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use std::ops::Deref;
use std::ops::DerefMut;
use crate::bindings as ll_bindings;
use crate::error::TskitError;
use crate::sys;
use crate::NodeId;
use crate::SimplificationOptions;
use crate::SizeType;
use crate::TableOutputOptions;
use crate::TreeFlags;
use crate::TreeInterface;
use crate::TreeSequenceFlags;
use crate::TskReturnValue;
use crate::{tsk_id_t, TableCollection};
use ll_bindings::tsk_tree_free;
use std::ptr::NonNull;
/// A Tree.
///
/// Wrapper around `tsk_tree_t`.
pub struct Tree<'treeseq> {
pub(crate) inner: mbox::MBox<ll_bindings::tsk_tree_t>,
// NOTE: this reference exists becaust tsk_tree_t
// contains a NON-OWNING pointer to tsk_treeseq_t.
// Thus, we could theoretically cause UB without
// tying the rust-side object liftimes together.
#[allow(dead_code)]
treeseq: &'treeseq TreeSequence,
api: TreeInterface,
current_tree: i32,
advanced: bool,
}
impl<'treeseq> Drop for Tree<'treeseq> {
fn drop(&mut self) {
// SAFETY: Mbox<_> cannot hold a NULL ptr
let rv = unsafe { tsk_tree_free(self.inner.as_mut()) };
assert_eq!(rv, 0);
}
}
impl<'treeseq> Deref for Tree<'treeseq> {
type Target = TreeInterface;
fn deref(&self) -> &Self::Target {
&self.api
}
}
impl<'treeseq> DerefMut for Tree<'treeseq> {
fn deref_mut(&mut self) -> &mut Self::Target {
&mut self.api
}
}
impl<'treeseq> Tree<'treeseq> {
fn new<F: Into<TreeFlags>>(ts: &'treeseq TreeSequence, flags: F) -> Result<Self, TskitError> {
let flags = flags.into();
// SAFETY: this is the type we want :)
let temp = unsafe {
libc::malloc(std::mem::size_of::<ll_bindings::tsk_tree_t>())
as *mut ll_bindings::tsk_tree_t
};
// Get our pointer into MBox ASAP
let nonnull = NonNull::<ll_bindings::tsk_tree_t>::new(temp)
.ok_or_else(|| TskitError::LibraryError("failed to malloc tsk_tree_t".to_string()))?;
// SAFETY: if temp is NULL, we have returned Err already.
let mut tree = unsafe { mbox::MBox::from_non_null_raw(nonnull) };
let mut rv =
unsafe { ll_bindings::tsk_tree_init(tree.as_mut(), ts.as_ptr(), flags.bits()) };
if rv < 0 {
return Err(TskitError::ErrorCode { code: rv });
}
// Gotta ask Jerome about this one--why isn't this handled in tsk_tree_init??
if !flags.contains(TreeFlags::NO_SAMPLE_COUNTS) {
// SAFETY: nobody is null here.
rv = unsafe {
ll_bindings::tsk_tree_set_tracked_samples(
tree.as_mut(),
ts.num_samples().into(),
(tree.as_mut()).samples,
)
};
}
let num_nodes = unsafe { (*(*ts.as_ptr()).tables).nodes.num_rows };
let api = TreeInterface::new(nonnull, num_nodes, num_nodes + 1, flags);
handle_tsk_return_value!(
rv,
Tree {
inner: tree,
treeseq: ts,
current_tree: 0,
advanced: false,
api
}
)
}
}
impl<'ts> streaming_iterator::StreamingIterator for Tree<'ts> {
type Item = Tree<'ts>;
fn advance(&mut self) {
let rv = if self.current_tree == 0 {
unsafe { ll_bindings::tsk_tree_first(self.as_mut_ptr()) }
} else {
unsafe { ll_bindings::tsk_tree_next(self.as_mut_ptr()) }
};
if rv == 0 {
self.advanced = false;
self.current_tree += 1;
} else if rv == 1 {
self.advanced = true;
self.current_tree += 1;
} else if rv < 0 {
panic_on_tskit_error!(rv);
}
}
fn get(&self) -> Option<&Self::Item> {
match self.advanced {
true => Some(self),
false => None,
}
}
}
impl<'ts> streaming_iterator::DoubleEndedStreamingIterator for Tree<'ts> {
fn advance_back(&mut self) {
let rv = if self.current_tree == 0 {
unsafe { ll_bindings::tsk_tree_last(self.as_mut_ptr()) }
} else {
unsafe { ll_bindings::tsk_tree_prev(self.as_mut_ptr()) }
};
if rv == 0 {
self.advanced = false;
self.current_tree -= 1;
} else if rv == 1 {
self.advanced = true;
self.current_tree -= 1;
} else if rv < 0 {
panic_on_tskit_error!(rv);
}
}
}
/// A tree sequence.
