Enum NucleotideCoordinate 

pub enum NucleotideCoordinate {
    Known {
        anchor: NucleotideAnchor,
        coordinate: i32,
        offset: i32,
    },
    Unknown,
}

Nucleotide coordinate written as a known position or ?.

Known coordinates keep the sign written in the HGVS string. For example, c.-1 becomes coordinate() == Some(-1), while c.*1 becomes coordinate() == Some(1). CDS-anchored intronic positions keep the same primary coordinate plus a signed secondary offset, e.g. c.-106+2 becomes coordinate() == Some(-106) and offset() == Some(2).

Examples

use tinyhgvs::{NucleotideAnchor, VariantDescription, parse_hgvs};

let five_prime = parse_hgvs("NM_007373.4:c.-1C>T").unwrap();
let three_prime = parse_hgvs("NM_001272071.2:c.*1C>T").unwrap();
let five_prime_intronic = parse_hgvs("NM_001385026.1:c.-106+2T>A").unwrap();

match five_prime.description {
    VariantDescription::Nucleotide(description) => {
        assert_eq!(description.location.start().unwrap().anchor(), Some(NucleotideAnchor::RelativeCdsStart));
        assert_eq!(description.location.start().unwrap().coordinate(), Some(-1));
        assert_eq!(description.location.start().unwrap().offset(), Some(0));
    }
    _ => unreachable!("expected nucleotide variant"),
}

match three_prime.description {
    VariantDescription::Nucleotide(description) => {
        assert_eq!(description.location.start().unwrap().anchor(), Some(NucleotideAnchor::RelativeCdsEnd));
        assert_eq!(description.location.start().unwrap().coordinate(), Some(1));
        assert_eq!(description.location.start().unwrap().offset(), Some(0));
    }
    _ => unreachable!("expected nucleotide variant"),
}

match five_prime_intronic.description {
    VariantDescription::Nucleotide(description) => {
        assert_eq!(description.location.start().unwrap().anchor(), Some(NucleotideAnchor::RelativeCdsStart));
        assert_eq!(description.location.start().unwrap().coordinate(), Some(-106));
        assert_eq!(description.location.start().unwrap().offset(), Some(2));
    }
    _ => unreachable!("expected nucleotide variant"),
}

Variants

Known

Known nucleotide coordinate with anchor and optional offset.

Fields

anchor: NucleotideAnchor

coordinate: i32

offset: i32

Unknown

Unknown nucleotide coordinate written as ?.

Implementations

impl NucleotideCoordinate

pub fn known(anchor: NucleotideAnchor, coordinate: i32, offset: i32) -> Self

Builds a known nucleotide coordinate.

pub fn is_known(&self) -> bool

Returns true when this coordinate is known.

pub fn is_unknown(&self) -> bool

Returns true when this coordinate is written as ?.

pub fn anchor(&self) -> Option<NucleotideAnchor>

Returns the anchor when this coordinate is known.

pub fn coordinate(&self) -> Option<i32>

Returns the primary coordinate when it is known.

pub fn offset(&self) -> Option<i32>

Returns the offset when this coordinate is known.

pub fn is_intronic(&self) -> bool

Returns true for intronic coordinates such as 357+1, -106+2, and *639-1.

pub fn is_cds_start_anchored(&self) -> bool

Returns true if variant’s location is relative to the CDS start, such as c.-1 and c.-106+2.

pub fn is_cds_end_anchored(&self) -> bool

Returns true if variant’s location is relative to the CDS end, such as c.*1 and c.*639-1.

pub fn is_five_prime_utr(&self) -> bool

Returns true for exonic 5’ UTR coordinates such as c.-81.

pub fn is_three_prime_utr(&self) -> bool

Returns true for exonic 3’ UTR coordinates such as c.*24.

Trait Implementations

impl Clone for NucleotideCoordinate

fn clone(&self) -> NucleotideCoordinate

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for NucleotideCoordinate

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

Formats the value using the given formatter.

impl PartialEq for NucleotideCoordinate

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl Copy for NucleotideCoordinate

impl Eq for NucleotideCoordinate

impl StructuralPartialEq for NucleotideCoordinate