
+    let nw = phylo2vec_quad(random_tree(2)).newick();
+    println!("{:?}", nw);
+    let x = newick2vec(&nw, 3, true);
+    println!("{:?}", x);
+
     // Define rate matrix
     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 = phylo2vec_quad(random_tree(27));
-
-    let end = Instant::now();
-    // let filename = "listeria0.aln";
+    let mut myvec: Vec<usize> = vec![0; 27];
+    let mut tr = phylo2vec_quad(myvec);
+    let filename = "listeria0.aln";
     tr.add_genetic_data(&args.alignment);
-
     tr.update_likelihood_postorder(&q);
-
     println!("{}", tr.get_tree_likelihood());
     println!("{:?}", tr.newick());
     println!("{:?}", tr.tree_vec);
 
     if !args.no_optimise {
         // tr.optimise(&q, 10);
-        tr.hillclimb(&q, 20);
+        // tr.hillclimb(&q, 20);
     }
 
     // let end = Instant::now();