Struct tskit::SimplificationOptions
source · #[repr(transparent)]pub struct SimplificationOptions { /* private fields */ }
Expand description
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
sourceimpl SimplificationOptions
impl SimplificationOptions
pub const FILTER_SITES: Self = _
sourcepub const FILTER_POPULATIONS: 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.
sourcepub const FILTER_INDIVIDUALS: Self = _
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.
sourcepub const REDUCE_TO_SITE_TOPOLOGY: Self = _
pub const REDUCE_TO_SITE_TOPOLOGY: Self = _
Whether to reduce the topology down to the trees that are present at sites.
sourcepub const KEEP_UNARY: Self = _
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.
sourcepub const KEEP_INPUT_ROOTS: Self = _
pub const KEEP_INPUT_ROOTS: Self = _
Whether to retain history ancestral to the MRCA of the samples.
sourcepub const KEEP_UNARY_IN_INDIVIDUALS: Self = _
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
.
sourcepub const fn from_bits(bits: RawFlags) -> Option<Self>
pub const fn from_bits(bits: RawFlags) -> Option<Self>
Convert from underlying bit representation, unless that representation contains bits that do not correspond to a flag.
sourcepub const fn from_bits_truncate(bits: RawFlags) -> Self
pub const fn from_bits_truncate(bits: RawFlags) -> Self
Convert from underlying bit representation, dropping any bits that do not correspond to flags.
sourcepub const unsafe fn from_bits_unchecked(bits: RawFlags) -> Self
pub const unsafe fn from_bits_unchecked(bits: RawFlags) -> Self
Convert from underlying bit representation, preserving all bits (even those not corresponding to a defined flag).
Safety
The caller of the bitflags!
macro can chose to allow or
disallow extra bits for their bitflags type.
The caller of from_bits_unchecked()
has to ensure that
all bits correspond to a defined flag or that extra bits
are valid for this bitflags type.
sourcepub const fn intersects(&self, other: Self) -> bool
pub const fn intersects(&self, other: Self) -> bool
Returns true
if there are flags common to both self
and other
.
sourcepub const fn contains(&self, other: Self) -> bool
pub const fn contains(&self, other: Self) -> bool
Returns true
if all of the flags in other
are contained within self
.
sourcepub fn set(&mut self, other: Self, value: bool)
pub fn set(&mut self, other: Self, value: bool)
Inserts or removes the specified flags depending on the passed value.
sourcepub const fn intersection(self, other: Self) -> Self
pub const fn intersection(self, other: Self) -> Self
Returns the intersection between the flags in self
and
other
.
Specifically, the returned set contains only the flags which are
present in both self
and other
.
This is equivalent to using the &
operator (e.g.
ops::BitAnd
), as in flags & other
.
sourcepub const fn union(self, other: Self) -> Self
pub const fn union(self, other: Self) -> Self
Returns the union of between the flags in self
and other
.
Specifically, the returned set contains all flags which are
present in either self
or other
, including any which are
present in both (see Self::symmetric_difference
if that
is undesirable).
This is equivalent to using the |
operator (e.g.
ops::BitOr
), as in flags | other
.
sourcepub const fn difference(self, other: Self) -> Self
pub const fn difference(self, other: Self) -> Self
Returns the difference between the flags in self
and other
.
Specifically, the returned set contains all flags present in
self
, except for the ones present in other
.
It is also conceptually equivalent to the “bit-clear” operation:
flags & !other
(and this syntax is also supported).
This is equivalent to using the -
operator (e.g.
ops::Sub
), as in flags - other
.
sourcepub const fn symmetric_difference(self, other: Self) -> Self
pub const fn symmetric_difference(self, other: Self) -> Self
Returns the symmetric difference between the flags
in self
and other
.
Specifically, the returned set contains the flags present which
are present in self
or other
, but that are not present in
both. Equivalently, it contains the flags present in exactly
one of the sets self
and other
.
This is equivalent to using the ^
operator (e.g.
ops::BitXor
), as in flags ^ other
.
sourcepub const fn complement(self) -> Self
pub const fn complement(self) -> Self
Returns the complement of this set of flags.
Specifically, the returned set contains all the flags which are
not set in self
, but which are allowed for this type.
Alternatively, it can be thought of as the set difference
between Self::all()
and self
(e.g. Self::all() - self
)
This is equivalent to using the !
operator (e.g.
ops::Not
), as in !flags
.
