parent
06baf0a053
commit
7e321a78c4
GPG Key ID:
7A3F8997BFE894E0
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@ -7,6 +7,7 @@ use super::{string_well_to_pt, TransferRecord, read_csv};
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use crate::plate::{PlateFormat, PlateType};
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use crate::plate_instances::PlateInstance;
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use crate::transfer::Transfer;
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use crate::well::Well;
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use crate::transfer_region::{CustomRegion, Region, TransferRegion};
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use std::collections::HashSet;
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@ -107,7 +108,7 @@ fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
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fn guess_plate_size(plate_filtered_records: &[&TransferRecord], which: PlateType) -> PlateFormat {
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let mut guess = PlateFormat::W96; // Never guess smaller than 96
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for record in plate_filtered_records {
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if let Some((row, col)) = string_well_to_pt(match which {
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if let Some(Well {col, row} ) = string_well_to_pt(match which {
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PlateType::Source => &record.source_well,
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PlateType::Destination => &record.destination_well,
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}) {
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@ -169,8 +170,8 @@ fn get_transfer_for_pair(
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return None;
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}
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let mut source_wells: HashSet<(u8, u8)> = HashSet::new();
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let mut destination_wells: HashSet<(u8, u8)> = HashSet::new();
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let mut source_wells: HashSet<Well> = HashSet::new();
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let mut destination_wells: HashSet<Well> = HashSet::new();
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for record in filtered_records {
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let source_point_opt = string_well_to_pt(&record.source_well);
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let destination_point_opt = string_well_to_pt(&record.destination_well);
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@ -183,8 +184,8 @@ fn get_transfer_for_pair(
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destination_wells.insert(destination_point);
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}
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}
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let source_wells_vec: Vec<(u8, u8)> = source_wells.into_iter().collect();
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let destination_wells_vec: Vec<(u8, u8)> = destination_wells.into_iter().collect();
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let source_wells_vec: Vec<Well> = source_wells.into_iter().collect();
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let destination_wells_vec: Vec<Well> = destination_wells.into_iter().collect();
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let custom_region: Region =
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Region::Custom(CustomRegion::new(source_wells_vec, destination_wells_vec));
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@ -1,4 +1,4 @@
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use crate::transfer::Transfer;
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use crate::{transfer::Transfer, well::Well};
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use crate::util::*;
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use super::{alternative_formats::EchoClientTransferRecord, mangle_headers::mangle_headers, transfer_record::TransferRecordDeserializeIntermediate, TransferRecord};
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@ -22,9 +22,9 @@ pub fn transfer_to_records(
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for d_well in dest_wells {
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records.push(TransferRecord {
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source_plate: src_barcode.to_string(),
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source_well: format!("{}{}", num_to_letters(s_well.0).unwrap(), s_well.1),
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source_well: format!("{}{}", num_to_letters(s_well.col).unwrap(), s_well.row),
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destination_plate: dest_barcode.to_string(),
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destination_well: format!("{}{}", num_to_letters(d_well.0).unwrap(), d_well.1),
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destination_well: format!("{}{}", num_to_letters(d_well.col).unwrap(), d_well.row),
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volume: tr.volume,
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concentration: None,
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})
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@ -53,7 +53,7 @@ pub fn records_to_echo_client_csv(trs: Vec<TransferRecord>) -> Result<String, Bo
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}
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/// Converts "spreadsheet format" well identification to coordinates
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pub fn string_well_to_pt(input: &str) -> Option<(u8, u8)> {
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pub fn string_well_to_pt(input: &str) -> Option<Well> {
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lazy_static! {
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static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap();
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@ -62,7 +62,7 @@ pub fn string_well_to_pt(input: &str) -> Option<(u8, u8)> {
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}
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if let Some(c1) = REGEX.captures(input) {
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if let (Some(row), Some(col)) = (letters_to_num(&c1[1]), c1[2].parse::<u8>().ok()) {
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return Some((row, col))
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return Some((row, col).into())
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} else {
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return None
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}
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@ -3,4 +3,6 @@ pub mod plate;
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pub mod plate_instances;
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pub mod transfer;
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pub mod transfer_region;
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pub mod transfer_volume;
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pub mod well;
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pub mod util;
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@ -2,30 +2,32 @@ use serde::{Deserialize, Serialize};
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use super::plate::Plate;
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use super::well::Well;
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#[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
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pub struct CustomRegion {
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src: Vec<(u8, u8)>,
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dest: Vec<(u8, u8)>,
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src: Vec<Well>,
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dest: Vec<Well>,
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}
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impl CustomRegion {
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pub fn new(src: Vec<(u8, u8)>, dest: Vec<(u8, u8)>) -> Self {
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pub fn new(src: Vec<Well>, dest: Vec<Well>) -> Self {
