Struct tskit::TableCollection

pub struct TableCollection { /* fields omitted */ }

A table collection.

This is a thin wrapper around the C type tsk_table_collection_t.

Current limitations

Examples

use tskit::TableAccess;
let mut tables = tskit::TableCollection::new(100.).unwrap();
assert_eq!(tables.sequence_length(), 100.);

// Adding edges:

let rv = tables.add_edge(0., 53., 1, 11).unwrap();

// Add node:

let rv = tables.add_node(0, 3.2, tskit::TSK_NULL, tskit::TSK_NULL).unwrap();

// Get immutable reference to edge table
let edges = tables.edges();
assert_eq!(edges.num_rows(), 1);

// Get immutable reference to node table
let nodes = tables.nodes();
assert_eq!(nodes.num_rows(), 1);

Metadata round trips and table iteration

use tskit;
use tskit::TableAccess;
use tskit::metadata::MetadataRoundtrip;

// Define a type for metadata
struct F {
    x: i32,
}

// Implement our metadata trait for type F.
// NOTE: this is hard because we are only using the
// rust standard library here.  See the examples/
// directory of the repository for examples using
// other, more convenient, crates.
impl tskit::metadata::MetadataRoundtrip for F {
    fn encode(&self) -> Result<Vec<u8>, tskit::metadata::MetadataError> {
        let mut rv = vec![];
        rv.extend(self.x.to_le_bytes().iter().copied());
        Ok(rv)
    }
    fn decode(md: &[u8]) -> Result<Self, tskit::metadata::MetadataError> {
        use std::convert::TryInto;
        let (x_int_bytes, rest) = md.split_at(std::mem::size_of::<i32>());
        Ok(Self {
            x: i32::from_le_bytes(x_int_bytes.try_into().unwrap()),
        })
    }
}

// Crate a table and add a mutation with metadata
let mut tables = tskit::TableCollection::new(100.).unwrap();

// The metadata takes a reference in the event that it could
// be data store in some container somewhere, and you don't want
// it moved.
tables.add_mutation_with_metadata(0, 0, 0, 0., None, Some(&F{x: -33})).unwrap();

// Iterate over each row in the table.
// The "true" means to include (a copy of) the
// encoded metadata, if any exist.
for row in tables.mutations().iter() {
    // Decode the metadata if any exists.
    if !row.metadata.is_none() {
        let md = F::decode(&row.metadata.unwrap()).unwrap();
        assert_eq!(md.x, -33);
    }
}

Future road map

1. Support all table types. Currently, we only support those needed for current goals in ongoing projects.
2. Strengthen some of the error handling.

Implementations

impl TableCollection

pub fn new(sequence_length: f64) -> Result<Self, TskitError>

Create a new table collection with a sequence length.

pub fn new_from_file(filename: &str) -> Result<Self, TskitError>

Load a table collection from a file.

pub fn sequence_length(&self) -> f64

Length of the sequence/“genome”.

pub fn add_edge(
    &mut self,
    left: f64,
    right: f64,
    parent: tsk_id_t,
    child: tsk_id_t
) -> TskReturnValue

Add a row to the edge table

pub fn add_edge_with_metadata(
    &mut self,
    left: f64,
    right: f64,
    parent: tsk_id_t,
    child: tsk_id_t,
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the edge table

pub fn add_individual(
    &mut self,
    flags: tsk_flags_t,
    location: &[f64],
    parents: &[tsk_id_t]
) -> TskReturnValue

Add a row to the individual table

pub fn add_individual_with_metadata(
    &mut self,
    flags: tsk_flags_t,
    location: &[f64],
    parents: &[tsk_id_t],
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the individual table

pub fn add_migration(
    &mut self,
    span: (f64, f64),
    node: tsk_id_t,
    source_dest: (tsk_id_t, tsk_id_t),
    time: f64
) -> TskReturnValue

Add a row to the migration table

Warnings

Migration tables are not currently supported by tree sequence simplification.

pub fn add_migration_with_metadata(
    &mut self,
    span: (f64, f64),
    node: tsk_id_t,
    source_dest: (tsk_id_t, tsk_id_t),
    time: f64,
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the migration table

Warnings

Migration tables are not currently supported by tree sequence simplification.

pub fn add_node(
    &mut self,
    flags: tsk_flags_t,
    time: f64,
    population: tsk_id_t,
    individual: tsk_id_t
) -> TskReturnValue

Add a row to the node table

pub fn add_node_with_metadata(
    &mut self,
    flags: tsk_flags_t,
    time: f64,
    population: tsk_id_t,
    individual: tsk_id_t,
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the node table

pub fn add_site(
    &mut self,
    position: f64,
    ancestral_state: Option<&[u8]>
) -> TskReturnValue

Add a row to the site table

pub fn add_site_with_metadata(
    &mut self,
    position: f64,
    ancestral_state: Option<&[u8]>,
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the site table

pub fn add_mutation(
    &mut self,
    site: tsk_id_t,
    node: tsk_id_t,
    parent: tsk_id_t,
    time: f64,
    derived_state: Option<&[u8]>
) -> TskReturnValue

Add a row to the mutation table.

pub fn add_mutation_with_metadata(
    &mut self,
    site: tsk_id_t,
    node: tsk_id_t,
    parent: tsk_id_t,
    time: f64,
    derived_state: Option<&[u8]>,
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the mutation table.

pub fn add_population(&mut self) -> TskReturnValue

Add a row to the population_table

pub fn add_population_with_metadata(
    &mut self,
    metadata: Option<&dyn MetadataRoundtrip>
) -> TskReturnValue

Add a row with metadata to the population_table

pub fn build_index(&mut self) -> TskReturnValue

Build the “input” and “output” indexes for the edge table.

