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Added some comments

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Ravi Shah 5 years ago
parent
commit
41f573fbca
  1. 35
      src/lib.rs

35
src/lib.rs

@ -1,3 +1,10 @@
// Copyright Ravi Shah 2021
// You should've got the GPL v3.0 with this software
// If ya didn't, it's available here:
// https://www.gnu.org/licenses/gpl-3.0.en.html
// Imports
mod utils; mod utils;
use wasm_bindgen::prelude::*; use wasm_bindgen::prelude::*;
@ -15,6 +22,8 @@ pub fn transcription(dna: String) -> String {
let mut transcribed_vec: Vec<char> = Vec::new(); let mut transcribed_vec: Vec<char> = Vec::new();
for i in char_vec { for i in char_vec {
// Basically converts DNA strand to mRNA
match i { match i {
'A' => transcribed_vec.push('U'), 'A' => transcribed_vec.push('U'),
'T' => transcribed_vec.push('A'), 'T' => transcribed_vec.push('A'),
@ -26,25 +35,30 @@ pub fn transcription(dna: String) -> String {
} }
} }
// Collect transcribed mRNA into a String
let transcribed_string: String = transcribed_vec.into_iter().collect(); let transcribed_string: String = transcribed_vec.into_iter().collect();
return transcribed_string; return transcribed_string;
} }
pub fn find_start(messenger_rna: String) -> String { pub fn find_start(messenger_rna: String) -> String {
let start_codon = "AUG"; let start_codon = "AUG";
// Find index of start codon
let start_index = messenger_rna.find(start_codon).unwrap(); let start_index = messenger_rna.find(start_codon).unwrap();
// Remove anything before start codon
let inter_rna: String = messenger_rna.chars().skip(start_index).collect(); let inter_rna: String = messenger_rna.chars().skip(start_index).collect();
return inter_rna; return inter_rna;
} }
pub fn break_into_codons(inter_rna: String) -> Vec<String> { pub fn break_into_codons(inter_rna: String) -> Vec<String> {
let sub_len = 3; let sub_len = 3;
// Split into codons (chunks of 3 bases each)
let subs = inter_rna.as_bytes() let subs = inter_rna.as_bytes()
.chunks(sub_len) .chunks(sub_len)
.map(str::from_utf8) .map(str::from_utf8)
.collect::<Result<Vec<&str>, _>>() .collect::<Result<Vec<&str>, _>>()
.unwrap(); .unwrap();
// Combine into a vector
let mut string_vec: Vec<String> = Vec::new(); let mut string_vec: Vec<String> = Vec::new();
for i in &subs { for i in &subs {
string_vec.push(i.to_string()); string_vec.push(i.to_string());
@ -58,6 +72,7 @@ pub fn find_stop(inter_codons: &[String]) -> usize {
let mut stop_index_2: usize = usize::MAX; let mut stop_index_2: usize = usize::MAX;
let mut stop_index_3: usize = usize::MAX; let mut stop_index_3: usize = usize::MAX;
// Find position of any stop codons
if inter_codons.iter().any(|i| i == "UAA") { if inter_codons.iter().any(|i| i == "UAA") {
stop_index_1 = inter_codons.iter().position(|r| r == "UAA").unwrap(); stop_index_1 = inter_codons.iter().position(|r| r == "UAA").unwrap();
} }
@ -76,6 +91,7 @@ pub fn find_stop(inter_codons: &[String]) -> usize {
pub fn find_first(stop_index_1: usize, stop_index_2: usize, stop_index_3: usize) -> usize { pub fn find_first(stop_index_1: usize, stop_index_2: usize, stop_index_3: usize) -> usize {
let mut stop_index: usize = 1; let mut stop_index: usize = 1;
// Find which stop codon actually occured first
if stop_index_1 < stop_index_2 { if stop_index_1 < stop_index_2 {
if stop_index_1 < stop_index_3{ if stop_index_1 < stop_index_3{
println!("UAA stop codon found!"); println!("UAA stop codon found!");
@ -105,6 +121,7 @@ pub fn find_first(stop_index_1: usize, stop_index_2: usize, stop_index_3: usize)
pub fn translation(inter_codons: Vec<String>) -> Vec<String> { pub fn translation(inter_codons: Vec<String>) -> Vec<String> {
let mut amino_acids_list: Vec<String> = Vec::new(); let mut amino_acids_list: Vec<String> = Vec::new();
// Matching codons to amino acids
for i in inter_codons { for i in inter_codons {
match i.as_str() { match i.as_str() {
"GUU" | "GUC" | "GUA" | "GUG" => amino_acids_list.push("Valine".to_string()), "GUU" | "GUC" | "GUA" | "GUG" => amino_acids_list.push("Valine".to_string()),
@ -142,30 +159,32 @@ pub fn translation(inter_codons: Vec<String>) -> Vec<String> {
pub fn main(mut strand: String) { pub fn main(mut strand: String) {
println!("Enter the DNA strand to be transcribed and translated: "); println!("Enter the DNA strand to be transcribed and translated: ");
strand = strand.to_string().to_uppercase();
strand = strand.to_string().to_uppercase(); // Convert to uppercase
let messenger_rna = transcription(strand);
let messenger_rna = transcription(strand); // Transcribe strand
println!("The transcribed strand is: {}", messenger_rna); println!("The transcribed strand is: {}", messenger_rna);
let inter_rna = find_start(messenger_rna);
let inter_rna = find_start(messenger_rna); // Find start codon
println!("{}", inter_rna); println!("{}", inter_rna);
let mut inter_codons = break_into_codons(inter_rna);
let mut stop_index = find_stop(&inter_codons);
let mut inter_codons = break_into_codons(inter_rna); // Break into codons
let mut stop_index = find_stop(&inter_codons); // Find index of stop codon
stop_index = stop_index + 1; stop_index = stop_index + 1;
println!("{}", stop_index); println!("{}", stop_index);
inter_codons.truncate(stop_index);
let amino_acids_list = translation(inter_codons);
inter_codons.truncate(stop_index); // Truncate at stop index
let amino_acids_list = translation(inter_codons); // Translate to amino acids
// Use `web_sys`'s global `window` function to get a handle on the global // Use `web_sys`'s global `window` function to get a handle on the global
// window object. // window object.
let window = web_sys::window().expect("no global `window` exists"); let window = web_sys::window().expect("no global `window` exists");
let document = window.document().expect("should have a document on window"); let document = window.document().expect("should have a document on window");
let codons_div = document.get_element_by_id("codons").expect("codons div should exist");
let codons_div = document.get_element_by_id("codons").expect("codons div should exist"); // Get codons div
// Insert codons header into the DOM
let val = document.create_element("h2").unwrap(); let val = document.create_element("h2").unwrap();
val.set_text_content(Some("Codons:")); val.set_text_content(Some("Codons:"));
codons_div.append_with_node_1(&val).unwrap(); codons_div.append_with_node_1(&val).unwrap();
print!("The translated amino acids are: "); print!("The translated amino acids are: ");
// Insert amino acids into the DOM
for i in amino_acids_list { for i in amino_acids_list {
let val = document.create_element("p").unwrap(); let val = document.create_element("p").unwrap();
val.set_text_content(Some(&i)); val.set_text_content(Some(&i));

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