refactor: Well struct

Will require bump to lib version!!
This commit is contained in:
Emilia Allison 2024-08-10 00:46:49 -04:00
parent 06baf0a053
commit 7e321a78c4
Signed by: emilia
GPG Key ID: 7A3F8997BFE894E0
6 changed files with 146 additions and 85 deletions

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@ -7,6 +7,7 @@ use super::{string_well_to_pt, TransferRecord, read_csv};
use crate::plate::{PlateFormat, PlateType}; use crate::plate::{PlateFormat, PlateType};
use crate::plate_instances::PlateInstance; use crate::plate_instances::PlateInstance;
use crate::transfer::Transfer; use crate::transfer::Transfer;
use crate::well::Well;
use crate::transfer_region::{CustomRegion, Region, TransferRegion}; use crate::transfer_region::{CustomRegion, Region, TransferRegion};
use std::collections::HashSet; use std::collections::HashSet;
@ -107,7 +108,7 @@ fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
fn guess_plate_size(plate_filtered_records: &[&TransferRecord], which: PlateType) -> PlateFormat { fn guess_plate_size(plate_filtered_records: &[&TransferRecord], which: PlateType) -> PlateFormat {
let mut guess = PlateFormat::W96; // Never guess smaller than 96 let mut guess = PlateFormat::W96; // Never guess smaller than 96
for record in plate_filtered_records { for record in plate_filtered_records {
if let Some((row, col)) = string_well_to_pt(match which { if let Some(Well {col, row} ) = string_well_to_pt(match which {
PlateType::Source => &record.source_well, PlateType::Source => &record.source_well,
PlateType::Destination => &record.destination_well, PlateType::Destination => &record.destination_well,
}) { }) {
@ -169,8 +170,8 @@ fn get_transfer_for_pair(
return None; return None;
} }
let mut source_wells: HashSet<(u8, u8)> = HashSet::new(); let mut source_wells: HashSet<Well> = HashSet::new();
let mut destination_wells: HashSet<(u8, u8)> = HashSet::new(); let mut destination_wells: HashSet<Well> = HashSet::new();
for record in filtered_records { for record in filtered_records {
let source_point_opt = string_well_to_pt(&record.source_well); let source_point_opt = string_well_to_pt(&record.source_well);
let destination_point_opt = string_well_to_pt(&record.destination_well); let destination_point_opt = string_well_to_pt(&record.destination_well);
@ -183,8 +184,8 @@ fn get_transfer_for_pair(
destination_wells.insert(destination_point); destination_wells.insert(destination_point);
} }
} }
let source_wells_vec: Vec<(u8, u8)> = source_wells.into_iter().collect(); let source_wells_vec: Vec<Well> = source_wells.into_iter().collect();
let destination_wells_vec: Vec<(u8, u8)> = destination_wells.into_iter().collect(); let destination_wells_vec: Vec<Well> = destination_wells.into_iter().collect();
let custom_region: Region = let custom_region: Region =
Region::Custom(CustomRegion::new(source_wells_vec, destination_wells_vec)); Region::Custom(CustomRegion::new(source_wells_vec, destination_wells_vec));

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@ -1,4 +1,4 @@
use crate::transfer::Transfer; use crate::{transfer::Transfer, well::Well};
use crate::util::*; use crate::util::*;
use super::{alternative_formats::EchoClientTransferRecord, mangle_headers::mangle_headers, transfer_record::TransferRecordDeserializeIntermediate, TransferRecord}; use super::{alternative_formats::EchoClientTransferRecord, mangle_headers::mangle_headers, transfer_record::TransferRecordDeserializeIntermediate, TransferRecord};
@ -22,9 +22,9 @@ pub fn transfer_to_records(
for d_well in dest_wells { for d_well in dest_wells {
records.push(TransferRecord { records.push(TransferRecord {
source_plate: src_barcode.to_string(), source_plate: src_barcode.to_string(),
source_well: format!("{}{}", num_to_letters(s_well.0).unwrap(), s_well.1), source_well: format!("{}{}", num_to_letters(s_well.col).unwrap(), s_well.row),
destination_plate: dest_barcode.to_string(), destination_plate: dest_barcode.to_string(),
destination_well: format!("{}{}", num_to_letters(d_well.0).unwrap(), d_well.1), destination_well: format!("{}{}", num_to_letters(d_well.col).unwrap(), d_well.row),
