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refactor: remove many unsafe calls from tree_interface.rs #428

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Dec 5, 2022
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refactor: remove many unsafe calls from tree_interface.rs #428

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59 changes: 30 additions & 29 deletions src/tree_interface.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ impl TreeInterface {
/// ```
pub fn samples_array(&self) -> Result<&[NodeId], TskitError> {
let num_samples =
unsafe { ll_bindings::tsk_treeseq_get_num_samples((*self.as_ptr()).tree_sequence) };
unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ref().tree_sequence) };
err_if_not_tracking_samples!(
self.flags,
sys::generate_slice(self.as_ref().samples, num_samples)
Expand Down Expand Up @@ -305,25 +305,28 @@ impl TreeInterface {
// error if we are not tracking samples,
// Ok(None) if u is out of range
fn left_sample<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.left_sample, self.num_nodes)
sys::tsk_column_access::<NodeId, _, _, _>(
u.into(),
self.as_ref().left_sample,
self.num_nodes,
)
}

// error if we are not tracking samples,
// Ok(None) if u is out of range
fn right_sample<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.right_sample, self.num_nodes)
sys::tsk_column_access::<NodeId, _, _, _>(
u.into(),
self.as_ref().right_sample,
self.num_nodes,
)
}

/// 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(),
self.as_ref().interval.left.into(),
self.as_ref().interval.right.into(),
)
}

Expand All @@ -338,45 +341,43 @@ impl TreeInterface {
///
/// Returns `None` if `u` is out of range.
pub fn parent<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.parent, self.array_len)
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), self.as_ref().parent, self.array_len)
}

/// Get the left child of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn left_child<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.left_child, self.array_len)
sys::tsk_column_access::<NodeId, _, _, _>(
u.into(),
self.as_ref().left_child,
self.array_len,
)
}

/// Get the right child of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn right_child<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.right_child, self.array_len)
sys::tsk_column_access::<NodeId, _, _, _>(
u.into(),
self.as_ref().right_child,
self.array_len,
)
}

/// Get the left sib of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn left_sib<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.left_sib, self.array_len)
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), self.as_ref().left_sib, self.array_len)
}

/// Get the right sib of node `u`.
///
/// Returns `None` if `u` is out of range.
pub fn right_sib<N: Into<NodeId> + Copy>(&self, u: N) -> Option<NodeId> {
// SAFETY: internal pointer cannot be NULL
let ptr = unsafe { *self.as_ptr() };
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), ptr.right_sib, self.array_len)
sys::tsk_column_access::<NodeId, _, _, _>(u.into(), self.as_ref().right_sib, self.array_len)
}

/// Obtain the list of samples for the current tree/tree sequence
Expand All @@ -388,12 +389,12 @@ impl TreeInterface {
#[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) };
unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ref().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) },
Ok(o) => unsafe { *(*(self.as_ref()).tree_sequence).samples.offset(o) },
Err(e) => panic!("{}", e),
};
rv.push(u.into());
Expand All @@ -404,7 +405,7 @@ impl TreeInterface {
/// 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) };
unsafe { ll_bindings::tsk_treeseq_get_num_samples(self.as_ref().tree_sequence) };
sys::generate_slice(self.as_ref().samples, num_samples)
}

Expand Down Expand Up @@ -561,7 +562,7 @@ impl TreeInterface {

/// Return the virtual root of the tree.
pub fn virtual_root(&self) -> NodeId {
unsafe { (*self.as_ptr()).virtual_root }.into()
self.as_ref().virtual_root.into()
}
}

Expand Down