Struct tskit::TableCollection

pub struct TableCollection { /* private fields */ }

A table collection.

This is a thin wrapper around the C type tsk_table_collection_t.

See also

• metadata

Examples

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::PopulationId::NULL, tskit::IndividualId::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);

Implementations

impl TableCollection

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

Create a new table collection with a sequence length.

Examples

let tables = tskit::TableCollection::new(55.0).unwrap();

Negative sequence lengths are errors:

let tables = tskit::TableCollection::new(-55.0).unwrap();

Examples found in repository

src/table_collection.rs (line 189)

    pub fn new_from_file(filename: impl AsRef<str>) -> Result<Self, TskitError> {
        // Arbitrary sequence_length.
        let mut tables = match TableCollection::new(1.0) {
            Ok(t) => t,
            Err(e) => return Err(e),
        };

        let c_str = std::ffi::CString::new(filename.as_ref()).map_err(|_| {
            TskitError::LibraryError("call to ffi::CString::new failed".to_string())
        })?;
        let rv = unsafe {
            ll_bindings::tsk_table_collection_load(
                tables.as_mut_ptr(),
                c_str.as_ptr(),
                ll_bindings::TSK_NO_INIT,
            )
        };

        handle_tsk_return_value!(rv, tables)
    }

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.

Examples found in repository

src/trees.rs (line 288)

    pub fn load(filename: impl AsRef<str>) -> Result<Self, TskitError> {
        let tables = TableCollection::new_from_file(filename.as_ref())?;

        Self::new(tables, TreeSequenceFlags::default())
    }

pub fn sequence_length(&self) -> Position

Length of the sequence/“genome”.

Examples

let tables = tskit::TableCollection::new(100.).unwrap();
assert_eq!(tables.sequence_length(), 100.0);

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

Examples

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

let metadata = EdgeMetadata{x: 1};
assert!(tables.add_edge_with_metadata(0., 53., 1, 11, &metadata).is_ok());

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

Examples

No flags, location, nor parents

tables.add_individual(0, None, None).unwrap();

No flags, a 3d location, no parents

tables.add_individual(0, &[-0.5, 0.3, 10.0], None).unwrap();

No flags, no location, two parents

tables.add_individual(0, None, &[1, 11]);

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

Examples

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

 
let metadata = IndividualMetadata{x: 1};
assert!(tables.add_individual_with_metadata(0, None, None,
                                            &metadata).is_ok());

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.

Examples

assert!(tables.add_migration((0.5, 100.0),
                             3,
                             (0, 1),
                             53.5).is_ok());

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

Add a row with optional metadata to the node table

Examples

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

let metadata = NodeMetadata{x: 1};
assert!(tables.add_node_with_metadata(0, 0.0, -1, -1, &metadata).is_ok());

pub fn add_site<P>(
    &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

Examples

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

let metadata = SiteMetadata{x: 1};
assert!(tables.add_site_with_metadata(tskit::Position::from(111.0),
                                      Some(&[111]),
                                      &metadata).is_ok());

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.

Examples

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

let metadata = MutationMetadata{x: 1};
assert!(tables.add_mutation_with_metadata(0, 0, 0, 100.0, None,
                                          &metadata).is_ok());

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

Add a row to the population_table

Examples

tables.add_population().unwrap();

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

Examples

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

let metadata = PopulationMetadata{x: 1};
assert!(tables.add_population_with_metadata(&metadata).is_ok());

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.

Examples found in repository

src/table_collection.rs (line 541)

    pub fn edge_insertion_order(&self) -> Option<&[EdgeId]> {
        if self.is_indexed() {
            Some(unsafe {
                std::slice::from_raw_parts(
                    (*self.as_ptr()).indexes.edge_insertion_order as *const EdgeId,
                    usize::try_from((*self.as_ptr()).indexes.num_edges).ok()?,
                )
            })
        } else {
            None
        }
    }

    /// If `self.is_indexed()` is `true`, return a non-owning
    /// slice containing the edge removal order.
    /// Otherwise, return `None`.
    pub fn edge_removal_order(&self) -> Option<&[EdgeId]> {
        if self.is_indexed() {
            Some(unsafe {
                std::slice::from_raw_parts(
                    (*self.as_ptr()).indexes.edge_removal_order as *const EdgeId,
                    usize::try_from((*self.as_ptr()).indexes.num_edges).ok()?,
                )
            })
        } else {
            None
        }
    }

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.

