Struct FastaSequenceStore 

pub struct FastaSequenceStore { /* private fields */ }

A sequence store that holds all sequences in memory, loaded from indexed FASTA files.

Supports loading multiple FASTA files incrementally via add_fasta. Digest computation is skipped when a fresh .refget.json cache exists.

Implementations

impl FastaSequenceStore

pub fn new() -> Self

Create an empty store.

pub fn add_fasta<P: AsRef<Path>>( &mut self, path: P, ) -> StoreResult<Vec<FastaSequenceSummary>>

Load a FASTA file into this store, appending to existing data.

Uses a digest cache if fresh, otherwise computes digests on the fly. Returns summaries for the sequences loaded from this file.

pub fn mark_circular(&mut self, circular_names: &[String])

Mark sequences with matching names as circular.

pub fn from_fasta<P: AsRef<Path>>( path: P, ) -> StoreResult<(Self, Vec<FastaSequenceSummary>)>

Convenience: load a single FASTA file and return the store + summaries.

Trait Implementations

impl Default for FastaSequenceStore

fn default() -> Self

Returns the “default value” for a type.

impl SequenceStore for FastaSequenceStore

fn get_sequence( &self, digest: &str, start: Option<u64>, end: Option<u64>, ) -> StoreResult<Option<Vec<u8>>>

Retrieve sequence bases by digest (MD5 or sha512t24u). Supports optional start/end for subsequence retrieval (0-based, half-open).

fn get_metadata(&self, digest: &str) -> StoreResult<Option<SequenceMetadata>>

Retrieve metadata for a sequence by digest.

fn get_length(&self, digest: &str) -> StoreResult<Option<u64>>

Retrieve the length of a sequence by digest.