Struct SiteTable 

pub struct SiteTable { /* private fields */ }

A site table.

Examples

use tskit::SiteTable;

let mut sites = SiteTable::default();
let rowid = sites.add_row(1., None).unwrap();
assert_eq!(rowid, 0);
assert_eq!(sites.num_rows(), 1);

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

use tskit::SiteTable;

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

let metadata = SiteMetadata{value: 42};

let mut sites = SiteTable::default();

let rowid = sites.add_row_with_metadata(0., None, &metadata).unwrap();
assert_eq!(rowid, 0);

match sites.metadata::<SiteMetadata>(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 SiteTable

pub fn num_rows(&self) -> SizeType

Return the number of rows

pub fn position<S: Into<SiteId> + Copy>(&self, row: S) -> Option<Position>

Return the position value from row row of the table.

Returns

• Some(position) if row is valid.
• None otherwise.

pub fn ancestral_state<S: Into<SiteId>>(&self, row: S) -> Option<&[u8]>

Get the ancestral_state value from row row of the table.

Returns

• Some(ancestral state) if row is valid.
• None otherwise.

pub fn metadata<T: SiteMetadata>( &self, row: impl Into<SiteId>, ) -> 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 or the row has no metadata.

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 = SiteTableRow> + '_

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

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

pub fn row<S: Into<SiteId> + Copy>(&self, r: S) -> Option<SiteTableRow>

Return row r of the table.

Parameters

• r: the row id.

Returns

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

pub fn row_view<S: Into<SiteId> + Copy>( &self, r: S, ) -> Option<SiteTableRowView<'_>>

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 position_slice(&self) -> &[Position]

Get the position column as a slice

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

Get the position column as a slice

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

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

Clear all data from the table

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

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

Trait Implementations

impl Debug for SiteTable

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

Formats the value using the given formatter.

impl Default for SiteTable

fn default() -> SiteTable

Returns the “default value” for a type.