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CustomRegion { src, dest }
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}
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}
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#[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
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pub enum Region {
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Rect((u8, u8), (u8, u8)),
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Point((u8, u8)),
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Rect(Well, Well),
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Point(Well),
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Custom(CustomRegion),
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}
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impl Default for Region {
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fn default() -> Self {
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Region::Point((1, 1))
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Region::Point(Well { row: 1, col: 1 })
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}
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}
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impl TryFrom<Region> for ((u8, u8), (u8, u8)) {
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impl TryFrom<Region> for (Well, Well) {
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type Error = &'static str;
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fn try_from(region: Region) -> Result<Self, Self::Error> {
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if let Region::Rect(c1, c2) = region {
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@ -37,12 +39,11 @@ impl TryFrom<Region> for ((u8, u8), (u8, u8)) {
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}
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}
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type Corner = (u8, u8);
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type Rectangle = (Corner, Corner);
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type Rectangle = (Well, Well);
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impl Region {
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pub fn new_custom(transfers: &Vec<Rectangle>) -> Self {
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let mut src_pts: Vec<(u8, u8)> = Vec::with_capacity(transfers.len());
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let mut dest_pts: Vec<(u8, u8)> = Vec::with_capacity(transfers.len());
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let mut src_pts: Vec<Well> = Vec::with_capacity(transfers.len());
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let mut dest_pts: Vec<Well> = Vec::with_capacity(transfers.len());
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for transfer in transfers {
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src_pts.push(transfer.0);
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@ -80,10 +81,10 @@ impl Default for TransferRegion {
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}
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impl TransferRegion {
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pub fn get_source_wells(&self) -> Vec<(u8, u8)> {
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pub fn get_source_wells(&self) -> Vec<Well> {
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match &self.source_region {
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Region::Rect(c1, c2) => {
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let mut wells = Vec::<(u8, u8)>::new();
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let mut wells = Vec::<Well>::new();
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let (ul, br) = standardize_rectangle(c1, c2);
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let (interleave_i, interleave_j) = self.interleave_source;
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// NOTE: This will panic if either is 0!
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@ -93,12 +94,12 @@ impl TransferRegion {
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let (interleave_i, interleave_j) =
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(i8::max(interleave_i, 1), i8::max(interleave_j, 1));
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for i in (ul.0..=br.0).step_by(i8::abs(interleave_i) as usize) {
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for j in (ul.1..=br.1).step_by(i8::abs(interleave_j) as usize) {
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for i in (ul.col..=br.col).step_by(i8::abs(interleave_i) as usize) {
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for j in (ul.row..=br.row).step_by(i8::abs(interleave_j) as usize) {
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// NOTE: It looks like we're ignoring negative interleaves,
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// because it wouldn't make a difference here---the same
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// wells will still be involved in the transfer.
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wells.push((i, j))
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wells.push(Well { col: i, row: j })
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}
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}
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wells
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@ -108,14 +109,14 @@ impl TransferRegion {
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}
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}
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pub fn get_destination_wells(&self) -> Vec<(u8, u8)> {
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pub fn get_destination_wells(&self) -> Vec<Well> {
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match &self.source_region {
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Region::Custom(c) => c.dest.clone(),
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_ => {
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let map = self.calculate_map();
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let source_wells = self.get_source_wells();
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let mut wells = Vec::<(u8, u8)>::new();
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let mut wells = Vec::<Well>::new();
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for well in source_wells {
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if let Some(mut dest_wells) = map(well) {
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@ -129,14 +130,14 @@ impl TransferRegion {
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}
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#[allow(clippy::type_complexity)] // Resolving gives inherent associated type error
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pub fn calculate_map(&self) -> Box<dyn Fn((u8, u8)) -> Option<Vec<(u8, u8)>> + '_> {
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pub fn calculate_map(&self) -> Box<dyn Fn(Well) -> Option<Vec<Well>> + '_> {
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// By validating first, we have a stronger guarantee that
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// this function will not panic. :)
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// log::debug!("Validating: {:?}", self.validate());
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if let Err(msg) = self.validate() {
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eprintln!("{}", msg);
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eprintln!("This transfer will be empty.");
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return Box::new(|(_, _)| None);
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return Box::new(|_| None);
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}
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// log::debug!("What is ild? {:?}", self);
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@ -144,10 +145,10 @@ impl TransferRegion {
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let il_dest = self.interleave_dest;
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let il_source = self.interleave_source;
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let source_corners: ((u8, u8), (u8, u8)) = match self.source_region {