Examples found in repository

src/table_collection.rs (line 613)

    pub fn full_sort<O: Into<TableSortOptions>>(&mut self, options: O) -> TskReturnValue {
        let b = Bookmark::new();
        self.sort(&b, options)
    }

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<N: Into<NodeId>, O: Into<SimplificationOptions>>(
    &mut self,
    samples: &[N],
    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.

Examples

There are many ways for a table colletion to be invalid. These examples are just the tip of the iceberg.

let mut tables = tskit::TableCollection::new(10.0).unwrap();
// Right position is > sequence_length
tables.add_edge(0.0, 11.0, 0, 0);
tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).unwrap();

// Left position is < 0.0
tables.add_edge(-1., 10.0, 0, 0);
tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).unwrap();

// Edges cannot have null node ids
tables.add_edge(0., 10.0, tskit::NodeId::NULL, 0);
tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).unwrap();

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.

Examples found in repository

src/table_collection.rs (line 216)

    pub fn sequence_length(&self) -> Position {
        unsafe { (*self.as_ptr()).sequence_length }.into()
    }

    edge_table_add_row!(
    /// Add a row to the edge table
    ///
    /// # Examples
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    ///
    /// // 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 mut tables = tskit::TableCollection::new(100.).unwrap();
    /// 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:
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// assert!(tables.add_edge(0., 53.,
    ///                         tskit::NodeId::NULL,
    ///                         tskit::NodeId::NULL).is_ok());
    /// # assert!(tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).is_err());
    /// ```
    ///
    /// See [`TableCollection::check_integrity`] for how to catch these data model
    /// violations.
    => add_edge, self, &mut(*self.as_mut_ptr()).edges);

    edge_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the edge table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::EdgeMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct EdgeMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = EdgeMetadata{x: 1};
    /// assert!(tables.add_edge_with_metadata(0., 53., 1, 11, &metadata).is_ok());
    /// # }
    /// ```
    => add_edge_with_metadata, self, &mut(*self.as_mut_ptr()).edges);

    individual_table_add_row!(
    /// Add a row to the individual table
    ///
    /// # Examples
    ///
    /// ## No flags, location, nor parents
    ///
    /// ```
    /// # 
    /// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
    /// tables.add_individual(0, None, None).unwrap();
    /// # assert!(tables.individuals().location(0).is_none());
    /// # assert!(tables.individuals().parents(0).is_none());
    /// ```
    ///
    /// ## No flags, a 3d location, no parents
    ///
    /// ```
    /// # 
    /// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
    /// tables.add_individual(0, &[-0.5, 0.3, 10.0], None).unwrap();
    /// # match tables.individuals().location(0) {
    /// #     Some(loc) => loc.iter().zip([-0.5, 0.3, 10.0].iter()).for_each(|(a,b)| assert_eq!(a, b)),
    /// #     None => panic!("expected a location"),
    /// # }
    /// ```
    ///
    /// ## No flags, no location, two parents
    /// ```
    /// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
    /// # 
    /// tables.add_individual(0, None, &[1, 11]);
    /// # match tables.individuals().parents(0) {
    /// #     Some(parents) => parents.iter().zip([1, 11].iter()).for_each(|(a,b)| assert_eq!(a, b)),
    /// #     None => panic!("expected parents"),
    /// # }
    /// ```
    => add_individual, self, &mut (*self.as_mut_ptr()).individuals);

    individual_table_add_row_with_metadata!(
    /// Add a row with metadata to the individual table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// 
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct IndividualMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = IndividualMetadata{x: 1};
    /// assert!(tables.add_individual_with_metadata(0, None, None,
    ///                                             &metadata).is_ok());
    /// # let decoded = tables.individuals().metadata::<IndividualMetadata>(0.into()).unwrap().unwrap();
    /// # assert_eq!(decoded.x, 1);
    /// # }
    => add_individual_with_metadata, self, &mut (*self.as_mut_ptr()).individuals);

    migration_table_add_row!(
    /// Add a row to the migration table
    ///
    /// # Warnings
    ///
    /// Migration tables are not currently supported
    /// by tree sequence simplification.
    /// # Examples
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// assert!(tables.add_migration((0.5, 100.0),
    ///                              3,
    ///                              (0, 1),
    ///                              53.5).is_ok());
    /// ```
    => add_migration, self, &mut (*self.as_mut_ptr()).migrations);

    migration_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the migration table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MigrationMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct MigrationMetadata {
    /// #    x: i32,
    /// # }
    /// 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.
    => add_migration_with_metadata, self, &mut (*self.as_mut_ptr()).migrations);

    node_table_add_row!(
    /// Add a row to the node table
    => add_node, self, &mut (*self.as_mut_ptr()).nodes);

