Struct noodles_bam::record::sequence::Sequence

pub struct Sequence { /* fields omitted */ }

A BAM record sequence.

Implementations

impl Sequence

pub fn new(seq: Vec<u8>, len: usize) -> Self

Creates a sequence by wrapping raw sequence data.

Examples

use noodles_bam::record::Sequence;
let sequence = Sequence::new(vec![0x12, 0x48], 4); // ACGT
assert_eq!(sequence.as_ref(), [0x12, 0x48]);

pub fn is_empty(&self) -> bool

Returns whether the sequence contains any bases.

Examples

use noodles_bam::record::Sequence;

let sequence = Sequence::default();
assert!(sequence.is_empty());

let sequence = Sequence::new(vec![0x12, 0x48], 4); // ACGT
assert!(!sequence.is_empty());

pub fn base_count(&self) -> usize

👎 Deprecated since 0.8.0:

Use Sequence::len instead.

Returns the number of bases in the sequence.

Examples

use noodles_bam::record::Sequence;
let sequence = Sequence::new(vec![0x12, 0x48], 4); // ACGT
assert_eq!(sequence.len(), 4);

pub fn len(&self) -> usize

Returns the number of bases in the sequence.

Examples

use noodles_bam::record::Sequence;
let sequence = Sequence::new(vec![0x12, 0x48], 4); // ACGT
assert_eq!(sequence.len(), 4);

pub fn set_len(&mut self, len: usize)

Returns a mutable reference to the base count.

Examples

use noodles_bam::record::Sequence;
let mut sequence = Sequence::default();
sequence.set_len(2);
assert_eq!(sequence.len(), 2);

pub fn get(&self, i: usize) -> Option<&Base>

Returns a reference to the base at the given index.

If the index is out of bounds, this returns None.

Examples

use noodles_bam::record::{sequence::Base, Sequence};

let sequence = Sequence::new(vec![0x12, 0x48], 4); // ACGT

assert_eq!(sequence.get(1), Some(&Base::C));
assert_eq!(sequence.get(8), None);

pub fn bases(&self) -> Bases<'_>

Returns a iterator over the bases in this sequence.

Examples

use noodles_bam::record::{sequence::Base, Sequence};

let sequence = Sequence::new(vec![0x12, 0x48], 4); // ACGT
let mut bases = sequence.bases();

assert_eq!(bases.next(), Some(Base::A));
assert_eq!(bases.next(), Some(Base::C));
assert_eq!(bases.next(), Some(Base::G));
assert_eq!(bases.next(), Some(Base::T));
assert_eq!(bases.next(), None);

pub fn push(&mut self, base: Base)

Appends a base to the end of the sequence.

Examples

use noodles_bam::record::{sequence::Base, Sequence};

let mut sequence = Sequence::new(vec![0x12, 0x40], 3); // ACG

sequence.push(Base::T);
assert_eq!(sequence.as_ref(), [0x12, 0x48]); // ACGT
assert_eq!(sequence.len(), 4);

sequence.push(Base::A);
assert_eq!(sequence.as_ref(), [0x12, 0x48, 0x10]); //ACGTA
assert_eq!(sequence.len(), 5);

Trait Implementations

impl AsMut<Vec<u8, Global>> for Sequence

fn as_mut(&mut self) -> &mut Vec<u8>

Performs the conversion.

impl AsRef<[u8]> for Sequence

fn as_ref(&self) -> &[u8]

Performs the conversion.

impl Clone for Sequence

fn clone(&self) -> Sequence

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<'a> Debug for Sequence

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

Formats the value using the given formatter.

impl Default for Sequence

fn default() -> Sequence

Returns the “default value” for a type.

impl Display for Sequence

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

Formats the value using the given formatter.

impl From<&'_ Sequence> for Sequence

fn from(sequence: &Sequence) -> Self

Performs the conversion.

impl From<Vec<Base, Global>> for Sequence

fn from(bases: Vec<Base>) -> Self

Performs the conversion.

impl PartialEq<Sequence> for Sequence

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

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

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

This method tests for !=.

impl Eq for Sequence

impl StructuralEq for Sequence

impl StructuralPartialEq for Sequence