Struct tskit::TableCollection

impl TableCollection

pub fn new<P: Into<Position>>(sequence_length: P) -> Result<Self, TskitError>

Create a new table collection with a sequence length.

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

Load a table collection from a file.

Examples

The function is generic over references to str:

let tables = tskit::TableCollection::new_from_file("trees.file").unwrap();

let filename = String::from("trees.file");
// Pass filename by reference
let tables = tskit::TableCollection::new_from_file(&filename).unwrap();

// Move filename
let tables = tskit::TableCollection::new_from_file(filename).unwrap();

// Boxed String are an unlikely use case, but can be made to work:
let filename = Box::new(String::from("trees.file"));
let tables = tskit::TableCollection::new_from_file(&*filename.as_ref()).unwrap();

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 sequence_length(&self) -> Position

Length of the sequence/“genome”.

pub fn add_edge<L, R, P, C>( &mut self, left: L, right: R, parent: P, child: C ) -> Result<EdgeId, TskitError>where L: Into<Position>, R: Into<Position>, P: Into<NodeId>, C: Into<NodeId>,

Add a row to the edge table

Examples


// left, right, parent, child
match tables.add_edge(0., 53., 1, 11) {
    // This is the first edge, so its id will be
    // zero (0).
    Ok(edge_id) => assert_eq!(edge_id, 0),
    Err(e) => panic!("{:?}", e),
}

You may also use Position and NodeId as inputs.

let left = tskit::Position::from(0.0);
let right = tskit::Position::from(53.0);
let parent = tskit::NodeId::from(1);
let child = tskit::NodeId::from(11);
match tables.add_edge(left, right, parent, child) {
    Ok(edge_id) => assert_eq!(edge_id, 0),
    Err(e) => panic!("{:?}", e),
}

Adding invalid data is allowed at this point:

assert!(tables.add_edge(0., 53.,
                        tskit::NodeId::NULL,
                        tskit::NodeId::NULL).is_ok());

See TableCollection::check_integrity for how to catch these data model violations.

pub fn add_edge_with_metadata<L, R, P, C, M>( &mut self, left: L, right: R, parent: P, child: C, metadata: &M ) -> Result<EdgeId, TskitError>where L: Into<Position>, R: Into<Position>, P: Into<NodeId>, C: Into<NodeId>, M: EdgeMetadata,

Add a row with optional metadata to the edge table

pub fn add_individual<F, L, P>( &mut self, flags: F, location: L, parents: P ) -> Result<IndividualId, TskitError>where F: Into<IndividualFlags>, L: IndividualLocation, P: IndividualParents,

Add a row to the individual table

pub fn add_individual_with_metadata<F, L, P, M>( &mut self, flags: F, location: L, parents: P, metadata: &M ) -> Result<IndividualId, TskitError>where F: Into<IndividualFlags>, L: IndividualLocation, P: IndividualParents, M: IndividualMetadata,

Add a row with metadata to the individual table

pub fn add_migration<LEFT, RIGHT, N, SOURCE, DEST, T>( &mut self, span: (LEFT, RIGHT), node: N, source_dest: (SOURCE, DEST), time: T ) -> Result<MigrationId, TskitError>where LEFT: Into<Position>, RIGHT: Into<Position>, N: Into<NodeId>, SOURCE: Into<PopulationId>, DEST: Into<PopulationId>, T: Into<Time>,

Add a row to the migration table

Warnings

Migration tables are not currently supported by tree sequence simplification.

pub fn add_migration_with_metadata<LEFT, RIGHT, N, SOURCE, DEST, T, M>( &mut self, span: (LEFT, RIGHT), node: N, source_dest: (SOURCE, DEST), time: T, metadata: &M ) -> Result<MigrationId, TskitError>where LEFT: Into<Position>, RIGHT: Into<Position>, N: Into<NodeId>, SOURCE: Into<PopulationId>, DEST: Into<PopulationId>, T: Into<Time>, M: MigrationMetadata,

Add a row with optional metadata to the migration table

Examples

See metadata for more details about required trait implementations. Those details have been omitted from this example.

