Struct Encoder 

pub struct Encoder<'a, I>
where
    I: Iterator<Item = PseudoAln> + Iterator,
{ /* private fields */ }

Encoder for an iterator over PseudoAlns.

Implementations

impl<'a, I> Encoder<'a, I>

where I: Iterator<Item = PseudoAln> + Iterator,

pub fn new_from_header_and_flags( records: &'a mut I, header: FileHeader, flags: FileFlags, ) -> Result<Self, Box<dyn Error>>

Construct from a FileHeader and FileFlags

Usage

use ahda::PseudoAln;
use ahda::encoder::Encoder;
use ahda::headers::file::{FileHeader, FileFlags};

let header = FileHeader::default();
let flags = FileFlags::default();
let records: Vec<PseudoAln> = Vec::new();
let mut iter = records.into_iter();
let encoder = Encoder::new_from_header_and_flags(&mut iter, header, flags);
assert!(encoder.is_ok());

pub fn new( records: &'a mut I, targets: &[Vec<u8>], sample_name: &[u8], n_queries: usize, ) -> Result<Self, Box<dyn Error>>

Construct from info needed to build the FileHeader and FileFlags.

Usage

use ahda::PseudoAln;
use ahda::encoder::Encoder;

let targets: Vec<Vec<u8>> = Vec::new();
let sample_name: Vec<u8> = Vec::new();
let n_queries: usize = 0;
let records: Vec<PseudoAln> = Vec::new();
let mut iter = records.into_iter();
let encoder = Encoder::new(&mut iter, &targets, &sample_name, n_queries);
assert!(encoder.is_ok());

pub fn set_metadata_compression( &mut self, metadata_compression: &MetadataCompression, )

Change the compression method for FileFlags and BlockFlags, see crate::compression::MetadataCompression for available options.

impl<I> Encoder<'_, I>

where I: Iterator<Item = PseudoAln> + Iterator,

pub fn encode_file_header_and_flags( &mut self, ) -> Result<Vec<u8>, Box<dyn Error>>

Encode the FileHeader and FileFlags and return the encoded bytes.

Will update the fields_present field of FileHeader if called before writing any blocks with Encoder::next.

Usage

use ahda::PseudoAln;
use ahda::encoder::Encoder;

let targets: Vec<Vec<u8>> = Vec::new();
let sample_name: Vec<u8> = Vec::new();
let n_queries: usize = 0;
let records: Vec<PseudoAln> = Vec::new();
let mut iter = records.into_iter();
let mut encoder = Encoder::new(&mut iter, &targets, &sample_name, n_queries).expect("Encoder");

let bytes = encoder.encode_file_header_and_flags();
assert!(bytes.is_ok());

let expected_bytes: Vec<u8> = vec![97, 104, 100, 97, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 22, 0, 0, 0, 0, 0, 0, 0, 31, 139, 8, 0, 0, 0, 0, 0, 0, 255, 99, 96, 0, 0, 255, 18, 217, 65, 2, 0, 0, 0];
assert_eq!(bytes.unwrap(), expected_bytes);

pub fn set_block_size( &mut self, block_size: usize, ) -> Result<(), Box<dyn Error>>

Change the number of PseudoAlns stored per block.

If the underlying bitmap uses a 32-bit address space, the block size is capped at u32::MAX / n_targets regardless of the input argument. For 64-bit address space, the block size is capped at u64::MAX / n_targets.

Trait Implementations

impl<I> Iterator for Encoder<'_, I>

where I: Iterator<Item = PseudoAln> + Iterator,

fn next(&mut self) -> Option<Result<Vec<u8>, Box<dyn Error>>>

Encode the next records block.

Returns bytes containing the encoded BlockHeader, BlockFlags, and PseudoAln vector.

Usage

use ahda::PseudoAln;
use ahda::encoder::Encoder;

let targets = vec!["chr.fasta".as_bytes().to_vec(), "plasmid.fasta".as_bytes().to_vec(), "virus.fasta".as_bytes().to_vec()];
let name = "sample".as_bytes().to_vec();

let records = vec![
    PseudoAln { ones: Some(vec![0]), ones_names: None, query_id: Some(0), query_name: None },
    PseudoAln { ones: Some(vec![0]), ones_names: None, query_id: Some(1), query_name: None },
    PseudoAln { ones: Some(vec![0, 1]), ones_names: None, query_id: Some(2), query_name: None },
    PseudoAln { ones: Some(vec![1]), ones_names: None, query_id: Some(3), query_name: None },
    PseudoAln { ones: Some(vec![]), ones_names: None, query_id: Some(4), query_name: None },
];
let n_records = records.len();
let mut iter = records.into_iter();

let mut encoder = Encoder::new(&mut iter, &targets, &name, n_records).expect("Encoder");