volume: tr.volume, volume: tr.volume,
concentration: None, concentration: None,
}) })
@ -53,7 +53,7 @@ pub fn records_to_echo_client_csv(trs: Vec<TransferRecord>) -> Result<String, Bo
} }
/// Converts "spreadsheet format" well identification to coordinates /// Converts "spreadsheet format" well identification to coordinates
pub fn string_well_to_pt(input: &str) -> Option<(u8, u8)> { pub fn string_well_to_pt(input: &str) -> Option<Well> {
lazy_static! { lazy_static! {
static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap(); static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap();
@ -62,7 +62,7 @@ pub fn string_well_to_pt(input: &str) -> Option<(u8, u8)> {
} }
if let Some(c1) = REGEX.captures(input) { if let Some(c1) = REGEX.captures(input) {
if let (Some(row), Some(col)) = (letters_to_num(&c1[1]), c1[2].parse::<u8>().ok()) { if let (Some(row), Some(col)) = (letters_to_num(&c1[1]), c1[2].parse::<u8>().ok()) {
return Some((row, col)) return Some((row, col).into())
} else { } else {
return None return None
} }

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@ -3,4 +3,6 @@ pub mod plate;
pub mod plate_instances; pub mod plate_instances;
pub mod transfer; pub mod transfer;
pub mod transfer_region; pub mod transfer_region;
pub mod transfer_volume;
pub mod well;
pub mod util; pub mod util;

View File

@ -2,30 +2,32 @@ use serde::{Deserialize, Serialize};
use super::plate::Plate; use super::plate::Plate;
use super::well::Well;
#[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)] #[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
pub struct CustomRegion { pub struct CustomRegion {
src: Vec<(u8, u8)>, src: Vec<Well>,
dest: Vec<(u8, u8)>, dest: Vec<Well>,
} }
impl CustomRegion { impl CustomRegion {
pub fn new(src: Vec<(u8, u8)>, dest: Vec<(u8, u8)>) -> Self { pub fn new(src: Vec<Well>, dest: Vec<Well>) -> Self {
CustomRegion { src, dest } CustomRegion { src, dest }
} }
} }
#[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)] #[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
pub enum Region { pub enum Region {
Rect((u8, u8), (u8, u8)), Rect(Well, Well),
Point((u8, u8)), Point(Well),
Custom(CustomRegion), Custom(CustomRegion),
} }
impl Default for Region { impl Default for Region {
fn default() -> Self { fn default() -> Self {
Region::Point((1, 1)) Region::Point(Well { row: 1, col: 1 })
} }
} }
impl TryFrom<Region> for ((u8, u8), (u8, u8)) { impl TryFrom<Region> for (Well, Well) {
type Error = &'static str; type Error = &'static str;
fn try_from(region: Region) -> Result<Self, Self::Error> { fn try_from(region: Region) -> Result<Self, Self::Error> {
if let Region::Rect(c1, c2) = region { if let Region::Rect(c1, c2) = region {
@ -37,12 +39,11 @@ impl TryFrom<Region> for ((u8, u8), (u8, u8)) {
} }
} }
type Corner = (u8, u8); type Rectangle = (Well, Well);
type Rectangle = (Corner, Corner);
impl Region { impl Region {
pub fn new_custom(transfers: &Vec<Rectangle>) -> Self { pub fn new_custom(transfers: &Vec<Rectangle>) -> Self {
let mut src_pts: Vec<(u8, u8)> = Vec::with_capacity(transfers.len()); let mut src_pts: Vec<Well> = Vec::with_capacity(transfers.len());
let mut dest_pts: Vec<(u8, u8)> = Vec::with_capacity(transfers.len()); let mut dest_pts: Vec<Well> = Vec::with_capacity(transfers.len());
for transfer in transfers { for transfer in transfers {
src_pts.push(transfer.0); src_pts.push(transfer.0);
@ -80,10 +81,10 @@ impl Default for TransferRegion {
} }
impl TransferRegion { impl TransferRegion {
pub fn get_source_wells(&self) -> Vec<(u8, u8)> { pub fn get_source_wells(&self) -> Vec<Well> {
match &self.source_region { match &self.source_region {
Region::Rect(c1, c2) => { Region::Rect(c1, c2) => {
let mut wells = Vec::<(u8, u8)>::new(); let mut wells = Vec::<Well>::new();
let (ul, br) = standardize_rectangle(c1, c2); let (ul, br) = standardize_rectangle(c1, c2);
let (interleave_i, interleave_j) = self.interleave_source; let (interleave_i, interleave_j) = self.interleave_source;
// NOTE: This will panic if either is 0! // NOTE: This will panic if either is 0!
