Struct tskit::SimplificationOptions [−][src]
pub struct SimplificationOptions { /* fields omitted */ }
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
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.
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.
Whether to reduce the topology down to the trees that are present at sites.
If True, preserve unary nodes (i.e. nodes with exactly one child) that exist on the path from samples to root.
Whether to retain history ancestral to the MRCA of the samples.
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
.
Returns the raw value of the flags currently stored.
Convert from underlying bit representation, unless that representation contains bits that do not correspond to a flag.
Convert from underlying bit representation, dropping any bits that do not correspond to flags.
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.
Returns true
if there are flags common to both self
and other
.
Returns true
if all of the flags in other
are contained within self
.
Inserts or removes the specified flags depending on the passed value.
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
.
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
.
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
.
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
.
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
Disables all flags disabled in the set.
Returns the union of the two sets of flags.
type Output = Self
type Output = Self
The resulting type after applying the |
operator.
Adds the set of flags.
Toggles the set of flags.
Returns the “default value” for a type. Read more
Extends a collection with the contents of an iterator. Read more
extend_one
)Extends a collection with exactly one element.
extend_one
)Reserves capacity in a collection for the given number of additional elements. Read more
Creates a value from an iterator. Read more
This method tests for self
and other
values to be equal, and is used
by ==
. Read more
This method tests for !=
.
This method returns an ordering between self
and other
values if one exists. Read more
This method tests less than (for self
and other
) and is used by the <
operator. Read more
This method tests less than or equal to (for self
and other
) and is used by the <=
operator. Read more
This method tests greater than (for self
and other
) and is used by the >
operator. Read more
Disables all flags enabled in the set.
Auto Trait Implementations
impl RefUnwindSafe for SimplificationOptions
impl Send for SimplificationOptions
impl Sync for SimplificationOptions
impl Unpin for SimplificationOptions
impl UnwindSafe for SimplificationOptions
Blanket Implementations
Mutably borrows from an owned value. Read more