let metadata = MigrationMetadata{x: 1};
assert!(tables.add_migration_with_metadata((0.5, 100.0),
                                           3,
                                           (0, 1),
                                           53.5,
                                           &metadata).is_ok());

Warnings

Migration tables are not currently supported by tree sequence simplification.

pub fn add_node<F, T, P, I>( &mut self, flags: F, time: T, population: P, individual: I ) -> Result<NodeId, TskitError>where F: Into<NodeFlags>, T: Into<Time>, P: Into<PopulationId>, I: Into<IndividualId>,

Add a row to the node table

pub fn add_node_with_defaults<T: Into<Time>, D: DefaultNodeData>( &mut self, time: T, defaults: &D ) -> Result<NodeId, TskitError>

Add a node using default values

pub fn add_node_with_metadata<F, T, P, I, N>( &mut self, flags: F, time: T, population: P, individual: I, metadata: &N ) -> Result<NodeId, TskitError>where F: Into<NodeFlags>, T: Into<Time>, P: Into<PopulationId>, I: Into<IndividualId>, N: NodeMetadata,

Add a row with optional metadata to the node table

pub fn add_site( &mut self, position: P, ancestral_state: Option<&[u8]> ) -> Result<SiteId, TskitError>where P: Into<Position>,

Add a row to the site table

pub fn add_site_with_metadata<P, M>( &mut self, position: P, ancestral_state: Option<&[u8]>, metadata: &M ) -> Result<SiteId, TskitError>where P: Into<Position>, M: SiteMetadata,

Add a row with optional metadata to the site table

pub fn add_mutation<S, N, P, T>( &mut self, site: S, node: N, parent: P, time: T, derived_state: Option<&[u8]> ) -> Result<MutationId, TskitError>where S: Into<SiteId>, N: Into<NodeId>, P: Into<MutationId>, T: Into<Time>,

Add a row to the mutation table.

pub fn add_mutation_with_metadata<S, N, P, T, M>( &mut self, site: S, node: N, parent: P, time: T, derived_state: Option<&[u8]>, metadata: &M ) -> Result<MutationId, TskitError>where S: Into<SiteId>, N: Into<NodeId>, P: Into<MutationId>, T: Into<Time>, M: MutationMetadata,

Add a row with optional metadata to the mutation table.

pub fn add_population(&mut self) -> Result<PopulationId, TskitError>

Add a row to the population_table

pub fn add_population_with_metadata<M>( &mut self, metadata: &M ) -> Result<PopulationId, TskitError>where M: PopulationMetadata,

Add a row with optional 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<&[EdgeId]>

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<&[EdgeId]>

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

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

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

Details

See full_sort for more details about which tables are sorted.

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

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

Details

This function only sorts the tables that have a strict sortedness requirement according to the tskit data model.

These tables are:

edges
mutations
sites

For some use cases it is desirable to have the individual table sorted so that parents appear before offspring. See topological_sort_individuals.

pub fn topological_sort_individuals<O: Into<IndividualTableSortOptions>>( &mut self, options: O ) -> TskReturnValue

Sorts the individual table in place, so that parents come before children, and the parent column is remapped as required. Node references to individuals are also updated.

This function is needed because neither sort nor full_sort sorts the individual table!

Examples

// Parent comes AFTER the child
let mut tables = tskit::TableCollection::new(1.0).unwrap();
let i0 = tables.add_individual(0, None, &[1]).unwrap();
assert_eq!(i0, 0);
let i1 = tables.add_individual(0, None, None).unwrap();
assert_eq!(i1, 1);
let n0 = tables.add_node(0, 0.0, -1, i1).unwrap();
assert_eq!(n0, 0);
let n1 = tables.add_node(0, 1.0, -1, i0).unwrap();
assert_eq!(n1, 1);

// Testing for valid individual order will Err:
match tables.check_integrity(tskit::TableIntegrityCheckFlags::CHECK_INDIVIDUAL_ORDERING) {
    Ok(_) => panic!("expected Err"),
    Err(_) => (),
};

// The standard sort doesn't fix the Err...:
tables.full_sort(tskit::TableSortOptions::default()).unwrap();
match tables.check_integrity(tskit::TableIntegrityCheckFlags::CHECK_INDIVIDUAL_ORDERING) {
    Ok(_) => panic!("expected Err"),
    Err(_) => (),
};

// ... so we need to intentionally sort the individuals.
let _ = tables.topological_sort_individuals(tskit::IndividualTableSortOptions::default()).unwrap();
tables.check_integrity(tskit::TableIntegrityCheckFlags::CHECK_INDIVIDUAL_ORDERING).unwrap();

Errors

Will return an error code if the underlying C function returns an error.

