refactor: Extract remove_leaf to its own ops function

[lsetiawan]

Need to extract the following remove_leaf method to its own ops function and then call it here so it can be used independently of TreeVec

phylo2vec/phylo2vec/src/tree_vec/mod.rs

Lines 121 to 169 in fb06aca

	pub fn remove_leaf(&mut self, leaf: usize) -> usize {
	let ancestry = self.get_ancestry();
	let leaf_coords = ops::find_coords_of_first_leaf(&ancestry, leaf);
	let leaf_row = leaf_coords.0;
	let leaf_col = leaf_coords.1;
	// Find the parent of the leaf to remove
	let parent = ancestry[leaf_row][2];
	let sister = ancestry[leaf_row][1 - leaf_col];
	let num_cherries = ancestry.len();
	let mut ancestry_rm = Vec::with_capacity(num_cherries - 1);
	for r in 0..num_cherries - 1 {
	let mut new_row = if r < leaf_row {
	ancestry[r].clone()
	} else {
	ancestry[r + 1].clone()
	};
	for c in 0..3 {
	let mut node = new_row[c];
	if node == parent {
	node = sister;
	}
	// Subtract 1 for leaves > "leaf"
	// (so that the vector is still valid)
	if node > leaf {
	node -= 1;
	if node >= parent {
	node -= 1;
	}
	}
	new_row[c] = node;
	}
	ancestry_rm.push(new_row);
	}
	ops::order_cherries(&mut ancestry_rm);
	ops::order_cherries_no_parents(&mut ancestry_rm);
	self.data = ops::build_vector(ancestry_rm);
	return sister;
	}
	}