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Dec 14, 2021
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support virtual root #205

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68 changes: 32 additions & 36 deletions src/trees.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ pub struct Tree {
current_tree: i32,
advanced: bool,
num_nodes: tsk_size_t,
array_len: tsk_size_t,
flags: TreeFlags,
}

Expand Down Expand Up @@ -58,6 +59,7 @@ impl Tree {
current_tree: 0,
advanced: false,
num_nodes,
array_len: num_nodes + 1,
flags,
}
}
Expand Down Expand Up @@ -100,7 +102,7 @@ impl Tree {
/// }
/// ```
pub fn parent_array(&self) -> &[NodeId] {
tree_array_slice!(self, parent, (*self.inner).num_nodes)
tree_array_slice!(self, parent, self.array_len)
}

/// # Failing examples
Expand Down Expand Up @@ -267,7 +269,7 @@ impl Tree {
/// }
/// ```
pub fn left_sib_array(&self) -> &[NodeId] {
tree_array_slice!(self, left_sib, (*self.inner).num_nodes)
tree_array_slice!(self, left_sib, self.array_len)
}

/// # Failing examples
Expand All @@ -287,7 +289,7 @@ impl Tree {
/// }
/// ```
pub fn right_sib_array(&self) -> &[NodeId] {
tree_array_slice!(self, right_sib, (*self.inner).num_nodes)
tree_array_slice!(self, right_sib, self.array_len)
}

/// # Failing examples
Expand All @@ -307,7 +309,7 @@ impl Tree {
/// }
/// ```
pub fn left_child_array(&self) -> &[NodeId] {
tree_array_slice!(self, left_child, (*self.inner).num_nodes)
tree_array_slice!(self, left_child, self.array_len)
}

/// # Failing examples
Expand All @@ -327,7 +329,7 @@ impl Tree {
/// }
/// ```
pub fn right_child_array(&self) -> &[NodeId] {
tree_array_slice!(self, right_child, (*self.inner).num_nodes)
tree_array_slice!(self, right_child, self.array_len)
}

fn left_sample(&self, u: NodeId) -> Result<NodeId, TskitError> {
Expand Down Expand Up @@ -367,7 +369,7 @@ impl Tree {
///
/// [`TskitError`] if `u` is out of range.
pub fn parent(&self, u: NodeId) -> Result<NodeId, TskitError> {
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, (*self.inner).parent, NodeId)
unsafe_tsk_column_access!(u.0, 0, self.array_len, (*self.inner).parent, NodeId)
}

/// Get the left child of node `u`.
Expand All @@ -376,7 +378,7 @@ impl Tree {
///
/// [`TskitError`] if `u` is out of range.
pub fn left_child(&self, u: NodeId) -> Result<NodeId, TskitError> {
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, (*self.inner).left_child, NodeId)
unsafe_tsk_column_access!(u.0, 0, self.array_len, (*self.inner).left_child, NodeId)
}

/// Get the right child of node `u`.
Expand All @@ -385,7 +387,7 @@ impl Tree {
///
/// [`TskitError`] if `u` is out of range.
pub fn right_child(&self, u: NodeId) -> Result<NodeId, TskitError> {
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, (*self.inner).right_child, NodeId)
unsafe_tsk_column_access!(u.0, 0, self.array_len, (*self.inner).right_child, NodeId)
}

/// Get the left sib of node `u`.
Expand All @@ -394,7 +396,7 @@ impl Tree {
///
/// [`TskitError`] if `u` is out of range.
pub fn left_sib(&self, u: NodeId) -> Result<NodeId, TskitError> {
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, (*self.inner).left_sib, NodeId)
unsafe_tsk_column_access!(u.0, 0, self.array_len, (*self.inner).left_sib, NodeId)
}

/// Get the right sib of node `u`.
Expand All @@ -403,7 +405,7 @@ impl Tree {
///
/// [`TskitError::IndexError`] if `u` is out of range.
pub fn right_sib(&self, u: NodeId) -> Result<NodeId, TskitError> {
unsafe_tsk_column_access!(u.0, 0, self.num_nodes, (*self.inner).right_sib, NodeId)
unsafe_tsk_column_access!(u.0, 0, self.array_len, (*self.inner).right_sib, NodeId)
}

/// Obtain the list of samples for the current tree/tree sequence
Expand Down Expand Up @@ -577,6 +579,11 @@ impl Tree {
};
handle_tsk_return_value!(code, kc)
}

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

impl streaming_iterator::StreamingIterator for Tree {
Expand Down Expand Up @@ -639,7 +646,7 @@ pub enum NodeTraversalOrder {
}

struct PreorderNodeIterator<'a> {
root_stack: Vec<NodeId>,
current_root: NodeId,
node_stack: Vec<NodeId>,
tree: &'a Tree,
current_node_: Option<NodeId>,
Expand All @@ -648,14 +655,15 @@ struct PreorderNodeIterator<'a> {
impl<'a> PreorderNodeIterator<'a> {
fn new(tree: &'a Tree) -> Self {
let mut rv = PreorderNodeIterator {
root_stack: tree.roots_to_vec(),
current_root: tree.right_child(tree.virtual_root()).unwrap(),
node_stack: vec![],
tree,
current_node_: None,
};
rv.root_stack.reverse();
if let Some(root) = rv.root_stack.pop() {
rv.node_stack.push(root);
let mut c = rv.current_root;
while !c.is_null() {
rv.node_stack.push(c);
c = rv.tree.left_sib(c).unwrap();
}
rv
}
Expand All @@ -664,26 +672,14 @@ impl<'a> PreorderNodeIterator<'a> {
impl NodeIterator for PreorderNodeIterator<'_> {
fn next_node(&mut self) {
self.current_node_ = self.node_stack.pop();
match self.current_node_ {
Some(u) => {
// NOTE: process children right-to-left
// because we later pop them from a steck
// to generate the expected left-to-right ordering.
let mut c = self.tree.right_child(u).unwrap();
while c != NodeId::NULL {
self.node_stack.push(c);
c = self.tree.left_sib(c).unwrap();
}
}
None => {
if let Some(r) = self.root_stack.pop() {
self.current_node_ = Some(r);
let mut c = self.tree.right_child(r).unwrap();
while c != NodeId::NULL {
self.node_stack.push(c);
c = self.tree.left_sib(c).unwrap();
}
}
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.
let mut c = self.tree.right_child(u).unwrap();
while c != NodeId::NULL {
self.node_stack.push(c);
c = self.tree.left_sib(c).unwrap();
}
};
}
Expand Down Expand Up @@ -763,7 +759,7 @@ impl<'a> RootIterator<'a> {
fn new(tree: &'a Tree) -> Self {
RootIterator {
current_root: None,
next_root: unsafe { ll_bindings::tsk_tree_get_left_root(tree.as_ptr()).into() },
next_root: tree.left_child(tree.virtual_root()).unwrap(),
tree,
}
}
Expand Down