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

Dump the table collection to file.

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 clear<O: Into<TableClearOptions>>( &mut self, options: O ) -> 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<O: Into<TableEqualityOptions>>( &self, other: &TableCollection, options: O ) -> 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<O: Into<SimplificationOptions>>( &mut self, samples: &[NodeId], options: O, idmap: bool ) -> Result<Option<&[NodeId]>, 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 NodeId::NULL if the input node is not part of the simplified history.

pub fn check_integrity(&self, flags: TableIntegrityCheckFlags) -> TskReturnValue

Validate the contents of the table collection

Parameters

flags is an instance of TableIntegrityCheckFlags

Return value

0 upon success, or an error code. However, if flags contains TableIntegrityCheckFlags::CHECK_TREES, and no error is returned, then the return value is the number of trees.

Note

Creating a crate::TreeSequence from a table collection will automatically run an integrity check. See TableCollection::tree_sequence.

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

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();
tables.add_provenance(&String::from("Some provenance")).unwrap();

// Get reference to the table
let prov_ref = tables.provenances();

// Get the first row
let row_0 = prov_ref.row(0).unwrap();

assert_eq!(row_0.record, "Some provenance");

// Get the first record
let record_0 = prov_ref.record(0).unwrap();
assert_eq!(record_0, row_0.record);

// Get the first time stamp
let timestamp = prov_ref.timestamp(0).unwrap();
assert_eq!(timestamp, row_0.timestamp);

// You can get the `humantime::Timestamp` object back from the `String`:
use core::str::FromStr;
let timestamp_string = humantime::Timestamp::from_str(&timestamp).unwrap();

// Provenance transfers to the tree sequences
let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
assert_eq!(treeseq.provenances().record(0).unwrap(), "Some provenance");
// We can still compare to row_0 because it is a copy of the row data:
assert_eq!(treeseq.provenances().record(0).unwrap(), row_0.record);

pub fn set_edges(&mut self, edges: &OwningEdgeTable) -> TskReturnValue

Set the edge table from an OwningEdgeTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut edges = tskit::OwningEdgeTable::default();
edges.add_row(0., 1., 0, 12).unwrap();
tables.set_edges(&edges).unwrap();
assert_eq!(tables.edges().num_rows(), 1);
assert_eq!(tables.edges().child(0).unwrap(), 12);

pub fn set_nodes(&mut self, nodes: &OwningNodeTable) -> TskReturnValue

Set the node table from an OwningNodeTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut nodes = tskit::OwningNodeTable::default();
nodes.add_row(0, 10.0, -1, -1).unwrap();
tables.set_nodes(&nodes).unwrap();
assert_eq!(tables.nodes().num_rows(), 1);
assert_eq!(tables.nodes().time(0).unwrap(), 10.0);

pub fn set_sites(&mut self, sites: &OwningSiteTable) -> TskReturnValue

Set the site table from an OwningSiteTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut sites = tskit::OwningSiteTable::default();
sites.add_row(11.0, None).unwrap();
tables.set_sites(&sites).unwrap();
assert_eq!(tables.sites().num_rows(), 1);
assert_eq!(tables.sites().position(0).unwrap(), 11.0);

pub fn set_mutations( &mut self, mutations: &OwningMutationTable ) -> TskReturnValue

Set the mutation table from an OwningMutationTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut mutations = tskit::OwningMutationTable::default();
mutations.add_row(14, 12, -1, 11.3, None).unwrap();
tables.set_mutations(&mutations).unwrap();
assert_eq!(tables.mutations().num_rows(), 1);
assert_eq!(tables.mutations().site(0).unwrap(), 14);

pub fn set_individuals( &mut self, individuals: &OwningIndividualTable ) -> TskReturnValue