///
/// This is a thin wrapper around the C type `tsk_treeseq_t`.
///
/// When created from a [`TableCollection`], the input tables are
/// moved into the `TreeSequence` object.
///
/// # Examples
///
/// ```
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// tables.add_node(0, 1.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// tables.add_edge(0., 1000., 0, 1).unwrap();
/// tables.add_edge(0., 1000., 0, 2).unwrap();
///
/// // index
/// tables.build_index();
///
/// // tables gets moved into our treeseq variable:
/// let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// assert_eq!(treeseq.nodes().num_rows(), 3);
/// assert_eq!(treeseq.edges().num_rows(), 2);
/// ```
///
/// This type does not provide access to mutable tables.
///
/// ```compile_fail
/// # let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// # tables.add_node(0, 1.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// # tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// # tables.add_node(0, 0.0, tskit::PopulationId::NULL, tskit::IndividualId::NULL).unwrap();
/// # tables.add_edge(0., 1000., 0, 1).unwrap();
/// # tables.add_edge(0., 1000., 0, 2).unwrap();
///
/// # // index
/// # tables.build_index();
///
/// # // tables gets moved into our treeseq variable:
/// # let treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// assert_eq!(treeseq.nodes_mut().num_rows(), 3);
/// ```
pub struct TreeSequence {
pub(crate) inner: sys::LLTreeSeq,
views: crate::table_views::TableViews,
}
unsafe impl Send for TreeSequence {}
unsafe impl Sync for TreeSequence {}
impl TreeSequence {
/// Create a tree sequence from a [`TableCollection`].
/// In general, [`TableCollection::tree_sequence`] may be preferred.
/// The table collection is moved/consumed.
///
/// # Parameters
///
/// * `tables`, a [`TableCollection`]
///
/// # Errors
///
/// * [`TskitError`] if the tables are not indexed.
/// * [`TskitError`] if the tables are not properly sorted.
/// See [`TableCollection::full_sort`](crate::TableCollection::full_sort).
///
/// # Examples
///
/// ```
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// tables.build_index();
/// let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();
/// ```
///
/// The following may be preferred to the previous example, and more closely
/// mimics the Python `tskit` interface:
///
/// ```
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// tables.build_index();
/// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// ```
///
/// The following raises an error because the tables are not indexed:
///
/// ```should_panic
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// let tree_sequence = tskit::TreeSequence::try_from(tables).unwrap();
/// ```
///
/// ## Note
///
/// This function makes *no extra copies* of the tables.
/// There is, however, a temporary allocation of an empty table collection
/// in order to convince rust that we are safely handling all memory.
pub fn new<F: Into<TreeSequenceFlags>>(
tables: TableCollection,
flags: F,
) -> Result<Self, TskitError> {
let raw_tables_ptr = tables.into_raw()?;
let mut inner = sys::LLTreeSeq::new(raw_tables_ptr, flags.into().bits())?;
let views = crate::table_views::TableViews::new_from_tree_sequence(inner.as_mut_ptr())?;
Ok(Self { inner, views })
}
fn as_ref(&self) -> &ll_bindings::tsk_treeseq_t {
self.inner.as_ref()
}
/// Pointer to the low-level C type.
pub fn as_ptr(&self) -> *const ll_bindings::tsk_treeseq_t {
self.inner.as_ptr()
}
/// Mutable pointer to the low-level C type.
pub fn as_mut_ptr(&mut self) -> *mut ll_bindings::tsk_treeseq_t {
self.inner.as_mut_ptr()
}
/// Dump the tree sequence to file.