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Region::Point((x, y)) => ((x, y), (x, y)),
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let source_corners: (Well, Well) = match self.source_region {
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Region::Point(well) => (well, well),
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Region::Rect(c1, c2) => (c1, c2),
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Region::Custom(_) => ((0, 0), (0, 0)),
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Region::Custom(_) => (Well { col: 0, row: 0 }, Well { col: 0, row: 0 }),
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};
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let (source_ul, _) = standardize_rectangle(&source_corners.0, &source_corners.1);
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// This map is not necessarily injective or surjective,
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@ -157,43 +158,43 @@ impl TransferRegion {
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// Non-replicate transfers:
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match &self.dest_region {
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Region::Point((x, y)) => {
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Box::new(move |(i, j)| {
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if source_wells.contains(&(i, j)) {
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Region::Point(well) => {
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Box::new(move |Well { col: i, row: j }| {
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if source_wells.contains(&Well { col: i, row: j }) {
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// Validity here already checked by self.validate()
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Some(vec![(
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x + i
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.checked_sub(source_ul.0)
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Some(vec![Well {
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col: well.col
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+ i.checked_sub(source_ul.col)
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.expect("Point cannot have been less than UL")
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.checked_div(il_source.0.unsigned_abs())
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.expect("Source interleave cannot be 0")
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.mul(il_dest.0.unsigned_abs()),
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y + j
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.checked_sub(source_ul.1)
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row: well.row
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+ j.checked_sub(source_ul.row)
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.expect("Point cannot have been less than UL")
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.checked_div(il_source.1.unsigned_abs())
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.expect("Source interleave cannot be 0")
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.mul(il_dest.1.unsigned_abs()),
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)])
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}])
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} else {
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None
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}
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})
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}
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Region::Rect(c1, c2) => {
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Box::new(move |(i, j)| {
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if source_wells.contains(&(i, j)) {
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Box::new(move |Well { col: i, row: j }| {
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if source_wells.contains(&Well { col: i, row: j }) {
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let possible_destination_wells = create_dense_rectangle(c1, c2);
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let (d_ul, d_br) = standardize_rectangle(c1, c2);
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let (s_ul, s_br) =
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standardize_rectangle(&source_corners.0, &source_corners.1);
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let s_dims = (
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s_br.0.checked_sub(s_ul.0).unwrap() + 1,
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s_br.1.checked_sub(s_ul.1).unwrap() + 1,
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s_br.col.checked_sub(s_ul.col).unwrap() + 1,
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s_br.row.checked_sub(s_ul.row).unwrap() + 1,
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);
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let d_dims = (
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d_br.0.checked_sub(d_ul.0).unwrap() + 1,
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d_br.1.checked_sub(d_ul.1).unwrap() + 1,
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d_br.col.checked_sub(d_ul.col).unwrap() + 1,
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d_br.row.checked_sub(d_ul.row).unwrap() + 1,
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);
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let number_used_src_wells = (
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// Number of used source wells
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@ -222,34 +223,34 @@ impl TransferRegion {
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.unwrap() as u8,
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);
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let i = i
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.saturating_sub(s_ul.0)
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.saturating_sub(s_ul.col)
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.saturating_div(il_source.0.unsigned_abs());
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let j = j
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.saturating_sub(s_ul.1)
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.saturating_sub(s_ul.row)
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.saturating_div(il_source.1.unsigned_abs());
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Some(
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possible_destination_wells
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.into_iter()
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.filter(|(x, _)| {
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x.checked_sub(d_ul.0).unwrap()
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.filter(|Well { col, .. }| {
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col.checked_sub(d_ul.col).unwrap()
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% (number_used_src_wells.0 * il_dest.0.unsigned_abs()) // Counter along x
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== (il_dest.0.unsigned_abs() *i)
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% (number_used_src_wells.0 * il_dest.0.unsigned_abs())
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})
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.filter(|(_, y)| {
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y.checked_sub(d_ul.1).unwrap()
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.filter(|Well { row, .. }| {
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row.checked_sub(d_ul.row).unwrap()
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% (number_used_src_wells.1 * il_dest.1.unsigned_abs()) // Counter along u
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== (il_dest.1.unsigned_abs() *j)
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% (number_used_src_wells.1 * il_dest.1.unsigned_abs())
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})
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.filter(|(x, y)| {
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.filter(|Well { col, row }| {
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// How many times have we replicated? < How many are we allowed
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// to replicate?
