Struct omnitigs::omnitigs::Omnitigs

impl<Graph: StaticGraph + SubgraphBase<RootGraph = Graph>> Omnitigs<Graph>

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

Computes the maximal omnitigs of the given graph.

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

Computes the maximal non-trivial omnitigs of the 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.

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

Computes the maximal multi-safe walks of the given graph.

pub fn transform_to_multi_safe_strict_model( &mut self, truncation_mode: TruncationMode )

The univocal extension of a multi-safe walk is not multi-safe in the strict model if the left and the right extension share any arcs. In this case, we can truncate the walk to remove the repetitions. However, there are multiple points at which we could truncate. The parameter truncation_mode decides which of the truncations should be reported.

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: GraphBase> Borrow<[Omnitig<Graph>]> for Omnitigs<Graph>

fn borrow(&self) -> &[Omnitig<Graph>]

Immutably borrows from an owned value. Read more

impl<Graph: GraphBase> BorrowMut<[Omnitig<Graph>]> for Omnitigs<Graph>

fn borrow_mut(&mut self) -> &mut [Omnitig<Graph>]

Mutably borrows from an owned value. Read more

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

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

Returns a copy of the value. Read more

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

Performs copy-assignment from source. Read more

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. Read more

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

fn default() -> Self

Returns the “default value” for a type. Read more

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

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

Converts to this type from the input type.

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

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

The returned type after indexing.

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

Performs the indexing (container[index]) operation. Read more

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

type Item = Omnitig<Graph>

The type of the elements being iterated over.

type IntoIter = IntoIter<<Omnitigs<Graph> as IntoIterator>::Item, Global>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value. Read more

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 ==.

1.0.0 · source§

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

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

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

Auto Trait Implementations§

impl<Graph> RefUnwindSafe for Omnitigs<Graph>where <Graph as GraphBase>::EdgeIndex: RefUnwindSafe,

impl<Graph> Send for Omnitigs<Graph>where <Graph as GraphBase>::EdgeIndex: Send,

impl<Graph> Sync for Omnitigs<Graph>where <Graph as GraphBase>::EdgeIndex: Sync,

impl<Graph> Unpin for Omnitigs<Graph>where <Graph as GraphBase>::EdgeIndex: Unpin,

impl<Graph> UnwindSafe for Omnitigs<Graph>where <Graph as GraphBase>::EdgeIndex: UnwindSafe,

Blanket Implementations§

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Compare self to key and return true if they are equal.

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Checks if this value is equivalent to the given key. Read more

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