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use crate::bindings as ll_bindings;
use crate::RawFlags;
use bitflags::bitflags;
bitflags! {
/// 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));
/// ```
#[derive(Default)]
#[repr(transparent)]
pub struct SimplificationOptions: RawFlags {
/// Default behavior
const NONE = 0;
const FILTER_SITES = ll_bindings::TSK_SIMPLIFY_FILTER_SITES;
/// 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.
const FILTER_POPULATIONS = ll_bindings::TSK_SIMPLIFY_FILTER_POPULATIONS;
/// 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.
const FILTER_INDIVIDUALS = ll_bindings::TSK_SIMPLIFY_FILTER_INDIVIDUALS;
/// Whether to reduce the topology down to the trees that are present at sites.
const REDUCE_TO_SITE_TOPOLOGY = ll_bindings::TSK_SIMPLIFY_REDUCE_TO_SITE_TOPOLOGY;
/// If True, preserve unary nodes (i.e. nodes with exactly one child)
/// that exist on the path from samples to root.
const KEEP_UNARY = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY;
/// Whether to retain history ancestral to the MRCA of the samples.
const KEEP_INPUT_ROOTS = ll_bindings::TSK_SIMPLIFY_KEEP_INPUT_ROOTS;
/// 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`.
const KEEP_UNARY_IN_INDIVIDUALS = ll_bindings::TSK_SIMPLIFY_KEEP_UNARY_IN_INDIVIDUALS;
}
}
bitflags! {
/// Modify behavior of [`crate::TableCollection::clear`].
#[derive(Default)]
#[repr(transparent)]
pub struct TableClearOptions : RawFlags {
/// Default behavior.
const NONE = 0;
const CLEAR_METADATA_SCHEMAS = ll_bindings::TSK_CLEAR_METADATA_SCHEMAS;
const CLEAR_TS_METADATA_SCHEMAS = ll_bindings::TSK_CLEAR_TS_METADATA_AND_SCHEMA;
const CLEAR_PROVENANCE = ll_bindings::TSK_CLEAR_PROVENANCE;
}
}
bitflags! {
/// Modify behavior of [`crate::TableCollection::equals`].
#[derive(Default)]
#[repr(transparent)]
pub struct TableEqualityOptions : RawFlags {
/// Default behavior.
const NONE = 0;
const IGNORE_METADATA = ll_bindings::TSK_CMP_IGNORE_METADATA;
const IGNORE_TS_METADATA = ll_bindings::TSK_CMP_IGNORE_TS_METADATA;
const IGNORE_PROVENANCE = ll_bindings::TSK_CMP_IGNORE_PROVENANCE;
const IGNORE_TIMESTAMPS = ll_bindings::TSK_CMP_IGNORE_TIMESTAMPS;
}
}
bitflags! {
/// Modify behavior of [`crate::TableCollection::sort`].
#[derive(Default)]
#[repr(transparent)]
pub struct TableSortOptions : RawFlags {
/// Default behavior.
const NONE = 0;
/// Do not validate contents of edge table.
const NO_CHECK_INTEGRITY = ll_bindings::TSK_NO_CHECK_INTEGRITY;
}
}
bitflags! {
/// Modify behavior of [`crate::TableCollection::sort_individuals`].
#[derive(Default)]
#[repr(transparent)]
pub struct IndividualTableSortOptions : RawFlags {
/// Default behavior.
const NONE = 0;
}
}
bitflags! {
/// Specify the behavior of iterating over [`Tree`] objects.
/// See [`TreeSequence::tree_iterator`].
#[derive(Default)]
#[repr(transparent)]
pub struct TreeFlags: RawFlags {
/// Default behavior.
const NONE = 0;
/// Update sample lists, enabling [`Tree::samples`].
const SAMPLE_LISTS = ll_bindings::TSK_SAMPLE_LISTS;
/// Do *not* update the number of samples descending
/// from each node. The default is to update these
/// counts.
const NO_SAMPLE_COUNTS = ll_bindings::TSK_NO_SAMPLE_COUNTS;
}
}
bitflags! {
/// Modify behavior of [`crate::TableCollection::dump`].
///
/// # Note
///
/// We intentionally do *not* provide the TSK_NO_BUILD_INDEXES
/// flag. Rather, we treat the various "dump" functions as
/// operations on immutable objects. Thus, if indexes are desired
/// when outputting a [`crate::TableCollection`], then
/// call [`crate::TableCollection::build_index`] prior to calling
/// [`crate::TableCollection::dump`].
#[derive(Default)]
#[repr(transparent)]
pub struct TableOutputOptions : RawFlags {
const NONE = 0;
}
}
bitflags! {
/// Modify behavior of [`crate::TableCollection::tree_sequence`]
/// and [`crate::TreeSequence::new`].
