Struct MutationTable 

pub struct MutationTable { /* private fields */ }

An immutable view of site table.

Examples

use tskit::MutationTable;

let mut mutations = MutationTable::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::MutationTable;

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

let metadata = MutationMetadata{value: 42};

let mut mutations = MutationTable::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 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: impl Into<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 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

pub fn node_column(&self) -> impl TableColumn<MutationId, NodeId> + '_

pub fn site_column(&self) -> impl TableColumn<MutationId, SiteId> + '_

pub fn time_column(&self) -> impl TableColumn<MutationId, Time> + '_

pub fn parent_column(&self) -> impl TableColumn<MutationId, MutationId> + '_

pub fn clear(&mut self) -> Result<i32, TskitError>

Clear all data from the table

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,

Trait Implementations

impl Debug for MutationTable

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for MutationTable

fn default() -> MutationTable

Returns the “default value” for a type.