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use crate::gene::Gene;
use crate::utils;
use rand::prelude::*;
pub struct DNA {
// The pool size, number of genes
pub pool_size: u16,
// The amount of marker each gene has, each marker is f32
pub gene_size: u16,
// The genes for this DNA sequence
pub genes: Vec<Gene>,
}
impl DNA {
/// Constructs a new `DNA`.
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna = DNA::new(2, 2);
/// ```
pub fn new(pool_size: u16, gene_size: u16) -> DNA {
DNA {
pool_size: pool_size,
gene_size: gene_size,
genes: (0..pool_size).map(|_| Gene::new(gene_size)).collect(),
}
}
/// Check if current DNA string is valid.
///
/// # Examples
///
/// ```
/// use genome::DNA;
/// let dna = DNA::new(2, 2);
///
/// let is_valid = DNA::is_valid(dna.to_string());
/// ```
pub fn is_valid(dna_str: String) -> bool {
let pool_size_hex = &dna_str[0..8];
let dna = DNA::from(dna_str.clone());
if dna.get_sum() == utils::f32_from_str(pool_size_hex) {
return true;
}
return false;
}
/// Merge two `DNA` into one
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(2, 2);
/// let dna2 = DNA::new(2, 2);
///
/// let merged = DNA::merge(dna1, dna2, false);
/// ```
pub fn merge(left_dna: DNA, right_dna: DNA, mutate: bool) -> Option<DNA> {
let mut ration_rng = thread_rng();
let mut mutate_rng = thread_rng();
match (left_dna.pool_size == right_dna.pool_size)
&& (left_dna.gene_size == right_dna.gene_size)
{
true => Some(DNA {
pool_size: left_dna.pool_size,
gene_size: left_dna.gene_size,
genes: (0..left_dna.pool_size)
.map(|i| {
if ration_rng.gen::<f32>() >= 0.5 {
left_dna.genes[i as usize].to_string()
} else {
right_dna.genes[i as usize].to_string()
}
})
.map(|g| {
let mut gene = Gene::from(g);
if mutate && mutate_rng.gen::<f32>() >= 0.9 {
gene.mutate();
}
gene
})
.collect(),
}),
false => None,
}
}
/// Compare two `DNA` similarity, return the percentage of same genes
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(256, 2);
/// let dna_str = dna1.to_string();
/// let dna2 = DNA::new(256, 2);
///
/// let merged = DNA::merge(dna1, dna2, false).unwrap();
///
/// let is_parent = DNA::compare(DNA::from(dna_str), merged) > 0.3;
/// ```
pub fn compare(left_dna: DNA, right_dna: DNA) -> f64 {
let mut same_markers = 0;
if left_dna.pool_size != right_dna.pool_size {
return 0 as f64;
}
(0..left_dna.pool_size).for_each(|i| {
if left_dna.genes[i as usize].to_string() == right_dna.genes[i as usize].to_string() {
same_markers = same_markers + 1;
}
});
same_markers as f64 / left_dna.pool_size as f64
}
/// Convert DNA to GAN latent vector
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(2, 2);
///
/// let latent = dna1.to_latent_vec();
/// ```
pub fn to_latent_vec(&self) -> Vec<f32> {
self.genes
.iter()
.map(|g| g.markers.iter().map(|m| m.value).collect::<Vec<f32>>())
.collect::<Vec<Vec<f32>>>()
.concat()
}
/// Convert DNA to string
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(2, 2);
///
/// let dna1_str = dna1.to_string();
/// ```
pub fn to_string(&self) -> String {
let pool_size_hex: String = utils::u16_to_string(self.pool_size);
let gene_size_hex: String = utils::u16_to_string(self.gene_size);
let check_sum: String = utils::f32_to_string(self.get_sum());
format!(
"{}{}{}{}",
check_sum,
pool_size_hex,
gene_size_hex,
self.genes.iter().map(|m| m.to_string()).collect::<String>()
)
}
/// Get checksum for the dna, return back f32 sum of all genes.
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(2, 2);
///
/// let dna1_str = dna1.get_sum();
/// ```
pub fn get_sum(&self) -> f32 {
self.genes.iter().map(|g| g.get_sum()).sum()
}
}
/// Convert DNA to string
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(2, 2);
///
/// let dna1_str = String::from(dna1);
/// ```
impl std::convert::From<DNA> for String {
fn from(dna: DNA) -> String {
let pool_size_hex: String = utils::u16_to_string(dna.pool_size);
let gene_size_hex: String = utils::u16_to_string(dna.gene_size);
let check_sum: String = utils::f32_to_string(dna.get_sum());
format!(
"{}{}{}{}",
check_sum,
pool_size_hex,
gene_size_hex,
dna.genes.iter().map(|m| m.to_string()).collect::<String>()
)
}
}
/// Convert DNA to string
///
/// # Examples
///
/// ```
/// use genome::DNA;
///
/// let dna1 = DNA::new(2, 2);
/// let dna1_str = dna1.to_string();
///
/// let dna_copy = DNA::from(dna1_str);
/// ```
impl std::convert::From<String> for DNA {
fn from(dna: String) -> DNA {
// Ignore the first 8 char for checksum
let pool_size_hex = &dna[8..12];
let gene_size_hex = &dna[12..16];
let genes_hex = &dna[16..];
let gene_size = utils::u16_from_str(gene_size_hex);
let genes = utils::partition_str(genes_hex, 8 * (gene_size + 1) as usize)
.iter()
.map(|s| String::from(*s))
.collect::<Vec<String>>();
DNA {
pool_size: utils::u16_from_str(pool_size_hex),
gene_size,
genes: genes.iter().map(|g| Gene::from(g.clone())).collect(),
}
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn can_be_converted_and_back() {
let dna = DNA::new(4, 2);
let dna2 = DNA::from(dna.to_string());
assert_eq!(dna.gene_size, dna2.gene_size);
assert_eq!(dna.pool_size, dna2.pool_size);
assert_eq!(dna.genes.len(), dna2.genes.len());
assert_eq!(dna.to_string(), dna2.to_string());
}
#[test]
fn can_be_merged() {
let dna1 = DNA::new(2, 2);
let dna2 = DNA::new(2, 2);
match DNA::merge(dna1, dna2, false) {
Some(_) => assert!(true),
None => assert!(false),
};
}
#[test]
fn cannot_be_merged() {
let dna1 = DNA::new(2, 2);
let dna2 = DNA::new(3, 2);
match DNA::merge(dna1, dna2, false) {
Some(_) => assert!(false),
None => assert!(true),
};
}
#[test]
fn check_merged_gene_ratio() {
let dna1 = DNA::new(512, 4);
let dna2 = DNA::new(512, 4);
let dna1str = dna1.to_string();
let dna2str = dna2.to_string();
let child = DNA::merge(dna1, dna2, false).unwrap();
let child_str = child.to_string();
let parent1_ratio = DNA::compare(DNA::from(child_str.clone()), DNA::from(dna1str));
let parent2_ratio = DNA::compare(DNA::from(child_str), DNA::from(dna2str));
assert!(parent1_ratio != 0 as f64);
assert!(parent2_ratio != 0 as f64);
assert!(parent1_ratio + parent2_ratio == 1 as f64);
}
}