Struct tskit::OwningMutationTable

pub struct OwningMutationTable { /* private fields */ }

A standalone mutation table that owns its data.

Examples

use tskit::OwningMutationTable;

let mut mutations = OwningMutationTable::default();
let rowid = mutations.add_row(1, 2, 0, 1.0, None).unwrap();
assert_eq!(rowid, 0);
assert_eq!(mutations.num_rows(), 1);

An example with metadata. This requires the cargo feature "derive" for tskit.

use tskit::OwningMutationTable;

#[derive(serde::Serialize,
         serde::Deserialize,
         tskit::metadata::MutationMetadata)]
#[serializer("serde_json")]
struct MutationMetadata {
    value: i32,
}

let metadata = MutationMetadata{value: 42};

let mut mutations = OwningMutationTable::default();

let rowid = mutations.add_row_with_metadata(0, 1, 5, 10.0, None, &metadata).unwrap();
assert_eq!(rowid, 0);

match mutations.metadata::<MutationMetadata>(rowid) {
    // rowid is in range, decoding succeeded
    Some(Ok(decoded)) => assert_eq!(decoded.value, 42),
    // rowid is in range, decoding failed
    Some(Err(e)) => panic!("error decoding metadata: {:?}", e),
    None => panic!("row id out of range")
}

Implementations

impl OwningMutationTable

pub fn clear(&mut self) -> TskReturnValue

Clear the table.

impl OwningMutationTable

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

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

impl OwningMutationTable

pub fn add_row<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>,

pub fn add_row_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,

Methods from Deref<Target = MutationTable>

pub fn num_rows(&self) -> SizeType

Return the number of rows.

pub fn site<M: Into<MutationId> + Copy>(&self, row: M) -> Option<SiteId>

Return the site value from row row of the table.

Errors

Will return IndexError if row is out of range.

pub fn node<M: Into<MutationId> + Copy>(&self, row: M) -> Option<NodeId>

Return the node value from row row of the table.

Errors

Will return IndexError if row is out of range.

pub fn parent<M: Into<MutationId> + Copy>(&self, row: M) -> Option<MutationId>

Return the parent value from row row of the table.

Errors

Will return IndexError if row is out of range.

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

Return the time value from row row of the table.

Errors

Will return IndexError if row is out of range.

pub fn derived_state<M: Into<MutationId>>(&self, row: M) -> Option<&[u8]>

Get the derived_state value from row row of the table.

Return

Will return None if there is no derived state.

Errors

Will return IndexError if row is out of range.

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

Retrieve decoded metadata for a row.

Returns

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

Errors

• TskitError::MetadataError if decoding fails.

Examples.

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

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

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

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

pub fn row<M: Into<MutationId> + Copy>(&self, r: M) -> Option<MutationTableRow>

Return row r of the table.

Parameters

• r: the row id.

Returns

• Some(row) if r is valid
• None otherwise

pub fn row_view<M: Into<MutationId> + Copy>( &self, r: M ) -> Option<MutationTableRowView<'_>>

Return a view of row r of the table.

Parameters

• r: the row id.

Returns

• Some(row view) if r is valid
• None otherwise

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

Get the node column as a slice

pub fn node_slice_raw(&self) -> &[tsk_id_t]

Get the node column as a slice

pub fn site_slice(&self) -> &[SiteId]

Get the site column as a slice

pub fn site_slice_raw(&self) -> &[tsk_id_t]

Get the site column as a slice

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

Get the time column as a slice

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

Get the time column as a slice

pub fn parent_slice(&self) -> &[MutationId]

Get the parent column as a slice

pub fn parent_slice_raw(&self) -> &[tsk_id_t]

Get the parent column as a slice

Trait Implementations

impl Default for OwningMutationTable

fn default() -> Self

Returns the “default value” for a type.

impl Deref for OwningMutationTable

type Target = MutationTable

The resulting type after dereferencing.

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

Dereferences the value.

impl DerefMut for OwningMutationTable

fn deref_mut(&mut self) -> &mut Self::Target

Mutably dereferences the value.