Trait bio_types::annot::loc::Loc

pub trait Loc {
    type RefID;
    type Strand;

    // Required methods
    fn refid(&self) -> &Self::RefID;
    fn start(&self) -> isize;
    fn length(&self) -> usize;
    fn strand(&self) -> Self::Strand
       where Self::Strand: Copy;
    fn pos_into<T>(&self, pos: &Pos<Self::RefID, T>) -> Option<Pos<(), T>>
       where Self::RefID: Eq,
             Self::Strand: Into<ReqStrand> + Copy,
             T: Neg<Output = T> + Copy;
    fn pos_outof<Q, T>(&self, pos: &Pos<Q, T>) -> Option<Pos<Self::RefID, T>>
       where Self::RefID: Clone,
             Self::Strand: Into<ReqStrand> + Copy,
             T: Neg<Output = T> + Copy;
    fn contig_intersection<T>(
        &self,
        other: &Contig<Self::RefID, T>
    ) -> Option<Self>
       where Self: Sized,
             Self::RefID: PartialEq + Clone,
             Self::Strand: Copy;

    // Provided methods
    fn contig(&self) -> Contig<Self::RefID, Self::Strand>
       where Self::RefID: Clone,
             Self::Strand: Copy { ... }
    fn first_pos(&self) -> Pos<Self::RefID, Self::Strand>
       where Self::RefID: Clone,
             Self::Strand: Into<ReqStrand> + Copy { ... }
    fn last_pos(&self) -> Pos<Self::RefID, Self::Strand>
       where Self::RefID: Clone,
             Self::Strand: Into<ReqStrand> + Copy { ... }
}

A trait for a sequence location – a defined region on a named chromosome (or other reference sequence), which may also have defined strand information. The trait is generic over the type of identifier for the reference sequence (allowing owned strings, sequence IDs, and other options) and the strand information (allowing type-level distinction between stranded and unstranded annotations).

Required Associated Types

type RefID

type Strand

Required Methods

fn refid(&self) -> &Self::RefID

Name of the reference sequence (chromosome name, etc.)

fn start(&self) -> isize

Starting (lowest, left-most, 5’-most) position on the reference sequence (0-based).

fn length(&self) -> usize

Length of the region

fn strand(&self) -> Self::Strandwhere Self::Strand: Copy,

Strand of the position

fn pos_into<T>(&self, pos: &Pos<Self::RefID, T>) -> Option<Pos<(), T>>where Self::RefID: Eq, Self::Strand: Into<ReqStrand> + Copy, T: Neg<Output = T> + Copy,

Map a sequence position on a reference sequence into a relative position within an annotated location on the reference sequence.

The first position of the annotated location is mapped to a position at 0, the next position of the annotated location is mapped to a position at 1, and so forth. The annotated location must have a known strandedness, which is taken into account. For reverse-strand annotations, the 3’-most position on the reference sequence is mapped to 0, and the strandedness of the position is reversed. When the sequence position lies on a different named reference sequence than the annotated location, or doesn’t fall within the annotated location, then None is returned.

This function serves as an inverse of @pos_outof.

fn pos_outof<Q, T>(&self, pos: &Pos<Q, T>) -> Option<Pos<Self::RefID, T>>where Self::RefID: Clone, Self::Strand: Into<ReqStrand> + Copy, T: Neg<Output = T> + Copy,

Map a relative position within an annotated location out of that location onto the enclosing reference sequence.

Position 0 within the annotated location is mapped to the first position of the annotated location, position 1 is mapped to the subsequent position, and so forth. The annotated location must have a known strandedness, which is taken into account. For reverse-strand annotations, position 0 is mapped to the 3’-most position of the reference sequence. When the sequence position is either negative, or greater than the length of the annotated location, then None is returned. The reference name for the sequence position is discarded; the mapped position receives a clone of the annotation’s reference sequence name.

This function serves as an inverse of @pos_into.

fn contig_intersection<T>(&self, other: &Contig<Self::RefID, T>) -> Option<Self>where Self: Sized, Self::RefID: PartialEq + Clone, Self::Strand: Copy,

Provided Methods

fn contig(&self) -> Contig<Self::RefID, Self::Strand>where Self::RefID: Clone, Self::Strand: Copy,

Contiguous sequence location that fully covers the location.

fn first_pos(&self) -> Pos<Self::RefID, Self::Strand>where Self::RefID: Clone, Self::Strand: Into<ReqStrand> + Copy,

The first Pos in a location, on the annotated strand.

The first position in a zero-length annotation will be the starting postion. This is the same as the first position in a length-1 annotation, on either strand.

fn last_pos(&self) -> Pos<Self::RefID, Self::Strand>where Self::RefID: Clone, Self::Strand: Into<ReqStrand> + Copy,

The last Pos in a location, on the annotated strand.

The last position in a zero-length annotation will be the starting postion. This is the same as the last position in a length-1 annotation, on either strand.

Implementors

impl<R, S> Loc for Contig<R, S>

type RefID = R

type Strand = S

impl<R, S> Loc for Pos<R, S>

type RefID = R

type Strand = S

impl<R, S> Loc for Spliced<R, S>

type RefID = R

type Strand = S