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Jun 9, 2022
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Add num_children C level #2316

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10 changes: 10 additions & 0 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
@@ -1,3 +1,13 @@
--------------------
[1.1.0] - 2022-XX-XX
--------------------

**Features**

- Add ``num_children`` to ``tsk_tree_t`` an array which contains counts of the number of child
nodes of each node in the tree. (:user:`GertjanBisschop`, :issue:`2274`, :pr:`2316`)


--------------------
[1.0.0] - 2022-05-24
--------------------
Expand Down
65 changes: 65 additions & 0 deletions c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,9 @@ check_trees_identical(tsk_tree_t *self, tsk_tree_t *other)
tsk_memcmp(self->left_sib, other->left_sib, N * sizeof(tsk_id_t)) == 0);
CU_ASSERT_FATAL(
tsk_memcmp(self->right_sib, other->right_sib, N * sizeof(tsk_id_t)) == 0);
CU_ASSERT_FATAL(
tsk_memcmp(self->num_children, other->num_children, N * sizeof(tsk_size_t))
== 0);

CU_ASSERT_EQUAL_FATAL(self->num_samples == NULL, other->num_samples == NULL)
CU_ASSERT_EQUAL_FATAL(
Expand Down Expand Up @@ -1149,6 +1152,7 @@ test_simplest_nonbinary_records(void)
"0 1 0";
const char *edges = "0 1 4 0,1,2,3\n";
tsk_treeseq_t ts, simplified;
tsk_tree_t t;
tsk_id_t sample_ids[] = { 0, 1, 2, 3 };
int ret;

Expand All @@ -1159,6 +1163,13 @@ test_simplest_nonbinary_records(void)
CU_ASSERT_EQUAL(tsk_treeseq_get_num_mutations(&ts), 0);
CU_ASSERT_EQUAL(tsk_treeseq_get_num_trees(&ts), 1);

ret = tsk_tree_init(&t, &ts, 0);
CU_ASSERT_EQUAL(ret, 0);
ret = tsk_tree_first(&t);
CU_ASSERT_EQUAL(t.num_children[4], 4);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&t), 1);
tsk_tree_free(&t);

ret = tsk_treeseq_simplify(&ts, sample_ids, 4, 0, &simplified, NULL);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_table_collection_equals(ts.tables, simplified.tables, 0));
Expand Down Expand Up @@ -1192,6 +1203,7 @@ test_simplest_unary_records(void)
"0 1 3 1\n"
"0 1 4 2,3\n";
tsk_treeseq_t ts, simplified, simplified_other;
tsk_tree_t t;
tsk_id_t sample_ids[] = { 0, 1 };

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
Expand All @@ -1202,6 +1214,14 @@ test_simplest_unary_records(void)
CU_ASSERT_EQUAL(tsk_treeseq_get_num_trees(&ts), 1);
CU_ASSERT_EQUAL(tsk_treeseq_get_num_populations(&ts), 1);

ret = tsk_tree_init(&t, &ts, 0);
CU_ASSERT_EQUAL(ret, 0);
ret = tsk_tree_first(&t);
CU_ASSERT_EQUAL(t.num_children[2], 1);
CU_ASSERT_EQUAL(t.num_children[4], 2);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&t), 1);
tsk_tree_free(&t);

ret = tsk_treeseq_simplify(&ts, sample_ids, 2, 0, &simplified, NULL);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL(tsk_treeseq_get_num_samples(&simplified), 2);
Expand Down Expand Up @@ -1408,6 +1428,8 @@ test_simplest_degenerate_multiple_root_records(void)
CU_ASSERT_EQUAL(t.num_edges, 2);
CU_ASSERT_EQUAL(t.right_sib[2], 3);
CU_ASSERT_EQUAL(t.right_sib[3], TSK_NULL);
CU_ASSERT_EQUAL(t.num_children[2], 1);
CU_ASSERT_EQUAL(t.num_children[0], 0);

