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pub mod allele;
pub use self::allele::Allele;
use std::{error, fmt, ops::Deref, str::FromStr};
use super::MISSING_FIELD;
const DELIMITER: char = ',';
#[derive(Clone, Debug, Default, PartialEq, Eq)]
pub struct AlternateBases(Vec<Allele>);
impl Deref for AlternateBases {
type Target = [Allele];
fn deref(&self) -> &Self::Target {
&self.0
}
}
impl fmt::Display for AlternateBases {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
if self.is_empty() {
f.write_str(MISSING_FIELD)
} else {
for (i, allele) in self.iter().enumerate() {
if i > 0 {
f.write_str(",")?;
}
write!(f, "{}", allele)?;
}
Ok(())
}
}
}
impl From<Vec<Allele>> for AlternateBases {
fn from(alleles: Vec<Allele>) -> Self {
Self(alleles)
}
}
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
Empty,
InvalidAllele(allele::ParseError),
}
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::InvalidAllele(e) => write!(f, "invalid allele: {}", e),
}
}
}
impl FromStr for AlternateBases {
type Err = ParseError;
fn from_str(s: &str) -> Result<Self, Self::Err> {
match s {
"" => Err(ParseError::Empty),
MISSING_FIELD => Ok(Self::default()),
_ => s
.split(DELIMITER)
.map(|s| s.parse().map_err(ParseError::InvalidAllele))
.collect::<Result<_, _>>()
.map(Self),
}
}
}
#[cfg(test)]
mod tests {
use crate::record::reference_bases::Base;
use super::*;
#[test]
fn test_fmt() {
let alternate_bases = AlternateBases(vec![Allele::Bases(vec![Base::G])]);
assert_eq!(alternate_bases.to_string(), "G");
let alternate_bases = AlternateBases(vec![
Allele::Bases(vec![Base::G]),
Allele::Bases(vec![Base::T]),
]);
assert_eq!(alternate_bases.to_string(), "G,T");
let alternate_bases = AlternateBases(vec![]);
assert_eq!(alternate_bases.to_string(), ".");
}
#[test]
fn test_from_str() {
assert_eq!(".".parse(), Ok(AlternateBases::default()));
assert_eq!(
"G".parse(),
Ok(AlternateBases::from(vec![Allele::Bases(vec![Base::G])]))
);
assert_eq!(
"G,T".parse(),
Ok(AlternateBases::from(vec![
Allele::Bases(vec![Base::G]),
Allele::Bases(vec![Base::T]),
]))
);
assert_eq!("".parse::<AlternateBases>(), Err(ParseError::Empty));
}
}