let next_block = encoder.next();
assert!(next_block.is_some());
assert!(next_block.as_ref().unwrap().is_ok());

let bytes = next_block.unwrap().unwrap();;
let expected_bytes: Vec<u8> = vec![5, 0, 0, 0, 1, 0, 0, 0, 40, 0, 0, 0, 28, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 31, 139, 8, 0, 0, 0, 0, 0, 0, 255, 99, 96, 100, 101, 96, 100, 98, 102, 1, 0, 191, 97, 224, 4, 8, 0, 0, 0, 31, 139, 8, 0, 0, 0, 0, 0, 0, 255, 179, 50, 96, 96, 96, 100, 0, 1, 22, 6, 1, 48, 205, 204, 192, 198, 192, 206, 192, 197, 0, 0, 124, 122, 116, 184, 26, 0, 0, 0];

assert_eq!(bytes, expected_bytes);

type Item = Result<Vec<u8>, Box<dyn Error>>

The type of the elements being iterated over.

fn next_chunk<const N: usize>( &mut self, ) -> Result<[Self::Item; N], IntoIter<Self::Item, N>>

where Self: Sized,

🔬This is a nightly-only experimental API. (iter_next_chunk)

Advances the iterator and returns an array containing the next N values.

fn size_hint(&self) -> (usize, Option<usize>)

Returns the bounds on the remaining length of the iterator.

fn count(self) -> usize

where Self: Sized,

Consumes the iterator, counting the number of iterations and returning it.

fn last(self) -> Option<Self::Item>

where Self: Sized,

Consumes the iterator, returning the last element.

fn advance_by(&mut self, n: usize) -> Result<(), NonZero<usize>>

🔬This is a nightly-only experimental API. (iter_advance_by)

Advances the iterator by n elements.

fn nth(&mut self, n: usize) -> Option<Self::Item>

Returns the nth element of the iterator.

fn step_by(self, step: usize) -> StepBy<Self>

where Self: Sized,

Creates an iterator starting at the same point, but stepping by the given amount at each iteration.

fn chain<U>(self, other: U) -> Chain<Self, <U as IntoIterator>::IntoIter>

where Self: Sized, U: IntoIterator<Item = Self::Item>,

Takes two iterators and creates a new iterator over both in sequence.

fn zip<U>(self, other: U) -> Zip<Self, <U as IntoIterator>::IntoIter>

where Self: Sized, U: IntoIterator,

‘Zips up’ two iterators into a single iterator of pairs.

fn intersperse(self, separator: Self::Item) -> Intersperse<Self>

where Self: Sized, Self::Item: Clone,

🔬This is a nightly-only experimental API. (iter_intersperse)

Creates a new iterator which places a copy of separator between items of the original iterator.

fn intersperse_with<G>(self, separator: G) -> IntersperseWith<Self, G>

where Self: Sized, G: FnMut() -> Self::Item,

🔬This is a nightly-only experimental API. (iter_intersperse)

Creates a new iterator which places an item generated by separator between items of the original iterator.

fn map<B, F>(self, f: F) -> Map<Self, F>

where Self: Sized, F: FnMut(Self::Item) -> B,

Takes a closure and creates an iterator which calls that closure on each element.

fn for_each<F>(self, f: F)

where Self: Sized, F: FnMut(Self::Item),

Calls a closure on each element of an iterator.

fn filter<P>(self, predicate: P) -> Filter<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator which uses a closure to determine if an element should be yielded.

fn filter_map<B, F>(self, f: F) -> FilterMap<Self, F>

where Self: Sized, F: FnMut(Self::Item) -> Option<B>,

Creates an iterator that both filters and maps.

fn enumerate(self) -> Enumerate<Self>

where Self: Sized,

Creates an iterator which gives the current iteration count as well as the next value.

fn peekable(self) -> Peekable<Self>

where Self: Sized,

Creates an iterator which can use the peek and peek_mut methods to look at the next element of the iterator without consuming it. See their documentation for more information.

fn skip_while<P>(self, predicate: P) -> SkipWhile<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator that skips elements based on a predicate.

fn take_while<P>(self, predicate: P) -> TakeWhile<Self, P>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Creates an iterator that yields elements based on a predicate.

fn map_while<B, P>(self, predicate: P) -> MapWhile<Self, P>

where Self: Sized, P: FnMut(Self::Item) -> Option<B>,

Creates an iterator that both yields elements based on a predicate and maps.

fn skip(self, n: usize) -> Skip<Self>

where Self: Sized,

Creates an iterator that skips the first n elements.

fn take(self, n: usize) -> Take<Self>

where Self: Sized,

Creates an iterator that yields the first n elements, or fewer if the underlying iterator ends sooner.

fn scan<St, B, F>(self, initial_state: St, f: F) -> Scan<Self, St, F>

where Self: Sized, F: FnMut(&mut St, Self::Item) -> Option<B>,

An iterator adapter which, like fold, holds internal state, but unlike fold, produces a new iterator.

