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mod field;
use std::{error, fmt, str::FromStr};
use self::field::Field;
const FIELD_DELIMITER: char = '\t';
const MAX_FIELDS: usize = 5;
/// A FASTA index record.
#[derive(Debug, Default, Eq, PartialEq)]
pub struct Record {
name: Vec<u8>,
length: u64,
offset: u64,
line_bases: u64,
line_width: u64,
}
impl Record {
/// Creates a FASTA index record.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 8, 4, 80, 81);
/// ```
pub fn new<N>(name: N, length: u64, offset: u64, line_bases: u64, line_width: u64) -> Self
where
N: Into<Vec<u8>>,
{
Self {
name: name.into(),
length,
offset,
line_bases,
line_width,
}
}
/// Returns the record name.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 8, 4, 80, 81);
/// assert_eq!(record.name(), b"sq0");
/// ```
pub fn name(&self) -> &[u8] {
&self.name
}
/// Returns the length of the sequence.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 8, 4, 80, 81);
/// assert_eq!(record.len(), 8);
/// ```
#[allow(clippy::len_without_is_empty)]
#[deprecated(since = "0.23.0", note = "Use `Record::length` instead.")]
pub fn len(&self) -> u64 {
self.length()
}
/// Returns the length of the sequence.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 8, 4, 80, 81);
/// assert_eq!(record.length(), 8);
/// ```
pub fn length(&self) -> u64 {
self.length
}
/// Returns the offset from the start.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 10946, 4, 80, 81);
/// assert_eq!(record.offset(), 4);
/// ```
pub fn offset(&self) -> u64 {
self.offset
}
/// Returns the number of bases in a line.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 10946, 4, 80, 81);
/// assert_eq!(record.line_bases(), 80);
/// ```
pub fn line_bases(&self) -> u64 {
self.line_bases
}
/// Returns the number of characters in a line.
///
/// # Examples
///
/// ```
/// use noodles_fasta::fai;
/// let record = fai::Record::new("sq0", 10946, 4, 80, 81);
/// assert_eq!(record.line_width(), 81);
/// ```
pub fn line_width(&self) -> u64 {
self.line_width
}
}
/// An error returned when a raw FASTA index record fails to parse.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
/// The input is empty.
Empty,
/// A field is missing.
MissingField(Field),
/// A field is invalid.
InvalidField(Field, std::num::ParseIntError),
}
impl error::Error for ParseError {
fn source(&self) -> Option<&(dyn error::Error + 'static)> {
match self {
Self::InvalidField(_, e) => Some(e),
_ => None,
}
}
}
impl fmt::Display for ParseError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::Empty => f.write_str("empty input"),
Self::MissingField(field) => write!(f, "missing field: {field:?}"),
Self::InvalidField(field, _) => write!(f, "invalid field: {field:?}"),
}
}
}
impl FromStr for Record {
type Err = ParseError;
fn from_str(s: &str) -> Result<Self, Self::Err> {
if s.is_empty() {
return Err(ParseError::Empty);
}
let mut fields = s.splitn(MAX_FIELDS, FIELD_DELIMITER);
let name = parse_string(&mut fields, Field::Name)?;
let len = parse_u64(&mut fields, Field::Length)?;
let offset = parse_u64(&mut fields, Field::Offset)?;
let line_bases = parse_u64(&mut fields, Field::LineBases)?;
let line_width = parse_u64(&mut fields, Field::LineWidth)?;
Ok(Self::new(name, len, offset, line_bases, line_width))
}
}
fn parse_string<'a, I>(fields: &mut I, field: Field) -> Result<String, ParseError>
where
I: Iterator<Item = &'a str>,
{
fields
.next()
.ok_or(ParseError::MissingField(field))
.map(|s| s.into())
}
fn parse_u64<'a, I>(fields: &mut I, field: Field) -> Result<u64, ParseError>
where
I: Iterator<Item = &'a str>,
{
fields
.next()
.ok_or(ParseError::MissingField(field))
.and_then(|s| s.parse().map_err(|e| ParseError::InvalidField(field, e)))
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_from_str() {
assert_eq!(
"sq0\t10946\t4\t80\t81".parse(),
Ok(Record::new("sq0", 10946, 4, 80, 81))
);
assert_eq!("".parse::<Record>(), Err(ParseError::Empty));
assert_eq!(
"sq0".parse::<Record>(),
Err(ParseError::MissingField(Field::Length))
);
assert!(matches!(
"sq0\tnoodles".parse::<Record>(),
Err(ParseError::InvalidField(Field::Length, _))
));
}
}