Struct tskit::TreeSequence

pub struct TreeSequence { /* private fields */ }

A tree sequence.

This is a thin wrapper around the C type tsk_treeseq_t.

When created from a TableCollection, the input tables are moved into the TreeSequence object.

Examples

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.add_node(0, 1.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
tables.add_edge(0., 1000., 0, 1).unwrap();
tables.add_edge(0., 1000., 0, 2).unwrap();

// index
tables.build_index();

// tables gets moved into our treeseq variable:
let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
assert_eq!(treeseq.nodes().num_rows(), 3);
assert_eq!(treeseq.edges().num_rows(), 2);

This type does not std::ops::DerefMut to crate::table_views::TableViews:

assert_eq!(treeseq.nodes_mut().num_rows(), 3);

Implementations

impl TreeSequence

pub fn new<F: Into<TreeSequenceFlags>>(
    tables: TableCollection,
    flags: F
) -> Result<Self, TskitError>

Create a tree sequence from a TableCollection. In general, TableCollection::tree_sequence may be preferred. The table collection is moved/consumed.

Parameters

• tables, a TableCollection

Errors

• TskitError if the tables are not indexed.
• TskitError if the tables are not properly sorted. See TableCollection::full_sort.

Examples

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();

The following may be preferred to the previous example, and more closely mimics the Python tskit interface:

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();

The following raises an error because the tables are not indexed:

let mut tables = tskit::TableCollection::new(1000.).unwrap();
let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();

Note

This function makes no extra copies of the tables. There is, however, a temporary allocation of an empty table collection in order to convince rust that we are safely handling all memory.

pub fn dump<O: Into<TableOutputOptions>>(
    &self,
    filename: &str,
    options: O
) -> TskReturnValue

Dump the tree sequence to file.

Note

• options is currently not used. Set to default value. This behavior may change in a future release, which could break API.

Panics

This function allocates a CString to pass the file name to the C API. A panic will occur if the system runs out of memory.

pub fn load(filename: impl AsRef<str>) -> Result<Self, TskitError>

Load from a file.

This function calls TableCollection::new_from_file with TreeSequenceFlags::default.

pub fn dump_tables(&self) -> Result<TableCollection, TskitError>

Obtain a copy of the TableCollection. The result is a “deep” copy of the tables.

Errors

TskitError will be raised if the underlying C library returns an error code.

pub fn tree_iterator<F: Into<TreeFlags>>(
    &self,
    flags: F
) -> Result<Tree, TskitError>

Create an iterator over trees.

Parameters

• flags A TreeFlags bit field.

Errors

Examples

// You must include streaming_iterator as a dependency
// and import this type.
use streaming_iterator::StreamingIterator;
// Import this to allow .next_back() for reverse
// iteration over trees.
use streaming_iterator::DoubleEndedStreamingIterator;

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
let mut tree_iterator = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap();
while let Some(tree) = tree_iterator.next() {
}

Warning

The following code results in an infinite loop. Be sure to note the difference from the previous example.

use streaming_iterator::StreamingIterator;

let mut tables = tskit::TableCollection::new(1000.).unwrap();
tables.build_index();
let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
while let Some(tree) = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap().next() {
}

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

👎Deprecated since 0.2.3: Please use TreeSequence::sample_nodes instead

Get the list of samples as a vector.

Panics

Will panic if the number of samples is too large to cast to a valid id.

pub fn sample_nodes(&self) -> &[NodeId]

Get the list of sample nodes as a slice.

pub fn num_trees(&self) -> SizeType

Get the number of trees.

pub fn kc_distance(
    &self,
    other: &TreeSequence,
    lambda: f64
) -> Result<f64, TskitError>

Calculate the average Kendall-Colijn (K-C) distance between pairs of trees whose intervals overlap.

Note

• Citation

Parameters

• lambda specifies the relative weight of topology and branch length. See TreeInterface::kc_distance for more details.

pub fn num_samples(&self) -> SizeType

pub fn simplify<O: Into<SimplificationOptions>>(
    &self,
    samples: &[NodeId],
    options: O,
    idmap: bool
) -> Result<(Self, Option<Vec<NodeId>>), TskitError>

Simplify tables and return a new tree sequence.

Parameters

• samples: a slice containing non-null node ids. The tables are simplified with respect to the ancestry of these nodes.
• options: A SimplificationOptions bit field controlling the behavior of simplification.
• idmap: if true, the return value contains a vector equal in length to the input node table. For each input node, this vector either contains the node’s new index or NodeId::NULL if the input node is not part of the simplified history.

pub fn add_provenance(
    &mut self,
    record: &str
) -> Result<ProvenanceId, TskitError>

Available on crate feature provenance only.

Add provenance record with a time stamp.

All implementation of this trait provided by tskit use an ISO 8601 format time stamp written using the RFC 3339 specification. This formatting approach has been the most straightforward method for supporting round trips to/from a crate::provenance::ProvenanceTable. The implementations used here use the humantime crate.

Parameters

• record: the provenance record

Examples

let mut tables = tskit::TableCollection::new(1000.).unwrap();
let mut treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
treeseq.add_provenance(&String::from("All your provenance r belong 2 us.")).unwrap();

let prov_ref = treeseq.provenances();
let row_0 = prov_ref.row(0).unwrap();
assert_eq!(row_0.record, "All your provenance r belong 2 us.");
let record_0 = prov_ref.record(0).unwrap();
assert_eq!(record_0, row_0.record);
let timestamp = prov_ref.timestamp(0).unwrap();
assert_eq!(timestamp, row_0.timestamp);
use core::str::FromStr;
let dt_utc = humantime::Timestamp::from_str(&timestamp).unwrap();
println!("utc = {}", dt_utc);

Methods from Deref<Target = TableViews>

pub fn edges(&self) -> &EdgeTable

Get reference to the EdgeTable.

pub fn nodes(&self) -> &NodeTable

Get 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);

Trait Implementations

impl Deref for TreeSequence

type Target = TableViews

The resulting type after dereferencing.

fn deref(&self) -> &Self::Target

Dereferences the value.

impl Drop for TreeSequence

fn drop(&mut self)

Executes the destructor for this type.

impl TryFrom<TableCollection> for TreeSequence

type Error = TskitError

The type returned in the event of a conversion error.

fn try_from(value: TableCollection) -> Result<Self, Self::Error>

Performs the conversion.

impl TskitTypeAccess<tsk_treeseq_t> for TreeSequence

fn as_ptr(&self) -> *const tsk_treeseq_t

Return const pointer

fn as_mut_ptr(&mut self) -> *mut tsk_treeseq_t

Return mutable pointer

impl Send for TreeSequence

impl Sync for TreeSequence