Struct NucleotideSequence

pub struct NucleotideSequence { /* private fields */ }

BLAST database representation of a nucleotide sequence.

This representation is divided into two different parts:

• Sequence encoding packed down to 2 bits per base. Ambiguous bases are resolved at random.
• Description of the ranges containing ambiguous bases.

This can easily converted to and from a FASTA string:

use blastdb_sequence_util::{Ncbi8naBase, NucleotideSequence};
let fasta = "acgtACGT";
let seq: NucleotideSequence = fasta.as_bytes().iter().map(|b| Ncbi8naBase::try_from(*b)).collect::<Result<_, _>>().unwrap();
let normalized_fasta: String = seq.iter().map(|b| char::from(b)).collect();  // ACGTACGT

Implementations

impl NucleotideSequence

pub fn new(seq: Vec<u8>, amb: Vec<u8>) -> NucleotideSequence

Create a NucleotideSequence from sequence and ambiguity streams.

pub fn len(&self) -> usize

Return the number of bases in the sequence.

pub fn is_empty(&self) -> bool

pub fn iter(&self) -> SequenceIter<'_, '_>

Iterate over Ncbi8na representation of sequence data.

pub fn sequence_bytes(&self) -> &[u8]

Return the raw sequence bytes for storage.

pub fn ambiguity_bytes(&self) -> &[u8]

Return the raw ambiguity bytes for storage.

Trait Implementations

impl Display for NucleotideSequence

Render the sequence as an IUPAC nucleic acide sequence.

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

Formats the value using the given formatter.

impl FromIterator<Ncbi8naBase> for NucleotideSequence

fn from_iter<T>(into_iter: T) -> Self

where T: IntoIterator<Item = Ncbi8naBase>,

Creates a value from an iterator.

impl FromStr for NucleotideSequence

type Err = NucleotideConversionError

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.