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use crate::bindings as ll_bindings;
use crate::tsk_id_t;
use crate::tsk_size_t;
use crate::NodeId;
use crate::Position;
use crate::SizeType;
use crate::Time;
use crate::TreeFlags;
use crate::TskitError;
use crate::TskitTypeAccess;
use std::ptr::NonNull;
pub struct TreeInterface {
non_owned_pointer: NonNull<ll_bindings::tsk_tree_t>,
num_nodes: tsk_size_t,
array_len: tsk_size_t,
flags: TreeFlags,
}
impl TskitTypeAccess<ll_bindings::tsk_tree_t> for TreeInterface {
fn as_ptr(&self) -> *const ll_bindings::tsk_tree_t {
self.non_owned_pointer.as_ptr()
}
fn as_mut_ptr(&mut self) -> *mut ll_bindings::tsk_tree_t {
self.non_owned_pointer.as_ptr()
}
}
impl TreeInterface {
pub(crate) fn new(
non_owned_pointer: NonNull<ll_bindings::tsk_tree_t>,
num_nodes: tsk_size_t,
array_len: tsk_size_t,
flags: TreeFlags,
) -> Self {
Self {
non_owned_pointer,
num_nodes,
array_len,
flags,
}
}
pub fn flags(&self) -> TreeFlags {
self.flags
}
/// # Failing examples
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let p = tree.parent_array();
/// drop(tree_iter);
/// for _ in p {} // ERROR
/// }
/// ```
pub fn parent_array(&self) -> &[NodeId] {
tree_array_slice!(self, parent, self.array_len)
}
/// # Failing examples
///
/// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
///
/// ```should_panic
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap(); // ERROR
/// while let Some(tree) = tree_iter.next() {
/// let s = tree.samples_array().unwrap();
/// for _ in s {}
/// }
/// ```
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::SAMPLE_LISTS).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let s = tree.samples_array().unwrap();
/// drop(tree_iter);
/// for _ in s {} // ERROR
/// }
/// ```
pub fn samples_array(&self) -> Result<&[NodeId], TskitError> {
let num_samples =
unsafe { ll_bindings::tsk_treeseq_get_num_samples((*self.as_ptr()).tree_sequence) };
err_if_not_tracking_samples!(self.flags, tree_array_slice!(self, samples, num_samples))
}
/// # Failing examples
///
/// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
///
/// ```should_panic
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap(); // ERROR
/// while let Some(tree) = tree_iter.next() {
/// let n = tree.next_sample_array().unwrap();
/// for _ in n {}
/// }
/// ```
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::SAMPLE_LISTS).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let n = tree.next_sample_array().unwrap();
/// drop(tree_iter);
/// for _ in n {} // ERROR
/// }
/// ```
pub fn next_sample_array(&self) -> Result<&[NodeId], TskitError> {
err_if_not_tracking_samples!(
self.flags,
tree_array_slice!(self, next_sample, (*self.as_ptr()).num_nodes)
)
}
/// # Failing examples
///
/// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
///
/// ```should_panic
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap(); // Error
/// while let Some(tree) = tree_iter.next() {
/// let l = tree.left_sample_array().unwrap();
/// for _ in l {}
/// }
/// ```
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::SAMPLE_LISTS).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let l = tree.left_sample_array().unwrap();
/// drop(tree_iter);
/// for _ in l {} // Error
/// }
/// ```
pub fn left_sample_array(&self) -> Result<&[NodeId], TskitError> {
err_if_not_tracking_samples!(
self.flags,
tree_array_slice!(self, left_sample, (*self.as_ptr()).num_nodes)
)
}
/// # Failing examples
///
/// An error will be returned if ['crate::TreeFlags::SAMPLE_LISTS`] is not used:
///
/// ```should_panic
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap(); // ERROR
/// while let Some(tree) = tree_iter.next() {
/// let r = tree.right_sample_array().unwrap();
/// for _ in r {}
/// }
/// ```
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::SAMPLE_LISTS).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let r = tree.right_sample_array().unwrap();
/// drop(tree_iter);
/// for _ in r {} // ERROR
/// }
/// ```
pub fn right_sample_array(&self) -> Result<&[NodeId], TskitError> {
err_if_not_tracking_samples!(
self.flags,
tree_array_slice!(self, right_sample, (*self.as_ptr()).num_nodes)
)
}
/// # Failing examples
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let r = tree.left_sib_array();
/// drop(tree_iter);
/// for _ in r {} // ERROR
/// }
/// ```
pub fn left_sib_array(&self) -> &[NodeId] {
tree_array_slice!(self, left_sib, self.array_len)
