Struct bio_seq::seq::Seq

pub struct Seq<A: Codec> { /* private fields */ }

A sequence of bit-packed characters of arbitrary length

Allocated to the heap

Implementations

impl Seq<Iupac>

pub fn contains(&self, rhs: &SeqSlice<Iupac>) -> bool

impl<A: Codec> Seq<A>

pub fn new() -> Self

pub fn with_capacity(len: usize) -> Self

pub fn nth(&self, i: usize) -> A

pub fn len(&self) -> usize

pub fn is_empty(&self) -> bool

pub fn bit_and(self, rhs: Seq<A>) -> Seq<A>

pub fn bit_or(self, rhs: Seq<A>) -> Seq<A>

pub fn push(&mut self, item: A)

pub fn clear(&mut self)

pub fn pop(&mut self) -> Option<A>

pub fn truncate(&mut self, _len: usize)

pub fn remove(&mut self, _index: usize) -> A

pub fn insert(&mut self, _index: usize, _element: A)

pub fn extend<I: IntoIterator<Item = A>>(&mut self, iter: I)

Methods from Deref<Target = SeqSlice<A>>

pub fn chain( self: &'a SeqSlice<A>, second: &'a SeqSlice<A> ) -> Chain<SeqIter<'a, A>, SeqIter<'a, A>>

pub fn kmers<const K: usize>(&self) -> KmerIter<'_, A, K>

Iterate over sliding windows of size K

pub fn rev(&self) -> RevIter<'_, A>

Iterate over the sequence in reverse order

pub fn windows(&self, width: usize) -> SeqChunks<'_, A>

Iterate over the sequence in overlapping windows of a specified width

This will panic if the length of the window is greater than the length of the sequence.

Example:

use bio_seq::prelude::*;

let seq: Seq<Dna> = "ACTGATCG".try_into().unwrap();
let windows: Vec<Seq<Dna>> = seq.windows(3).collect();
assert_eq!(windows, vec!["ACT", "CTG", "TGA", "GAT", "ATC", "TCG"]);

pub fn chunks(&self, width: usize) -> SeqChunks<'_, A>

Iterate over the sequence in non-overlapping chunks of a specified width

The last incomplete chunk will be excluded if the sequence length is not divisible by the specified width.

Example:

use bio_seq::prelude::*;

let seq: Seq<Dna> = "ACTGATCG".try_into().unwrap();
let chunks: Vec<Seq<Dna>> = seq.chunks(3).collect();
assert_eq!(chunks, vec!["ACT", "GAT"]);

pub fn nth(&self, i: usize) -> A

pub fn len(&self) -> usize

pub fn is_empty(&self) -> bool

pub fn bit_and(&self, rhs: &SeqSlice<A>) -> Seq<A>

pub fn bit_or(&self, rhs: &SeqSlice<A>) -> Seq<A>

Trait Implementations

impl<A: Codec> AsRef<SeqSlice<A>> for Seq<A>

fn as_ref(&self) -> &SeqSlice<A>

Converts this type into a shared reference of the (usually inferred) input type.

impl BitAnd for Seq<Iupac>

type Output = Seq<Iupac>

The resulting type after applying the & operator.

fn bitand(self, rhs: Self) -> Self::Output

Performs the & operation.

impl BitOr for Seq<Iupac>

type Output = Seq<Iupac>

The resulting type after applying the | operator.

fn bitor(self, rhs: Self) -> Self::Output

Performs the | operation.

impl<A: Codec> Borrow<SeqSlice<A>> for Seq<A>

fn borrow(&self) -> &SeqSlice<A>

Immutably borrows from an owned value.

impl<A: Codec> Clone for Seq<A>

fn clone(&self) -> Self

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<A: Debug + Codec> Debug for Seq<A>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<A: Codec> Default for Seq<A>

fn default() -> Self

Returns the “default value” for a type.

impl<A: Codec> Deref for Seq<A>

type Target = SeqSlice<A>

The resulting type after dereferencing.

fn deref(&self) -> &Self::Target

Dereferences the value.

impl<A: Codec> Display for Seq<A>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<A: Codec> Extend<A> for Seq<A>

fn extend<T: IntoIterator<Item = A>>(&mut self, iter: T)

Extends a collection with the contents of an iterator.

fn extend_one(&mut self, item: A)

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

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

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

Reserves capacity in a collection for the given number of additional elements.

