Struct NodeTable

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pub struct NodeTable { /* private fields */ }

Expand description

An immtable view of a node table.

Implementations§

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impl NodeTable

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pub fn num_rows(&self) -> SizeType

Return the number of rows

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pub fn time<N: Into<NodeId> + Copy>(&self, row: N) -> Option<Time>

Return the time value from row row of the table.

§Returns

Some(time) if row is valid.
None otherwise.

§Examples

if let Some(time) = tables.nodes().time(0) {
// then node id 0 is a valid row id
}

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pub fn flags<N: Into<NodeId> + Copy>(&self, row: N) -> Option<NodeFlags>

Return the flags value from row row of the table.

§Returns

Some(flags) if row is valid.
None otherwise.

§Examples

if let Some(flags) = tables.nodes().flags(0) {
// then node id 0 is a valid row id
}

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pub fn flags_array_mut(&mut self) -> &mut [NodeFlags]

👎Deprecated since 0.12.0: use flags_slice_mut instead

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pub fn time_array_mut(&mut self) -> &mut [Time]

👎Deprecated since 0.12.0: use time_slice_mut instead

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pub fn population<N: Into<NodeId> + Copy>(&self, row: N) -> Option<PopulationId>

Return the population value from row row of the table.

§Examples

if let Some(pop) = tables.nodes().population(0) {
// then node id 0 is a valid row id
}

§Returns

Some(population) if row is valid.
None otherwise.

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pub fn deme<N: Into<NodeId> + Copy>(&self, row: N) -> Option<PopulationId>

Return the population value from row row of the table.

§Examples

See NodeTable::population for examples.

§Returns

Some(population) if row is valid.
None otherwise.

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pub fn individual<N: Into<NodeId> + Copy>(&self, row: N) -> Option<IndividualId>

Return the individual value from row row of the table.

§Examples

if let Some(individual) = tables.nodes().individual(0) {
// then node id 0 is a valid row id
}

§Returns

Some(individual) if row is valid.
None otherwise.

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pub fn metadata<T: NodeMetadata>( &self, row: NodeId, ) -> Option<Result<T, TskitError>>

Retrieve decoded metadata for a row.

§Returns

Some(Ok(T)) if row is valid and decoding succeeded.
Some(Err(_)) if row is not valid and decoding failed.
None if row is not valid.

§Errors

TskitError::MetadataError if decoding fails.

§Examples.

The big-picture semantics are the same for all table types. See crate::IndividualTable::metadata for examples.

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

Return an iterator over rows of the table. The value of the iterator is NodeTableRow.

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pub fn lending_iter(&self) -> NodeTableRowView<'_>

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pub fn row<N: Into<NodeId> + Copy>(&self, r: N) -> Option<NodeTableRow>

Return row r of the table.

§Parameters

r: the row id.

§Returns

Some(row) if r is valid
None otherwise

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pub fn row_view<N: Into<NodeId> + Copy>( &self, r: N, ) -> Option<NodeTableRowView<'_>>

Return a view of row r of the table.

§Parameters

r: the row id.

§Returns

Some(row view) if r is valid
None otherwise

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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.

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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.

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pub fn time_slice(&self) -> &[Time]

Get the time column as a slice

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pub fn time_slice_raw(&self) -> &[f64]

Get the time column as a slice

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pub fn time_slice_mut(&mut self) -> &mut [Time]

Get the time column as a mutable slice

§Examples

For a crate::TableCollection, accessing the table creates a temporary that will be dropped, causing this code to not compile:

let time = tables.nodes().time_slice_mut();
println!("{}", time.len()); // ERROR: the temporary node table is dropped by now

Treating the returned slice as an iterable succeeds:

for time in tables.nodes_mut().time_slice_mut() {
    *time = 55.0.into(); // change each node's time value
}
assert!(tables.nodes_mut().time_slice_mut().iter().all(|t| t == &55.0));

§Panics

Internally, we rely on a conversion of u64 to usize. This conversion is fallible on some platforms. If the conversion fails, this function will panic.

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pub fn time_slice_raw_mut(&mut self) -> &mut [f64]

Get the time column as a mutable slice

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pub fn flags_slice(&self) -> &[NodeFlags]

Get the flags column as a slice

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pub fn flags_slice_raw(&self) -> &[tsk_flags_t]

Get the flags column as a slice

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pub fn flags_slice_mut(&mut self) -> &mut [NodeFlags]

Get the flags column as a mutable slice

§Examples

let flags = tables.nodes_mut().flags_slice_mut();
for flag in flags {
// Can do something...
}

for flag in  tables.nodes_mut().flags_slice_mut() {
}

The returned slice is mutable, allowing one to do things like clear the sample status of all nodes:

A copy of the flags can be obtained by collecting results into Vec:

for flag in tables.nodes_mut().flags_slice_mut() {
    flag.remove(tskit::NodeFlags::IS_SAMPLE);
}
assert!(!tables.nodes_mut().flags_slice_mut().iter().any(|f| f.is_sample()));
assert!(tables.nodes().samples_as_vector().is_empty());

let flags = tables.nodes_mut().flags_slice_mut().to_vec();

§Owning tables

The ownership semantics differ when tables are not part of a table collection:

let mut nodes = tskit::OwningNodeTable::default();
assert!(nodes.add_row(tskit::NodeFlags::IS_SAMPLE, 10., -1, -1).is_ok());
let flags = nodes.flags_slice_mut();
assert!(flags.iter().all(|f| f.is_sample()));

// while we are at it, let's use our node
// table to populate a table collection.
let mut tables = tskit::TableCollection::new(10.0).unwrap();
tables.set_nodes(&nodes);
assert_eq!(tables.nodes().num_rows(), 1);
assert_eq!(tables.nodes_mut().flags_slice_mut().iter().filter(|f| f.is_sample()).count(), 1);

§Panics

Internally, we rely on a conversion of u64 to usize. This conversion is fallible on some platforms. If the conversion fails, this function will panic.

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