Struct nafcodec::DecoderBuilder

pub struct DecoderBuilder { /* private fields */ }

A builder to configure and initialize a Decoder.

The fields to decode are opt-out: by default, the Decoder will extract all available fields found in the archive into each Record. Use the provided methods to avoid decoding uneeded fields.

For instance, to read a nucleotide archive and only extract sequences names, skipping decoding of sequences:

let decoder = nafcodec::DecoderBuilder::new()
    .sequence(false)
    .quality(false)
    .with_path("../data/phix.naf")
    .unwrap();
for record in decoder.map(Result::unwrap) {
    println!(">{}", record.id.unwrap());
}

Implementations

impl DecoderBuilder

pub fn new() -> Self

Create a new decoder builder with default parameters.

By default, all fields are extracted if they are available in the header.

pub fn from_flags<F: Into<Flags>>(flags: F) -> Self

Create a new decoder builder from the given flags.

This constructor can be used as a shortcut to setup decoding of a subset of supported fields. For instance, to read only the sequence identifiers and quality lines from an archive:

let mut decoder = DecoderBuilder::from_flags(Flag::Id | Flag::Quality)
    .with_path("../data/phix.naf")
    .unwrap();

let record = decoder.next().unwrap().unwrap();
assert!(record.sequence.is_none());
assert!(record.quality.is_some());

pub fn buffer_size(&mut self, buffer_size: usize) -> &mut Self

The buffer size to use while reading.

Note that Decoder uses a lot of buffered I/O, and that more than one buffer will be created. Nevertheless, a higher value will reduce the necessity to seek the reader while reading the different blocks.

By default, a buffer size of 4KiB is used for each internal buffer.

pub fn id(&mut self, id: bool) -> &mut Self

Whether or not to decode the sequence identifiers if available.

pub fn comment(&mut self, comment: bool) -> &mut Self

Whether or not to decode the sequence comment if available.

pub fn sequence(&mut self, sequence: bool) -> &mut Self

Whether or not to decode the sequence string if available.

pub fn quality(&mut self, quality: bool) -> &mut Self

Whether or not to decode the quality string if available.

pub fn mask(&mut self, mask: bool) -> &mut Self

Whether or not to perform region masking in the output sequence.

pub fn with_bytes<'data, 'z>( &self, bytes: &'data [u8] ) -> Result<Decoder<'z, BufReader<Cursor<&'data [u8]>>>, Error>

Consume the builder to get a decoder reading data from the given buffer.

pub fn with_path<'z, P: AsRef<Path>>( &self, path: P ) -> Result<Decoder<'z, BufReader<File>>, Error>

Consume the builder to get a decoder reading a file at the given path.

pub fn with_reader<'z, R: BufRead + Seek>( &self, reader: R ) -> Result<Decoder<'z, R>, Error>

Consume the builder to get a decoder reading data from reader.

Trait Implementations

impl Clone for DecoderBuilder

fn clone(&self) -> DecoderBuilder

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for DecoderBuilder

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

Formats the value using the given formatter.

impl Default for DecoderBuilder

fn default() -> Self

Returns the “default value” for a type.