    node_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the node table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::NodeMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct NodeMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = NodeMetadata{x: 1};
    /// assert!(tables.add_node_with_metadata(0, 0.0, -1, -1, &metadata).is_ok());
    /// # }
    /// ```
    => add_node_with_metadata, self, &mut (*self.as_mut_ptr()).nodes);

    site_table_add_row!(
    /// Add a row to the site table
    => add_site, self, &mut (*self.as_mut_ptr()).sites);

    site_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the site table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::SiteMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct SiteMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = SiteMetadata{x: 1};
    /// assert!(tables.add_site_with_metadata(tskit::Position::from(111.0),
    ///                                       Some(&[111]),
    ///                                       &metadata).is_ok());
    /// # }
    /// ```
    => add_site_with_metadata, self, &mut (*self.as_mut_ptr()).sites);

    mutation_table_add_row!(
    /// Add a row to the mutation table.
    => add_mutation, self, &mut (*self.as_mut_ptr()).mutations);

    mutation_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the mutation table.
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct MutationMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = MutationMetadata{x: 1};
    /// assert!(tables.add_mutation_with_metadata(0, 0, 0, 100.0, None,
    ///                                           &metadata).is_ok());
    /// # }
    /// ```
    => add_mutation_with_metadata, self, &mut (*self.as_mut_ptr()).mutations);

    population_table_add_row!(
    /// Add a row to the population_table
    ///
    /// # Examples
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(55.0).unwrap();
    /// tables.add_population().unwrap();
    /// ```
    => add_population, self, &mut (*self.as_mut_ptr()).populations);

    population_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the population_table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::PopulationMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct PopulationMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = PopulationMetadata{x: 1};
    /// assert!(tables.add_population_with_metadata(&metadata).is_ok());
    /// # }
    => add_population_with_metadata, self, &mut (*self.as_mut_ptr()).populations);

    /// 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 build_index(&mut self) -> TskReturnValue {
        let rv = unsafe { ll_bindings::tsk_table_collection_build_index(self.as_mut_ptr(), 0) };
        handle_tsk_return_value!(rv)
    }

    /// Return `true` if tables are indexed.
    pub fn is_indexed(&self) -> bool {
        unsafe { ll_bindings::tsk_table_collection_has_index(self.as_ptr(), 0) }
    }

    /// If `self.is_indexed()` is `true`, return a non-owning
    /// slice containing the edge insertion order.
    /// Otherwise, return `None`.
    pub fn edge_insertion_order(&self) -> Option<&[EdgeId]> {
        if self.is_indexed() {
            Some(unsafe {
                std::slice::from_raw_parts(
                    (*self.as_ptr()).indexes.edge_insertion_order as *const EdgeId,
                    usize::try_from((*self.as_ptr()).indexes.num_edges).ok()?,
                )
            })
        } else {
            None
        }
    }

    /// If `self.is_indexed()` is `true`, return a non-owning
    /// slice containing the edge removal order.
    /// Otherwise, return `None`.
    pub fn edge_removal_order(&self) -> Option<&[EdgeId]> {
        if self.is_indexed() {
            Some(unsafe {
                std::slice::from_raw_parts(
                    (*self.as_ptr()).indexes.edge_removal_order as *const EdgeId,
                    usize::try_from((*self.as_ptr()).indexes.num_edges).ok()?,
                )
            })
        } else {
            None
        }
    }

    /// Sort the tables.  
    /// The [``bookmark``](crate::types::Bookmark) can
    /// be used to affect where sorting starts from for each table.
    ///
    /// # Details
    ///
    /// See [`full_sort`](crate::TableCollection::full_sort)
    /// for more details about which tables are sorted.
    pub fn sort<O: Into<TableSortOptions>>(
        &mut self,
        start: &Bookmark,
        options: O,
    ) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_sort(
                self.as_mut_ptr(),
                &start.offsets,
                options.into().bits(),
            )
        };

        handle_tsk_return_value!(rv)
    }

    /// Fully sort all tables.
    /// Implemented via a call to [``sort``](crate::TableCollection::sort).
    ///
    /// # Details
    ///
    /// This function only sorts the tables that have a strict sortedness
    /// requirement according to the `tskit` [data
    /// model](https://tskit.dev/tskit/docs/stable/data-model.html).
    ///
    /// 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``](crate::TableCollection::topological_sort_individuals).
    pub fn full_sort<O: Into<TableSortOptions>>(&mut self, options: O) -> TskReturnValue {
        let b = Bookmark::new();
        self.sort(&b, options)
    }

