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
Default behavior
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 an empty set of flags
Returns the set containing all flags.
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).
Returns true
if there are flags common to both self
and other
.
Returns true
all of the flags in other
are contained within self
.
Inserts the specified flags in-place.
Removes the specified flags in-place.
Toggles the specified flags in-place.
Inserts or removes the specified flags depending on the passed value.
Trait Implementations
Returns the intersection between the two sets of flags.
type Output = SimplificationOptions
type Output = SimplificationOptions
The resulting type after applying the &
operator.
Disables all flags disabled in the set.
Returns the union of the two sets of flags.
type Output = SimplificationOptions
type Output = SimplificationOptions
The resulting type after applying the |
operator.
Adds the set of flags.
Returns the left flags, but with all the right flags toggled.
type Output = SimplificationOptions
type Output = SimplificationOptions
The resulting type after applying the ^
operator.
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
fn from_iter<T: IntoIterator<Item = SimplificationOptions>>(
iterator: T
) -> SimplificationOptions
fn from_iter<T: IntoIterator<Item = SimplificationOptions>>(
iterator: T
) -> SimplificationOptions
Creates a value from an iterator. Read more
Returns the complement of this set of flags.
type Output = SimplificationOptions
type Output = SimplificationOptions
The resulting type after applying the !
operator.
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
Returns the set difference of the two sets of flags.
type Output = SimplificationOptions
type Output = SimplificationOptions
The resulting type after applying the -
operator.
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