Struct FastaImporter 

pub struct FastaImporter { /* private fields */ }

Imports FASTA records and emits SBOL 3 Documents.

FastaImporter::new takes the namespace IRI that the resulting SBOL 3 top-level objects will be rooted under — typically the owning lab or repository (e.g. https://example.org/lab). Component identities are derived as {namespace}/{record-id}.

By default, the alphabet of each record is detected automatically from the sequence text. Call FastaImporter::with_alphabet to override that detection when the data is ambiguous.

Implementations

impl FastaImporter

pub fn new(namespace: impl AsRef<str>) -> Result<Self, ImportError>

Builds a new importer scoped to the supplied namespace IRI.

pub fn with_alphabet(self, alphabet: Alphabet) -> Self

Skips alphabet detection and forces every record to be imported as the supplied Alphabet.

pub fn read<R: Read>( &self, reader: R, ) -> Result<(Document, ImportReport), ImportError>

Reads every record from the supplied reader and returns one SBOL 3 Document containing the emitted Components + Sequences plus an ImportReport tallying what was produced.

pub fn read_str( &self, input: &str, ) -> Result<(Document, ImportReport), ImportError>

Reads from a string slice.

pub fn read_path( &self, path: impl AsRef<Path>, ) -> Result<(Document, ImportReport), ImportError>

Reads from a file on disk (.fasta / .fa / .fna / .faa — the importer doesn’t actually care about the extension).

Trait Implementations

impl Clone for FastaImporter

fn clone(&self) -> FastaImporter

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FastaImporter

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

Formats the value using the given formatter.