Added peturb vector MoveFn, put moves in their own file

src/genetic_data.rs

@@ -4,7 +4,7 @@ use needletail::parse_fastx_file;
 use crate::topology::Topology;
 use ndarray::s;
 use logaddexp::LogAddExp;
-use rand::Rng;
+use crate::moves::MoveFn;
 
 const NEGINF: f64 = -f64::INFINITY;
 // (A, C, G, T)
@@ -153,63 +153,9 @@ pub fn base_freq_logse(muta: ndarray::ArrayBase<ndarray::ViewRepr<&f64>, ndarray
         .fold(0.0, |tot, (muta, bf)| tot + muta.exp() * bf)
         .ln()
 }
-
-// A move produces a vector of nodes that have a new parent node
-// Now Likelihood update
-// Iterate over nodes that need changing from Topology
-// Calculate new likelihoods at internal nodes, add to HashMap
-// Get whole Topology likelihood at root node from HashMap
-// If better, can move HashMap likelihoods into GeneticData
-
-
-// A TryTopology struct that contains old Topology, new tree_vec, changes, reference to gen_data?, HashMap?
-
 pub struct CandidateTopology{
-    new_topology: Topology,
-    changes: Option<Vec<usize>>,
-}
-
-pub fn peturb_vector(topology: &Topology) -> CandidateTopology {
-
-    let mut vout = topology.tree_vec.to_vec();
-    let n = vout.len().div_ceil(5);
-    let mut rng = rand::thread_rng();
-    let ind_rng = rand::thread_rng();
-    let distr = rand::distributions::Bernoulli::new(0.5).unwrap();
-    let ind_distr = rand::distributions::Uniform::new(0, vout.len());
-
-    let mut inds: Vec<usize> = ind_rng.sample_iter(ind_distr).take(n).collect();
-    inds.sort();
-
-    for ind in inds {
-        if ind.eq(&0) {
-            continue;
-        }
-
-        match rng.sample(distr) {
-            true => {
-                if vout[ind].lt(&(2 * (ind - 1))) {
-                    vout[ind] += 1;
-                }
-            }
-            false => {
-                if vout[ind].gt(&0) {
-                    vout[ind] -= 1;
-                }
-            }
-        };
-    }
-
-    let new_topology: Topology = Topology::from_vec(&vout);
-    let changes: Option<Vec<usize>> = topology.find_changes(&new_topology);
-    CandidateTopology{
-        new_topology,
-        changes,
-    }
-}
-
-pub fn hillclimb_accept(old_ll: &f64, new_ll: &f64) -> bool {
-    new_ll.gt(old_ll)
+    pub new_topology: Topology,
+    pub changes: Option<Vec<usize>>,
 }
 
 impl Topology {
@@ -306,22 +252,3 @@ impl Topology {
     }
 }
 
-pub trait MoveFn {
-    fn generate_move(&self, current_topology: &Topology) -> CandidateTopology;
-}
-
-pub struct ExactMove {
-    pub target_vector: Vec<usize>,
-}
-
-impl MoveFn for ExactMove {
-    fn generate_move(&self, current_topology: &Topology) -> CandidateTopology {
-
-        let new_topology: Topology = Topology::from_vec(&self.target_vector);
-        let changes: Option<Vec<usize>> = current_topology.find_changes(&new_topology);
-        CandidateTopology{
-            new_topology,
-            changes,
-        }
-    }
-}

src/lib.rs

@@ -4,6 +4,7 @@ mod iterators;
 mod rate_matrix;
 mod topology;
 mod genetic_data;
+mod moves;
 
 use rate_matrix::RateMatrix;
 use topology::Topology;
@@ -15,6 +16,7 @@ use crate::cli::*;
 use std::env::args;
 use std::time::Instant;
 use crate::genetic_data::*;
+use crate::moves::*;
 
 pub fn main() {
     let args = cli_args();

src/moves.rs

@@ -0,0 +1,76 @@
+use crate::Topology;
+use crate::CandidateTopology;
+use rand::Rng;
+
+pub trait MoveFn {
+    fn generate_move(&self, current_topology: &Topology) -> CandidateTopology;
+}
+
+pub struct ExactMove {
+    pub target_vector: Vec<usize>,
+}
+
+impl MoveFn for ExactMove {
+    fn generate_move(&self, current_topology: &Topology) -> CandidateTopology {
+
+        let new_topology: Topology = Topology::from_vec(&self.target_vector);
+        let changes: Option<Vec<usize>> = current_topology.find_changes(&new_topology);
+        CandidateTopology{
+            new_topology,
+            changes,
+        }
+    }
+}
+
+pub struct PeturbVec {
+    pub n: usize,
+}
+
+impl MoveFn for PeturbVec {
+    fn generate_move(&self, current_topology: &Topology) -> CandidateTopology {
+        let mut vout = current_topology.tree_vec.to_vec();
+        let mut rng = rand::thread_rng();
+        let ind_rng = rand::thread_rng();
+        let distr = rand::distributions::Bernoulli::new(0.5).unwrap();
+        let ind_distr = rand::distributions::Uniform::new(0, vout.len());
+
+        let samp_n: usize = match self.n.gt(&vout.len()) {
+            true => {vout.len()},
+            false => {self.n},
+        };
+
+        let mut inds: Vec<usize> = ind_rng.sample_iter(ind_distr).take(samp_n).collect();
+        inds.sort();
+
+        for ind in inds {
+            if ind.eq(&0) {
+                continue;
+            }
+
+            match rng.sample(distr) {
+                true => {
+                    if vout[ind].lt(&(2 * (ind - 1))) {
+                        vout[ind] += 1;
+                    }
+                }
+                false => {
+                    if vout[ind].gt(&0) {
+                        vout[ind] -= 1;
+                    }
+                }
+            };
+        };
+
+        let new_topology: Topology = Topology::from_vec(&vout);
+        let changes: Option<Vec<usize>> = current_topology.find_changes(&new_topology);
+        CandidateTopology{
+            new_topology,
+            changes,
+        }
+    }
+}
+
+
+pub fn hillclimb_accept(old_ll: &f64, new_ll: &f64) -> bool {
+    new_ll.gt(old_ll)
+}