Struct noodles_core::region::Region

pub struct Region { /* private fields */ }

A genomic region.

A genomic region describes a region on a reference sequence. It consists of reference sequence name and an interval.

They are represented in text as reference-sequence-name[:start[-end]], where the start and end positions are 1-based, inclusive. If no end position is given, it is assumed to span from the start to the end of the reference sequence. If no interval is given, it is assumed to span the entirety of the reference sequence.

Implementations

impl Region

pub fn new<N, I>(name: N, interval: I) -> Self

where N: Into<BString>, I: Into<Interval>,

Creates a region.

Positions are assumed to be 1-based.

Examples

use noodles_core::{Region, Position};

let start = Position::try_from(5)?;
let end = Position::try_from(8)?;
let region = Region::new("sq0", start..=end);

pub fn name(&self) -> &BStr

Returns the reference name of the region.

Examples

use noodles_core::{Position, Region};

let start = Position::try_from(5)?;
let end = Position::try_from(8)?;
let region = Region::new("sq0", start..=end);

assert_eq!(region.name(), &b"sq0"[..]);

pub fn start(&self) -> Bound<Position>

Returns the start position of the region (1-based).

Examples

use noodles_core::{Position, Region};

let start = Position::try_from(5)?;
let region = Region::new("sq0", start..);

assert_eq!(region.start(), Bound::Included(start));

pub fn end(&self) -> Bound<Position>

Returns the end position of the region (1-based).

Examples

use noodles_core::{Position, Region};

let end = Position::try_from(8)?;
let region = Region::new("sq0", ..=end);

assert_eq!(region.end(), Bound::Included(end));

pub fn interval(&self) -> Interval

Returns the start and end positions as an interval.

Examples

use noodles_core::{region::Interval, Position, Region};

let start = Position::try_from(5)?;
let end = Position::try_from(8)?;
let region = Region::new("sq0", start..=end);

assert_eq!(region.interval(), Interval::from(start..=end));

Trait Implementations

impl Clone for Region

fn clone(&self) -> Region

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Region

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Display for Region

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl FromStr for Region

type Err = ParseError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl PartialEq for Region

fn eq(&self, other: &Region) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for Region

impl StructuralPartialEq for Region