}
/// # Failing examples
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let r = tree.right_sib_array();
/// drop(tree_iter);
/// for _ in r {} // ERROR
/// }
/// ```
pub fn right_sib_array(&self) -> &[NodeId] {
tree_array_slice!(self, right_sib, self.array_len)
}
/// # Failing examples
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let l = tree.left_child_array();
/// drop(tree_iter);
/// for _ in l {} // ERROR
/// }
/// ```
pub fn left_child_array(&self) -> &[NodeId] {
tree_array_slice!(self, left_child, self.array_len)
}
/// # Failing examples
///
/// The lifetime of the slice is tied to the parent object:
///
/// ```compile_fail
/// use streaming_iterator::StreamingIterator;
/// let tables = tskit::TableCollection::new(1.).unwrap();
/// let treeseq =
/// tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// let mut tree_iter = treeseq.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// while let Some(tree) = tree_iter.next() {
/// let r = tree.right_child_array();
/// drop(tree_iter);
/// for _ in r {} // ERROR
/// }
/// ```
pub fn right_child_array(&self) -> &[NodeId] {
tree_array_slice!(self, right_child, self.array_len)
}
// error if we are not tracking samples,
// Ok(None) if u is out of range
fn left_sample(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, ptr, left_sample, NodeId)
}
// error if we are not tracking samples,
// Ok(None) if u is out of range
fn right_sample(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, ptr, right_sample, NodeId)
}
/// Return the `[left, right)` coordinates of the tree.
pub fn interval(&self) -> (Position, Position) {
(
// SAFETY: internal pointer cannot be NULL
unsafe { (*self.as_ptr()).interval }.left.into(),
unsafe { (*self.as_ptr()).interval }.right.into(),
)
}
/// Return the length of the genome for which this
/// tree is the ancestry.
pub fn span(&self) -> Position {
let i = self.interval();
i.1 - i.0
}
/// Get the parent of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn parent(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.array_len, ptr, parent, NodeId)
}
/// Get the left child of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn left_child(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.array_len, ptr, left_child, NodeId)
}
/// Get the right child of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn right_child(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.array_len, ptr, right_child, NodeId)
}
/// Get the left sib of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn left_sib(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.array_len, ptr, left_sib, NodeId)
}
/// Get the right sib of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn right_sib(&self, u: NodeId) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
unsafe_tsk_column_access!(u.0, 0, self.array_len, ptr, right_sib, NodeId)
}
/// Obtain the list of samples for the current tree/tree sequence
/// as a vector.
///
/// # Panics
///
/// Will panic if the number of samples is too large to cast to a valid id.
#[deprecated(since = "0.2.3", note = "Please use Tree::sample_nodes instead")]
pub fn samples_to_vec(&self) -> Vec<NodeId> {
let num_samples =
unsafe { ll_bindings::tsk_treeseq_get_num_samples((*self.as_ptr()).tree_sequence) };
let mut rv = vec![];
for i in 0..num_samples {
let u = match isize::try_from(i) {
Ok(o) => unsafe { *(*(*self.as_ptr()).tree_sequence).samples.offset(o) },
Err(e) => panic!("{}", e),
};
rv.push(u.into());
}
rv
}
/// Get the list of sample nodes as a slice.
pub fn sample_nodes(&self) -> &[NodeId] {
let num_samples =
unsafe { ll_bindings::tsk_treeseq_get_num_samples((*self.as_ptr()).tree_sequence) };
tree_array_slice!(self, samples, num_samples)
}
/// Return an [`Iterator`] from the node `u` to the root of the tree.
///
/// # Returns
///
/// * `Some(iterator)` if `u` us valid
/// * `None` otherwise
#[deprecated(since = "0.2.3", note = "Please use Tree::parents instead")]
pub fn path_to_root(&self, u: NodeId) -> Option<impl Iterator<Item = NodeId> + '_> {
self.parents(u)
}
/// Return an [`Iterator`] from the node `u` to the root of the tree,
/// travering all parent nodes.
///
/// # Returns
///
/// * `Some(iterator)` if `u` is valid
/// * `None` otherwise
pub fn parents(&self, u: NodeId) -> Option<impl Iterator<Item = NodeId> + '_> {
ParentsIterator::new(self, u)
}
/// Return an [`Iterator`] over the children of node `u`.
