Wrote code to strip leaf labels and branch length from rapidNJ newick…

… string. Now need to compile this into a Newick string that newick_to_vec can convert into a tree vector

Cargo.toml

@@ -11,6 +11,7 @@ needletail = "0.5.1"
 nalgebra = "0.32.3"
 clap = { version = "4.5", features = ["derive"]}
 cxx = "1.0"
+regex = "1.10"
 
 [dev-dependencies]
 # testing

src/lib.rs

@@ -7,28 +7,78 @@ mod tests;
 mod tree;
 mod dspsa;
 
+use cxx::kind;
 use cxx::let_cxx_string;
 use cxx::CxxString;
 use rand::Rng;
 use rand::random;
+use regex::{RegexSet, RegexSetBuilder};
 
 use crate::dspsa::hill_peturb;
 use crate::gen_list::*;
 use crate::phylo2vec::*;
 use crate::tree::Tree;
 use crate::likelihoods::logse;
 use crate::node::Node;
-use std::collections::HashSet;
+use std::collections::HashMap;
 use std::thread::current;
 use std::time::Instant;
 extern crate nalgebra as na;
 
+
 pub mod cli;
 use crate::cli::*;
 
 pub fn main() {
     let args = cli_args();
 
+    let nstr: String = String::from("(((((('9':0.00066056,'4':0.0012556):0.00030238,('25':0.00042479,'19':0.00030083):0.00039731):0.00012351,'7':0.00039526):8.5797e-05,'18':0.00068249):0.00011977,'20':0.00056004):9.6199e-05,(((((((('17':0.0045802,'8':0.0021951):0.00019116,(((('24':0.0021162,'12':0.0017684):0.00074803,'13':0.0043482):0.00026831,('27':0.00063335,'5':0.00071804):0.0024273):4.8521e-05,((('23':0.0012435,'2':0.0012676):0.00011672,('21':0.00085695,'6':0.00096101):0.001509):0.00046989,'10':0.0020611):0.00092726):0.00022606):0.00019029,'26':0.0027488):0.00030355,('14':0.0021462,'0':0.0018751):0.00061029):0.00035469,'1':0.00096653):0.00015559,'22':0.0013558):7.0943e-05,('16':0.00054383,'15':0.00076666):0.00015841):0.00016779,'11':0.0021712):9.9157e-05,'3':0.00081132);");
+
+    // Chops into nodes
+    let mut v: Vec<&str> = nstr.split_inclusive(|c: char| c.eq(&')') || c.eq(&',')).filter(|s| !s.is_empty() && s.ne(&";")).collect();
+    // Pop off the semi-colon
+    // v.pop();
+    // println!("{:?}", v);
+
+    let n_nodes = v.len();
+    let mut branch_len: Vec<f64> = Vec::with_capacity(n_nodes);
+    let mut name_dict: HashMap<usize, String> = HashMap::with_capacity(n_nodes);
+    let internal_index = ((n_nodes - 1) / 2) + 1;
+    let mut node_index: usize = 0;
+
+    // println!("{}", n_nodes);
+    // println!("{}", internal_index);
+
+    // Iterate over nodes
+    for node in v {
+        let cleaned_node: String = node.replace(&['(', '\'', ')', ','], "");
+        // println!("{:?}", cleaned_node);
+        let split_node: Vec<&str> = cleaned_node.split(':').collect();
+        // println!("{:?}", split_node);
+
+        let node_name: String = match split_node[0].is_empty() {
+            true => node_index.to_string(),
+            false => split_node[0].to_string(),
+        };
+        name_dict.insert(node_index, node_name);
+
+        let blen: f64 = split_node[1].parse().unwrap();
+        branch_len.push(blen);
+        node_index += 1;
+
+        // Need to reconstruct new newick string using new node labels
+
+        // let new_el: Vec<&str> = node.split_inclusive(|c: char| c.eq(&')') || c.eq(&',') || c.eq(&'(') || c.eq(&':') || c.eq(&',')).collect();
+
+        // println!("{:?}", node);
+    }
+
+    // for (key, val) in name_dict.iter() {
+    //     println!("key: {key} val: {val}");
+    // }
+    // let v = newick_to_vec(&nstr, 27);
+
+
     // 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,
@@ -47,10 +97,9 @@ pub fn main() {
     println!("{}", tr.get_tree_likelihood());
     println!("{:?}", tr.newick());
     println!("{:?}", tr.tree_vec);
-    // println!("{:?}", tr.mutation_lists);
 
     if !args.no_optimise {
-        tr.hillclimb(&q, 100);
+        // tr.hillclimb(&q, 100);
     }
 
     // let end = Instant::now();