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mod lazy_line;
use futures::{stream, Stream, TryStreamExt};
use tokio::io::{self, AsyncBufRead, AsyncBufReadExt};
use self::lazy_line::read_lazy_line;
use crate::{lazy, Directive, Line, Record};
/// An async GFF reader.
pub struct Reader<R> {
inner: R,
buf: String,
}
impl<R> Reader<R> {
/// Returns a reference to the underlying reader.
///
/// # Examples
///
/// ```
/// use noodles_gff as gff;
/// use tokio::io;
/// let reader = gff::r#async::io::Reader::new(io::empty());
/// let _inner = reader.get_ref();
/// ```
pub fn get_ref(&self) -> &R {
&self.inner
}
/// Returns a mutable reference to the underlying reader.
///
/// # Examples
///
/// ```
/// use noodles_gff as gff;
/// use tokio::io;
/// let mut reader = gff::r#async::io::Reader::new(io::empty());
/// let _inner = reader.get_mut();
/// ```
pub fn get_mut(&mut self) -> &mut R {
&mut self.inner
}
/// Unwraps and returns the underlying reader.
///
/// # Examples
///
/// ```
/// use noodles_gff as gff;
/// use tokio::io;
/// let reader = gff::r#async::io::Reader::new(io::empty());
/// let _inner = reader.into_inner();
/// ```
pub fn into_inner(self) -> R {
self.inner
}
}
impl<R> Reader<R>
where
R: AsyncBufRead + Unpin,
{
/// Creates an async GFF reader.
///
/// # Examples
///
/// ```
/// use noodles_gff as gff;
/// use tokio::io;
/// let reader = gff::r#async::io::Reader::new(io::empty());
/// ```
pub fn new(inner: R) -> Self {
Self {
inner,
buf: String::new(),
}
}
/// Reads a raw GFF line.
///
/// # Examples
///
/// ```
/// # #[tokio::main]
/// # async fn main() -> tokio::io::Result<()> {
/// use noodles_gff as gff;
///
/// let data = b"##gff-version 3\n";
/// let mut reader = gff::r#async::io::Reader::new(&data[..]);
///
/// let mut buf = String::new();
/// reader.read_line(&mut buf).await?;
/// assert_eq!(buf, "##gff-version 3");
/// # Ok(())
/// # }
/// ```
pub async fn read_line(&mut self, buf: &mut String) -> io::Result<usize> {
read_line(&mut self.inner, buf).await
}
/// Reads a lazy line.
///
/// # Examples
///
/// ```
/// # #[tokio::main]
/// # async fn main() -> tokio::io::Result<()> {
/// use noodles_gff::{self as gff, lazy};
///
/// let data = b"##gff-version 3\n";
/// let mut reader = gff::r#async::io::Reader::new(&data[..]);
///
/// let mut line = lazy::Line::default();
/// reader.read_lazy_line(&mut line).await?;
/// assert_eq!(line, lazy::Line::Directive(String::from("##gff-version 3")));
/// # Ok(())
/// # }
/// ```
pub async fn read_lazy_line(&mut self, line: &mut lazy::Line) -> io::Result<usize> {
read_lazy_line(&mut self.inner, &mut self.buf, line).await
}
/// Returns a stream over lines.
///
/// # Examples
///
/// ```
/// # #[tokio::main]
/// # async fn main() -> tokio::io::Result<()> {
/// use noodles_gff as gff;
/// use futures::TryStreamExt;
///
/// let data = b"##gff-version 3\n";
/// let mut reader = gff::r#async::io::Reader::new(&data[..]);
/// let mut lines = reader.lines();
///
/// let line = lines.try_next().await?;
/// assert!(matches!(line, Some(gff::Line::Directive(_))));
///
/// assert!(lines.try_next().await?.is_none());
/// # Ok(())
/// # }
/// ```
pub fn lines(&mut self) -> impl Stream<Item = io::Result<Line>> + '_ {
Box::pin(stream::try_unfold(
(self, String::new()),
|(reader, mut buf)| async {
buf.clear();
reader.read_line(&mut buf).await.and_then(|n| match n {
0 => Ok(None),
_ => match buf.parse() {
Ok(line) => Ok(Some((line, (reader, buf)))),
Err(e) => Err(io::Error::new(io::ErrorKind::InvalidData, e)),
},
})
},
))
}
/// Returns a stream over records.
///
/// # Examples
///
/// ```
/// # #[tokio::main]
/// # async fn main() -> tokio::io::Result<()> {
/// use noodles_gff as gff;
/// use futures::TryStreamExt;
///
/// let data = b"##gff-version 3\n";
/// let mut reader = gff::r#async::io::Reader::new(&data[..]);
/// let mut records = reader.records();
///
/// assert!(records.try_next().await?.is_none());
/// # Ok(())
/// # }
/// ```
pub fn records(&mut self) -> impl Stream<Item = io::Result<Record>> + '_ {
Box::pin(stream::try_unfold(self.lines(), |mut lines| async {
loop {
match lines.try_next().await? {
None | Some(Line::Directive(Directive::StartOfFasta)) => return Ok(None),
Some(Line::Record(record)) => return Ok(Some((record, lines))),
_ => {}
}
}
}))
}
}
async fn read_line<R>(reader: &mut R, buf: &mut String) -> io::Result<usize>
where
R: AsyncBufRead + Unpin,
{
const LINE_FEED: char = '\n';
const CARRIAGE_RETURN: char = '\r';
match reader.read_line(buf).await {
Ok(0) => Ok(0),
Ok(n) => {
if buf.ends_with(LINE_FEED) {
buf.pop();
if buf.ends_with(CARRIAGE_RETURN) {
buf.pop();
}
}
Ok(n)
}
Err(e) => Err(e),
}
}
#[cfg(test)]
mod tests {
use super::*;
#[tokio::test]
async fn test_read_line() -> io::Result<()> {
async fn t(buf: &mut String, mut data: &[u8], expected: &str) -> io::Result<()> {
buf.clear();
read_line(&mut data, buf).await?;
assert_eq!(buf, expected);
Ok(())
}
let mut buf = String::new();
t(&mut buf, b"noodles\n", "noodles").await?;
t(&mut buf, b"noodles\r\n", "noodles").await?;
t(&mut buf, b"noodles", "noodles").await?;
Ok(())
}
}