Struct consalign::Reader

pub struct Reader<B> { /* private fields */ }

A FASTA reader.

Implementations

impl Reader<BufReader<File>>

pub fn from_file<P>(path: P) -> Result<Reader<BufReader<File>>, Error>where P: AsRef<Path> + Debug,

Read FASTA from given file path.

pub fn from_file_with_capacity<P>( capacity: usize, path: P ) -> Result<Reader<BufReader<File>>, Error>where P: AsRef<Path> + Debug,

Read FASTA from give file path and a capacity

impl<R> Reader<BufReader<R>>where R: Read,

pub fn new(reader: R) -> Reader<BufReader<R>>

Create a new Fasta reader given an instance of io::Read.

Example

let reader = Reader::new(fasta_file);

pub fn with_capacity(capacity: usize, reader: R) -> Reader<BufReader<R>>

Create a new Fasta reader given a capacity and an instance of io::Read.

Example

let reader = Reader::with_capacity(16384, fasta_file);

impl<B> Reader<B>where B: BufRead,

pub fn from_bufread(bufreader: B) -> Reader<B>

Create a new Fasta reader with an object that implements io::BufRead.

Example

let buffer = io::BufReader::with_capacity(16384, fasta_file);
let reader = Reader::from_bufread(buffer);

pub fn records(self) -> Records<B>

Return an iterator over the records of this Fasta file.

Example

for record in reader.records() {
    let record = record.unwrap();
    assert_eq!(record.id(), "id");
    assert_eq!(record.desc().unwrap(), "desc");
    assert_eq!(record.seq().to_vec(), b"AAAA");
}

Trait Implementations

impl<B> Clone for Reader<B>where B: Clone,

fn clone(&self) -> Reader<B>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<B> Debug for Reader<B>where B: Debug,

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

Formats the value using the given formatter.

impl<B> Default for Reader<B>where B: Default,

fn default() -> Reader<B>

Returns the “default value” for a type.

impl<'de, B> Deserialize<'de> for Reader<B>where B: Deserialize<'de>,

fn deserialize<__D>( __deserializer: __D ) -> Result<Reader<B>, <__D as Deserializer<'de>>::Error>where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl<B> FastaRead for Reader<B>where B: BufRead,

fn read(&mut self, record: &mut Record) -> Result<(), Error>

Read the next FASTA record into the given Record. An empty record indicates that no more records can be read.

Use this method when you want to read records as fast as possible because it allows the reuse of a Record allocation.

The records iterator provides a more ergonomic approach to accessing FASTA records.

Errors

This function will return an error if the record is incomplete, syntax is violated or any form of I/O error is encountered.

Example

use bio::io::fasta::Record;
use bio::io::fasta::{FastaRead, Reader};

const fasta_file: &'static [u8] = b">id desc
AAAA
";
let mut reader = Reader::new(fasta_file);
let mut record = Record::new();

// Check for errors parsing the record
reader
    .read(&mut record)
    .expect("fasta reader: got an io::Error or could not read_line()");

assert_eq!(record.id(), "id");
assert_eq!(record.desc().unwrap(), "desc");
assert_eq!(record.seq().to_vec(), b"AAAA");

impl<B> Hash for Reader<B>where B: Hash,

fn hash<__H>(&self, state: &mut __H)where __H: Hasher,

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl<B> Ord for Reader<B>where B: Ord,

fn cmp(&self, other: &Reader<B>) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Selfwhere Self: Sized + PartialOrd<Self>,

Restrict a value to a certain interval.

impl<B> PartialEq<Reader<B>> for Reader<B>where B: PartialEq<B>,

fn eq(&self, other: &Reader<B>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<B> PartialOrd<Reader<B>> for Reader<B>where B: PartialOrd<B>,

fn partial_cmp(&self, other: &Reader<B>) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl<B> Serialize for Reader<B>where B: Serialize,

fn serialize<__S>( &self, __serializer: __S ) -> Result<<__S as Serializer>::Ok, <__S as Serializer>::Error>where __S: Serializer,

Serialize this value into the given Serde serializer.

impl<B> Eq for Reader<B>where B: Eq,

impl<B> StructuralEq for Reader<B>

impl<B> StructuralPartialEq for Reader<B>