Struct SequenceSearchRepository 

pub struct SequenceSearchRepository { /* private fields */ }

Implementations

impl SequenceSearchRepository

pub fn new(pool: PgPool) -> Self

pub async fn reindex( &self, conn: &mut PgConnection, object_id: Uuid, elements: Option<&str>, alphabet: Option<&str>, ) -> Result<usize, DomainError>

Rebuild the k-mer index for one sequence. Idempotent: deletes all existing rows then inserts the current set. Skips sequences whose alphabet is not DNA/RNA, whose elements is empty, or whose length is shorter than K.

pub async fn search( &self, pattern: &str, options: SequenceSearchOptions, ) -> Result<Vec<SequenceMatch>, DomainError>

Exact substring search with reverse-complement awareness. Returns every (sequence, start, strand) where the pattern (or its reverse complement) appears in sbol_sequences.elements.

pub async fn search_many( &self, patterns: &[String], options: SequenceSearchOptions, ) -> Result<Vec<BatchSequenceMatch>, DomainError>

Run search for each pattern. Patterns are independent; the implementation is a simple loop. Use this to amortise HTTP / CLI round-trips when scanning N motifs against the same corpus.

pub async fn align_candidates( &self, query: &str, ) -> Result<Vec<(String, String)>, DomainError>

Candidate sequences for the banded aligner: every indexed DNA/RNA sequence sharing at least one canonical k-mer with query. Unlike candidates_seeded, which seeds only on the query’s first k-mer, this aggregates over every canonical query k-mer so a gapped hit whose head does not match is still admitted. A query shorter than K has no seed and every nucleotide sequence is a candidate.

pub async fn all_nucleotide_sequences( &self, ) -> Result<Vec<(String, String)>, DomainError>

pub async fn sequences_by_iris( &self, iris: &[String], ) -> Result<Vec<(String, String)>, DomainError>

Trait Implementations

impl Clone for SequenceSearchRepository

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.