@ -93,12 +94,12 @@ impl TransferRegion {
let (interleave_i, interleave_j) = let (interleave_i, interleave_j) =
(i8::max(interleave_i, 1), i8::max(interleave_j, 1)); (i8::max(interleave_i, 1), i8::max(interleave_j, 1));
for i in (ul.0..=br.0).step_by(i8::abs(interleave_i) as usize) { for i in (ul.col..=br.col).step_by(i8::abs(interleave_i) as usize) {
for j in (ul.1..=br.1).step_by(i8::abs(interleave_j) as usize) { for j in (ul.row..=br.row).step_by(i8::abs(interleave_j) as usize) {
// NOTE: It looks like we're ignoring negative interleaves, // NOTE: It looks like we're ignoring negative interleaves,
// because it wouldn't make a difference here---the same // because it wouldn't make a difference here---the same
// wells will still be involved in the transfer. // wells will still be involved in the transfer.
wells.push((i, j)) wells.push(Well { col: i, row: j })
} }
} }
wells wells
@ -108,14 +109,14 @@ impl TransferRegion {
} }
} }
pub fn get_destination_wells(&self) -> Vec<(u8, u8)> { pub fn get_destination_wells(&self) -> Vec<Well> {
match &self.source_region { match &self.source_region {
Region::Custom(c) => c.dest.clone(), Region::Custom(c) => c.dest.clone(),
_ => { _ => {
let map = self.calculate_map(); let map = self.calculate_map();
let source_wells = self.get_source_wells(); let source_wells = self.get_source_wells();
let mut wells = Vec::<(u8, u8)>::new(); let mut wells = Vec::<Well>::new();
for well in source_wells { for well in source_wells {
if let Some(mut dest_wells) = map(well) { if let Some(mut dest_wells) = map(well) {
@ -129,14 +130,14 @@ impl TransferRegion {
} }
#[allow(clippy::type_complexity)] // Resolving gives inherent associated type error #[allow(clippy::type_complexity)] // Resolving gives inherent associated type error
pub fn calculate_map(&self) -> Box<dyn Fn((u8, u8)) -> Option<Vec<(u8, u8)>> + '_> { pub fn calculate_map(&self) -> Box<dyn Fn(Well) -> Option<Vec<Well>> + '_> {
// By validating first, we have a stronger guarantee that // By validating first, we have a stronger guarantee that
// this function will not panic. :) // this function will not panic. :)
// log::debug!("Validating: {:?}", self.validate()); // log::debug!("Validating: {:?}", self.validate());
if let Err(msg) = self.validate() { if let Err(msg) = self.validate() {
eprintln!("{}", msg); eprintln!("{}", msg);
eprintln!("This transfer will be empty."); eprintln!("This transfer will be empty.");
return Box::new(|(_, _)| None); return Box::new(|_| None);
} }
// log::debug!("What is ild? {:?}", self); // log::debug!("What is ild? {:?}", self);
@ -144,10 +145,10 @@ impl TransferRegion {
let il_dest = self.interleave_dest; let il_dest = self.interleave_dest;
let il_source = self.interleave_source; let il_source = self.interleave_source;
let source_corners: ((u8, u8), (u8, u8)) = match self.source_region { let source_corners: (Well, Well) = match self.source_region {
Region::Point((x, y)) => ((x, y), (x, y)), Region::Point(well) => (well, well),
Region::Rect(c1, c2) => (c1, c2), Region::Rect(c1, c2) => (c1, c2),
Region::Custom(_) => ((0, 0), (0, 0)), Region::Custom(_) => (Well { col: 0, row: 0 }, Well { col: 0, row: 0 }),
}; };