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x.checked_sub(d_ul.0).unwrap().div_euclid(
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col.checked_sub(d_ul.col).unwrap().div_euclid(
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number_used_src_wells.0 * il_dest.0.unsigned_abs(),
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) < count.0
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&& y.checked_sub(d_ul.1).unwrap().div_euclid(
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&& row.checked_sub(d_ul.row).unwrap().div_euclid(
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number_used_src_wells.1 * il_dest.1.unsigned_abs(),
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) < count.1
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})
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@ -260,14 +261,14 @@ impl TransferRegion {
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}
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})
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}
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Region::Custom(c) => Box::new(move |(i, j)| {
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Region::Custom(c) => Box::new(move |Well { col: i, row: j }| {
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let src = c.src.clone();
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let dest = c.dest.clone();
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let points: Vec<(u8, u8)> = src
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let points: Vec<Well> = src
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.iter()
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.enumerate()
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.filter(|(_index, (x, y))| *x == i && *y == j)
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.filter(|(_index, Well { col, row })| *col == i && *row == j)
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.map(|(index, _)| dest[index])
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.collect();
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if points.is_empty() {
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@ -296,15 +297,15 @@ impl TransferRegion {
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// later
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Region::Rect(s1, s2) => {
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// Check if all source wells exist:
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if s1.0 == 0 || s1.1 == 0 || s2.0 == 0 || s2.1 == 0 {
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if s1.col == 0 || s1.row == 0 || s2.col == 0 || s2.row == 0 {
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return Err("Source region is out-of-bounds! (Too small)");
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}
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// Sufficient to check if the corners are in-bounds
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let source_max = self.source_plate.size();
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if s1.0 > source_max.0 || s2.0 > source_max.0 {
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if s1.col > source_max.0 || s2.col > source_max.0 {
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return Err("Source region is out-of-bounds! (Too tall)");
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}
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if s1.1 > source_max.1 || s2.1 > source_max.1 {
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if s1.row > source_max.1 || s2.row > source_max.1 {
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// log::debug!("s1.1: {}, max.1: {}", s1.1, source_max.1);
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return Err("Source region is out-of-bounds! (Too wide)");
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}
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@ -325,28 +326,34 @@ impl TransferRegion {
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}
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}
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fn create_dense_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> Vec<(u8, u8)> {
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fn create_dense_rectangle(c1: &Well, c2: &Well) -> Vec<Well> {
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// Creates a vector of every point between two corners
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let (c1, c2) = standardize_rectangle(c1, c2);
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let mut points = Vec::<(u8, u8)>::new();
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for i in c1.0..=c2.0 {
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for j in c1.1..=c2.1 {
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points.push((i, j));
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let mut points = Vec::<Well>::new();
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for i in c1.col..=c2.col {
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for j in c1.row..=c2.row {
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points.push(Well { col: i, row: j });
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}
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}
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points
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}
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fn standardize_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> ((u8, u8), (u8, u8)) {
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let upper_left_i = u8::min(c1.0, c2.0);
|
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let upper_left_j = u8::min(c1.1, c2.1);
|
||||
let bottom_right_i = u8::max(c1.0, c2.0);
|
||||
let bottom_right_j = u8::max(c1.1, c2.1);
|
||||
fn standardize_rectangle(c1: &Well, c2: &Well) -> (Well, Well) {
|
||||
let upper_left_i = u8::min(c1.col, c2.col);
|
||||
let upper_left_j = u8::min(c1.row, c2.row);
|
||||
let bottom_right_i = u8::max(c1.col, c2.col);
|
||||
let bottom_right_j = u8::max(c1.row, c2.row);
|
||||
(
|
||||
(upper_left_i, upper_left_j),
|
||||
(bottom_right_i, bottom_right_j),
|
||||
Well {
|
||||
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();
|
||||
for i in 1..=source_dims.0 {
|
||||
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')
|
||||
} else {
|
||||
source_string.push('.')
|
||||
|
|
@ -379,7 +386,7 @@ impl fmt::Display for TransferRegion {
|
|||
let mut dest_string = String::new();
|
||||
for i in 1..=dest_dims.0 {
|
||||
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')
|
||||
} else {
|
||||
dest_string.push('.')
|
||||
|
|
|
|||
|
|
@ -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<>),
|
||||
}
|
||||
*/
|
||||
|
|
@ -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,
|
||||
}
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue