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Switch extension trait from IntoIterators to Interators
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@swooster
swooster committed Dec 1, 2022
1 parent 47b9188 commit 6e79826
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Showing 2 changed files with 54 additions and 50 deletions.
13 changes: 9 additions & 4 deletions benches/all_windows.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ use rand::{rngs::OsRng, seq::SliceRandom};
use smallvec::SmallVec;

use quickdna::{
BaseSequence, DnaSequence, Nucleotide, NucleotideLike, Nucleotides, TranslationTable,
BaseSequence, DnaSequence, Nucleotide, NucleotideIter, NucleotideLike, TranslationTable,
};

static PROTEIN_WINDOW_LEN: usize = 20;
Expand Down Expand Up @@ -111,12 +111,13 @@ impl IterBasedSequenceWindows {
fn from_dna(dna: &[Nucleotide], dna_window_len: usize, protein_window_len: usize) -> Self {
let mut aas = SmallVec::new();
let ncbi1 = TranslationTable::Ncbi1.to_fn();
aas.extend(dna.self_reading_frames().into_iter().map(|codons| {
aas.extend(dna.iter().self_reading_frames().into_iter().map(|codons| {
let translated: Vec<_> = codons.map(ncbi1).collect();
String::from_utf8(translated).unwrap()
}));
aas.extend(
dna.reverse_complement()
dna.iter()
.reverse_complement()
.self_reading_frames()
.into_iter()
.map(|codons| {
Expand All @@ -125,7 +126,11 @@ impl IterBasedSequenceWindows {
}),
);

let dna_rc = (&dna).reverse_complement().map(|n| n.to_ascii()).collect();
let dna_rc = dna
.iter()
.reverse_complement()
.map(|n| n.to_ascii())
.collect();
let dna_rc = String::from_utf8(dna_rc).unwrap();

let dna = dna.iter().map(|n| n.to_ascii()).collect();
Expand Down
91 changes: 45 additions & 46 deletions src/iter.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,8 +46,8 @@ impl ToNucleotideLike for &NucleotideAmbiguous {
}
}

/// Extension trait for nucleotide sequences
pub trait Nucleotides: IntoIterator {
/// Extension trait for nucleotide iterators
pub trait NucleotideIter: Iterator + Sized {
/// Returns up to 6 non-empty codon iterators for forward and reverse complement reading frames.
///
/// The foward codon iterators are given before the reverse complement ones, with the forward
Expand All @@ -58,12 +58,12 @@ pub trait Nucleotides: IntoIterator {
/// # Examples
///
/// ```
/// use quickdna::{Nucleotide, Nucleotides};
/// use quickdna::{Nucleotide, NucleotideIter};
///
/// use Nucleotide::*;
/// let dna = [C, G, A, T, C, G, A, T];
///
/// let frames = dna.all_reading_frames();
/// let frames = dna.iter().all_reading_frames();
/// assert_eq!(frames.len(), 6);
/// assert!(frames[0].clone().eq([
/// [C, G, A].into(),
Expand Down Expand Up @@ -92,7 +92,7 @@ pub trait Nucleotides: IntoIterator {
///
/// // The last forward and RC reading frames are omitted
/// // because they would only have 2 nucleotides.
/// let frames = dna[..4].all_reading_frames();
/// let frames = dna[..4].iter().all_reading_frames();
/// assert_eq!(frames.len(), 4);
/// assert!(frames[0].clone().eq([
/// [C, G, A].into(),
Expand All @@ -108,12 +108,12 @@ pub trait Nucleotides: IntoIterator {
/// ]));
///
/// // All reading frames are omitted due to insufficient nucleotides.
/// let frames = dna[..2].all_reading_frames();
/// let frames = dna[..2].iter().all_reading_frames();
/// assert!(frames.is_empty());
/// ```
fn all_reading_frames(self) -> SmallVec<[ForwardOrRcCodons<Self::IntoIter>; 6]>
fn all_reading_frames(self) -> SmallVec<[ForwardOrRcCodons<Self>; 6]>
where
Self::IntoIter: Clone + DoubleEndedIterator + ExactSizeIterator;
Self: Clone + DoubleEndedIterator + ExactSizeIterator;

/// Returns iterator of codons for the first reading frame of this nucleotide sequence.
/// If the number of nucleotides isn't divisible by 3, excess nucleotides are silently
Expand All @@ -123,7 +123,7 @@ pub trait Nucleotides: IntoIterator {
/// # Examples
///
/// ```
/// use quickdna::{Codons, Nucleotide, Nucleotides};
/// use quickdna::{Codons, Nucleotide, NucleotideIter};
///
/// use Nucleotide::*;
/// let dna = [C, G, A, T, C, G, A, T];
Expand All @@ -132,41 +132,41 @@ pub trait Nucleotides: IntoIterator {
/// [C, G, A].into(),
/// [T, C, G].into(),
/// ];
/// assert!(dna.codons().eq(expected_codons));
/// assert!(dna.iter().codons().eq(expected_codons));
///
/// assert!(dna.codons().eq(dna.self_reading_frames().remove(0)));
/// assert!(dna.iter().codons().eq(dna.iter().self_reading_frames().remove(0)));
/// ```
fn codons(self) -> Codons<Self::IntoIter>;
fn codons(self) -> Codons<Self>;

/// Returns iterator of complementary nucleotides.
///
/// # Examples
///
/// ```
/// use quickdna::{Nucleotide, Nucleotides};
/// use quickdna::{Nucleotide, NucleotideIter};
///
/// use Nucleotide::*;
/// let dna = [C, G, A, T];
///
/// assert!(dna.complement().eq([G, C, T, A]));
/// assert!(dna.iter().complement().eq([G, C, T, A]));
/// ```
fn complement(self) -> Complement<Self::IntoIter>;
fn complement(self) -> Complement<Self>;

/// Returns iterator of reverse complement of contained nucleotides.
///
/// # Examples
///
/// ```
/// use quickdna::{Nucleotide, Nucleotides};
/// use quickdna::{Nucleotide, NucleotideIter};
///
/// use Nucleotide::*;
/// let dna = [C, G, A, T];
///
/// assert!(dna.reverse_complement().eq([A, T, C, G]));
/// assert!(dna.iter().reverse_complement().eq([A, T, C, G]));
/// ```
fn reverse_complement(self) -> std::iter::Rev<Complement<Self::IntoIter>>
fn reverse_complement(self) -> std::iter::Rev<Complement<Self>>
where
Self::IntoIter: DoubleEndedIterator;
Self: DoubleEndedIterator;

/// Returns up to 3 non-empty codon iterators for reading frames.
///
Expand All @@ -176,12 +176,12 @@ pub trait Nucleotides: IntoIterator {
/// # Examples
///
/// ```
/// use quickdna::{Nucleotide, Nucleotides};
/// use quickdna::{Nucleotide, NucleotideIter};
///
/// use Nucleotide::*;
/// let dna = [C, G, A, T, C, G, A, T];
///
/// let frames = dna.self_reading_frames();
/// let frames = dna.iter().self_reading_frames();
/// assert_eq!(frames.len(), 3);
/// assert!(frames[0].clone().eq([
/// [C, G, A].into(),
Expand All @@ -197,7 +197,7 @@ pub trait Nucleotides: IntoIterator {
/// ]));
///
/// // The last reading frame is omitted because it would only have 2 nucleotides.
/// let frames = dna[..4].self_reading_frames();
/// let frames = dna[..4].iter().self_reading_frames();
/// assert_eq!(frames.len(), 2);
/// assert!(frames[0].clone().eq([
/// [C, G, A].into(),
Expand All @@ -207,25 +207,24 @@ pub trait Nucleotides: IntoIterator {
/// ]));
///
/// // All reading frames are omitted due to insufficient nucleotides.
/// let frames = dna[..2].self_reading_frames();
/// let frames = dna[..2].iter().self_reading_frames();
/// assert!(frames.is_empty());
/// ```
fn self_reading_frames(self) -> SmallVec<[Codons<Self::IntoIter>; 3]>
fn self_reading_frames(self) -> SmallVec<[Codons<Self>; 3]>
where
Self::IntoIter: Clone + ExactSizeIterator;
Self: Clone + ExactSizeIterator;
}

impl<N, I, T> Nucleotides for T
impl<N, I> NucleotideIter for I
where
N: ToNucleotideLike,
I: Iterator<Item = N>,
T: IntoIterator<IntoIter = I>,
{
fn all_reading_frames(self) -> SmallVec<[ForwardOrRcCodons<Self::IntoIter>; 6]>
fn all_reading_frames(self) -> SmallVec<[ForwardOrRcCodons<Self>; 6]>
where
Self::IntoIter: Clone + DoubleEndedIterator + ExactSizeIterator,
Self: Clone + DoubleEndedIterator + ExactSizeIterator,
{
let iter1 = self.into_iter();
let iter1 = self;
let mut iter2 = iter1.clone();
iter2.next();
let mut iter3 = iter2.clone();
Expand All @@ -249,26 +248,26 @@ where
frames
}

fn codons(self) -> Codons<Self::IntoIter> {
Codons(self.into_iter())
fn codons(self) -> Codons<Self> {
Codons(self)
}

fn complement(self) -> Complement<Self::IntoIter> {
Complement(self.into_iter())
fn complement(self) -> Complement<Self> {
Complement(self)
}

fn reverse_complement(self) -> std::iter::Rev<Complement<Self::IntoIter>>
fn reverse_complement(self) -> std::iter::Rev<Complement<Self>>
where
Self::IntoIter: DoubleEndedIterator,
Self: DoubleEndedIterator,
{
self.complement().rev()
}

fn self_reading_frames(self) -> SmallVec<[Codons<Self::IntoIter>; 3]>
fn self_reading_frames(self) -> SmallVec<[Codons<Self>; 3]>
where
Self::IntoIter: Clone + ExactSizeIterator,
Self: Clone + ExactSizeIterator,
{
let iter1 = self.into_iter();
let iter1 = self;
let mut iter2 = iter1.clone();
iter2.next();
let mut iter3 = iter2.clone();
Expand All @@ -281,8 +280,8 @@ where

/// Adapter yielding codons of the contained iterator.
///
/// This `struct` is created by the [`codons`](Nucleotides::codons)
/// method on [`Nucleotides`]. See its documentation for more.
/// This `struct` is created by the [`codons`](NucleotideIter::codons)
/// method on [`NucleotideIter`]. See its documentation for more.
#[derive(Clone, Debug)]
pub struct Codons<I>(I);

Expand Down Expand Up @@ -339,8 +338,8 @@ where

/// Adapter yielding complementary nucleotide of the contained iterator.
///
/// This `struct` is created by the [`complement`](Nucleotides::complement)
/// method on [`Nucleotides`]. See its documentation for more.
/// This `struct` is created by the [`complement`](NucleotideIter::complement)
/// method on [`NucleotideIter`]. See its documentation for more.
#[derive(Clone, Debug)]
pub struct Complement<I>(I);

Expand Down Expand Up @@ -384,8 +383,8 @@ where

/// Adapter capable of holding either forward codon iterators or reverse complement codon iterators.
///
/// This `struct` is created by the [`all_reading_frames`](Nucleotides::all_reading_frames)
/// method on [`Nucleotides`]. See its documentation for more.
/// This `struct` is created by the [`all_reading_frames`](NucleotideIter::all_reading_frames)
/// method on [`NucleotideIter`]. See its documentation for more.
#[derive(Clone, Debug)]
pub enum ForwardOrRcCodons<I> {
Forward(Codons<I>),
Expand Down Expand Up @@ -449,7 +448,7 @@ mod test {
fn test_reverse_codons() {
use Nucleotide::*;
let dna = [A, A, T, T, C, C, G, G];
let rev_codons: Vec<_> = dna.codons().rev().collect();
let rev_codons: Vec<_> = dna.iter().codons().rev().collect();
let expected = [[T, C, C].into(), [A, A, T].into()];
assert_eq!(rev_codons, expected);
}
Expand Down

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