Struct Reader

Source

pub struct Reader<T>(/* private fields */)
where
    T: BufRead;

Expand description

A chain file reader.

Implementations§

Source §

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

Source

pub fn new(inner: T) -> Self

Creates a chain file reader.

§Examples

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let reader = chainfile::Reader::new(&data[..]);

Source

pub fn inner(&self) -> &T

Gets a reference to the inner reader.

§Examples

use std::io;

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let cursor = io::Cursor::new(data);

let reader = chainfile::Reader::new(cursor);
assert_eq!(reader.inner().position(), 0);

Source

pub fn inner_mut(&mut self) -> &mut T

Gets a mutable reference to the inner reader.

§Examples

use std::io::Read;

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let mut reader = chainfile::Reader::new(&data[..]);
let mut buffer = vec![0; data.len()];

reader.inner_mut().read_exact(&mut buffer).unwrap();
assert_eq!(buffer, data[..]);

Source

pub fn into_inner(self) -> T

Consumes self and returns the inner reader.

§Examples

use std::io::BufRead;

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let reader = chainfile::Reader::new(&data[..]);
let mut lines = reader.into_inner().lines().map(|line| line.unwrap());

assert_eq!(
    lines.next(),
    Some(String::from("chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1"))
);
assert_eq!(lines.next(), Some(String::from("3\t0\t1")));
assert_eq!(lines.next(), Some(String::from("1")));
assert_eq!(lines.next(), None);

Source

pub fn read_line_raw(&mut self, buffer: &mut String) -> Result<usize>

Reads a raw, textual line from the underlying reader.

§Examples

use std::io;

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let mut reader = chainfile::Reader::new(&data[..]);

let mut buffer = String::new();

assert_eq!(reader.read_line_raw(&mut buffer)?, 36);
assert_eq!(buffer, "chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1");

assert_eq!(reader.read_line_raw(&mut buffer)?, 6);
assert_eq!(buffer, "3\t0\t1");

assert_eq!(reader.read_line_raw(&mut buffer)?, 1);
assert_eq!(buffer, "1");

assert_eq!(reader.read_line_raw(&mut buffer)?, 0);

Source

pub fn read_line(&mut self, buffer: &mut String) -> Result<Option<Line>, Error>

Attempts to read a Line from the underlying reader.

§Examples

use std::io;

use chainfile::Line;

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let mut reader = chainfile::Reader::new(&data[..]);

let mut buffer = String::new();
assert!(matches!(
    reader.read_line(&mut buffer)?,
    Some(Line::Header(_))
));
assert!(matches!(
    reader.read_line(&mut buffer)?,
    Some(Line::AlignmentData(_))
));
assert!(matches!(
    reader.read_line(&mut buffer)?,
    Some(Line::AlignmentData(_))
));
assert!(matches!(reader.read_line(&mut buffer)?, None));

Source

pub fn lines(&mut self) -> impl Iterator<Item = Result<Line>> + '_

Returns an iterator over the Lines in the underlying reader.

§Examples

use std::io::BufRead;

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let mut reader = chainfile::Reader::new(&data[..]);

let lines = reader.lines().collect::<Vec<_>>();
assert_eq!(lines.len(), 3);

Source

pub fn sections(&mut self) -> Sections<'_, T> ⓘ

Returns an iterator over the alignment sections in the underlying reader.

§Examples

let data = b"chain 0 seq0 4 + 0 4 seq0 5 - 0 5 1\n3\t0\t1\n1";
let mut reader = chainfile::Reader::new(&data[..]);

let sections = reader
    .sections()
    .map(|result| result.unwrap())
    .collect::<Vec<_>>();
assert_eq!(sections.len(), 1);