Struct omnitigs::omnitigs::Omnitigs

pub struct Omnitigs<Graph: GraphBase> { /* fields omitted */ }

A structure containing omnitigs of a graph.

Implementations

impl<Graph: StaticGraph> Omnitigs<Graph>

pub fn compute(graph: &Graph) -> Self

Computes the maximal omnitigs of the given graph.

pub fn compute_trivial_only(graph: &Graph) -> Self

Computes the maximal trivial omnitigs of the given graph, including those that are subwalks of maximal non-trivial omnitigs.

pub fn compute_trivial_only_non_scc(graph: &Graph) -> Self

Computes the maximal trivial omnitigs of the given graph, including those that are subwalks of maximal non-trivial omnitigs. This algorithm allows the graph to be not strongly connected, but it is a bit slower, especially for long trivial omnitigs.

impl<Graph: StaticEdgeCentricBigraph> Omnitigs<Graph> where
    Graph::EdgeData: BidirectedData + Eq,
    Graph::NodeData: Debug, 

pub fn remove_reverse_complements(&mut self, graph: &Graph)

Retains only one direction of each pair of reverse-complemental omnitigs.

Note: I am not sure if this method is correct in all cases, but it will panic if it finds a case where it is not correct. For practical genomes it seems to work.

impl<Graph: GraphBase> Omnitigs<Graph>

pub fn new(
    omnitigs: Vec<Omnitig<Graph>>,
    omnitigs_per_macrotig: Vec<usize>
) -> Self

Creates a new Omnitigs struct from the given omnitigs and statistics.

pub fn iter(&self) -> impl Iterator<Item = &Omnitig<Graph>>

Returns an iterator over the omnitigs in this struct.

pub fn len(&self) -> usize

Returns the amount of omnitigs in this struct.

pub fn is_empty(&self) -> bool

Returns true if this struct contains no omnitigs.

pub fn push(&mut self, omnitig: Omnitig<Graph>)

Adds the given omnitig to this struct.

pub fn omnitigs_per_macrotig(&self) -> &[usize]

Returns a slice of omnitig counts per macrotig.

Trait Implementations

impl<Graph: Clone + GraphBase> Clone for Omnitigs<Graph>

fn clone(&self) -> Omnitigs<Graph>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<Graph: GraphBase> Debug for Omnitigs<Graph> where
    Graph::NodeIndex: Debug, 

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

Formats the value using the given formatter.

impl<Graph: GraphBase> Default for Omnitigs<Graph>

fn default() -> Self

Returns the “default value” for a type.

impl<Graph: GraphBase> Eq for Omnitigs<Graph> where
    Graph::EdgeIndex: Eq, 

impl<Graph: GraphBase> From<Vec<Omnitig<Graph>, Global>> for Omnitigs<Graph>

fn from(omnitigs: Vec<Omnitig<Graph>>) -> Self

Performs the conversion.

impl<Graph: GraphBase, IndexType> Index<IndexType> for Omnitigs<Graph> where
    Vec<Omnitig<Graph>>: Index<IndexType>, 

type Output = <Vec<Omnitig<Graph>> as Index<IndexType>>::Output

The returned type after indexing.

fn index(&self, index: IndexType) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<Graph: GraphBase> PartialEq<Omnitigs<Graph>> for Omnitigs<Graph> where
    Graph::EdgeIndex: PartialEq, 

fn eq(&self, rhs: &Self) -> bool

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

#[must_use]

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

This method tests for !=.