/// # Returns
///
/// * `Some(iterator)` if `u` is valid
/// * `None` otherwise
pub fn children(&self, u: NodeId) -> Option<impl Iterator<Item = NodeId> + '_> {
ChildIterator::new(self, u)
}
/// Return an [`Iterator`] over the sample nodes descending from node `u`.
///
/// # Note
///
/// If `u` is itself a sample, then it is included in the values returned.
///
/// # Returns
///
/// * Some(Ok(iterator)) if [`TreeFlags::SAMPLE_LISTS`] is in [`TreeInterface::flags`]
/// * Some(Err(_)) if [`TreeFlags::SAMPLE_LISTS`] is not in [`TreeInterface::flags`]
/// * None if `u` is not valid.
pub fn samples(
&self,
u: NodeId,
) -> Option<Result<impl Iterator<Item = NodeId> + '_, TskitError>> {
SamplesIterator::new(self, u)
}
/// Return an [`Iterator`] over the roots of the tree.
///
/// # Note
///
/// For a tree with multiple roots, the iteration starts
/// at the left root.
pub fn roots(&self) -> impl Iterator<Item = NodeId> + '_ {
RootIterator::new(self)
}
/// Return all roots as a vector.
pub fn roots_to_vec(&self) -> Vec<NodeId> {
let mut v = vec![];
for r in self.roots() {
v.push(r);
}
v
}
/// Return an [`Iterator`] over all nodes in the tree.
///
/// # Parameters
///
/// * `order`: A value from [`NodeTraversalOrder`] specifying the
/// iteration order.
// Return value is dyn for later addition of other traversal orders
pub fn traverse_nodes(
&self,
order: NodeTraversalOrder,
) -> Box<dyn Iterator<Item = NodeId> + '_> {
match order {
NodeTraversalOrder::Preorder => Box::new(PreorderNodeIterator::new(self)),
NodeTraversalOrder::Postorder => Box::new(PostorderNodeIterator::new(self)),
}
}
/// Return the [`crate::NodeTable`] for this current tree
/// (and the tree sequence from which it came).
///
/// This is a convenience function for accessing node times, etc..
pub fn node_table(&self) -> crate::NodeTable {
unimplemented!("this needs to return &NodeTable");
// crate::NodeTable::new_from_table(unsafe {
// &(*(*(*self.as_ptr()).tree_sequence).tables).nodes
// })
}
/// Calculate the total length of the tree via a preorder traversal.
///
/// # Parameters
///
/// * `by_span`: if `true`, multiply the return value by [`TreeInterface::span`].
///
/// # Errors
///
/// [`TskitError`] may be returned if a node index is out of range.
pub fn total_branch_length(&self, by_span: bool) -> Result<Time, TskitError> {
let nt = self.node_table();
let mut b = Time::from(0.);
for n in self.traverse_nodes(NodeTraversalOrder::Preorder) {
let p = self.parent(n).ok_or(TskitError::IndexError {})?;
if p != NodeId::NULL {
b += nt.time(p).ok_or(TskitError::IndexError {})?
- nt.time(n).ok_or(TskitError::IndexError {})?;
}
}
match by_span {
true => Ok(b * self.span()),
false => Ok(b),
}
}
/// Get the number of samples below node `u`.
///
/// # Errors
///
/// * [`TskitError`] if [`TreeFlags::NO_SAMPLE_COUNTS`].
pub fn num_tracked_samples(&self, u: NodeId) -> Result<SizeType, TskitError> {
let mut n = SizeType(tsk_size_t::MAX);
let np: *mut tsk_size_t = &mut n.0;
let code = unsafe { ll_bindings::tsk_tree_get_num_tracked_samples(self.as_ptr(), u.0, np) };
handle_tsk_return_value!(code, n)
}
/// Calculate the average Kendall-Colijn (`K-C`) distance between
/// pairs of trees whose intervals overlap.
///
/// # Note
///
/// * [Citation](https://doi.org/10.1093/molbev/msw124)
///
/// # Parameters
///
/// * `lambda` specifies the relative weight of topology and branch length.
/// If `lambda` is 0, we only consider topology.