///
/// # Note
///
/// * `options` is currently not used. Set to default value.
/// This behavior may change in a future release, which could
/// break `API`.
///
/// # Panics
///
/// This function allocates a `CString` to pass the file name to the C API.
/// A panic will occur if the system runs out of memory.
pub fn dump<O: Into<TableOutputOptions>>(&self, filename: &str, options: O) -> TskReturnValue {
let c_str = std::ffi::CString::new(filename).map_err(|_| {
TskitError::LibraryError("call to ffi::Cstring::new failed".to_string())
})?;
self.inner
.dump(c_str, options.into().bits())
.map_err(|e| e.into())
}
/// Load from a file.
///
/// This function calls [`TableCollection::new_from_file`] with
/// [`TreeSequenceFlags::default`].
pub fn load(filename: impl AsRef<str>) -> Result<Self, TskitError> {
let tables = TableCollection::new_from_file(filename.as_ref())?;
Self::new(tables, TreeSequenceFlags::default())
}
/// Obtain a copy of the [`TableCollection`].
/// The result is a "deep" copy of the tables.
///
/// # Errors
///
/// [`TskitError`] will be raised if the underlying C library returns an error code.
pub fn dump_tables(&self) -> Result<TableCollection, TskitError> {
let mut inner = crate::table_collection::uninit_table_collection();
let rv = unsafe {
ll_bindings::tsk_table_collection_copy((*self.as_ptr()).tables, &mut *inner, 0)
};
// SAFETY: we just initialized it.
// The C API doesn't free NULL pointers.
handle_tsk_return_value!(rv, unsafe { TableCollection::new_from_mbox(inner)? })
}
/// Create an iterator over trees.
///
/// # Parameters
///
/// * `flags` A [`TreeFlags`] bit field.
///
/// # Errors
///
/// # Examples
///
/// ```
/// // You must include streaming_iterator as a dependency
/// // and import this type.
/// use streaming_iterator::StreamingIterator;
/// // Import this to allow .next_back() for reverse
/// // iteration over trees.
/// use streaming_iterator::DoubleEndedStreamingIterator;
///
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// tables.build_index();
/// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// let mut tree_iterator = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// while let Some(tree) = tree_iterator.next() {
/// }
/// ```
///
/// ## Coupled liftimes
///
/// A `Tree`'s lifetime is tied to that of its tree sequence:
///
/// ```{compile_fail}
/// # use streaming_iterator::StreamingIterator;
/// # use streaming_iterator::DoubleEndedStreamingIterator;
/// # let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// # tables.build_index();
/// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// let mut tree_iterator = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap();
/// drop(tree_sequence);
/// while let Some(tree) = tree_iterator.next() { // compile fail.
/// }
/// ```
/// # Warning
///
/// The following code results in an infinite loop.
/// Be sure to note the difference from the previous example.
///
/// ```no_run
/// use streaming_iterator::StreamingIterator;
///
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// tables.build_index();
/// let tree_sequence = tables.tree_sequence(tskit::TreeSequenceFlags::default()).unwrap();
/// while let Some(tree) = tree_sequence.tree_iterator(tskit::TreeFlags::default()).unwrap().next() {
/// }
/// ```
pub fn tree_iterator<F: Into<TreeFlags>>(&self, flags: F) -> Result<Tree, TskitError> {
let tree = Tree::new(self, flags)?;
Ok(tree)
}
/// Get the list of samples 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 TreeSequence::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()) };
let mut rv = vec![];
for i in 0..num_samples {
let u = match isize::try_from(i) {
Ok(o) => NodeId::from(unsafe { *(*self.as_ptr()).samples.offset(o) }),
Err(e) => panic!("{}", e),
};
rv.push(u);
}
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()) };
sys::generate_slice(self.as_ref().samples, num_samples)
}
/// Get the number of trees.
pub fn num_trees(&self) -> SizeType {
self.inner.num_trees().into()
}
/// 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.