Set the individual table from an OwningIndividualTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut individuals = tskit::OwningIndividualTable::default();
individuals.add_row(0, [0.1, 10.0], None).unwrap();
tables.set_individuals(&individuals).unwrap();
assert_eq!(tables.individuals().num_rows(), 1);
let expected = vec![tskit::Location::from(0.1), tskit::Location::from(10.0)];
assert_eq!(tables.individuals().location(0), Some(expected.as_slice()));

pub fn set_migrations( &mut self, migrations: &OwningMigrationTable ) -> TskReturnValue

Set the migration table from an OwningMigrationTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut migrations = tskit::OwningMigrationTable::default();
migrations.add_row((0.25, 0.37), 1, (0, 1), 111.0).unwrap();
tables.set_migrations(&migrations).unwrap();
assert_eq!(tables.migrations().num_rows(), 1);
assert_eq!(tables.migrations().time(0).unwrap(), 111.0);

pub fn set_populations( &mut self, populations: &OwningPopulationTable ) -> TskReturnValue

Set the population table from an OwningPopulationTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut populations = tskit::OwningPopulationTable::default();
populations.add_row().unwrap();
tables.set_populations(&populations).unwrap();
assert_eq!(tables.populations().num_rows(), 1);

pub fn set_provenances( &mut self, provenances: &OwningProvenanceTable ) -> TskReturnValue

Available on crate feature provenance only.

Set the provenance table from an OwningProvenanceTable

Errors

Any errors from the C API propagate.

Example

let mut tables = tskit::TableCollection::new(1.0).unwrap();
let mut provenances = tskit::provenance::OwningProvenanceTable::default();
provenances.add_row("I like pancakes").unwrap();
tables.set_provenances(&provenances).unwrap();
assert_eq!(tables.provenances().num_rows(), 1);
assert_eq!(tables.provenances().record(0).unwrap(), "I like pancakes");

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

Get mutable reference to the NodeTable.

pub fn edges(&self) -> &EdgeTable

Get reference to the EdgeTable.

pub fn individuals(&self) -> &IndividualTable

Get reference to the IndividualTable.

pub fn migrations(&self) -> &MigrationTable

Get reference to the MigrationTable.

pub fn mutations(&self) -> &MutationTable

Get reference to the MutationTable.

pub fn nodes(&self) -> &NodeTable

Get reference to the NodeTable.

pub fn populations(&self) -> &PopulationTable

Get reference to the PopulationTable.

pub fn sites(&self) -> &SiteTable

Get reference to the SiteTable.

pub fn provenances(&self) -> &ProvenanceTable

Available on crate feature provenance only.

Get reference to the ProvenanceTable

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

Return an iterator over the individuals.

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

Return an iterator over the nodes.

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

Return an iterator over the edges.

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

Return an iterator over the migrations.

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

Return an iterator over the mutations.

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

Return an iterator over the populations.

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

Return an iterator over the sites.

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:

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);

pub fn as_ptr(&self) -> *const tsk_table_collection_t

Pointer to the low-level C type.

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

Mutable pointer to the low-level C type.

Trait Implementations§

impl Drop for TableCollection

fn drop(&mut self)

Executes the destructor for this type. Read more

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.

Auto Trait Implementations§

impl UnwindSafe for TableCollection

Blanket Implementations§

impl<T> Any for Twhere T: 'static + ?Sized,

fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

impl<T> Borrow<T> for Twhere T: ?Sized,

const: unstable · source§

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

impl<T> BorrowMut<T> for Twhere T: ?Sized,

const: unstable · source§

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

impl<T> Free for T

unsafe default fn free(ptr_ref: NonNull<T>)

Drops the content pointed by this pointer and frees it. Read more

impl<T> From<T> for T

const: unstable · source§

fn from(t: T) -> T

Returns the argument unchanged.

impl<T, U> Into for Twhere U: From<T>,

const: unstable · source§

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

impl<T, U> TryFrom for Twhere U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source§

fn try_from(value: U) -> Result<T, <T as TryFrom>::Error>

Performs the conversion.

impl<T, U> TryInto for Twhere U: TryFrom<T>,