#[derive(Default)]
#[repr(transparent)]
pub struct TreeSequenceFlags: RawFlags {
/// Default behavior
const NONE = 0;
/// If used, then build table indexes if they are not present.
const BUILD_INDEXES = ll_bindings::TSK_TS_INIT_BUILD_INDEXES;
}
}
bitflags! {
#[derive(Default)]
#[repr(transparent)]
pub struct TableIntegrityCheckFlags: RawFlags {
/// Default behavior is a set of basic checks
const NONE = 0;
/// Check that edges are ordered
const CHECK_EDGE_ORDERING =ll_bindings::TSK_CHECK_EDGE_ORDERING;
/// Check that sites are ordered
const CHECK_SITE_ORDERING =ll_bindings::TSK_CHECK_SITE_ORDERING;
/// Check for duplicated sites
const CHECK_SITE_DUPLICATES=ll_bindings::TSK_CHECK_SITE_DUPLICATES;
/// Check that mutations are ordered
const CHECK_MUTATION_ORDERING =ll_bindings::TSK_CHECK_MUTATION_ORDERING;
/// Check that individuals are ordered
const CHECK_INDIVIDUAL_ORDERING=ll_bindings::TSK_CHECK_INDIVIDUAL_ORDERING;
/// Check that migrations are ordered
const CHECK_MIGRATION_ORDERING= ll_bindings::TSK_CHECK_MIGRATION_ORDERING;
/// Check that table indexes are valid
const CHECK_INDEXES=ll_bindings::TSK_CHECK_INDEXES;
/// Check tree integrity. Enables most or all of the preceding options.
const CHECK_TREES=ll_bindings::TSK_CHECK_TREES;
}
}
bitflags! {
#[derive(Default)]
#[repr(transparent)]
/// Node flags
pub struct NodeFlags : RawFlags {
/// Default (empty)
const NONE = 0;
/// Node is a sample
const IS_SAMPLE = ll_bindings::TSK_NODE_IS_SAMPLE;
}
}
bitflags! {
#[derive(Default)]
#[repr(transparent)]
/// Individual flags
pub struct IndividualFlags : RawFlags {
/// Default (empty)
const NONE = 0;
}
}
impl_flags!(SimplificationOptions);
impl_flags!(TableClearOptions);
impl_flags!(TableEqualityOptions);
impl_flags!(TreeSequenceFlags);
impl_flags!(TableSortOptions);
impl_flags!(TreeFlags);
impl_flags!(IndividualTableSortOptions);
impl_flags!(TableIntegrityCheckFlags);
impl_flags!(TableOutputOptions);
impl_from_for_flag_types!(SimplificationOptions);
impl_from_for_flag_types!(TableClearOptions);
impl_from_for_flag_types!(TableEqualityOptions);
impl_from_for_flag_types!(TreeSequenceFlags);
impl_from_for_flag_types!(TableSortOptions);
impl_from_for_flag_types!(TreeFlags);
impl_from_for_flag_types!(IndividualTableSortOptions);
impl_from_for_flag_types!(TableIntegrityCheckFlags);
impl_from_for_flag_types!(TableOutputOptions);
impl From<RawFlags> for NodeFlags {
fn from(flags: RawFlags) -> Self {
// Safety: node flags can contain user-defined values.
// It is an error on the user's part to define flags
// in the first 16 bits, as per the C API docs.
unsafe { Self::from_bits_unchecked(flags) }
}
}
impl From<RawFlags> for IndividualFlags {
fn from(flags: RawFlags) -> Self {
// Safety: node flags can contain user-defined values.
// It is an error on the user's part to define flags
// in the first 16 bits, as per the C API docs.
unsafe { Self::from_bits_unchecked(flags) }
}
}
impl NodeFlags {
/// Create a new flags instance with `IS_SAMPLE` set.
pub fn new_sample() -> Self {
Self::IS_SAMPLE
}
/// We do not enforce valid flags in the library.
/// This function will return `true` if any bits
/// are set that do not correspond to allowed flags.
pub fn is_valid(&self) -> bool {
true
}
/// Returns `true` if flags contains `IS_SAMPLE`,
/// and `false` otherwise.
pub fn is_sample(&self) -> bool {
self.contains(NodeFlags::IS_SAMPLE)
}
}
impl IndividualFlags {
/// We do not enforce valid flags in the library.
/// This function will return `true` if any bits
/// are set that do not correspond to allowed flags.
pub fn is_valid(&self) -> bool {
true
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn node_is_not_sample() {
let n = NodeFlags::default();
assert!(!n.is_sample());
}
#[test]
fn node_is_sample() {
let n = NodeFlags::new_sample();
assert!(n.is_sample());
}
}