/// See [`TreeInterface::kc_distance`] for more details.
pub fn kc_distance(&self, other: &TreeSequence, lambda: f64) -> Result<f64, TskitError> {
self.inner
.kc_distance(&other.inner, lambda)
.map_err(|e| e.into())
}
// FIXME: document
pub fn num_samples(&self) -> SizeType {
self.inner.num_samples().into()
}
/// Simplify tables and return a new tree sequence.
///
/// # Parameters
///
/// * `samples`: a slice containing non-null node ids.
/// The tables are simplified with respect to the ancestry
/// of these nodes.
/// * `options`: A [`SimplificationOptions`] bit field controlling
/// the behavior of simplification.
/// * `idmap`: if `true`, the return value contains a vector equal
/// in length to the input node table. For each input node,
/// this vector either contains the node's new index or [`NodeId::NULL`]
/// if the input node is not part of the simplified history.
pub fn simplify<O: Into<SimplificationOptions>>(
&self,
samples: &[NodeId],
options: O,
idmap: bool,
) -> Result<(Self, Option<Vec<NodeId>>), TskitError> {
let mut output_node_map: Vec<NodeId> = vec![];
if idmap {
output_node_map.resize(usize::try_from(self.nodes().num_rows())?, NodeId::NULL);
}
let llsamples = unsafe {
std::slice::from_raw_parts(samples.as_ptr().cast::<tsk_id_t>(), samples.len())
};
let mut inner = self.inner.simplify(
llsamples,
options.into().bits(),
match idmap {
true => output_node_map.as_mut_ptr().cast::<tsk_id_t>(),
false => std::ptr::null_mut(),
},
)?;
let views = crate::table_views::TableViews::new_from_tree_sequence(inner.as_mut_ptr())?;
Ok((
Self { inner, views },
match idmap {
true => Some(output_node_map),
false => None,
},
))
}
#[cfg(feature = "provenance")]
#[cfg_attr(doc_cfg, doc(cfg(feature = "provenance")))]
/// Add provenance record with a time stamp.
///
/// All implementation of this trait provided by `tskit` use
/// an `ISO 8601` format time stamp
/// written using the [RFC 3339](https://tools.ietf.org/html/rfc3339)
/// specification.
/// This formatting approach has been the most straightforward method
/// for supporting round trips to/from a [`crate::provenance::ProvenanceTable`].
/// The implementations used here use the [`humantime`](https://docs.rs/humantime/latest/humantime/) crate.
///
/// # Parameters
///
/// * `record`: the provenance record
///
/// # Examples
///
/// ```
/// let mut tables = tskit::TableCollection::new(1000.).unwrap();
/// let mut treeseq = tables.tree_sequence(tskit::TreeSequenceFlags::BUILD_INDEXES).unwrap();
/// # #[cfg(feature = "provenance")] {
/// treeseq.add_provenance(&String::from("All your provenance r belong 2 us.")).unwrap();
///
/// let prov_ref = treeseq.provenances();
/// let row_0 = prov_ref.row(0).unwrap();
/// assert_eq!(row_0.record, "All your provenance r belong 2 us.");
/// let record_0 = prov_ref.record(0).unwrap();
/// assert_eq!(record_0, row_0.record);
/// let timestamp = prov_ref.timestamp(0).unwrap();
/// assert_eq!(timestamp, row_0.timestamp);
/// use core::str::FromStr;
/// let dt_utc = humantime::Timestamp::from_str(×tamp).unwrap();
/// println!("utc = {}", dt_utc);
/// # }
/// ```
pub fn add_provenance(&mut self, record: &str) -> Result<crate::ProvenanceId, TskitError> {
if record.is_empty() {
return Err(TskitError::ValueError {
got: "empty string".to_string(),
expected: "provenance record".to_string(),
});
}
let timestamp = humantime::format_rfc3339(std::time::SystemTime::now()).to_string();
let rv = unsafe {
ll_bindings::tsk_provenance_table_add_row(
&mut (*self.inner.as_ref().tables).provenances,
timestamp.as_ptr() as *mut i8,
timestamp.len() as ll_bindings::tsk_size_t,
record.as_ptr() as *mut i8,
record.len() as ll_bindings::tsk_size_t,
)
};
handle_tsk_return_value!(rv, crate::ProvenanceId::from(rv))
}
delegate_table_view_api!();
/// Build a lending iterator over edge differences.
///
/// # Errors
///
/// * [`TskitError`] if the `C` back end is unable to allocate
/// needed memory
pub fn edge_differences_iter(
&self,
) -> Result<crate::edge_differences::EdgeDifferencesIterator, TskitError> {
crate::edge_differences::EdgeDifferencesIterator::new_from_treeseq(self, 0)
}
}
impl TryFrom<TableCollection> for TreeSequence {
type Error = TskitError;
fn try_from(value: TableCollection) -> Result<Self, Self::Error> {
Self::new(value, TreeSequenceFlags::default())
}
}
#[cfg(test)]
pub(crate) mod test_trees {
use super::*;
use crate::test_fixtures::{
make_small_table_collection, make_small_table_collection_two_trees,
treeseq_from_small_table_collection, treeseq_from_small_table_collection_two_trees,
};
use crate::NodeTraversalOrder;
use streaming_iterator::DoubleEndedStreamingIterator;
use streaming_iterator::StreamingIterator;
#[test]
fn test_create_treeseq_new_from_tables() {
let tables = make_small_table_collection();
let treeseq = TreeSequence::new(tables, TreeSequenceFlags::default()).unwrap();
let samples = treeseq.sample_nodes();
assert_eq!(samples.len(), 2);
for i in 1..3 {
assert_eq!(samples[i - 1], NodeId::from(i as tsk_id_t));
}
}
#[test]
fn test_create_treeseq_from_tables() {
let tables = make_small_table_collection();
let _treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
}
#[test]
fn test_iterate_tree_seq_with_one_tree() {
let tables = make_small_table_collection();
let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
let mut ntrees = 0;
let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
while let Some(tree) = tree_iter.next() {
ntrees += 1;
assert_eq!(tree.current_tree, ntrees);
let samples = tree.sample_nodes();
assert_eq!(samples.len(), 2);
for i in 1..3 {
assert_eq!(samples[i - 1], NodeId::from(i as tsk_id_t));
let mut nsteps = 0;
for _ in tree.parents(samples[i - 1]) {
nsteps += 1;
}
assert_eq!(nsteps, 2);
}
// These nodes are all out of range
for i in 100..110 {
let mut nsteps = 0;
for _ in tree.parents(i) {
nsteps += 1;
}
assert_eq!(nsteps, 0);
}
assert_eq!(tree.parents(-1_i32).count(), 0);
assert_eq!(tree.children(-1_i32).count(), 0);
let roots = tree.roots_to_vec();
for r in roots.iter() {
let mut num_children = 0;
for _ in tree.children(*r) {
num_children += 1;
}
assert_eq!(num_children, 2);
}
}
assert_eq!(ntrees, 1);
}
#[test]
fn test_iterate_no_roots() {
let mut tables = TableCollection::new(100.).unwrap();
tables.build_index().unwrap();
let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
while let Some(tree) = tree_iter.next() {
let mut num_roots = 0;
for _ in tree.roots() {
num_roots += 1;
}
assert_eq!(num_roots, 0);
}
}
#[test]
fn test_samples_iterator_error_when_not_tracking_samples() {
let tables = make_small_table_collection();
let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
if let Some(tree) = tree_iter.next() {
for n in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
match tree.samples(n) {
Err(_) => (),
_ => panic!("should not be Ok(_) or None"),
