Struct tskit::SimplificationOptions [−][src]
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
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impl SimplificationOptions
[src]pub const NONE: SimplificationOptions
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Default behavior
pub const FILTER_SITES: SimplificationOptions
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pub const FILTER_POPULATIONS: SimplificationOptions
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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
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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
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Whether to reduce the topology down to the trees that are present at sites.
pub const KEEP_UNARY: SimplificationOptions
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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
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Whether to retain history ancestral to the MRCA of the samples.
pub const KEEP_UNARY_IN_INDIVIDUALS: SimplificationOptions
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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
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Returns an empty set of flags
pub const fn all() -> SimplificationOptions
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Returns the set containing all flags.
pub const fn bits(&self) -> tsk_flags_t
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Returns the raw value of the flags currently stored.
pub fn from_bits(bits: tsk_flags_t) -> Option<SimplificationOptions>
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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
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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
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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
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Returns true
if no flags are currently stored.
pub const fn is_all(&self) -> bool
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Returns true
if all flags are currently set.
pub const fn intersects(&self, other: SimplificationOptions) -> bool
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Returns true
if there are flags common to both self
and other
.
pub const fn contains(&self, other: SimplificationOptions) -> bool
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Returns true
all of the flags in other
are contained within self
.
pub fn insert(&mut self, other: SimplificationOptions)
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Inserts the specified flags in-place.
pub fn remove(&mut self, other: SimplificationOptions)
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Removes the specified flags in-place.
pub fn toggle(&mut self, other: SimplificationOptions)
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Toggles the specified flags in-place.
pub fn set(&mut self, other: SimplificationOptions, value: bool)
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Inserts or removes the specified flags depending on the passed value.
Trait Implementations
impl BitAnd<SimplificationOptions> for SimplificationOptions
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impl BitAnd<SimplificationOptions> for SimplificationOptions
[src]type Output = SimplificationOptions
The resulting type after applying the &
operator.
fn bitand(self, other: SimplificationOptions) -> SimplificationOptions
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Returns the intersection between the two sets of flags.
impl BitAndAssign<SimplificationOptions> for SimplificationOptions
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impl BitAndAssign<SimplificationOptions> for SimplificationOptions
[src]fn bitand_assign(&mut self, other: SimplificationOptions)
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Disables all flags disabled in the set.
impl BitOr<SimplificationOptions> for SimplificationOptions
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impl BitOr<SimplificationOptions> for SimplificationOptions
[src]type Output = SimplificationOptions
The resulting type after applying the |
operator.
fn bitor(self, other: SimplificationOptions) -> SimplificationOptions
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Returns the union of the two sets of flags.
impl BitOrAssign<SimplificationOptions> for SimplificationOptions
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impl BitOrAssign<SimplificationOptions> for SimplificationOptions
[src]fn bitor_assign(&mut self, other: SimplificationOptions)
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Adds the set of flags.
impl BitXor<SimplificationOptions> for SimplificationOptions
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impl BitXor<SimplificationOptions> for SimplificationOptions
[src]type Output = SimplificationOptions
The resulting type after applying the ^
operator.
fn bitxor(self, other: SimplificationOptions) -> SimplificationOptions
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Returns the left flags, but with all the right flags toggled.
impl BitXorAssign<SimplificationOptions> for SimplificationOptions
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impl BitXorAssign<SimplificationOptions> for SimplificationOptions
[src]fn bitxor_assign(&mut self, other: SimplificationOptions)
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Toggles the set of flags.
impl Clone for SimplificationOptions
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impl Clone for SimplificationOptions
[src]fn clone(&self) -> SimplificationOptions
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pub fn clone_from(&mut self, source: &Self)
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impl Copy for SimplificationOptions
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impl Copy for SimplificationOptions
[src]impl Default for SimplificationOptions
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impl Default for SimplificationOptions
[src]fn default() -> SimplificationOptions
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impl Eq for SimplificationOptions
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impl Eq for SimplificationOptions
[src]impl Extend<SimplificationOptions> for SimplificationOptions
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impl Extend<SimplificationOptions> for SimplificationOptions
[src]fn extend<T: IntoIterator<Item = SimplificationOptions>>(&mut self, iterator: T)
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pub fn extend_one(&mut self, item: A)
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pub fn extend_reserve(&mut self, additional: usize)
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impl FromIterator<SimplificationOptions> for SimplificationOptions
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impl FromIterator<SimplificationOptions> for SimplificationOptions
[src]fn from_iter<T: IntoIterator<Item = SimplificationOptions>>(
iterator: T
) -> SimplificationOptions
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iterator: T
) -> SimplificationOptions
impl Hash for SimplificationOptions
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impl Hash for SimplificationOptions
[src]impl Not for SimplificationOptions
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impl Not for SimplificationOptions
[src]type Output = SimplificationOptions
The resulting type after applying the !
operator.
fn not(self) -> SimplificationOptions
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Returns the complement of this set of flags.
impl Ord for SimplificationOptions
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impl Ord for SimplificationOptions
[src]impl PartialEq<SimplificationOptions> for SimplificationOptions
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impl PartialEq<SimplificationOptions> for SimplificationOptions
[src]fn eq(&self, other: &SimplificationOptions) -> bool
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fn ne(&self, other: &SimplificationOptions) -> bool
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impl PartialOrd<SimplificationOptions> for SimplificationOptions
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impl PartialOrd<SimplificationOptions> for SimplificationOptions
[src]fn partial_cmp(&self, other: &SimplificationOptions) -> Option<Ordering>
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#[must_use]pub fn lt(&self, other: &Rhs) -> bool
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#[must_use]pub fn le(&self, other: &Rhs) -> bool
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#[must_use]pub fn gt(&self, other: &Rhs) -> bool
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#[must_use]pub fn ge(&self, other: &Rhs) -> bool
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impl StructuralEq for SimplificationOptions
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impl StructuralEq for SimplificationOptions
[src]impl Sub<SimplificationOptions> for SimplificationOptions
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impl Sub<SimplificationOptions> for SimplificationOptions
[src]type Output = SimplificationOptions
The resulting type after applying the -
operator.
fn sub(self, other: SimplificationOptions) -> SimplificationOptions
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Returns the set difference of the two sets of flags.
impl SubAssign<SimplificationOptions> for SimplificationOptions
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impl SubAssign<SimplificationOptions> for SimplificationOptions
[src]fn sub_assign(&mut self, other: SimplificationOptions)
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Disables all flags enabled in the set.
Auto Trait Implementations
impl RefUnwindSafe for SimplificationOptions
impl RefUnwindSafe for SimplificationOptions
impl Send for SimplificationOptions
impl Send for SimplificationOptions
impl Sync for SimplificationOptions
impl Sync for SimplificationOptions
impl Unpin for SimplificationOptions
impl Unpin for SimplificationOptions
impl UnwindSafe for SimplificationOptions
impl UnwindSafe for SimplificationOptions