Struct Mapping 

pub struct Mapping { /* private fields */ }

An alignment between a substring of a query sequence and a single node using a single edit operation.

This can also represent unaligned insertions.

Implementations

impl Mapping

pub fn new( seq_offset: usize, handle: usize, node_len: usize, node_offset: usize, edit: Difference, ) -> Self

Creates a new mapping starting at the given position.

Panics

Will panic if the edit extends past the end of the node. Will panic if handle is gbz::ENDMARKER.

pub fn unaligned(seq_offset: usize, edit: Difference) -> Self

Creates a mapping for an unaligned insertion.

Panics

Will panic if the edit is not an insertion.

pub fn seq_interval(&self) -> &Range<usize>

Returns the aligned interval of the query sequence.

pub fn query_len(&self) -> usize

Returns the length of the query interval.

pub fn handle(&self) -> usize

Returns the handle of the target node.

Returns gbz::ENDMARKER for an unaligned insertion.

pub fn is_unaligned(&self) -> bool

Returns true if this mapping is an unaligned insertion.

pub fn node_len(&self) -> usize

Returns the length of the target node.

pub fn node_interval(&self) -> &Range<usize>

Returns the aligned interval of the target node.

pub fn target_len(&self) -> usize

Returns the length of the target interval.

pub fn edit(&self) -> &Difference

Returns the edit operation.

pub fn follows(&self, other: &Self) -> bool

Returns true this mapping follows the given one in the same node.

pub fn is_at_start(&self) -> bool

Returns true if this mapping is at the start of the target node.

pub fn is_at_end(&self) -> bool

Returns true if this mapping is at the end of the target node.

Trait Implementations

impl Clone for Mapping

fn clone(&self) -> Mapping

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Mapping

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

Formats the value using the given formatter.

impl PartialEq for Mapping

fn eq(&self, other: &Mapping) -> 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 Eq for Mapping

impl StructuralPartialEq for Mapping