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mod base;
pub use self::base::Base;
use std::{convert::TryFrom, error, fmt, ops::Deref, str::FromStr};
use super::NULL_FIELD;
#[derive(Clone, Debug, Default, Eq, PartialEq)]
pub struct Sequence(Vec<Base>);
impl Deref for Sequence {
type Target = [Base];
fn deref(&self) -> &Self::Target {
&self.0
}
}
impl From<Vec<Base>> for Sequence {
fn from(bases: Vec<Base>) -> Self {
Self(bases)
}
}
impl fmt::Display for Sequence {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
if self.0.is_empty() {
write!(f, "{}", NULL_FIELD)
} else {
for base in &self.0 {
write!(f, "{}", base)?;
}
Ok(())
}
}
}
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
Empty,
InvalidBase(base::TryFromCharError),
}
impl error::Error for ParseError {}
impl fmt::Display for ParseError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::Empty => f.write_str("empty input"),
Self::InvalidBase(e) => write!(f, "invalid base: {}", e),
}
}
}
impl FromStr for Sequence {
type Err = ParseError;
fn from_str(s: &str) -> Result<Self, Self::Err> {
match s {
"" => Err(ParseError::Empty),
NULL_FIELD => Ok(Self::default()),
_ => s
.chars()
.map(|c| c.to_ascii_uppercase())
.map(Base::try_from)
.collect::<Result<Vec<_>, _>>()
.map(Self::from)
.map_err(ParseError::InvalidBase),
}
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_fmt() {
let sequence = Sequence::from(vec![Base::A, Base::T, Base::C, Base::G]);
assert_eq!(sequence.to_string(), "ATCG");
}
#[test]
fn test_from_str() {
let expected = Sequence(vec![Base::A, Base::T, Base::C, Base::G]);
assert_eq!("ATCG".parse::<Sequence>(), Ok(expected));
let expected = Sequence(vec![Base::A, Base::T, Base::C, Base::G]);
assert_eq!("atcg".parse::<Sequence>(), Ok(expected));
let expected = Sequence(vec![Base::A, Base::T, Base::C, Base::G]);
assert_eq!("aTcG".parse::<Sequence>(), Ok(expected));
assert_eq!("*".parse::<Sequence>(), Ok(Sequence::default()));
assert_eq!("".parse::<Sequence>(), Err(ParseError::Empty));
}
}