Struct tskit::table_views::TableViews

pub struct TableViews { /* private fields */ }

Implementations

impl TableViews

pub fn edges(&self) -> &EdgeTable

Get reference to the EdgeTable.

pub fn nodes(&self) -> &NodeTable

Get reference to the NodeTable.

pub fn nodes_mut(&mut self) -> &mut NodeTable

Get mutable reference to the NodeTable.

pub fn sites(&self) -> &SiteTable

Get reference to the SiteTable.

pub fn mutations(&self) -> &MutationTable

Get reference to the MutationTable.

pub fn individuals(&self) -> &IndividualTable

Get reference to the IndividualTable.

pub fn populations(&self) -> &PopulationTable

Get reference to the PopulationTable.

pub fn migrations(&self) -> &MigrationTable

Get reference to the MigrationTable.

pub fn provenances(&self) -> &ProvenanceTable

Available on crate feature provenance only.

Get reference to the ProvenanceTable

pub fn edges_iter(&self) -> impl Iterator<Item = EdgeTableRow> + '_

Return an iterator over the edges.

pub fn nodes_iter(&self) -> impl Iterator<Item = NodeTableRow> + '_

Return an iterator over the nodes.

pub fn sites_iter(&self) -> impl Iterator<Item = SiteTableRow> + '_

Return an iterator over the sites.

pub fn mutations_iter(&self) -> impl Iterator<Item = MutationTableRow> + '_

Return an iterator over the mutations.

pub fn individuals_iter(&self) -> impl Iterator<Item = IndividualTableRow> + '_

Return an iterator over the individuals.

pub fn populations_iter(&self) -> impl Iterator<Item = PopulationTableRow> + '_

Return an iterator over the populations.

pub fn migrations_iter(&self) -> impl Iterator<Item = MigrationTableRow> + '_

Return an iterator over the migrations.

pub fn provenances_iter(&self) -> impl Iterator<Item = ProvenanceTableRow> + '_

Available on crate feature provenance only.

Return an iterator over provenances

pub fn samples_as_vector(&self) -> Vec<NodeId>

Obtain a vector containing the indexes (“ids”) of all nodes for which crate::TSK_NODE_IS_SAMPLE is true.

The provided implementation dispatches to crate::NodeTable::samples_as_vector.

pub fn create_node_id_vector(
    &self,
    f: impl FnMut(&NodeTableRow) -> bool
) -> Vec<NodeId>

Obtain a vector containing the indexes (“ids”) of all nodes satisfying a certain criterion.

The provided implementation dispatches to crate::NodeTable::create_node_id_vector.

Parameters

• f: a function. The function is passed the current table collection and each crate::node_table::NodeTableRow. If f returns true, the index of that row is included in the return value.

Examples

Get all nodes with time > 0.0:

use tskit::bindings::tsk_id_t;

let mut tables = tskit::TableCollection::new(100.).unwrap();
tables
    .add_node(tskit::TSK_NODE_IS_SAMPLE, 0.0, tskit::PopulationId::NULL,
    tskit::IndividualId::NULL)
    .unwrap();
tables
    .add_node(tskit::TSK_NODE_IS_SAMPLE, 1.0, tskit::PopulationId::NULL,
    tskit::IndividualId::NULL)
    .unwrap();
let samples = tables.create_node_id_vector(
    |row: &tskit::NodeTableRow| row.time > 0.,
);
assert_eq!(samples[0], 1);

// Get all nodes that have a mutation:

fn node_has_mutation(
    // dyn trait here means this
    // will work with TreeSequence, too.
    tables_type: &dyn std::ops::Deref<Target=tskit::table_views::TableViews>,
    row: &tskit::NodeTableRow,
) -> bool {
    for mrow in tables_type.mutations_iter() {
        if mrow.node == row.id {
            return true;
        }
    }
    false
}

// Get all nodes that have a mutation:

tables.add_mutation(0, 0, tskit::MutationId::NULL, 0.0, None).unwrap();
let samples_with_mut = tables.create_node_id_vector(
    |row: &tskit::NodeTableRow| node_has_mutation(&tables, row));
assert_eq!(samples_with_mut[0], 0);