1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
#[test]
fn initialize_from_table_collection() {
// ANCHOR: build_tables
use tskit::prelude::*;
use tskit::TableCollection;
use tskit::TableSortOptions;
use tskit::TreeFlags;
use tskit::TreeSequenceFlags;
let mut tables = TableCollection::new(1000.).unwrap();
tables
.add_node(0, 2.0, PopulationId::NULL, IndividualId::NULL)
.unwrap();
tables
.add_node(0, 1.0, PopulationId::NULL, IndividualId::NULL)
.unwrap();
tables
.add_node(
tskit::NodeFlags::new_sample(),
0.0,
PopulationId::NULL,
IndividualId::NULL,
)
.unwrap();
tables
.add_node(
tskit::NodeFlags::new_sample(),
0.0,
PopulationId::NULL,
IndividualId::NULL,
)
.unwrap();
tables
.add_node(
tskit::NodeFlags::new_sample(),
0.0,
PopulationId::NULL,
IndividualId::NULL,
)
.unwrap();
tables
.add_node(
tskit::NodeFlags::new_sample(),
0.0,
PopulationId::NULL,
IndividualId::NULL,
)
.unwrap();
tables.add_edge(500., 1000., 0, 1).unwrap();
tables.add_edge(0., 500., 0, 2).unwrap();
tables.add_edge(0., 1000., 0, 3).unwrap();
tables.add_edge(500., 1000., 1, 2).unwrap();
tables.add_edge(0., 1000., 1, 4).unwrap();
tables.add_edge(0., 1000., 1, 5).unwrap();
// ANCHOR_END: build_tables
// ANCHOR: sort_tables
tables.full_sort(TableSortOptions::default()).unwrap();
// ANCHOR_END: sort_tables
// ANCHOR: index_tables
tables.build_index().unwrap();
// ANCHOR_END: index_tables
// ANCHOR: create_tree_sequence
let treeseq = tables.tree_sequence(TreeSequenceFlags::default()).unwrap();
// ANCHOR_END: create_tree_sequence
// ANCHOR: iterate_trees
let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
while let Some(_tree) = tree_iterator.next() {
// _tree is a tskit::Tree
}
// ANCHOR_END: iterate_trees
let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
// ANCHOR: iterate_node_siblings
// This is an enum defining supported
// traversal orders through a Tree.
use tskit::NodeTraversalOrder;
while let Some(tree) = tree_iterator.next() {
for node in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
if let Some(parent) = tree.parent(node) {
// Collect the siblings of node into a Vec
// The children function returns another iterator
let _siblings = tree
.children(parent)
.filter(|child| child != node)
.collect::<Vec<_>>();
}
}
}
// ANCHOR_END: iterate_node_siblings
let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
// ANCHOR: iterate_node_siblings_via_arrays
while let Some(tree) = tree_iterator.next() {
let parents = tree.parent_array();
let rsibs = tree.right_sib_array();
let lchildren = tree.left_child_array();
for node in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
let mut siblings = vec![];
assert!(!node.is_null());
if let Some(parent) = parents.get(usize::try_from(node).unwrap()) {
if !parent.is_null() {
if let Some(child) = lchildren.get(usize::try_from(*parent).unwrap()) {
let mut u = *child;
while !u.is_null() {
if u != node {
siblings.push(u);
}
if let Some(sib) = rsibs.get(usize::try_from(u).unwrap()) {
u = *sib;
}
}
}
}
}
}
}
// ANCHOR_END: iterate_node_siblings_via_arrays
let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
// ANCHOR: iterate_node_siblings_via_array_getters
while let Some(tree) = tree_iterator.next() {
for node in tree.traverse_nodes(NodeTraversalOrder::Preorder) {
let mut siblings = vec![];
if let Some(parent) = tree.parent(node) {
if let Some(child) = tree.left_child(parent) {
let mut u = child;
while !u.is_null() {
if u != node {
siblings.push(u);
}
if let Some(sib) = tree.right_sib(u) {
u = sib;
}
}
}
}
}
}
// ANCHOR_END: iterate_node_siblings_via_array_getters
// let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
// let mut total_branch_lengths = vec![];
// while let Some(tree) = tree_iterator.next() {
// total_branch_lengths.push(tree.total_branch_length(false).unwrap());
// }
// let mut tree_iterator = treeseq.tree_iterator(TreeFlags::default()).unwrap();
// let mut total_branch_lengths_ll = vec![];
// let mut x = 0.0;
// while let Some(tree) = tree_iterator.next() {
// let l =
// unsafe { tskit::bindings::tsk_tree_get_total_branch_length(tree.as_ptr(), -1, &mut x) };
// assert!(l >= 0);
// total_branch_lengths_ll.push(x);
// }
// for (i, j) in total_branch_lengths
// .iter()
// .zip(total_branch_lengths_ll.iter())
// {
// assert_eq!(i, j, "{} {}", i, j);
// }
// ANCHOR: iterate_edge_differences
for diffs in treeseq.edge_differences_iter() {
for edge_removal in diffs.removals() {
println!("edge removal: {}", edge_removal);
}
for edge_insertion in diffs.insertions() {
println!("edge insertion: {}", edge_insertion);
}
}
// ANCHOR_END: iterate_edge_differences
// ANCHOR: iterate_edge_differences_update_parents
let num_nodes = treeseq.nodes().num_rows().as_usize();
// num_nodes + 1 to reflect a "virtual root" present in
// the tree arrays
let mut parents = vec![NodeId::NULL; num_nodes + 1];
let mut tree_iter = treeseq.tree_iterator(0).unwrap();
for diffs in treeseq.edge_differences_iter() {
let tree = tree_iter.next().unwrap();
for edge_out in diffs.removals() {
let c = edge_out.child();
parents[c.as_usize()] = NodeId::NULL;
}
for edge_in in diffs.insertions() {
let c = edge_in.child();
parents[c.as_usize()] = edge_in.parent();
}
assert_eq!(tree.parent_array(), &parents);
}
// ANCHOR_END: iterate_edge_differences_update_parents
}