fn flat_map<U, F>(self, f: F) -> FlatMap<Self, U, F>

where Self: Sized, U: IntoIterator, F: FnMut(Self::Item) -> U,

Creates an iterator that works like map, but flattens nested structure.

fn flatten(self) -> Flatten<Self>

where Self: Sized, Self::Item: IntoIterator,

Creates an iterator that flattens nested structure.

fn map_windows<F, R, const N: usize>(self, f: F) -> MapWindows<Self, F, N>

where Self: Sized, F: FnMut(&[Self::Item; N]) -> R,

🔬This is a nightly-only experimental API. (iter_map_windows)

Calls the given function f for each contiguous window of size N over self and returns an iterator over the outputs of f. Like slice::windows(), the windows during mapping overlap as well.

fn fuse(self) -> Fuse<Self>

where Self: Sized,

Creates an iterator which ends after the first None.

fn inspect<F>(self, f: F) -> Inspect<Self, F>

where Self: Sized, F: FnMut(&Self::Item),

Does something with each element of an iterator, passing the value on.

fn by_ref(&mut self) -> &mut Self

where Self: Sized,

Creates a “by reference” adapter for this instance of Iterator.

fn collect<B>(self) -> B

where B: FromIterator<Self::Item>, Self: Sized,

Transforms an iterator into a collection.

fn try_collect<B>( &mut self, ) -> <<Self::Item as Try>::Residual as Residual<B>>::TryType

where Self: Sized, Self::Item: Try, <Self::Item as Try>::Residual: Residual<B>, B: FromIterator<<Self::Item as Try>::Output>,

🔬This is a nightly-only experimental API. (iterator_try_collect)

Fallibly transforms an iterator into a collection, short circuiting if a failure is encountered.

fn collect_into<E>(self, collection: &mut E) -> &mut E

where E: Extend<Self::Item>, Self: Sized,

🔬This is a nightly-only experimental API. (iter_collect_into)

Collects all the items from an iterator into a collection.

fn partition<B, F>(self, f: F) -> (B, B)

where Self: Sized, B: Default + Extend<Self::Item>, F: FnMut(&Self::Item) -> bool,

Consumes an iterator, creating two collections from it.

fn is_partitioned<P>(self, predicate: P) -> bool

where Self: Sized, P: FnMut(Self::Item) -> bool,

🔬This is a nightly-only experimental API. (iter_is_partitioned)

Checks if the elements of this iterator are partitioned according to the given predicate, such that all those that return true precede all those that return false.

fn try_fold<B, F, R>(&mut self, init: B, f: F) -> R

where Self: Sized, F: FnMut(B, Self::Item) -> R, R: Try<Output = B>,

An iterator method that applies a function as long as it returns successfully, producing a single, final value.

fn try_for_each<F, R>(&mut self, f: F) -> R

where Self: Sized, F: FnMut(Self::Item) -> R, R: Try<Output = ()>,

An iterator method that applies a fallible function to each item in the iterator, stopping at the first error and returning that error.

fn fold<B, F>(self, init: B, f: F) -> B

where Self: Sized, F: FnMut(B, Self::Item) -> B,

Folds every element into an accumulator by applying an operation, returning the final result.

fn reduce<F>(self, f: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(Self::Item, Self::Item) -> Self::Item,

Reduces the elements to a single one, by repeatedly applying a reducing operation.

fn try_reduce<R>( &mut self, f: impl FnMut(Self::Item, Self::Item) -> R, ) -> <<R as Try>::Residual as Residual<Option<<R as Try>::Output>>>::TryType

where Self: Sized, R: Try<Output = Self::Item>, <R as Try>::Residual: Residual<Option<Self::Item>>,

🔬This is a nightly-only experimental API. (iterator_try_reduce)

Reduces the elements to a single one by repeatedly applying a reducing operation. If the closure returns a failure, the failure is propagated back to the caller immediately.

fn all<F>(&mut self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> bool,

Tests if every element of the iterator matches a predicate.

fn any<F>(&mut self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> bool,

Tests if any element of the iterator matches a predicate.

fn find<P>(&mut self, predicate: P) -> Option<Self::Item>

where Self: Sized, P: FnMut(&Self::Item) -> bool,

Searches for an element of an iterator that satisfies a predicate.

fn find_map<B, F>(&mut self, f: F) -> Option<B>

where Self: Sized, F: FnMut(Self::Item) -> Option<B>,

Applies function to the elements of iterator and returns the first non-none result.

fn try_find<R>( &mut self, f: impl FnMut(&Self::Item) -> R, ) -> <<R as Try>::Residual as Residual<Option<Self::Item>>>::TryType

where Self: Sized, R: Try<Output = bool>, <R as Try>::Residual: Residual<Option<Self::Item>>,

