From ef1720abdb25245b472e38195e0451dff606234a Mon Sep 17 00:00:00 2001
From: Joel Hellewell <joel@ebi.ac.uk>
Date: Thu, 20 Jul 2023 09:33:02 +0100
Subject: [PATCH] rewrote function to combine genetic lists to take references
 and not destroy previous lists

---
 src/gen_list.rs | 89 ++++++++++++++++++++++++++++++-------------------
 src/main.rs     | 20 ++++-------
 2 files changed, 61 insertions(+), 48 deletions(-)

diff --git a/src/gen_list.rs b/src/gen_list.rs
index 69e2c3a..e01280f 100644
--- a/src/gen_list.rs
+++ b/src/gen_list.rs
@@ -41,45 +41,66 @@ pub fn create_list(refseq: &[char], seq: &[char]) -> Vec<Mutation> {
 }
 
 // Combines two vectors of Mutations into a single vector
-pub fn combine_lists(seq1: &mut Vec<Mutation>, seq2: &mut Vec<Mutation>) -> Vec<Mutation> {
+pub fn combine_lists(seq1: Option<&Vec<Mutation>>, seq2: Option<&Vec<Mutation>>) -> Vec<Mutation> {
     let mut out: Vec<Mutation> = Vec::new();
-
-    seq1.reverse();
-    seq2.reverse();
-
-    let mut j = seq2.pop();
-    let mut i = seq1.pop();
-
-    while i.is_some() | j.is_some() {
-        if j.is_none() {
-            out.push(i.unwrap());
-            i = seq1.pop();
-        } else if i.is_none() {
-            out.push(j.unwrap());
-            j = seq2.pop();
-        } else {
-            let i0 = i.unwrap().0;
-            let j0 = j.unwrap().0;
-
-            match i0.cmp(&j0) {
-                Ordering::Equal => {
-                    // This should call another function to handle the calculation
-                    out.push(Mutation(i0, 5.0, 5.0, 5.0, 5.0));
-                    i = seq1.pop();
-                    j = seq2.pop();
-                }
-                Ordering::Less => {
-                    out.push(i.unwrap());
-                    i = seq1.pop();
-                }
-                Ordering::Greater => {
-                    out.push(j.unwrap());
-                    j = seq2.pop();
-                }
+    let seq1 = seq1.unwrap();
+    let seq2 = seq2.unwrap();
+
+    // Index in each vector of mutations
+    let mut s1_i = seq1.len() - 1;
+    let mut s2_i = seq2.len() - 1;
+
+    // Mutation at each index
+    let mut s1_node = seq1.get(s1_i);
+    let mut s2_node = seq2.get(s2_i);
+
+    // Location of mutation in sequence
+    let mut s1_loc = s1_node.unwrap().0;
+    let mut s2_loc = s2_node.unwrap().0;
+
+    while (s1_i < 0) | (s2_i > 0) {
+        match s1_loc.cmp(&s2_loc) {
+            Ordering::Equal => {
+                out.push(Mutation(s1_loc, 5.0, 5.0, 5.0, 5.0));
+                
+                s1_i -= 1;
+                s1_node = seq1.get(s1_i);
+                s1_loc = s1_node.unwrap().0;
+
+                s2_i -= 1;
+                s2_node = seq2.get(s2_i);
+                s2_loc = s2_node.unwrap().0;
+            },
+            Ordering::Greater => {
+                out.push(*s1_node.unwrap());
+                s1_i -= 1;
+                s1_node = seq1.get(s1_i);
+                s1_loc = s1_node.unwrap().0;
+            },
+            Ordering::Less => {
+                out.push(*s2_node.unwrap());
+                s2_i -= 1;
+                s2_node = seq2.get(s2_i);
+                s2_loc = s2_node.unwrap().0;
             }
         }
     }
 
+    // Push last entries
+    match s1_loc.cmp(&s2_loc) {
+        Ordering::Equal => {
+            out.push(Mutation(s1_loc, 5.0, 5.0, 5.0, 5.0));},
+        Ordering::Greater => {
+            out.push(*s1_node.unwrap());
+            out.push(*s2_node.unwrap());},
+        Ordering::Less => {
+            out.push(*s2_node.unwrap());
+            out.push(*s1_node.unwrap());
+        },
+    }
+
+    out.reverse();
+
     out
 }
 
diff --git a/src/main.rs b/src/main.rs
index 7a85f37..d991aca 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -17,22 +17,14 @@ fn main() {
     let filename = "listeria0.aln";
     let mut ll = create_genetic_data(filename);
 
-    println!("{:?}", ll.likelihood_lists.len());
+    // println!("{:?}", ll.likelihood_lists.get_mut());
+    
+    let combo = combine_lists(ll.likelihood_lists.get(0), ll.likelihood_lists.get(1));
+    // println!("seq1: {:?}",ll.likelihood_lists);
+    println!("combined seq: {:?}", combo);
 
-    // let record2 = reader.next().unwrap().unwrap();
-    // let seq2: Vec<char> = record2.seq().iter().map(|l| *l as char).collect();
-
-    // let record3 = reader.next().unwrap().unwrap();
-    // let seq3: Vec<char> = record3.seq().iter().map(|l| *l as char).collect();
-
-    // let mut out: Vec<Mutation> = create_list(&seq_vec, &seq2);
-    // let mut out2: Vec<Mutation> = create_list(&seq_vec, &seq3);
-
-    // let mut lists: Vec<&mut Vec<Mutation>> = vec![&mut out, &mut out2];
-
-    // let combined_out = combine_lists(&mut out, &mut out2);
-    // println!("combined seq: {:?}", combined_out[0..25].to_vec());
 
+    // println!("{:?}", ll.likelihood_lists.get(0).unwrap().get(0));
     // let tr = phylo2vec_quad(vec![0, 1, 0]);
     // let tr2 = phylo2vec_lin(vec![0, 0, 2, 3], false);