let (source_ul, _) = standardize_rectangle(&source_corners.0, &source_corners.1); let (source_ul, _) = standardize_rectangle(&source_corners.0, &source_corners.1);
// This map is not necessarily injective or surjective, // This map is not necessarily injective or surjective,
@ -157,43 +158,43 @@ impl TransferRegion {
// Non-replicate transfers: // Non-replicate transfers:
match &self.dest_region { match &self.dest_region {
Region::Point((x, y)) => { Region::Point(well) => {
Box::new(move |(i, j)| { Box::new(move |Well { col: i, row: j }| {
if source_wells.contains(&(i, j)) { if source_wells.contains(&Well { col: i, row: j }) {
// Validity here already checked by self.validate() // Validity here already checked by self.validate()
Some(vec![( Some(vec![Well {
x + i col: well.col
.checked_sub(source_ul.0) + i.checked_sub(source_ul.col)
.expect("Point cannot have been less than UL") .expect("Point cannot have been less than UL")
.checked_div(il_source.0.unsigned_abs()) .checked_div(il_source.0.unsigned_abs())
.expect("Source interleave cannot be 0") .expect("Source interleave cannot be 0")
.mul(il_dest.0.unsigned_abs()), .mul(il_dest.0.unsigned_abs()),
y + j row: well.row
.checked_sub(source_ul.1) + j.checked_sub(source_ul.row)
.expect("Point cannot have been less than UL") .expect("Point cannot have been less than UL")
.checked_div(il_source.1.unsigned_abs()) .checked_div(il_source.1.unsigned_abs())
.expect("Source interleave cannot be 0") .expect("Source interleave cannot be 0")
.mul(il_dest.1.unsigned_abs()), .mul(il_dest.1.unsigned_abs()),
)]) }])
} else { } else {
None None
} }
}) })
} }
Region::Rect(c1, c2) => { Region::Rect(c1, c2) => {
Box::new(move |(i, j)| { Box::new(move |Well { col: i, row: j }| {
if source_wells.contains(&(i, j)) { if source_wells.contains(&Well { col: i, row: j }) {
let possible_destination_wells = create_dense_rectangle(c1, c2); let possible_destination_wells = create_dense_rectangle(c1, c2);
let (d_ul, d_br) = standardize_rectangle(c1, c2); let (d_ul, d_br) = standardize_rectangle(c1, c2);
let (s_ul, s_br) = let (s_ul, s_br) =
standardize_rectangle(&source_corners.0, &source_corners.1); standardize_rectangle(&source_corners.0, &source_corners.1);
let s_dims = ( let s_dims = (
s_br.0.checked_sub(s_ul.0).unwrap() + 1, s_br.col.checked_sub(s_ul.col).unwrap() + 1,
s_br.1.checked_sub(s_ul.1).unwrap() + 1, s_br.row.checked_sub(s_ul.row).unwrap() + 1,
); );
let d_dims = ( let d_dims = (
d_br.0.checked_sub(d_ul.0).unwrap() + 1, d_br.col.checked_sub(d_ul.col).unwrap() + 1,
d_br.1.checked_sub(d_ul.1).unwrap() + 1, d_br.row.checked_sub(d_ul.row).unwrap() + 1,
); );
let number_used_src_wells = ( let number_used_src_wells = (
// Number of used source wells // Number of used source wells
@ -222,34 +223,34 @@ impl TransferRegion {
.unwrap() as u8, .unwrap() as u8,
); );
let i = i let i = i
.saturating_sub(s_ul.0) .saturating_sub(s_ul.col)
.saturating_div(il_source.0.unsigned_abs()); .saturating_div(il_source.0.unsigned_abs());
let j = j let j = j
.saturating_sub(s_ul.1) .saturating_sub(s_ul.row)
.saturating_div(il_source.1.unsigned_abs()); .saturating_div(il_source.1.unsigned_abs());
Some( Some(
possible_destination_wells possible_destination_wells
.into_iter() .into_iter()
.filter(|(x, _)| { .filter(|Well { col, .. }| {