Trait Implementations
sourceimpl Binary for SimplificationOptions
impl Binary for SimplificationOptions
sourceimpl BitAnd<SimplificationOptions> for SimplificationOptions
impl BitAnd<SimplificationOptions> for SimplificationOptions
type Output = SimplificationOptions
type Output = SimplificationOptions
&
operator.sourceimpl BitAndAssign<SimplificationOptions> for SimplificationOptions
impl BitAndAssign<SimplificationOptions> for SimplificationOptions
sourcefn bitand_assign(&mut self, other: Self)
fn bitand_assign(&mut self, other: Self)
Disables all flags disabled in the set.
sourceimpl BitOr<SimplificationOptions> for SimplificationOptions
impl BitOr<SimplificationOptions> for SimplificationOptions
sourcefn bitor(self, other: SimplificationOptions) -> Self
fn bitor(self, other: SimplificationOptions) -> Self
Returns the union of the two sets of flags.
type Output = SimplificationOptions
type Output = SimplificationOptions
|
operator.sourceimpl BitOrAssign<SimplificationOptions> for SimplificationOptions
impl BitOrAssign<SimplificationOptions> for SimplificationOptions
sourcefn bitor_assign(&mut self, other: Self)
fn bitor_assign(&mut self, other: Self)
Adds the set of flags.
sourceimpl BitXor<SimplificationOptions> for SimplificationOptions
impl BitXor<SimplificationOptions> for SimplificationOptions
sourcefn bitxor(self, other: Self) -> Self
fn bitxor(self, other: Self) -> Self
Returns the left flags, but with all the right flags toggled.
type Output = SimplificationOptions
type Output = SimplificationOptions
^
operator.sourceimpl BitXorAssign<SimplificationOptions> for SimplificationOptions
impl BitXorAssign<SimplificationOptions> for SimplificationOptions
sourcefn bitxor_assign(&mut self, other: Self)
fn bitxor_assign(&mut self, other: Self)
Toggles the set of flags.
sourceimpl Clone for SimplificationOptions
impl Clone for SimplificationOptions
sourcefn clone(&self) -> SimplificationOptions
fn clone(&self) -> SimplificationOptions
1.0.0 · sourcefn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
source
. Read moresourceimpl Debug for SimplificationOptions
impl Debug for SimplificationOptions
sourceimpl Default for SimplificationOptions
impl Default for SimplificationOptions
sourcefn default() -> SimplificationOptions
fn default() -> SimplificationOptions
sourceimpl Extend<SimplificationOptions> for SimplificationOptions
impl Extend<SimplificationOptions> for SimplificationOptions
sourcefn extend<T: IntoIterator<Item = Self>>(&mut self, iterator: T)
fn extend<T: IntoIterator<Item = Self>>(&mut self, iterator: T)
sourcefn extend_one(&mut self, item: A)
fn extend_one(&mut self, item: A)
extend_one
)sourcefn extend_reserve(&mut self, additional: usize)
fn extend_reserve(&mut self, additional: usize)
extend_one
)sourceimpl From<u32> for SimplificationOptions
impl From<u32> for SimplificationOptions
sourceimpl FromIterator<SimplificationOptions> for SimplificationOptions
impl FromIterator<SimplificationOptions> for SimplificationOptions
sourcefn from_iter<T: IntoIterator<Item = Self>>(iterator: T) -> Self
fn from_iter<T: IntoIterator<Item = Self>>(iterator: T) -> Self
sourceimpl Hash for SimplificationOptions
impl Hash for SimplificationOptions
sourceimpl LowerHex for SimplificationOptions
impl LowerHex for SimplificationOptions
sourceimpl Not for SimplificationOptions
impl Not for SimplificationOptions
type Output = SimplificationOptions
type Output = SimplificationOptions
!
operator.sourceimpl Octal for SimplificationOptions
impl Octal for SimplificationOptions
sourceimpl Ord for SimplificationOptions
impl Ord for SimplificationOptions
sourcefn cmp(&self, other: &SimplificationOptions) -> Ordering
fn cmp(&self, other: &SimplificationOptions) -> Ordering
1.21.0 · sourcefn max(self, other: Self) -> Selfwhere
Self: Sized,
fn max(self, other: Self) -> Selfwhere
Self: Sized,
1.21.0 · sourcefn min(self, other: Self) -> Selfwhere
Self: Sized,
fn min(self, other: Self) -> Selfwhere
Self: Sized,
1.50.0 · sourcefn clamp(self, min: Self, max: Self) -> Selfwhere
Self: Sized + PartialOrd<Self>,
fn clamp(self, min: Self, max: Self) -> Selfwhere
Self: Sized + PartialOrd<Self>,
sourceimpl PartialEq<SimplificationOptions> for SimplificationOptions
impl PartialEq<SimplificationOptions> for SimplificationOptions
sourcefn eq(&self, other: &SimplificationOptions) -> bool
fn eq(&self, other: &SimplificationOptions) -> bool
sourceimpl PartialOrd<SimplificationOptions> for SimplificationOptions
impl PartialOrd<SimplificationOptions> for SimplificationOptions
sourcefn partial_cmp(&self, other: &SimplificationOptions) -> Option<Ordering>
fn partial_cmp(&self, other: &SimplificationOptions) -> Option<Ordering>
1.0.0 · sourcefn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
self
and other
) and is used by the <=
operator. Read moresourceimpl Sub<SimplificationOptions> for SimplificationOptions
impl Sub<SimplificationOptions> for SimplificationOptions
type Output = SimplificationOptions
type Output = SimplificationOptions
-
operator.sourceimpl SubAssign<SimplificationOptions> for SimplificationOptions
impl SubAssign<SimplificationOptions> for SimplificationOptions
sourcefn sub_assign(&mut self, other: Self)
fn sub_assign(&mut self, other: Self)
Disables all flags enabled in the set.