}
}
}
}
#[test]
fn test_num_tracked_samples() {
let treeseq = treeseq_from_small_table_collection();
assert_eq!(treeseq.num_samples(), 2);
let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
if let Some(tree) = tree_iter.next() {
assert_eq!(tree.num_tracked_samples(2).unwrap(), 1);
assert_eq!(tree.num_tracked_samples(1).unwrap(), 1);
assert_eq!(tree.num_tracked_samples(0).unwrap(), 2);
}
}
#[should_panic]
#[test]
fn test_num_tracked_samples_not_tracking_sample_counts() {
let treeseq = treeseq_from_small_table_collection();
assert_eq!(treeseq.num_samples(), 2);
let mut tree_iter = treeseq.tree_iterator(TreeFlags::NO_SAMPLE_COUNTS).unwrap();
if let Some(tree) = tree_iter.next() {
assert_eq!(tree.num_tracked_samples(2).unwrap(), 0);
assert_eq!(tree.num_tracked_samples(1).unwrap(), 0);
assert_eq!(tree.num_tracked_samples(0).unwrap(), 0);
}
}
#[test]
fn test_iterate_samples() {
let tables = make_small_table_collection();
let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
let mut tree_iter = treeseq.tree_iterator(TreeFlags::SAMPLE_LISTS).unwrap();
if let Some(tree) = tree_iter.next() {
assert!(!tree.flags().contains(TreeFlags::NO_SAMPLE_COUNTS));
assert!(tree.flags().contains(TreeFlags::SAMPLE_LISTS));
let mut s = vec![];
if let Ok(iter) = tree.samples(0) {
for i in iter {
s.push(i);
}
}
assert_eq!(s.len(), 2);
assert_eq!(
s.len(),
usize::try_from(tree.num_tracked_samples(0).unwrap()).unwrap()
);
assert_eq!(s[0], 1);
assert_eq!(s[1], 2);
for u in 1..3 {
let mut s = vec![];
if let Ok(iter) = tree.samples(u) {
for i in iter {
s.push(i);
}
}
assert_eq!(s.len(), 1);
assert_eq!(s[0], u);
assert_eq!(
s.len(),
usize::try_from(tree.num_tracked_samples(u).unwrap()).unwrap()
);
}
} else {
panic!("Expected a tree");
}
}
#[test]
fn test_iterate_samples_two_trees() {
use super::ll_bindings::tsk_size_t;
let treeseq = treeseq_from_small_table_collection_two_trees();
assert_eq!(treeseq.num_trees(), 2);
let mut tree_iter = treeseq.tree_iterator(TreeFlags::SAMPLE_LISTS).unwrap();
let expected_number_of_roots = vec![2, 1];
let mut expected_root_ids = vec![
vec![NodeId::from(0)],
vec![NodeId::from(1), NodeId::from(0)],
];
while let Some(tree) = tree_iter.next() {
let mut num_roots = 0;
let eroot_ids = expected_root_ids.pop().unwrap();
for (i, r) in tree.roots().enumerate() {
num_roots += 1;
assert_eq!(r, eroot_ids[i]);
}
assert_eq!(
expected_number_of_roots[(tree.current_tree - 1) as usize],
num_roots
);
assert_eq!(tree.roots().count(), eroot_ids.len());
let mut preoder_nodes = vec![];
let mut postoder_nodes = vec![];
for n in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
let mut nsamples = 0;
preoder_nodes.push(n);
if let Ok(iter) = tree.samples(n) {
for _ in iter {
nsamples += 1;
}
}
assert!(nsamples > 0);
assert_eq!(nsamples, tree.num_tracked_samples(n).unwrap());
}
for n in tree.traverse_nodes(NodeTraversalOrder::Postorder) {
let mut nsamples = 0;
postoder_nodes.push(n);
if let Ok(iter) = tree.samples(n) {
for _ in iter {