    /// 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``](crate::TableCollection::sort) nor
    /// [``full_sort``](crate::TableCollection::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 topological_sort_individuals<O: Into<IndividualTableSortOptions>>(
        &mut self,
        options: O,
    ) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_individual_topological_sort(
                self.as_mut_ptr(),
                options.into().bits(),
            )
        };
        handle_tsk_return_value!(rv)
    }

    /// 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 dump<O: Into<TableOutputOptions>>(&self, filename: &str, options: O) -> TskReturnValue {
        let c_str = std::ffi::CString::new(filename).map_err(|_| {
            TskitError::LibraryError("call to ffi::CString::new failed".to_string())
        })?;
        let rv = unsafe {
            ll_bindings::tsk_table_collection_dump(
                self.as_ptr(),
                c_str.as_ptr(),
                options.into().bits(),
            )
        };

        handle_tsk_return_value!(rv)
    }

    /// Clear the contents of all tables.
    /// Does not release memory.
    /// Memory will be released when the object goes out
    /// of scope.
    pub fn clear<O: Into<TableClearOptions>>(&mut self, options: O) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_clear(self.as_mut_ptr(), options.into().bits())
        };

        handle_tsk_return_value!(rv)
    }

    /// Free all memory allocated on the C side.
    /// Not public b/c not very safe.
    #[allow(dead_code)]
    fn free(&mut self) -> TskReturnValue {
        let rv = unsafe { ll_bindings::tsk_table_collection_free(self.as_mut_ptr()) };

        handle_tsk_return_value!(rv)
    }

    /// Return ``true`` if ``self`` contains the same
    /// data as ``other``, and ``false`` otherwise.
    pub fn equals<O: Into<TableEqualityOptions>>(
        &self,
        other: &TableCollection,
        options: O,
    ) -> bool {
        unsafe {
            ll_bindings::tsk_table_collection_equals(
                self.as_ptr(),
                other.as_ptr(),
                options.into().bits(),
            )
        }
    }

    /// Return a "deep" copy of the tables.
    pub fn deepcopy(&self) -> Result<TableCollection, TskitError> {
        // The output is UNINITIALIZED tables,
        // else we leak memory
        let mut inner = uninit_table_collection();

        let rv = unsafe { ll_bindings::tsk_table_collection_copy(self.as_ptr(), &mut *inner, 0) };

        // SAFETY: we just initialized it.
        // The C API doesn't free NULL pointers.
        handle_tsk_return_value!(rv, unsafe { Self::new_from_mbox(inner)? })
    }

    /// 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 tree_sequence(
        self,
        flags: TreeSequenceFlags,
    ) -> Result<crate::TreeSequence, TskitError> {
        crate::TreeSequence::new(self, flags)
    }

    /// 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 simplify<N: Into<NodeId>, O: Into<SimplificationOptions>>(
        &mut self,
        samples: &[N],
        options: O,
        idmap: bool,
    ) -> Result<Option<&[NodeId]>, TskitError> {
        if idmap {
            self.idmap.resize(
                usize::try_from(self.views.nodes().num_rows())?,
                NodeId::NULL,
            );
        }
        let rv = unsafe {
            ll_bindings::tsk_table_collection_simplify(
                self.as_mut_ptr(),
                samples.as_ptr().cast::<tsk_id_t>(),
                samples.len() as tsk_size_t,
                options.into().bits(),
                match idmap {
                    true => self.idmap.as_mut_ptr().cast::<tsk_id_t>(),
                    false => std::ptr::null_mut(),
                },
            )
        };
        handle_tsk_return_value!(
            rv,
            match idmap {
                true => Some(&self.idmap),
                false => None,
            }
        )
    }

    /// 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`].
    ///
    /// # Examples
    ///
    /// There are many ways for a table colletion to be invalid.
    /// These examples are just the tip of the iceberg.
    ///
    /// ```should_panic
    /// let mut tables = tskit::TableCollection::new(10.0).unwrap();
    /// // Right position is > sequence_length
    /// tables.add_edge(0.0, 11.0, 0, 0);
    /// tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).unwrap();
    /// ```
    ///
    /// ```should_panic
    /// # let mut tables = tskit::TableCollection::new(10.0).unwrap();
    /// // Left position is < 0.0
    /// tables.add_edge(-1., 10.0, 0, 0);
    /// tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).unwrap();
    /// ```
    ///
    /// ```should_panic
    /// # let mut tables = tskit::TableCollection::new(10.0).unwrap();
    /// // Edges cannot have null node ids
    /// tables.add_edge(0., 10.0, tskit::NodeId::NULL, 0);
    /// tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).unwrap();
    /// ```
    pub fn check_integrity(&self, flags: TableIntegrityCheckFlags) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_check_integrity(self.as_ptr(), flags.bits())
        };
        handle_tsk_return_value!(rv)
    }

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

Mutable pointer to the low-level C type.

