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//! Inner VCF header contig map value.
mod builder;
pub mod name;
pub(crate) mod tag;
pub use self::{name::Name, tag::Tag};
use std::{error, fmt, num};
use self::tag::StandardTag;
use super::{Fields, Indexed, Inner, Map, OtherFields};
/// An inner VCF header contig map value.
#[derive(Clone, Debug, Default, Eq, PartialEq)]
pub struct Contig {
length: Option<usize>,
md5: Option<String>,
url: Option<String>,
idx: Option<usize>,
}
impl Inner for Contig {
type StandardTag = StandardTag;
type Builder = builder::Builder;
}
impl Indexed for Contig {
fn idx(&self) -> Option<usize> {
self.idx
}
fn idx_mut(&mut self) -> &mut Option<usize> {
&mut self.idx
}
}
impl Map<Contig> {
/// Creates a VCF header contig map value.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
/// let map = Map::<Contig>::new();
/// ```
pub fn new() -> Self {
Self::default()
}
/// Returns the length.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
/// let map = Map::<Contig>::new();
/// assert!(map.length().is_none());
/// ```
pub fn length(&self) -> Option<usize> {
self.inner.length
}
/// Returns a mutable reference to the length.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
///
/// let mut map = Map::<Contig>::new();
/// assert!(map.length().is_none());
///
/// *map.length_mut() = Some(8);
/// assert_eq!(map.length(), Some(8));
/// ```
pub fn length_mut(&mut self) -> &mut Option<usize> {
&mut self.inner.length
}
/// Returns the MD5 hexdigest.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
/// let map = Map::<Contig>::new();
/// assert!(map.md5().is_none());
/// ```
pub fn md5(&self) -> Option<&str> {
self.inner.md5.as_deref()
}
/// Returns a mutable reference to the MD5 hexdigest.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
///
/// let mut map = Map::<Contig>::new();
/// assert!(map.md5().is_none());
///
/// *map.md5_mut() = Some(String::from("d7eba311421bbc9d3ada44709dd61534"));
/// assert_eq!(map.md5(), Some("d7eba311421bbc9d3ada44709dd61534"));
/// ```
pub fn md5_mut(&mut self) -> &mut Option<String> {
&mut self.inner.md5
}
/// Returns the URL.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
/// let map = Map::<Contig>::new();
/// assert!(map.url().is_none());
/// ```
pub fn url(&self) -> Option<&str> {
self.inner.url.as_deref()
}
/// Returns a mutable reference to the URL.
///
/// # Examples
///
/// ```
/// use noodles_vcf::header::record::value::{map::Contig, Map};
///
/// let mut map = Map::<Contig>::new();
/// assert!(map.url().is_none());
///
/// *map.url_mut() = Some(String::from("https://example.com/reference.fa"));
/// assert_eq!(map.url(), Some("https://example.com/reference.fa"));
/// ```
pub fn url_mut(&mut self) -> &mut Option<String> {
&mut self.inner.url
}
}
impl fmt::Display for Map<Contig> {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
if let Some(length) = self.length() {
write!(f, ",{tag}={length}", tag = tag::LENGTH)?;
}
if let Some(md5) = self.md5() {
write!(f, ",{tag}={md5}", tag = tag::MD5)?;
}
if let Some(url) = self.url() {
write!(f, ",{tag}={url}", tag = tag::URL)?;
}
super::fmt_display_other_fields(f, self.other_fields())?;
if let Some(idx) = self.idx() {
super::fmt_display_idx_field(f, idx)?;
}
Ok(())
}
}
/// An error returned when a raw contig record fails to parse.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
/// A field is missing.
MissingField(Tag),
/// A tag is duplicated.
DuplicateTag(Tag),
/// The ID is invalid.
InvalidId(name::ParseError),
/// The length is invalid.
InvalidLength(num::ParseIntError),
/// The IDX is invalid.
InvalidIdx(num::ParseIntError),
}
impl error::Error for ParseError {
fn source(&self) -> Option<&(dyn error::Error + 'static)> {
match self {
Self::InvalidId(e) => Some(e),
Self::InvalidLength(e) => Some(e),
Self::InvalidIdx(e) => Some(e),
_ => None,
}
}
}
impl fmt::Display for ParseError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
match self {
Self::MissingField(tag) => write!(f, "missing field: {tag}"),
Self::DuplicateTag(tag) => write!(f, "duplicate tag: {tag}"),
Self::InvalidId(_) => write!(f, "invalid ID"),
Self::InvalidLength(_) => write!(f, "invalid length"),
Self::InvalidIdx(_) => write!(f, "invalid IDX"),
}
}
}
impl TryFrom<Fields> for Map<Contig> {
type Error = ParseError;
fn try_from(fields: Fields) -> Result<Self, Self::Error> {
let mut length = None;
let mut md5 = None;
let mut url = None;
let mut idx = None;
let mut other_fields = OtherFields::new();
for (key, value) in fields {
match Tag::from(key) {
tag::ID => return Err(ParseError::DuplicateTag(tag::ID)),
tag::LENGTH => {
parse_length(&value).and_then(|v| try_replace(&mut length, tag::LENGTH, v))?
}
tag::MD5 => try_replace(&mut md5, tag::MD5, value)?,
tag::URL => try_replace(&mut url, tag::URL, value)?,
tag::IDX => parse_idx(&value).and_then(|v| try_replace(&mut idx, tag::IDX, v))?,
Tag::Other(t) => try_insert(&mut other_fields, t, value)?,
}
}
Ok(Self {
inner: Contig {
length,
md5,
url,
idx,
},
other_fields,
})
}
}
fn parse_length(s: &str) -> Result<usize, ParseError> {
s.parse().map_err(ParseError::InvalidLength)
}
fn parse_idx(s: &str) -> Result<usize, ParseError> {
s.parse().map_err(ParseError::InvalidIdx)
}
fn try_replace<T>(option: &mut Option<T>, tag: Tag, value: T) -> Result<(), ParseError> {
if option.replace(value).is_none() {
Ok(())
} else {
Err(ParseError::DuplicateTag(tag))
}
}
fn try_insert(
other_fields: &mut OtherFields<StandardTag>,
tag: super::tag::Other<StandardTag>,
value: String,
) -> Result<(), ParseError> {
use indexmap::map::Entry;
match other_fields.entry(tag) {
Entry::Vacant(entry) => {
entry.insert(value);
Ok(())
}
Entry::Occupied(entry) => {
let (t, _) = entry.remove_entry();
Err(ParseError::DuplicateTag(Tag::Other(t)))
}
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_fmt() -> Result<(), ParseError> {
let map = Map::<Contig>::try_from(vec![
(String::from("length"), String::from("8")),
(
String::from("md5"),
String::from("d7eba311421bbc9d3ada44709dd61534"),
),
(
String::from("URL"),
String::from("https://example.com/reference.fa"),
),
])?;
let expected = r#",length=8,md5=d7eba311421bbc9d3ada44709dd61534,URL=https://example.com/reference.fa"#;
assert_eq!(map.to_string(), expected);
Ok(())
}
#[test]
fn test_try_from_fields_for_map_contig() -> Result<(), Box<dyn std::error::Error>> {
let actual = Map::<Contig>::try_from(Vec::new())?;
let expected = Map::<Contig>::new();
assert_eq!(actual, expected);
Ok(())
}
}