x.checked_sub(d_ul.0).unwrap() col.checked_sub(d_ul.col).unwrap()
% (number_used_src_wells.0 * il_dest.0.unsigned_abs()) // Counter along x % (number_used_src_wells.0 * il_dest.0.unsigned_abs()) // Counter along x
== (il_dest.0.unsigned_abs() *i) == (il_dest.0.unsigned_abs() *i)
% (number_used_src_wells.0 * il_dest.0.unsigned_abs()) % (number_used_src_wells.0 * il_dest.0.unsigned_abs())
}) })
.filter(|(_, y)| { .filter(|Well { row, .. }| {
y.checked_sub(d_ul.1).unwrap() row.checked_sub(d_ul.row).unwrap()
% (number_used_src_wells.1 * il_dest.1.unsigned_abs()) // Counter along u % (number_used_src_wells.1 * il_dest.1.unsigned_abs()) // Counter along u
== (il_dest.1.unsigned_abs() *j) == (il_dest.1.unsigned_abs() *j)
% (number_used_src_wells.1 * il_dest.1.unsigned_abs()) % (number_used_src_wells.1 * il_dest.1.unsigned_abs())
}) })
.filter(|(x, y)| { .filter(|Well { col, row }| {
// How many times have we replicated? < How many are we allowed // How many times have we replicated? < How many are we allowed
// to replicate? // to replicate?
x.checked_sub(d_ul.0).unwrap().div_euclid( col.checked_sub(d_ul.col).unwrap().div_euclid(
number_used_src_wells.0 * il_dest.0.unsigned_abs(), number_used_src_wells.0 * il_dest.0.unsigned_abs(),
) < count.0 ) < count.0
&& y.checked_sub(d_ul.1).unwrap().div_euclid( && row.checked_sub(d_ul.row).unwrap().div_euclid(
number_used_src_wells.1 * il_dest.1.unsigned_abs(), number_used_src_wells.1 * il_dest.1.unsigned_abs(),
) < count.1 ) < count.1
}) })
@ -260,14 +261,14 @@ impl TransferRegion {
} }
}) })
} }
Region::Custom(c) => Box::new(move |(i, j)| { Region::Custom(c) => Box::new(move |Well { col: i, row: j }| {
let src = c.src.clone(); let src = c.src.clone();
let dest = c.dest.clone(); let dest = c.dest.clone();
let points: Vec<(u8, u8)> = src let points: Vec<Well> = src
.iter() .iter()
.enumerate() .enumerate()
.filter(|(_index, (x, y))| *x == i && *y == j) .filter(|(_index, Well { col, row })| *col == i && *row == j)
.map(|(index, _)| dest[index]) .map(|(index, _)| dest[index])
.collect(); .collect();
if points.is_empty() { if points.is_empty() {
@ -296,15 +297,15 @@ impl TransferRegion {
// later // later
Region::Rect(s1, s2) => { Region::Rect(s1, s2) => {
// Check if all source wells exist: // Check if all source wells exist:
if s1.0 == 0 || s1.1 == 0 || s2.0 == 0 || s2.1 == 0 { if s1.col == 0 || s1.row == 0 || s2.col == 0 || s2.row == 0 {
return Err("Source region is out-of-bounds! (Too small)"); return Err("Source region is out-of-bounds! (Too small)");
} }
// Sufficient to check if the corners are in-bounds // Sufficient to check if the corners are in-bounds
let source_max = self.source_plate.size(); let source_max = self.source_plate.size();
if s1.0 > source_max.0 || s2.0 > source_max.0 { if s1.col > source_max.0 || s2.col > source_max.0 {
return Err("Source region is out-of-bounds! (Too tall)"); return Err("Source region is out-of-bounds! (Too tall)");
} }
if s1.1 > source_max.1 || s2.1 > source_max.1 { if s1.row > source_max.1 || s2.row > source_max.1 {
// log::debug!("s1.1: {}, max.1: {}", s1.1, source_max.1); // log::debug!("s1.1: {}, max.1: {}", s1.1, source_max.1);
return Err("Source region is out-of-bounds! (Too wide)"); return Err("Source region is out-of-bounds! (Too wide)");
} }