Examples found in repository

src/table_collection.rs (line 63)

    fn drop(&mut self) {
        let rv = unsafe { tsk_table_collection_free(self.as_mut_ptr()) };
        assert_eq!(rv, 0);
    }
}

/// Returns a pointer to an uninitialized tsk_table_collection_t
pub(crate) fn uninit_table_collection() -> MBox<ll_bindings::tsk_table_collection_t> {
    let temp = unsafe {
        libc::malloc(std::mem::size_of::<ll_bindings::tsk_table_collection_t>())
            as *mut ll_bindings::tsk_table_collection_t
    };
    let nonnull = match std::ptr::NonNull::<ll_bindings::tsk_table_collection_t>::new(temp) {
        Some(x) => x,
        None => panic!("out of memory"),
    };
    unsafe { MBox::from_non_null_raw(nonnull) }
}

impl TableCollection {
    /// Create a new table collection with a sequence length.
    ///
    /// # Examples
    ///
    /// ```
    /// let tables = tskit::TableCollection::new(55.0).unwrap();
    /// ```
    ///
    /// Negative sequence lengths are errors:
    ///
    /// ```{should_panic}
    /// let tables = tskit::TableCollection::new(-55.0).unwrap();
    /// ```
    pub fn new<P: Into<Position>>(sequence_length: P) -> Result<Self, TskitError> {
        let sequence_length = sequence_length.into();
        if sequence_length <= 0. {
            return Err(TskitError::ValueError {
                got: f64::from(sequence_length).to_string(),
                expected: "sequence_length >= 0.0".to_string(),
            });
        }
        let mut mbox = uninit_table_collection();
        let rv = unsafe { ll_bindings::tsk_table_collection_init(&mut *mbox, 0) };
        if rv < 0 {
            return Err(crate::error::TskitError::ErrorCode { code: rv });
        }
        let views = crate::table_views::TableViews::new_from_mbox_table_collection(&mut mbox)?;
        // AHA?
        assert!(std::ptr::eq(
            &mbox.as_ref().edges as *const ll_bindings::tsk_edge_table_t,
            views.edges().as_ref() as *const ll_bindings::tsk_edge_table_t
        ));
        let mut tables = Self {
            inner: mbox,
            idmap: vec![],
            views,
        };
        unsafe {
            (*tables.as_mut_ptr()).sequence_length = f64::from(sequence_length);
        }
        Ok(tables)
    }

    /// # Safety
    ///
    /// It is possible that the mbox's inner pointer has not be run through
    /// tsk_table_collection_init, meaning that it is in an uninitialized state.
    /// Or, it may be initialized and about to be used in a part of the C API
    /// requiring an uninitialized table collection.
    /// Consult the C API docs before using!
    pub(crate) unsafe fn new_from_mbox(
        mbox: MBox<ll_bindings::tsk_table_collection_t>,
    ) -> Result<Self, TskitError> {
        let mut mbox = mbox;
        let views = crate::table_views::TableViews::new_from_mbox_table_collection(&mut mbox)?;
        Ok(Self {
            inner: mbox,
            idmap: vec![],
            views,
        })
    }

    pub(crate) fn into_raw(self) -> Result<*mut ll_bindings::tsk_table_collection_t, TskitError> {
        let mut tables = self;
        // rust won't let use move inner out b/c this type implements Drop.
        // So we have to replace the existing pointer with a new one.
        let table_ptr = unsafe {
            libc::malloc(std::mem::size_of::<ll_bindings::tsk_table_collection_t>())
                as *mut ll_bindings::tsk_table_collection_t
        };
        let rv = unsafe { ll_bindings::tsk_table_collection_init(table_ptr, 0) };

        let mut temp = unsafe { MBox::from_raw(table_ptr) };
        std::mem::swap(&mut temp, &mut tables.inner);
        handle_tsk_return_value!(rv, MBox::into_raw(temp))
    }

