Struct mutexpect::SeqAnnotation

pub struct SeqAnnotation {
    pub name: String,
    pub chr: String,
    pub range: Interval,
    pub strand: Strand,
    pub exons: Vec<Interval>,
    pub coding_sequences: Vec<CDS>,
}

Fields

name: String

chr: String

range: Interval

strand: Strand

exons: Vec<Interval>

coding_sequences: Vec<CDS>

Implementations

impl SeqAnnotation

pub fn new(
    name: String,
    chr: String,
    range: Interval,
    strand: Strand,
    exons: Vec<Interval>,
    coding_sequences: Vec<CDS>
) -> Self

pub fn find_intron(&self, genomic_position: usize) -> Option<Interval>

Find introns based on the exons Assumption: Every intron is flanked by exons

Cases: a b c d e exons | –|– | –|– | DNA –––––––––––––

a) Not an intron, because it is before the first exon b,d) Not an intron, because it is inside an exon c) An intron, because it is between two exons e) 3’ UTR region. Not an intron.

pub fn get_introns(&self) -> Vec<Interval>

Determine all intron locations based on the exons

Note that exons may overlap. But in any case, this function only returns regions that are not covered by any exons (assuming that the exons are sorted by start and then by stop position).

pub fn get_end_minus50(&self) -> usize

pub fn find_exon(&self, genomic_position: usize) -> Option<Interval>

pub fn find_cds(&self, genomic_position: usize) -> Option<CDS>

Trait Implementations

impl Debug for SeqAnnotation

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

Formats the value using the given formatter.

impl PartialEq<SeqAnnotation> for SeqAnnotation

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

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

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

This method tests for !=.

impl StructuralPartialEq for SeqAnnotation