Struct Path 

pub struct Path { /* private fields */ }

A path thought a BaseGraph

class to keep track of paths

Implementations

impl Path

pub fn new(last_vertex: NodeIndex, edges_in_order: Vec<EdgeIndex>) -> Self

Create a new Path containing no edges and starting at initialVertex @param initialVertex the starting vertex of the path @param graph the graph this path will follow through

pub fn new_add_edge<V: BaseVertex, E: BaseEdge>( &self, edge: EdgeIndex, graph: &BaseGraph<V, E>, ) -> Path

Create a new Path extending p with edge

@param p the path to extend. @param edge the edge to extend path with.

@throws IllegalArgumentException if {@code p} or {@code edge} are {@code null}, or {@code edge} is not part of {@code p}’s graph, or {@code edge} does not have as a source the last vertex in {@code p}.

pub fn new_prepend_edge<V: BaseVertex, E: BaseEdge>( &self, edge: EdgeIndex, graph: &BaseGraph<V, E>, ) -> Path

Creates a new path continuing on from #self that prepends the given edge index to the beginning of the path, checking that the edge is contiguous with the rest of the path

pub fn new_add_edges<V: BaseVertex, E: BaseEdge>( &self, edges: Vec<EdgeIndex>, graph: &BaseGraph<V, E>, ) -> Path

Create a new Path extending p with edge

@param p the path to extend. @param edges list of edges to extend. Does not check arguments’ validity i.e. doesn’t check that edges are in order

@throws IllegalArgumentException if {@code p} or {@code edges} are {@code null} or empty, or {@code edges} is not part of {@code p}’s graph, or {@code edges} does not have as a source the last vertex in {@code p}.

pub fn contains_vertex<V: BaseVertex, E: BaseEdge>( &self, v: NodeIndex, graph: &BaseGraph<V, E>, ) -> bool

Does this path contain the given vertex?

@param v a non-null vertex @return true if v occurs within this path, false otherwise

pub fn to_string<V: BaseVertex, E: BaseEdge>( &self, graph: &BaseGraph<V, E>, ) -> String

pub fn get_edges(&self) -> &Vec<EdgeIndex>

Get the edges of this path in order. Returns an unmodifiable view of the underlying list @return a non-null list of edges

pub fn get_last_edge(&self) -> EdgeIndex

pub fn get_vertices<V: BaseVertex, E: BaseEdge>( &self, graph: &BaseGraph<V, E>, ) -> Vec<NodeIndex>

Get the list of vertices in this path in order defined by the edges of the path @return a non-null, non-empty list of vertices

pub fn get_first_vertex<V: BaseVertex, E: BaseEdge>( &self, graph: &BaseGraph<V, E>, ) -> NodeIndex

Get the first vertex in this path @return a non-null vertex

pub fn get_last_vertex(&self) -> NodeIndex

Get the final vertex of the path @return a non-null vertex

pub fn get_bases<V: BaseVertex, E: BaseEdge>( &self, graph: &BaseGraph<V, E>, ) -> Vec<u8>

The base sequence for this path. Pull the full sequence for source nodes and then the suffix for all subsequent nodes @return non-null sequence of bases corresponding to this path

pub fn get_max_multiplicity<V: BaseVertex, E: BaseEdge>( &self, graph: &BaseGraph<V, E>, ) -> usize

pub fn calculate_cigar<V: BaseVertex, E: BaseEdge>( &self, ref_seq: &[u8], graph: &BaseGraph<V, E>, avx_mode: AVXMode, ) -> CigarString

Calculate the cigar elements for this path against the reference sequence

@param refSeq the reference sequence that all of the bases in this path should align to @param aligner @return a Cigar mapping this path to refSeq, or null if no reasonable alignment could be found

pub fn len(&self) -> usize

Length of the path in edges.

@return {@code 0} or greater.

Trait Implementations

impl Clone for Path

fn clone(&self) -> Path

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Path

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

Formats the value using the given formatter.

impl Hash for Path

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl PartialEq for Path

fn eq(&self, other: &Self) -> 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 Path