    /// Load a table collection from a file.
    ///
    /// # Examples
    ///
    /// The function is generic over references to `str`:
    ///
    /// ```
    /// # let empty_tables = tskit::TableCollection::new(100.).unwrap();
    /// # empty_tables.dump("trees.file", tskit::TableOutputOptions::default()).unwrap();
    /// 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();
    /// # std::fs::remove_file("trees.file").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 new_from_file(filename: impl AsRef<str>) -> Result<Self, TskitError> {
        // Arbitrary sequence_length.
        let mut tables = match TableCollection::new(1.0) {
            Ok(t) => t,
            Err(e) => return Err(e),
        };

        let c_str = std::ffi::CString::new(filename.as_ref()).map_err(|_| {
            TskitError::LibraryError("call to ffi::CString::new failed".to_string())
        })?;
        let rv = unsafe {
            ll_bindings::tsk_table_collection_load(
                tables.as_mut_ptr(),
                c_str.as_ptr(),
                ll_bindings::TSK_NO_INIT,
            )
        };

        handle_tsk_return_value!(rv, tables)
    }

    /// Length of the sequence/"genome".
    /// # Examples
    ///
    /// ```
    /// let tables = tskit::TableCollection::new(100.).unwrap();
    /// assert_eq!(tables.sequence_length(), 100.0);
    /// ```
    pub fn sequence_length(&self) -> Position {
        unsafe { (*self.as_ptr()).sequence_length }.into()
    }

    edge_table_add_row!(
    /// Add a row to the edge table
    ///
    /// # Examples
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    ///
    /// // 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 mut tables = tskit::TableCollection::new(100.).unwrap();
    /// 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:
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// assert!(tables.add_edge(0., 53.,
    ///                         tskit::NodeId::NULL,
    ///                         tskit::NodeId::NULL).is_ok());
    /// # assert!(tables.check_integrity(tskit::TableIntegrityCheckFlags::default()).is_err());
    /// ```
    ///
    /// See [`TableCollection::check_integrity`] for how to catch these data model
    /// violations.
    => add_edge, self, &mut(*self.as_mut_ptr()).edges);

    edge_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the edge table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::EdgeMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct EdgeMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = EdgeMetadata{x: 1};
    /// assert!(tables.add_edge_with_metadata(0., 53., 1, 11, &metadata).is_ok());
    /// # }
    /// ```
    => add_edge_with_metadata, self, &mut(*self.as_mut_ptr()).edges);

    individual_table_add_row!(
    /// Add a row to the individual table
    ///
    /// # Examples
    ///
    /// ## No flags, location, nor parents
    ///
    /// ```
    /// # 
    /// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
    /// tables.add_individual(0, None, None).unwrap();
    /// # assert!(tables.individuals().location(0).is_none());
    /// # assert!(tables.individuals().parents(0).is_none());
    /// ```
    ///
    /// ## No flags, a 3d location, no parents
    ///
    /// ```
    /// # 
    /// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
    /// tables.add_individual(0, &[-0.5, 0.3, 10.0], None).unwrap();
    /// # match tables.individuals().location(0) {
    /// #     Some(loc) => loc.iter().zip([-0.5, 0.3, 10.0].iter()).for_each(|(a,b)| assert_eq!(a, b)),
    /// #     None => panic!("expected a location"),
    /// # }
    /// ```
    ///
    /// ## No flags, no location, two parents
    /// ```
    /// # let mut tables = tskit::TableCollection::new(1.0).unwrap();
    /// # 
    /// tables.add_individual(0, None, &[1, 11]);
    /// # match tables.individuals().parents(0) {
    /// #     Some(parents) => parents.iter().zip([1, 11].iter()).for_each(|(a,b)| assert_eq!(a, b)),
    /// #     None => panic!("expected parents"),
    /// # }
    /// ```
    => add_individual, self, &mut (*self.as_mut_ptr()).individuals);

    individual_table_add_row_with_metadata!(
    /// Add a row with metadata to the individual table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// 
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::IndividualMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct IndividualMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = IndividualMetadata{x: 1};
    /// assert!(tables.add_individual_with_metadata(0, None, None,
    ///                                             &metadata).is_ok());
    /// # let decoded = tables.individuals().metadata::<IndividualMetadata>(0.into()).unwrap().unwrap();
    /// # assert_eq!(decoded.x, 1);
    /// # }
    => add_individual_with_metadata, self, &mut (*self.as_mut_ptr()).individuals);

    migration_table_add_row!(
    /// Add a row to the migration table
    ///
    /// # Warnings
    ///
    /// Migration tables are not currently supported
    /// by tree sequence simplification.
    /// # Examples
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// assert!(tables.add_migration((0.5, 100.0),
    ///                              3,
    ///                              (0, 1),
    ///                              53.5).is_ok());
    /// ```
    => add_migration, self, &mut (*self.as_mut_ptr()).migrations);

    migration_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the migration table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MigrationMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct MigrationMetadata {
    /// #    x: i32,
    /// # }
    /// 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.
    => add_migration_with_metadata, self, &mut (*self.as_mut_ptr()).migrations);

