Struct seq_io::fasta::RefRecord

pub struct RefRecord<'a> { /* private fields */ }

A FASTA record that borrows data from a buffer.

Implementations

impl<'a> RefRecord<'a>

pub fn seq_lines(&self) -> SeqLines<'_>

Return an iterator over all sequence lines in the data

pub fn num_seq_lines(&self) -> usize

Returns the number of sequence lines. Equivalent to self.seq_lines().len()

pub fn full_seq(&self) -> Cow<'_, [u8]>

Returns the full sequence. If the sequence consists of a single line, then the sequence will be borrowed from the underlying buffer (equivalent to calling RefRecord::seq()). If there are multiple lines, an owned copy will be created (equivalent to RefRecord::owned_seq()).

pub fn owned_seq(&self) -> Vec<u8>

Returns the sequence as owned Vec. Note: This function must be called in order to obtain a sequence that does not contain line endings (as returned by seq())

pub fn to_owned_record(&self) -> OwnedRecord

Creates an owned copy of the record.

pub fn write_unchanged<W: Write>(&self, writer: W) -> Result<()>

Writes a record to the given io::Write instance by just writing the unmodified input, which is faster than RefRecord::write

Trait Implementations

impl<'a> Clone for RefRecord<'a>

fn clone(&self) -> RefRecord<'a>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<'a> Debug for RefRecord<'a>

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

Formats the value using the given formatter.

impl<'a> Record for RefRecord<'a>

fn seq(&self) -> &[u8]

Return the FASTA sequence as byte slice. Note that this method of RefRecord returns the raw sequence, which may contain line breaks. Use seq_lines() to iterate over all lines without breaks, or use full_seq() to access the whole sequence at once.

fn head(&self) -> &[u8]

Return the header line of the record as byte slice

fn write<W: Write>(&self, writer: W) -> Result<()>

Write the record to the given io::Write instance. The sequence will occupy one line only.

fn write_wrap<W: Write>(&self, writer: W, wrap: usize) -> Result<()>

Write the record to the given io::Write instance. The sequence is wrapped to produce multi-line FASTA with a maximum width specified by wrap.

fn id_bytes(&self) -> &[u8]

fn id(&self) -> Result<&str, Utf8Error>

Return the ID of the record (everything before an optional space) as string slice

fn desc_bytes(&self) -> Option<&[u8]>

fn desc(&self) -> Option<Result<&str, Utf8Error>>

Return the description of the record as string slice, if present. Otherwise, None is returned.

fn id_desc_bytes(&self) -> (&[u8], Option<&[u8]>)

Return both the ID and the description of the record (if present) This should be faster than calling id() and desc() separately.

fn id_desc(&self) -> Result<(&str, Option<&str>), Utf8Error>

Return both the ID and the description of the record (if present) This should be faster than calling id() and desc() separately.