/// If `lambda` is 1, we only consider branch lengths.
pub fn kc_distance(&self, other: &TreeInterface, lambda: f64) -> Result<f64, TskitError> {
let mut kc = f64::NAN;
let kcp: *mut f64 = &mut kc;
let code = unsafe {
ll_bindings::tsk_tree_kc_distance(self.as_ptr(), other.as_ptr(), lambda, kcp)
};
handle_tsk_return_value!(code, kc)
}
/// Return the virtual root of the tree.
pub fn virtual_root(&self) -> NodeId {
unsafe { (*self.as_ptr()).virtual_root }.into()
}
}
/// Specify the traversal order used by
/// [`TreeInterface::traverse_nodes`].
pub enum NodeTraversalOrder {
///Preorder traversal, starting at the root(s) of a [`TreeInterface`].
///For trees with multiple roots, start at the left root,
///traverse to tips, proceeed to the next root, etc..
Preorder,
///Postorder traversal, starting at the root(s) of a [`TreeInterface`].
///For trees with multiple roots, start at the left root,
///traverse to tips, proceeed to the next root, etc..
Postorder,
}
// Trait defining iteration over nodes.
trait NodeIterator {
fn next_node(&mut self);
fn current_node(&mut self) -> Option<NodeId>;
}
struct PreorderNodeIterator<'a> {
current_root: NodeId,
node_stack: Vec<NodeId>,
tree: &'a TreeInterface,
current_node_: Option<NodeId>,
}
impl<'a> PreorderNodeIterator<'a> {
fn new(tree: &'a TreeInterface) -> Self {
debug_assert!(tree.right_child(tree.virtual_root()).is_some());
let mut rv = PreorderNodeIterator {
current_root: tree
.right_child(tree.virtual_root())
.unwrap_or(NodeId::NULL),
node_stack: vec![],
tree,
current_node_: None,
};
let mut c = rv.current_root;
while !c.is_null() {
rv.node_stack.push(c);
debug_assert!(rv.tree.left_sib(c).is_some());
c = rv.tree.left_sib(c).unwrap_or(NodeId::NULL);
}
rv
}
}
impl NodeIterator for PreorderNodeIterator<'_> {
fn next_node(&mut self) {
self.current_node_ = self.node_stack.pop();
if let Some(u) = self.current_node_ {
// NOTE: process children right-to-left
// because we later pop them from a steck
// to generate the expected left-to-right ordering.
debug_assert!(self.tree.right_child(u).is_some());
let mut c = self.tree.right_child(u).unwrap_or(NodeId::NULL);
while c != NodeId::NULL {
self.node_stack.push(c);
debug_assert!(self.tree.right_child(c).is_some());
c = self.tree.left_sib(c).unwrap_or(NodeId::NULL);
}
};
}
fn current_node(&mut self) -> Option<NodeId> {
self.current_node_
}
}
iterator_for_nodeiterator!(PreorderNodeIterator<'_>);
struct PostorderNodeIterator<'a> {
nodes: Vec<NodeId>,
current_node_index: usize,
num_nodes_current_tree: usize,
// Make the lifetime checker happy.
tree: std::marker::PhantomData<&'a TreeInterface>,
}
impl<'a> PostorderNodeIterator<'a> {
fn new(tree: &'a TreeInterface) -> Self {
let mut num_nodes_current_tree: tsk_size_t = 0;
let ptr = std::ptr::addr_of_mut!(num_nodes_current_tree);
let mut nodes = vec![
NodeId::NULL;
// NOTE: this fn does not return error codes
usize::try_from(unsafe {
ll_bindings::tsk_tree_get_size_bound(tree.as_ptr())
}).unwrap_or(usize::MAX)
];
let rv = unsafe {
ll_bindings::tsk_tree_postorder(
tree.as_ptr(),
nodes.as_mut_ptr().cast::<tsk_id_t>(),
ptr,
)
};
// This is either out of memory
// or node out of range.
// The former is fatal, and the latter
// not relevant (for now), as we start at roots.
