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
Default flags
let flags = tskit::SimplificationOptions::default();
assert_eq!(flags, tskit::SimplificationOptions::NONE);
Using a “builder” API
let flags =
tskit::SimplificationOptions::default().keep_unary().filter_populations().filter_sites();
assert!(flags.contains(tskit::SimplificationOptions::KEEP_UNARY));
assert!(flags.contains(tskit::SimplificationOptions::FILTER_POPULATIONS));
assert!(flags.contains(tskit::SimplificationOptions::FILTER_SITES));
Implementations§
source§impl 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
.
source§impl SimplificationOptions
impl SimplificationOptions
sourcepub fn keep_input_roots(self) -> Self
pub fn keep_input_roots(self) -> Self
Update to set KEEP_INPUT_ROOTS
.
Examples
let f = tskit::SimplificationOptions::default().keep_input_roots();
assert!(f.contains(tskit::SimplificationOptions::KEEP_INPUT_ROOTS));
sourcepub fn keep_unary(self) -> Self
pub fn keep_unary(self) -> Self
Update to set KEEP_UNARY
.
Examples
let f = tskit::SimplificationOptions::default().keep_unary();
assert!(f.contains(tskit::SimplificationOptions::KEEP_UNARY));
sourcepub fn keep_unary_in_individuals(self) -> Self
pub fn keep_unary_in_individuals(self) -> Self
Update to set KEEP_UNARY_IN_INDIVIDUALS
.
Examples
let f = tskit::SimplificationOptions::default().keep_unary_in_individuals();
assert!(f.contains(tskit::SimplificationOptions::KEEP_UNARY_IN_INDIVIDUALS));
sourcepub fn filter_populations(self) -> Self
pub fn filter_populations(self) -> Self
Update to set FILTER_POPULATIONS
.
Examples
let f = tskit::SimplificationOptions::default().filter_populations();
assert!(f.contains(tskit::SimplificationOptions::FILTER_POPULATIONS));
sourcepub fn filter_sites(self) -> Self
pub fn filter_sites(self) -> Self
Update to set FILTER_SITES
.
Examples
let f = tskit::SimplificationOptions::default().filter_sites();
assert!(f.contains(tskit::SimplificationOptions::FILTER_SITES));
sourcepub fn reduce_to_site_topology(self) -> Self
pub fn reduce_to_site_topology(self) -> Self
Update to set REDUCE_TO_SITE_TOPOLOGY
.
Examples
let f = tskit::SimplificationOptions::default().reduce_to_site_topology();
assert!(f.contains(tskit::SimplificationOptions::REDUCE_TO_SITE_TOPOLOGY));
sourcepub fn filter_individuals(self) -> Self
pub fn filter_individuals(self) -> Self
Update to set FILTER_INDIVIDUALS
.
Examples
let f = tskit::SimplificationOptions::default().filter_individuals();
assert!(f.contains(tskit::SimplificationOptions::FILTER_INDIVIDUALS));
Trait Implementations§
source§impl Binary for SimplificationOptions
impl Binary for SimplificationOptions
source§impl BitAndAssign<SimplificationOptions> for SimplificationOptions
impl BitAndAssign<SimplificationOptions> for SimplificationOptions
source§fn bitand_assign(&mut self, other: Self)
fn bitand_assign(&mut self, other: Self)
Disables all flags disabled in the set.
source§impl BitOr<SimplificationOptions> for SimplificationOptions
impl BitOr<SimplificationOptions> for SimplificationOptions
source§fn 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.source§impl BitOrAssign<SimplificationOptions> for SimplificationOptions
impl BitOrAssign<SimplificationOptions> for SimplificationOptions
source§fn bitor_assign(&mut self, other: Self)
fn bitor_assign(&mut self, other: Self)
Adds the set of flags.
source§impl BitXorAssign<SimplificationOptions> for SimplificationOptions
impl BitXorAssign<SimplificationOptions> for SimplificationOptions
source§fn bitxor_assign(&mut self, other: Self)
fn bitxor_assign(&mut self, other: Self)
Toggles the set of flags.
source§impl Clone for SimplificationOptions
impl Clone for SimplificationOptions
source§fn clone(&self) -> SimplificationOptions
fn clone(&self) -> SimplificationOptions
1.0.0 · source§fn clone_from(&mut self, source: &Self)
fn clone_from(&mut self, source: &Self)
source
. Read moresource§impl Debug for SimplificationOptions
impl Debug for SimplificationOptions
source§impl Default for SimplificationOptions
impl Default for SimplificationOptions
source§fn default() -> SimplificationOptions
fn default() -> SimplificationOptions
source§impl Extend<SimplificationOptions> for SimplificationOptions
impl Extend<SimplificationOptions> for SimplificationOptions
source§fn extend<T: IntoIterator<Item = Self>>(&mut self, iterator: T)
fn extend<T: IntoIterator<Item = Self>>(&mut self, iterator: T)
source§fn extend_one(&mut self, item: A)
fn extend_one(&mut self, item: A)
extend_one
)source§fn extend_reserve(&mut self, additional: usize)
fn extend_reserve(&mut self, additional: usize)
extend_one
)source§impl From<u32> for SimplificationOptions
impl From<u32> for SimplificationOptions
source§impl FromIterator<SimplificationOptions> for SimplificationOptions
impl FromIterator<SimplificationOptions> for SimplificationOptions
source§fn from_iter<T: IntoIterator<Item = Self>>(iterator: T) -> Self
fn from_iter<T: IntoIterator<Item = Self>>(iterator: T) -> Self
source§impl Hash for SimplificationOptions
impl Hash for SimplificationOptions
source§impl LowerHex for SimplificationOptions
impl LowerHex for SimplificationOptions
source§impl Not for SimplificationOptions
impl Not for SimplificationOptions
source§impl Octal for SimplificationOptions
impl Octal for SimplificationOptions
source§impl Ord for SimplificationOptions
impl Ord for SimplificationOptions
source§fn cmp(&self, other: &SimplificationOptions) -> Ordering
fn cmp(&self, other: &SimplificationOptions) -> Ordering
1.21.0 · source§fn max(self, other: Self) -> Selfwhere
Self: Sized,
fn max(self, other: Self) -> Selfwhere Self: Sized,
source§impl PartialEq<SimplificationOptions> for SimplificationOptions
impl PartialEq<SimplificationOptions> for SimplificationOptions
source§fn eq(&self, other: &SimplificationOptions) -> bool
fn eq(&self, other: &SimplificationOptions) -> bool
self
and other
values to be equal, and is used
by ==
.source§impl PartialOrd<SimplificationOptions> for SimplificationOptions
impl PartialOrd<SimplificationOptions> for SimplificationOptions
source§fn partial_cmp(&self, other: &SimplificationOptions) -> Option<Ordering>
fn partial_cmp(&self, other: &SimplificationOptions) -> Option<Ordering>
1.0.0 · source§fn le(&self, other: &Rhs) -> bool
fn le(&self, other: &Rhs) -> bool
self
and other
) and is used by the <=
operator. Read moresource§impl SubAssign<SimplificationOptions> for SimplificationOptions
impl SubAssign<SimplificationOptions> for SimplificationOptions
source§fn sub_assign(&mut self, other: Self)
fn sub_assign(&mut self, other: Self)
Disables all flags enabled in the set.