@ -325,28 +326,34 @@ impl TransferRegion {
} }
} }
fn create_dense_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> Vec<(u8, u8)> { fn create_dense_rectangle(c1: &Well, c2: &Well) -> Vec<Well> {
// Creates a vector of every point between two corners // Creates a vector of every point between two corners
let (c1, c2) = standardize_rectangle(c1, c2); let (c1, c2) = standardize_rectangle(c1, c2);
let mut points = Vec::<(u8, u8)>::new(); let mut points = Vec::<Well>::new();
for i in c1.0..=c2.0 { for i in c1.col..=c2.col {
for j in c1.1..=c2.1 { for j in c1.row..=c2.row {
points.push((i, j)); points.push(Well { col: i, row: j });
} }
} }
points points
} }
fn standardize_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> ((u8, u8), (u8, u8)) { fn standardize_rectangle(c1: &Well, c2: &Well) -> (Well, Well) {
let upper_left_i = u8::min(c1.0, c2.0); let upper_left_i = u8::min(c1.col, c2.col);
let upper_left_j = u8::min(c1.1, c2.1); let upper_left_j = u8::min(c1.row, c2.row);
let bottom_right_i = u8::max(c1.0, c2.0); let bottom_right_i = u8::max(c1.col, c2.col);
let bottom_right_j = u8::max(c1.1, c2.1); let bottom_right_j = u8::max(c1.row, c2.row);
( (
(upper_left_i, upper_left_j), Well {
(bottom_right_i, bottom_right_j), col: upper_left_i,
row: upper_left_j,
},
Well {
col: bottom_right_i,
row: bottom_right_j,
},
) )
} }
@ -363,7 +370,7 @@ impl fmt::Display for TransferRegion {
let mut source_string = String::new(); let mut source_string = String::new();
for i in 1..=source_dims.0 { for i in 1..=source_dims.0 {
for j in 1..=source_dims.1 { for j in 1..=source_dims.1 {
if source_wells.contains(&(i, j)) { if source_wells.contains(&Well { col: i, row: j }) {
source_string.push('x') source_string.push('x')
} else { } else {
source_string.push('.') source_string.push('.')
@ -379,7 +386,7 @@ impl fmt::Display for TransferRegion {
let mut dest_string = String::new(); let mut dest_string = String::new();
for i in 1..=dest_dims.0 { for i in 1..=dest_dims.0 {
for j in 1..=dest_dims.1 { for j in 1..=dest_dims.1 {
if dest_wells.contains(&(i, j)) { if dest_wells.contains(&Well{col: i, row: j}) {
dest_string.push('x') dest_string.push('x')
} else { } else {
dest_string.push('.') dest_string.push('.')

View File

@ -0,0 +1,11 @@
use std::collections::HashMap;
use serde::{Serialize, Deserialize};
/*
#[non_exhaustive]
#[derive(Serialize, Deserialize, Debug, PartialEq)]
pub enum TransferVolume {
Single(f32),
WellMap(HashMap<>),
}
*/

View File

@ -0,0 +1,40 @@
use lazy_static::lazy_static;
use regex::Regex;
use serde::{Deserialize, Serialize};
use super::util::letters_to_num;
#[derive(Clone, Copy, Eq, PartialEq, Serialize, Deserialize, Debug, Hash)]
pub struct Well {
pub row: u8,
pub col: u8,
}
impl Well {
pub fn string_well_to_pt(input: &str) -> Option<Self> {
lazy_static! {
static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap();
// Can this be removed?
static ref REGEX_ALT: Regex = Regex::new(r"(\d+)").unwrap();
}
if let Some(c1) = REGEX.captures(input) {
if let (Some(row), Some(col)) = (letters_to_num(&c1[1]), c1[2].parse::<u8>().ok()) {
return Some(Well { row, col });
} else {
return None;
}
}
None
}
}
impl Into<Well> for (u8, u8) {
fn into(self) -> Well {
Well {
col: self.0,
row: self.1,
}
}
}