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 { ... }
}Expand description
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§
Required Methods§
sourcefn start(&self) -> isize
fn start(&self) -> isize
Starting (lowest, left-most, 5’-most) position on the reference sequence (0-based).
sourcefn pos_into<T>(&self, pos: &Pos<Self::RefID, T>) -> Option<Pos<(), T>>
fn pos_into<T>(&self, pos: &Pos<Self::RefID, T>) -> Option<Pos<(), T>>
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.
sourcefn pos_outof<Q, T>(&self, pos: &Pos<Q, T>) -> Option<Pos<Self::RefID, T>>
fn pos_outof<Q, T>(&self, pos: &Pos<Q, T>) -> Option<Pos<Self::RefID, T>>
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>
Provided Methods§
sourcefn contig(&self) -> Contig<Self::RefID, Self::Strand>
fn contig(&self) -> Contig<Self::RefID, Self::Strand>
Contiguous sequence location that fully covers the location.
sourcefn first_pos(&self) -> Pos<Self::RefID, Self::Strand>
fn first_pos(&self) -> Pos<Self::RefID, Self::Strand>
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.