Struct GraphSection

pub struct GraphSection {
    pub id: BString,
    pub attributes: HashMap<BString, Attribute>,
    pub node_indices: HashMap<BString, NodeIndex>,
    pub edge_indices: HashMap<BString, EdgeIndex>,
    pub groups: HashMap<BString, Group>,
    pub chains: HashMap<BString, Group>,
    /* private fields */
}

Represents a graph section within the TSG file

Fields

id: BString

attributes: HashMap<BString, Attribute>

node_indices: HashMap<BString, NodeIndex>

edge_indices: HashMap<BString, EdgeIndex>

groups: HashMap<BString, Group>

chains: HashMap<BString, Group>

Implementations

impl GraphSection

pub fn builder() -> GraphSectionBuilder

Create an instance of GraphSection using the builder syntax

impl GraphSection

pub fn new(id: BString) -> Self

Create a new empty GraphSection

pub fn new_default_graph() -> Self

pub fn node_indices_to_ids(&self) -> HashMap<NodeIndex, BString>

pub fn edge_indices_to_ids(&self) -> HashMap<EdgeIndex, BString>

pub fn node_weight(&self, node_idx: NodeIndex) -> Option<&NodeData>

pub fn edge_weight(&self, edge_idx: EdgeIndex) -> Option<&EdgeData>

pub fn in_degree(&self, node_idx: NodeIndex) -> usize

pub fn out_degree(&self, node_idx: NodeIndex) -> usize

pub fn add_node(&mut self, node_data: NodeData) -> Result<NodeIndex>

Add a node to the graph

pub fn add_edge( &mut self, source_id: &BStr, sink_id: &BStr, edge_data: EdgeData, ) -> Result<EdgeIndex>

Add an edge to the graph

pub fn node_by_idx(&self, node_idx: NodeIndex) -> Option<&NodeData>

pub fn node_by_id(&self, id: &str) -> Option<&NodeData>

pub fn edge_by_id(&self, id: &str) -> Option<&EdgeData>

pub fn edge_by_idx(&self, edge_idx: EdgeIndex) -> Option<&EdgeData>

pub fn nodes(&self) -> Vec<&NodeData>

pub fn edges(&self) -> Vec<&EdgeData>

pub fn find_node_id_by_idx(&self, node_idx: NodeIndex) -> Option<&BString>

Helper method to find a node’s ID by its index

pub fn traverse(&self) -> Result<Vec<TSGPath<'_>>>

Traverse the graph and return all valid paths from source nodes to sink nodes.

A valid path must respect read continuity, especially for nodes with Intermediary (IN) reads. For nodes with IN reads, we ensure that:

1. The node shares at least one read with previous nodes in the path
2. The node can connect to at least one subsequent node that shares a read with it

Example: n1 (r1) -> n3 (r1,r2) -> n4 (r1) n2 (r2) -> n3 (r1,r2) -> n5 (r2)

If n3 has IN reads, then only these paths are valid:

• n1 -> n3 -> n4 (valid because they all share read r1)
• n2 -> n3 -> n5 (valid because they all share read r2)

These paths would be invalid:

• n1 -> n3 -> n5 (invalid because n1 and n5 don’t share a common read)
• n2 -> n3 -> n4 (invalid because n2 and n4 don’t share a common read)

pub fn to_dot(&self, node_label: bool, edge_label: bool) -> Result<String>

pub fn to_json(&self) -> Result<Value>

pub fn annotate_node_with_sequence<P: AsRef<Path>>( &mut self, reference_genome_path: P, ) -> Result<()>

Trait Implementations

impl Clone for GraphSection

fn clone(&self) -> GraphSection

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for GraphSection

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

Formats the value using the given formatter.

impl Default for GraphSection

fn default() -> GraphSection

Returns the “default value” for a type.

impl GraphAnalysis for GraphSection

fn is_connected(&self) -> Result<bool>

Determines whether the graph is connected.

fn is_cyclic(&self) -> Result<bool>

Determines whether the graph contains any cycles.

fn is_bubble(&self) -> Result<bool>

Determines whether the graph contains any bubbles.

fn is_simple(&self) -> Result<bool>

Determines whether the graph is simple.

fn topo(&self) -> Result<GraphTopology>

fn is_directed_acyclic_graph(&self) -> Result<bool>

Determines whether the graph is a directed acyclic graph (DAG).

fn is_fade_in(&self) -> Result<bool>

Determines whether the directed graph is a fade-in structure.

fn is_fade_out(&self) -> Result<bool>

Determines whether the directed graph is a fade-out structure.

fn is_bipartite(&self) -> Result<bool>

Determines whether the graph is bipartite.

fn is_unique_path(&self) -> Result<bool>

Determines whether the graph contains a unique path.

fn is_equi_path(&self) -> Result<bool>

Determines whether the graph contains equi-paths.

fn is_hetero_path(&self) -> Result<bool>

Determines whether the graph contains hetero-paths.

fn matches_topology(&self, topology: GraphTopology) -> Result<bool>

Helper method to check if the graph matches a specific topology.