if rv < 0 {
panic!("fatal error calculating postoder node list");
}
Self {
nodes,
current_node_index: 0,
num_nodes_current_tree: usize::try_from(num_nodes_current_tree).unwrap_or(0),
tree: std::marker::PhantomData,
}
}
}
impl<'a> Iterator for PostorderNodeIterator<'a> {
type Item = NodeId;
fn next(&mut self) -> Option<Self::Item> {
match self.current_node_index < self.num_nodes_current_tree {
true => {
let rv = self.nodes[self.current_node_index];
self.current_node_index += 1;
Some(rv)
}
false => None,
}
}
}
struct RootIterator<'a> {
current_root: Option<NodeId>,
next_root: NodeId,
tree: &'a TreeInterface,
}
impl<'a> RootIterator<'a> {
fn new(tree: &'a TreeInterface) -> Self {
debug_assert!(tree.left_child(tree.virtual_root()).is_some());
RootIterator {
current_root: None,
next_root: tree.left_child(tree.virtual_root()).unwrap_or(NodeId::NULL),
tree,
}
}
}
impl NodeIterator for RootIterator<'_> {
fn next_node(&mut self) {
self.current_root = match self.next_root {
NodeId::NULL => None,
r => {
assert!(r >= 0);
let cr = Some(r);
debug_assert!(self.tree.right_sib(r).is_some());
self.next_root = self.tree.right_sib(r).unwrap_or(NodeId::NULL);
cr
}
};
}
fn current_node(&mut self) -> Option<NodeId> {
self.current_root
}
}
iterator_for_nodeiterator!(RootIterator<'_>);
struct ChildIterator<'a> {
current_child: Option<NodeId>,
next_child: NodeId,
tree: &'a TreeInterface,
}
impl<'a> ChildIterator<'a> {
fn new(tree: &'a TreeInterface, u: NodeId) -> Option<Self> {
let c = tree.left_child(u)?;
Some(ChildIterator {
current_child: None,
next_child: c,
tree,
})
}
}
impl NodeIterator for ChildIterator<'_> {
fn next_node(&mut self) {
self.current_child = match self.next_child {
NodeId::NULL => None,
r => {
assert!(r >= 0);
let cr = Some(r);
debug_assert!(self.tree.right_sib(r).is_some());
self.next_child = self.tree.right_sib(r).unwrap_or(NodeId::NULL);
cr
}
};
}
fn current_node(&mut self) -> Option<NodeId> {
self.current_child
}
}
iterator_for_nodeiterator!(ChildIterator<'_>);
struct ParentsIterator<'a> {
current_node: Option<NodeId>,
next_node: NodeId,
tree: &'a TreeInterface,
}
impl<'a> ParentsIterator<'a> {
fn new(tree: &'a TreeInterface, u: NodeId) -> Option<Self> {
let num_nodes = tsk_id_t::try_from(tree.num_nodes).ok()?;
match u {
x if x < num_nodes => Some(ParentsIterator {
current_node: None,
next_node: u,
tree,
}),
_ => None,
}
}
}
impl NodeIterator for ParentsIterator<'_> {
fn next_node(&mut self) {
self.current_node = match self.next_node {
NodeId::NULL => None,
r => {
assert!(r >= 0);
let cr = Some(r);
debug_assert!(self.tree.parent(r).is_some());
self.next_node = self.tree.parent(r).unwrap_or(NodeId::NULL);
cr
}
};
}
fn current_node(&mut self) -> Option<NodeId> {
self.current_node
}
}
iterator_for_nodeiterator!(ParentsIterator<'_>);
struct SamplesIterator<'a> {
current_node: Option<NodeId>,
next_sample_index: NodeId,
last_sample_index: NodeId,
tree: &'a TreeInterface,
//next_sample: crate::ffi::TskIdArray,
//samples: crate::ffi::TskIdArray,
}
impl<'a> SamplesIterator<'a> {
fn new(tree: &'a TreeInterface, u: NodeId) -> Option<Result<Self, TskitError>> {
match tree.flags.contains(TreeFlags::SAMPLE_LISTS) {
false => Some(Err(TskitError::NotTrackingSamples {})),
true => {
let next_sample_index = tree.left_sample(u)?;
let last_sample_index = tree.right_sample(u)?;
Some(Ok(SamplesIterator {
current_node: None,
next_sample_index,
last_sample_index,
tree,
}))
}
}
}
}
impl NodeIterator for SamplesIterator<'_> {
fn next_node(&mut self) {
self.current_node = match self.next_sample_index {
NodeId::NULL => None,
r => {
if r == self.last_sample_index {
let cr =
Some(unsafe { *(*self.tree.as_ptr()).samples.offset(r.0 as isize) }.into());
self.next_sample_index = NodeId::NULL;
cr
} else {
assert!(r >= 0);
let cr =
Some(unsafe { *(*self.tree.as_ptr()).samples.offset(r.0 as isize) }.into());
//self.next_sample_index = self.next_sample[r];
self.next_sample_index =
unsafe { *(*self.tree.as_ptr()).next_sample.offset(r.0 as isize) }.into();
cr
}
}
};
}
fn current_node(&mut self) -> Option<NodeId> {
self.current_node
}
}
iterator_for_nodeiterator!(SamplesIterator<'_>);