impl<A: Codec> From<&SeqSlice<A>> for Seq<A>

fn from(slice: &SeqSlice<A>) -> Self

Converts to this type from the input type.

impl<A: Codec> From<&Vec<A>> for Seq<A>

fn from(vec: &Vec<A>) -> Self

Converts to this type from the input type.

impl<A: Codec, const K: usize> From<Kmer<A, K>> for Seq<A>

fn from(kmer: Kmer<A, K>) -> Self

Converts to this type from the input type.

impl<A: Codec> From<Seq<A>> for String

fn from(seq: Seq<A>) -> Self

Converts to this type from the input type.

impl<A: Codec> From<Seq<A>> for usize

fn from(slice: Seq<A>) -> usize

Converts to this type from the input type.

impl From<Vec<u8>> for Seq<Dna>

fn from(vec: Vec<u8>) -> Self

Converts to this type from the input type.

impl<A: Codec> FromIterator<A> for Seq<A>

fn from_iter<T: IntoIterator<Item = A>>(iter: T) -> Self

Creates a value from an iterator.

impl<A: Codec> FromStr for Seq<A>

type Err = ParseBioError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl<A: Hash + Codec> Hash for Seq<A>

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl<A: Codec> Index<Range<usize>> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, range: Range<usize>) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> Index<RangeFrom<usize>> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, range: RangeFrom<usize>) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> Index<RangeFull> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, _range: RangeFull) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> Index<RangeInclusive<usize>> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, range: RangeInclusive<usize>) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> Index<RangeTo<usize>> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, range: RangeTo<usize>) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> Index<RangeToInclusive<usize>> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, range: RangeToInclusive<usize>) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> Index<usize> for Seq<A>

type Output = SeqSlice<A>

The returned type after indexing.

fn index(&self, i: usize) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: Codec> IndexMut<usize> for Seq<A>

fn index_mut(&mut self, _index: usize) -> &mut SeqSlice<A>

Performs the mutable indexing (container[index]) operation.

impl<'a, A: Codec> IntoIterator for &'a Seq<A>

type Item = A

The type of the elements being iterated over.

type IntoIter = SeqIter<'a, A>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl<A: Ord + Codec> Ord for Seq<A>

fn cmp(&self, other: &Seq<A>) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized + PartialOrd,

Restrict a value to a certain interval.

impl<A: Codec> PartialEq<&Seq<A>> for Seq<A>

fn eq(&self, other: &&Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<&Seq<A>> for SeqSlice<A>

fn eq(&self, other: &&Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<&SeqSlice<A>> for Seq<A>

fn eq(&self, other: &&SeqSlice<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<&str> for Seq<A>

fn eq(&self, other: &&str) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<Seq<A>> for &Seq<A>

fn eq(&self, other: &Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<Seq<A>> for &SeqSlice<A>

fn eq(&self, other: &Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec, const K: usize> PartialEq<Seq<A>> for Kmer<A, K>

fn eq(&self, seq: &Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<Seq<A>> for SeqSlice<A>

fn eq(&self, other: &Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Codec> PartialEq<SeqSlice<A>> for Seq<A>

fn eq(&self, other: &SeqSlice<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: PartialEq + Codec> PartialEq for Seq<A>

fn eq(&self, other: &Seq<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: PartialOrd + Codec> PartialOrd for Seq<A>

fn partial_cmp(&self, other: &Seq<A>) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl<A: Codec + Complement> ReverseComplement for Seq<A>

type Output = Seq<A>

fn revcomp(&self) -> Seq<A>

Reverse complement of a sequence

impl<A: Codec> TryFrom<&[u8]> for Seq<A>

type Error = ParseBioError

The type returned in the event of a conversion error.

fn try_from(s: &[u8]) -> Result<Self, Self::Error>

Performs the conversion.

impl<A: Codec> TryFrom<&str> for Seq<A>

type Error = ParseBioError

The type returned in the event of a conversion error.

fn try_from(s: &str) -> Result<Self, Self::Error>

Performs the conversion.

impl<A: Codec, const K: usize> TryFrom<Seq<A>> for Kmer<A, K>

type Error = ParseBioError

The type returned in the event of a conversion error.

fn try_from(seq: Seq<A>) -> Result<Self, Self::Error>

Performs the conversion.

impl<A: Eq + Codec> Eq for Seq<A>

impl<A: Codec> StructuralPartialEq for Seq<A>