🔬This is a nightly-only experimental API. (try_find)

Applies function to the elements of iterator and returns the first true result or the first error.

fn position<P>(&mut self, predicate: P) -> Option<usize>

where Self: Sized, P: FnMut(Self::Item) -> bool,

Searches for an element in an iterator, returning its index.

fn max(self) -> Option<Self::Item>

where Self: Sized, Self::Item: Ord,

Returns the maximum element of an iterator.

fn min(self) -> Option<Self::Item>

where Self: Sized, Self::Item: Ord,

Returns the minimum element of an iterator.

fn max_by_key<B, F>(self, f: F) -> Option<Self::Item>

where B: Ord, Self: Sized, F: FnMut(&Self::Item) -> B,

Returns the element that gives the maximum value from the specified function.

fn max_by<F>(self, compare: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> Ordering,

Returns the element that gives the maximum value with respect to the specified comparison function.

fn min_by_key<B, F>(self, f: F) -> Option<Self::Item>

where B: Ord, Self: Sized, F: FnMut(&Self::Item) -> B,

Returns the element that gives the minimum value from the specified function.

fn min_by<F>(self, compare: F) -> Option<Self::Item>

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> Ordering,

Returns the element that gives the minimum value with respect to the specified comparison function.

fn unzip<A, B, FromA, FromB>(self) -> (FromA, FromB)

where FromA: Default + Extend<A>, FromB: Default + Extend<B>, Self: Sized + Iterator<Item = (A, B)>,

Converts an iterator of pairs into a pair of containers.

fn copied<'a, T>(self) -> Copied<Self>

where T: Copy + 'a, Self: Sized + Iterator<Item = &'a T>,

Creates an iterator which copies all of its elements.

fn cloned<'a, T>(self) -> Cloned<Self>

where T: Clone + 'a, Self: Sized + Iterator<Item = &'a T>,

Creates an iterator which clones all of its elements.

fn array_chunks<const N: usize>(self) -> ArrayChunks<Self, N>

where Self: Sized,

🔬This is a nightly-only experimental API. (iter_array_chunks)

Returns an iterator over N elements of the iterator at a time.

fn sum<S>(self) -> S

where Self: Sized, S: Sum<Self::Item>,

Sums the elements of an iterator.

fn product<P>(self) -> P

where Self: Sized, P: Product<Self::Item>,

Iterates over the entire iterator, multiplying all the elements.

fn cmp<I>(self, other: I) -> Ordering

where I: IntoIterator<Item = Self::Item>, Self::Item: Ord, Self: Sized,

Lexicographically compares the elements of this Iterator with those of another.

fn cmp_by<I, F>(self, other: I, cmp: F) -> Ordering

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Ordering,

🔬This is a nightly-only experimental API. (iter_order_by)

Lexicographically compares the elements of this Iterator with those of another with respect to the specified comparison function.

fn partial_cmp<I>(self, other: I) -> Option<Ordering>

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Lexicographically compares the PartialOrd elements of this Iterator with those of another. The comparison works like short-circuit evaluation, returning a result without comparing the remaining elements. As soon as an order can be determined, the evaluation stops and a result is returned.

fn partial_cmp_by<I, F>(self, other: I, partial_cmp: F) -> Option<Ordering>

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> Option<Ordering>,

🔬This is a nightly-only experimental API. (iter_order_by)

Lexicographically compares the elements of this Iterator with those of another with respect to the specified comparison function.

fn eq<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialEq<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are equal to those of another.

fn eq_by<I, F>(self, other: I, eq: F) -> bool

where Self: Sized, I: IntoIterator, F: FnMut(Self::Item, <I as IntoIterator>::Item) -> bool,

🔬This is a nightly-only experimental API. (iter_order_by)

Determines if the elements of this Iterator are equal to those of another with respect to the specified equality function.

fn ne<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialEq<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are not equal to those of another.

fn lt<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically less than those of another.

fn le<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically less or equal to those of another.

fn gt<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically greater than those of another.

fn ge<I>(self, other: I) -> bool

where I: IntoIterator, Self::Item: PartialOrd<<I as IntoIterator>::Item>, Self: Sized,

Determines if the elements of this Iterator are lexicographically greater than or equal to those of another.

fn is_sorted(self) -> bool

where Self: Sized, Self::Item: PartialOrd,

Checks if the elements of this iterator are sorted.

fn is_sorted_by<F>(self, compare: F) -> bool

where Self: Sized, F: FnMut(&Self::Item, &Self::Item) -> bool,

Checks if the elements of this iterator are sorted using the given comparator function.

fn is_sorted_by_key<F, K>(self, f: F) -> bool

where Self: Sized, F: FnMut(Self::Item) -> K, K: PartialOrd,

Checks if the elements of this iterator are sorted using the given key extraction function.