Struct tskit::SimplificationOptions

pub struct SimplificationOptions { /* fields omitted */ }

Control the behavior of crate::TableCollection::simplify and crate::TreeSequence::simplify

Inclusion of values sets an option to true. The default behavior (NONE) 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

// Initial flags set to 0:
let mut flags = tskit::SimplificationOptions::default();

// Add some options:
flags.insert(tskit::SimplificationOptions::KEEP_UNARY);
flags.insert(tskit::SimplificationOptions::FILTER_POPULATIONS);

assert!(flags.contains(tskit::SimplificationOptions::KEEP_UNARY));
assert!(flags.contains(tskit::SimplificationOptions::FILTER_POPULATIONS));

All-in-one initialization

use tskit::SimplificationOptions as SO;
let flags = SO::FILTER_SITES | SO::KEEP_UNARY;
assert!(flags.contains(SO::FILTER_SITES));
assert!(flags.contains(SO::KEEP_UNARY));
assert!(!flags.contains(SO::FILTER_POPULATIONS));

Implementations

impl SimplificationOptions

pub const NONE: SimplificationOptions

Default behavior

pub const FILTER_SITES: SimplificationOptions

pub const FILTER_POPULATIONS: SimplificationOptions

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: SimplificationOptions

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: SimplificationOptions

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

pub const KEEP_UNARY: SimplificationOptions

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: SimplificationOptions

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

pub const KEEP_UNARY_IN_INDIVIDUALS: SimplificationOptions

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 const fn empty() -> SimplificationOptions

Returns an empty set of flags

pub const fn all() -> SimplificationOptions

Returns the set containing all flags.

pub const fn bits(&self) -> tsk_flags_t

Returns the raw value of the flags currently stored.

pub fn from_bits(bits: tsk_flags_t) -> Option<SimplificationOptions>

Convert from underlying bit representation, unless that representation contains bits that do not correspond to a flag.

pub const fn from_bits_truncate(bits: tsk_flags_t) -> SimplificationOptions

Convert from underlying bit representation, dropping any bits that do not correspond to flags.

pub const unsafe fn from_bits_unchecked(
    bits: tsk_flags_t
) -> SimplificationOptions

Convert from underlying bit representation, preserving all bits (even those not corresponding to a defined flag).

pub const fn is_empty(&self) -> bool

Returns true if no flags are currently stored.

pub const fn is_all(&self) -> bool

Returns true if all flags are currently set.

pub const fn intersects(&self, other: SimplificationOptions) -> bool

Returns true if there are flags common to both self and other.

pub const fn contains(&self, other: SimplificationOptions) -> bool

Returns true all of the flags in other are contained within self.

pub fn insert(&mut self, other: SimplificationOptions)

Inserts the specified flags in-place.

pub fn remove(&mut self, other: SimplificationOptions)

Removes the specified flags in-place.

pub fn toggle(&mut self, other: SimplificationOptions)

Toggles the specified flags in-place.

pub fn set(&mut self, other: SimplificationOptions, value: bool)

Inserts or removes the specified flags depending on the passed value.

Trait Implementations

impl Binary for SimplificationOptions

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

Formats the value using the given formatter.

impl BitAnd<SimplificationOptions> for SimplificationOptions

fn bitand(self, other: SimplificationOptions) -> SimplificationOptions

Returns the intersection between the two sets of flags.

type Output = SimplificationOptions

The resulting type after applying the & operator.

impl BitAndAssign<SimplificationOptions> for SimplificationOptions

fn bitand_assign(&mut self, other: SimplificationOptions)

Disables all flags disabled in the set.

impl BitOr<SimplificationOptions> for SimplificationOptions

fn bitor(self, other: SimplificationOptions) -> SimplificationOptions

Returns the union of the two sets of flags.

type Output = SimplificationOptions

The resulting type after applying the | operator.

impl BitOrAssign<SimplificationOptions> for SimplificationOptions

fn bitor_assign(&mut self, other: SimplificationOptions)

Adds the set of flags.

impl BitXor<SimplificationOptions> for SimplificationOptions

fn bitxor(self, other: SimplificationOptions) -> SimplificationOptions

Returns the left flags, but with all the right flags toggled.

type Output = SimplificationOptions

The resulting type after applying the ^ operator.

impl BitXorAssign<SimplificationOptions> for SimplificationOptions

fn bitxor_assign(&mut self, other: SimplificationOptions)

Toggles the set of flags.

impl Clone for SimplificationOptions

fn clone(&self) -> SimplificationOptions

Returns a copy 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 Extend<SimplificationOptions> for SimplificationOptions

fn extend<T: IntoIterator<Item = SimplificationOptions>>(&mut self, iterator: T)

Extends a collection with the contents of an iterator.

fn extend_one(&mut self, item: A)

🔬 This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬 This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl FromIterator<SimplificationOptions> for SimplificationOptions

fn from_iter<T: IntoIterator<Item = SimplificationOptions>>(
    iterator: T
) -> SimplificationOptions

Creates a value from an iterator.

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, 

Feeds a slice of this type into the given Hasher.

impl LowerHex for SimplificationOptions

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

Formats the value using the given formatter.

impl Not for SimplificationOptions

fn not(self) -> SimplificationOptions

Returns the complement of this set of flags.

type Output = SimplificationOptions

The resulting type after applying the ! operator.

impl Octal for SimplificationOptions

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

Formats the value using the given formatter.

impl Ord for SimplificationOptions

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

This method returns an Ordering between self and other.

#[must_use]

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

Compares and returns the maximum of two values.

#[must_use]

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

Compares and returns the minimum of two values.

#[must_use]

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

Restrict a value to a certain interval.

impl PartialEq<SimplificationOptions> for SimplificationOptions

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

This method tests for self and other values to be equal, and is used by ==.

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

This method tests for !=.

impl PartialOrd<SimplificationOptions> for SimplificationOptions

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

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

#[must_use]

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

This method tests less than (for self and other) and is used by the < operator.

#[must_use]

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

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

#[must_use]

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

This method tests greater than (for self and other) and is used by the > operator.

#[must_use]

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

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

impl Sub<SimplificationOptions> for SimplificationOptions

fn sub(self, other: SimplificationOptions) -> SimplificationOptions

Returns the set difference of the two sets of flags.

type Output = SimplificationOptions

The resulting type after applying the - operator.

impl SubAssign<SimplificationOptions> for SimplificationOptions

fn sub_assign(&mut self, other: SimplificationOptions)

Disables all flags enabled in the set.

impl UpperHex for SimplificationOptions

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

Formats the value using the given formatter.

impl Copy for SimplificationOptions

impl Eq for SimplificationOptions

impl StructuralEq for SimplificationOptions

impl StructuralPartialEq for SimplificationOptions