nsamples += 1;
}
}
assert!(nsamples > 0);
assert_eq!(nsamples, tree.num_tracked_samples(n).unwrap());
}
assert_eq!(preoder_nodes.len(), postoder_nodes.len());
// Test our preorder against the tskit functions in 0.99.15
{
let mut nodes: Vec<NodeId> = vec![
NodeId::NULL;
unsafe { ll_bindings::tsk_tree_get_size_bound(tree.as_ptr()) }
as usize
];
let mut num_nodes: tsk_size_t = 0;
let ptr = std::ptr::addr_of_mut!(num_nodes);
unsafe {
ll_bindings::tsk_tree_preorder(
tree.as_ptr(),
nodes.as_mut_ptr() as *mut tsk_id_t,
ptr,
);
}
assert_eq!(num_nodes as usize, preoder_nodes.len());
for i in 0..num_nodes as usize {
assert_eq!(preoder_nodes[i], nodes[i]);
}
}
}
}
#[test]
fn test_kc_distance_naive_test() {
let ts1 = treeseq_from_small_table_collection();
let ts2 = treeseq_from_small_table_collection();
let kc = ts1.kc_distance(&ts2, 0.0).unwrap();
assert!(kc.is_finite());
assert!((kc - 0.).abs() < f64::EPSILON);
}
#[test]
fn test_dump_tables() {
let tables = make_small_table_collection_two_trees();
// Have to make b/c tables will no longer exist after making the treeseq
let tables_copy = tables.deepcopy().unwrap();
let ts = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
let dumped = ts.dump_tables().unwrap();
assert!(tables_copy.equals(&dumped, crate::TableEqualityOptions::default()));
}
#[test]
fn test_reverse_tree_iteration() {
let treeseq = treeseq_from_small_table_collection_two_trees();
let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
let mut starts_fwd = vec![];
let mut stops_fwd = vec![];
let mut starts_rev = vec![];
let mut stops_rev = vec![];
while let Some(tree) = tree_iter.next() {
let interval = tree.interval();
starts_fwd.push(interval.0);
stops_fwd.push(interval.1);
}
assert_eq!(stops_fwd.len(), 2);
assert_eq!(stops_fwd.len(), 2);
// NOTE: we do NOT need to create a new iterator.
while let Some(tree) = tree_iter.next_back() {
let interval = tree.interval();
starts_rev.push(interval.0);
stops_rev.push(interval.1);
}
assert_eq!(starts_fwd.len(), starts_rev.len());
assert_eq!(stops_fwd.len(), stops_rev.len());
starts_rev.reverse();
assert!(starts_fwd == starts_rev);
stops_rev.reverse();
assert!(stops_fwd == stops_rev);
}
// FIXME: remove later
#[test]
fn test_array_lifetime() {
let treeseq = treeseq_from_small_table_collection_two_trees();
let mut tree_iter = treeseq.tree_iterator(TreeFlags::default()).unwrap();
if let Some(tree) = tree_iter.next() {
let pa = tree.parent_array();
let mut pc = vec![];
for i in pa.iter() {
pc.push(*i);
}
for (i, p) in pc.iter().enumerate() {
assert_eq!(pa[i], *p);
}
} else {
panic!("Expected a tree.");
}
}
}
#[cfg(test)]
mod test_treeeseq_send_sync {
use crate::test_fixtures::treeseq_from_small_table_collection_two_trees;
use std::sync::Arc;
use std::thread;
#[test]
fn build_arc() {
let t = treeseq_from_small_table_collection_two_trees();
let a = Arc::new(t);
let join_handle = thread::spawn(move || a.num_trees());
let ntrees = join_handle.join().unwrap();
assert_eq!(ntrees, 2);
}
}