    node_table_add_row!(
    /// Add a row to the node table
    => add_node, self, &mut (*self.as_mut_ptr()).nodes);

    node_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the node table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::NodeMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct NodeMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = NodeMetadata{x: 1};
    /// assert!(tables.add_node_with_metadata(0, 0.0, -1, -1, &metadata).is_ok());
    /// # }
    /// ```
    => add_node_with_metadata, self, &mut (*self.as_mut_ptr()).nodes);

    site_table_add_row!(
    /// Add a row to the site table
    => add_site, self, &mut (*self.as_mut_ptr()).sites);

    site_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the site table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::SiteMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct SiteMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = SiteMetadata{x: 1};
    /// assert!(tables.add_site_with_metadata(tskit::Position::from(111.0),
    ///                                       Some(&[111]),
    ///                                       &metadata).is_ok());
    /// # }
    /// ```
    => add_site_with_metadata, self, &mut (*self.as_mut_ptr()).sites);

    mutation_table_add_row!(
    /// Add a row to the mutation table.
    => add_mutation, self, &mut (*self.as_mut_ptr()).mutations);

    mutation_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the mutation table.
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct MutationMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = MutationMetadata{x: 1};
    /// assert!(tables.add_mutation_with_metadata(0, 0, 0, 100.0, None,
    ///                                           &metadata).is_ok());
    /// # }
    /// ```
    => add_mutation_with_metadata, self, &mut (*self.as_mut_ptr()).mutations);

    population_table_add_row!(
    /// Add a row to the population_table
    ///
    /// # Examples
    ///
    /// ```
    /// # let mut tables = tskit::TableCollection::new(55.0).unwrap();
    /// tables.add_population().unwrap();
    /// ```
    => add_population, self, &mut (*self.as_mut_ptr()).populations);

    population_table_add_row_with_metadata!(
    /// Add a row with optional metadata to the population_table
    ///
    /// # Examples
    ///
    /// See [`metadata`](crate::metadata) for more details about required
    /// trait implementations.
    /// Those details have been omitted from this example.
    ///
    /// ```
    /// # #[cfg(feature = "derive")] {
    /// # let mut tables = tskit::TableCollection::new(100.).unwrap();
    /// # #[derive(serde::Serialize, serde::Deserialize, tskit::metadata::PopulationMetadata)]
    /// # #[serializer("serde_json")]
    /// # struct PopulationMetadata {
    /// #    x: i32,
    /// # }
    /// let metadata = PopulationMetadata{x: 1};
    /// assert!(tables.add_population_with_metadata(&metadata).is_ok());
    /// # }
    => add_population_with_metadata, self, &mut (*self.as_mut_ptr()).populations);

    /// 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 build_index(&mut self) -> TskReturnValue {
        let rv = unsafe { ll_bindings::tsk_table_collection_build_index(self.as_mut_ptr(), 0) };
        handle_tsk_return_value!(rv)
    }

    /// Return `true` if tables are indexed.
    pub fn is_indexed(&self) -> bool {
        unsafe { ll_bindings::tsk_table_collection_has_index(self.as_ptr(), 0) }
    }

    /// If `self.is_indexed()` is `true`, return a non-owning
    /// slice containing the edge insertion order.
    /// Otherwise, return `None`.
    pub fn edge_insertion_order(&self) -> Option<&[EdgeId]> {
        if self.is_indexed() {
            Some(unsafe {
                std::slice::from_raw_parts(
                    (*self.as_ptr()).indexes.edge_insertion_order as *const EdgeId,
                    usize::try_from((*self.as_ptr()).indexes.num_edges).ok()?,
                )
            })
        } else {
            None
        }
    }

    /// If `self.is_indexed()` is `true`, return a non-owning
    /// slice containing the edge removal order.
    /// Otherwise, return `None`.
    pub fn edge_removal_order(&self) -> Option<&[EdgeId]> {
        if self.is_indexed() {
            Some(unsafe {
                std::slice::from_raw_parts(
                    (*self.as_ptr()).indexes.edge_removal_order as *const EdgeId,
                    usize::try_from((*self.as_ptr()).indexes.num_edges).ok()?,
                )
            })
        } else {
            None
        }
    }

