Struct SimplificationOptions 

pub struct SimplificationOptions(/* private fields */);

Control the behavior of table simplification.

Inclusion of values sets an option to true. The default behavior is to perform the algorithm as described in Kelleher et al. (2018), 10.1371/journal.pcbi.1006581.

The documentation for each field is taken from the tskit primary docs.

Examples

Building up flags

Default flags

let flags = SimplificationOptions::default();

Using a “builder” API

let flags =
SimplificationOptions::default().keep_unary().filter_populations().filter_sites();
assert!(flags.contains(SimplificationOptions::KEEP_UNARY));
assert!(flags.contains(SimplificationOptions::FILTER_POPULATIONS));
assert!(flags.contains(SimplificationOptions::FILTER_SITES));

Implementations

impl SimplificationOptions

pub const FILTER_SITES: Self

pub const FILTER_POPULATIONS: Self

If True, remove any populations that are not referenced by nodes after simplification; new population IDs are allocated sequentially from zero. If False, the population table will not be altered in any way.

pub const FILTER_INDIVIDUALS: Self

If True, remove any individuals that are not referenced by nodes after simplification; new individual IDs are allocated sequentially from zero. If False, the individual table will not be altered in any way.

pub const REDUCE_TO_SITE_TOPOLOGY: Self

Whether to reduce the topology down to the trees that are present at sites.

pub const KEEP_UNARY: Self

If True, preserve unary nodes (i.e. nodes with exactly one child) that exist on the path from samples to root.

pub const KEEP_INPUT_ROOTS: Self

Whether to retain history ancestral to the MRCA of the samples.

pub const KEEP_UNARY_IN_INDIVIDUALS: Self

If True, preserve unary nodes that exist on the path from samples to root, but only if they are associated with an individual in the individuals table. Cannot be specified at the same time as KEEP_UNARY.

pub fn keep_input_roots(self) -> Self

Update to set KEEP_INPUT_ROOTS.

Examples

let f = SimplificationOptions::default().keep_input_roots();
assert!(f.contains(SimplificationOptions::KEEP_INPUT_ROOTS));

pub fn keep_unary(self) -> Self

Update to set KEEP_UNARY.

Examples

let f = SimplificationOptions::default().keep_unary();
assert!(f.contains(SimplificationOptions::KEEP_UNARY));

pub fn keep_unary_in_individuals(self) -> Self

Update to set KEEP_UNARY_IN_INDIVIDUALS.

Examples

let f = SimplificationOptions::default().keep_unary_in_individuals();
assert!(f.contains(SimplificationOptions::KEEP_UNARY_IN_INDIVIDUALS));

pub fn filter_populations(self) -> Self

Update to set FILTER_POPULATIONS.

Examples

let f = SimplificationOptions::default().filter_populations();
assert!(f.contains(SimplificationOptions::FILTER_POPULATIONS));

pub fn filter_sites(self) -> Self

Update to set FILTER_SITES.

Examples

let f = SimplificationOptions::default().filter_sites();
assert!(f.contains(SimplificationOptions::FILTER_SITES));

pub fn reduce_to_site_topology(self) -> Self

Update to set REDUCE_TO_SITE_TOPOLOGY.

Examples

let f = SimplificationOptions::default().reduce_to_site_topology();
assert!(f.contains(SimplificationOptions::REDUCE_TO_SITE_TOPOLOGY));

pub fn filter_individuals(self) -> Self

Update to set FILTER_INDIVIDUALS.

Examples

let f = SimplificationOptions::default().filter_individuals();
assert!(f.contains(SimplificationOptions::FILTER_INDIVIDUALS));

pub fn bits(&self) -> RawFlags

pub fn all() -> Self

pub fn contains<I>(&self, bit: I) -> bool

where I: Into<Self> + Copy,

Trait Implementations

impl BitAnd for SimplificationOptions

type Output = SimplificationOptions

The resulting type after applying the & operator.

fn bitand(self, rhs: Self) -> Self::Output

Performs the & operation.

impl BitAndAssign for SimplificationOptions

fn bitand_assign(&mut self, rhs: Self)

Performs the &= operation.

impl BitOr for SimplificationOptions

type Output = SimplificationOptions

The resulting type after applying the | operator.

fn bitor(self, rhs: Self) -> Self::Output

Performs the | operation.

impl BitOrAssign for SimplificationOptions

fn bitor_assign(&mut self, rhs: Self)

Performs the |= operation.

impl BitXor for SimplificationOptions

type Output = SimplificationOptions

The resulting type after applying the ^ operator.

fn bitxor(self, rhs: Self) -> Self::Output

Performs the ^ operation.

impl BitXorAssign for SimplificationOptions

fn bitxor_assign(&mut self, rhs: Self)

Performs the ^= operation.

impl Clone for SimplificationOptions

fn clone(&self) -> SimplificationOptions

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for SimplificationOptions

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

Formats the value using the given formatter.

impl Default for SimplificationOptions

fn default() -> SimplificationOptions

Returns the “default value” for a type.

impl From<u32> for SimplificationOptions

fn from(value: RawFlags) -> Self

Converts to this type from the input type.

impl Hash for SimplificationOptions

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for SimplificationOptions

fn cmp(&self, other: &SimplificationOptions) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for SimplificationOptions

fn eq(&self, other: &SimplificationOptions) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for SimplificationOptions

fn partial_cmp(&self, other: &SimplificationOptions) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Copy for SimplificationOptions

impl Eq for SimplificationOptions

impl StructuralPartialEq for SimplificationOptions