Note

The C API call behind this takes a flags argument that is currently unused. A future release may break API here if the C library is updated to use flags.

pub fn is_indexed(&self) -> bool

Return true if tables are indexed.

pub fn edge_insertion_order(&self) -> Option<&[tsk_id_t]>

If self.is_indexed() is true, return a non-owning slice containing the edge insertion order. Otherwise, return None.

pub fn edge_removal_order(&self) -> Option<&[tsk_id_t]>

If self.is_indexed() is true, return a non-owning slice containing the edge removal order. Otherwise, return None.

pub fn sort(
    &mut self,
    start: &Bookmark,
    options: TableSortOptions
) -> TskReturnValue

Sort the tables.
The bookmark can be used to affect where sorting starts from for each table.

pub fn full_sort(&mut self, options: TableSortOptions) -> TskReturnValue

Fully sort all functions. Implemented via a call to sort.

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

Dump the table collection to file.

pub fn clear(&mut self, options: TableClearOptions) -> TskReturnValue

Clear the contents of all tables. Does not release memory. Memory will be released when the object goes out of scope.

pub fn equals(
    &self,
    other: &TableCollection,
    options: TableEqualityOptions
) -> bool

Return true if self contains the same data as other, and false otherwise.

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

Return a “deep” copy of the tables.

pub fn tree_sequence(
    self,
    flags: TreeSequenceFlags
) -> Result<TreeSequence, TskitError>

Return a crate::TreeSequence based on the tables. This function will raise errors if tables are not sorted, not indexed, or invalid in any way.

pub fn simplify(
    &mut self,
    samples: &[tsk_id_t],
    options: SimplificationOptions,
    idmap: bool
) -> Result<Option<Vec<tsk_id_t>>, TskitError>

Simplify tables in place.

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 TSK_NULL if the input node is not part of the simplified history.

Trait Implementations

impl Drop for TableCollection

fn drop(&mut self)

Executes the destructor for this type.

impl NodeListGenerator for TableCollection

fn samples_as_vector(&self) -> Vec<tsk_id_t>

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

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

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

impl Provenance for TableCollection

fn add_provenance(&mut self, record: &str) -> TskReturnValue

Add provenance record with a time stamp.

fn provenances(&self) -> ProvenanceTable<'_>

Return an immutable reference to the table, type ProvenanceTable

fn provenances_iter(&self) -> TableIterator<ProvenanceTable<'_>>

Return an iterator over the rows of the ProvenanceTable. See ProvenanceTable::iter for details.

impl TableAccess for TableCollection

fn edges(&self) -> EdgeTable<'_>

Get reference to the EdgeTable.

fn individuals(&self) -> IndividualTable<'_>

Get reference to the IndividualTable.

fn migrations(&self) -> MigrationTable<'_>

Get reference to the MigrationTable.

fn nodes(&self) -> NodeTable<'_>

Get reference to the NodeTable.

fn sites(&self) -> SiteTable<'_>

Get reference to the SiteTable.

fn mutations(&self) -> MutationTable<'_>

Get reference to the MutationTable.

fn populations(&self) -> PopulationTable<'_>

Get reference to the PopulationTable.

fn edges_iter(&self) -> TableIterator<EdgeTable<'_>>

Return an iterator over the edges. See EdgeTable::iter for details.

fn nodes_iter(&self) -> TableIterator<NodeTable<'_>>

Return an iterator over the nodes. See NodeTable::iter for details.

fn mutations_iter(&self) -> TableIterator<MutationTable<'_>>

Return an iterator over the mutations. See MutationTable::iter for details.

fn sites_iter(&self) -> TableIterator<SiteTable<'_>>

Return an iterator over the sites. See SiteTable::iter for details.

fn populations_iter(&self) -> TableIterator<PopulationTable<'_>>

Return an iterator over the populations. See PopulationTable::iter for details.

fn migrations_iter(&self) -> TableIterator<MigrationTable<'_>>

Return an iterator over the migration events. See MigrationTable::iter for details.

fn individuals_iter(&self) -> TableIterator<IndividualTable<'_>>

Return an iterator over the individuals. See IndividualTable::iter for details.

impl TskitTypeAccess<tsk_table_collection_t> for TableCollection

fn as_ptr(&self) -> *const tsk_table_collection_t

Return const pointer

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

Return mutable pointer