    /// Sort the tables.  
    /// The [``bookmark``](crate::types::Bookmark) can
    /// be used to affect where sorting starts from for each table.
    ///
    /// # Details
    ///
    /// See [`full_sort`](crate::TableCollection::full_sort)
    /// for more details about which tables are sorted.
    pub fn sort<O: Into<TableSortOptions>>(
        &mut self,
        start: &Bookmark,
        options: O,
    ) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_sort(
                self.as_mut_ptr(),
                &start.offsets,
                options.into().bits(),
            )
        };

        handle_tsk_return_value!(rv)
    }

    /// Fully sort all tables.
    /// Implemented via a call to [``sort``](crate::TableCollection::sort).
    ///
    /// # Details
    ///
    /// This function only sorts the tables that have a strict sortedness
    /// requirement according to the `tskit` [data
    /// model](https://tskit.dev/tskit/docs/stable/data-model.html).
    ///
    /// 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``](crate::TableCollection::topological_sort_individuals).
    pub fn full_sort<O: Into<TableSortOptions>>(&mut self, options: O) -> TskReturnValue {
        let b = Bookmark::new();
        self.sort(&b, options)
    }

    /// 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``](crate::TableCollection::sort) nor
    /// [``full_sort``](crate::TableCollection::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 topological_sort_individuals<O: Into<IndividualTableSortOptions>>(
        &mut self,
        options: O,
    ) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_individual_topological_sort(
                self.as_mut_ptr(),
                options.into().bits(),
            )
        };
        handle_tsk_return_value!(rv)
    }

    /// 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 dump<O: Into<TableOutputOptions>>(&self, filename: &str, options: O) -> TskReturnValue {
        let c_str = std::ffi::CString::new(filename).map_err(|_| {
            TskitError::LibraryError("call to ffi::CString::new failed".to_string())
        })?;
        let rv = unsafe {
            ll_bindings::tsk_table_collection_dump(
                self.as_ptr(),
                c_str.as_ptr(),
                options.into().bits(),
            )
        };

        handle_tsk_return_value!(rv)
    }

    /// Clear the contents of all tables.
    /// Does not release memory.
    /// Memory will be released when the object goes out
    /// of scope.
    pub fn clear<O: Into<TableClearOptions>>(&mut self, options: O) -> TskReturnValue {
        let rv = unsafe {
            ll_bindings::tsk_table_collection_clear(self.as_mut_ptr(), options.into().bits())
        };

        handle_tsk_return_value!(rv)
    }

    /// Free all memory allocated on the C side.
    /// Not public b/c not very safe.
    #[allow(dead_code)]
    fn free(&mut self) -> TskReturnValue {
        let rv = unsafe { ll_bindings::tsk_table_collection_free(self.as_mut_ptr()) };

        handle_tsk_return_value!(rv)
    }

    /// Return ``true`` if ``self`` contains the same
    /// data as ``other``, and ``false`` otherwise.
    pub fn equals<O: Into<TableEqualityOptions>>(
        &self,
        other: &TableCollection,
        options: O,
    ) -> bool {
        unsafe {
            ll_bindings::tsk_table_collection_equals(
                self.as_ptr(),
                other.as_ptr(),
                options.into().bits(),
            )
        }
    }

    /// Return a "deep" copy of the tables.
    pub fn deepcopy(&self) -> Result<TableCollection, TskitError> {
        // The output is UNINITIALIZED tables,
        // else we leak memory
        let mut inner = uninit_table_collection();

        let rv = unsafe { ll_bindings::tsk_table_collection_copy(self.as_ptr(), &mut *inner, 0) };

        // SAFETY: we just initialized it.
        // The C API doesn't free NULL pointers.
        handle_tsk_return_value!(rv, unsafe { Self::new_from_mbox(inner)? })
    }

    /// 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 tree_sequence(
        self,
        flags: TreeSequenceFlags,
    ) -> Result<crate::TreeSequence, TskitError> {
        crate::TreeSequence::new(self, flags)
    }

    /// 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 simplify<N: Into<NodeId>, O: Into<SimplificationOptions>>(
        &mut self,
        samples: &[N],
        options: O,
        idmap: bool,
    ) -> Result<Option<&[NodeId]>, TskitError> {
        if idmap {
            self.idmap.resize(
                usize::try_from(self.views.nodes().num_rows())?,
                NodeId::NULL,
            );
        }
        let rv = unsafe {
            ll_bindings::tsk_table_collection_simplify(
                self.as_mut_ptr(),
                samples.as_ptr().cast::<tsk_id_t>(),
                samples.len() as tsk_size_t,
                options.into().bits(),
                match idmap {
                    true => self.idmap.as_mut_ptr().cast::<tsk_id_t>(),
                    false => std::ptr::null_mut(),
                },
            )
        };
        handle_tsk_return_value!(
            rv,
            match idmap {
                true => Some(&self.idmap),
                false => None,
            }
        )
    }

Trait Implementations

impl Drop for TableCollection

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.