ret = tsk_treeseq_simplify(&ts, sample_ids, 2, 0, &simplified, NULL);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand Down Expand Up @@ -1501,6 +1523,8 @@ test_simplest_zero_root_tree(void)
CU_ASSERT_EQUAL(tsk_tree_get_right_root(&t), TSK_NULL);
CU_ASSERT_EQUAL(t.right_sib[2], 3);
CU_ASSERT_EQUAL(t.right_sib[3], TSK_NULL);
CU_ASSERT_EQUAL(t.num_children[0], 0);
CU_ASSERT_EQUAL(t.num_children[4], 2);

tsk_tree_free(&t);
tsk_treeseq_free(&ts);
Expand Down Expand Up @@ -1544,6 +1568,8 @@ test_simplest_multi_root_tree(void)
CU_ASSERT_EQUAL(tsk_tree_get_left_root(&t), 0);
CU_ASSERT_EQUAL(t.right_sib[0], 3);
CU_ASSERT_EQUAL(t.num_edges, 2);
CU_ASSERT_EQUAL(t.num_children[0], 0);
CU_ASSERT_EQUAL(t.num_children[3], 2);

tsk_tree_print_state(&t, _devnull);

Expand Down Expand Up @@ -1889,12 +1915,14 @@ test_simplest_initial_gap_zero_roots(void)
CU_ASSERT_EQUAL(ret, TSK_TREE_OK);
CU_ASSERT_EQUAL(tsk_tree_get_left_root(&tree), TSK_NULL);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 0);

ret = tsk_tree_next(&tree);
CU_ASSERT_EQUAL(ret, TSK_TREE_OK);
CU_ASSERT_EQUAL(tsk_tree_get_left_root(&tree), TSK_NULL);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 0);
CU_ASSERT_EQUAL(tree.parent[0], 2);
CU_ASSERT_EQUAL(tree.parent[1], 2);
CU_ASSERT_EQUAL(tree.num_children[2], 2);

tsk_tree_free(&tree);
tsk_treeseq_free(&ts);
Expand Down Expand Up @@ -1944,18 +1972,21 @@ test_simplest_holey_tsk_treeseq_zero_roots(void)
CU_ASSERT_EQUAL(tree.parent[0], 2);
CU_ASSERT_EQUAL(tree.parent[1], 2);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 0);
CU_ASSERT_EQUAL(tree.num_children[2], 2);

ret = tsk_tree_next(&tree);
CU_ASSERT_EQUAL(ret, TSK_TREE_OK);
CU_ASSERT_EQUAL(tsk_tree_get_left_root(&tree), TSK_NULL);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 0);
CU_ASSERT_EQUAL(tree.num_children[2], 0);

ret = tsk_tree_next(&tree);
CU_ASSERT_EQUAL(ret, TSK_TREE_OK);
CU_ASSERT_EQUAL(tsk_tree_get_left_root(&tree), TSK_NULL);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 0);
CU_ASSERT_EQUAL(tree.parent[0], 2);
CU_ASSERT_EQUAL(tree.parent[1], 2);
CU_ASSERT_EQUAL(tree.num_children[2], 2);

tsk_tree_free(&tree);
tsk_treeseq_free(&ts);
Expand Down Expand Up @@ -2708,6 +2739,7 @@ test_simplest_overlapping_parents(void)
CU_ASSERT_EQUAL(tree.right_sib[0], 1);
CU_ASSERT_EQUAL(tree.left_sib[1], 0);
CU_ASSERT_EQUAL(tree.right_sib[1], TSK_NULL);
CU_ASSERT_EQUAL(tree.num_children[2], 2);

tsk_tree_free(&tree);
tsk_treeseq_free(&ts);
Expand Down Expand Up @@ -3859,6 +3891,8 @@ test_single_tree_iter(void)
CU_ASSERT_EQUAL(ret, TSK_TREE_OK);
CU_ASSERT_EQUAL(tsk_treeseq_get_num_nodes(&ts), num_nodes);
CU_ASSERT_EQUAL(tsk_treeseq_get_num_trees(&ts), 1);
CU_ASSERT_EQUAL(tree.num_children[4], 2);
CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 1);
tsk_tree_print_state(&tree, _devnull);

for (u = 0; u < (tsk_id_t) num_nodes; u++) {
Expand Down Expand Up @@ -3945,6 +3979,7 @@ test_single_nonbinary_tree_iter(void)
CU_ASSERT_EQUAL(tree.left_sib[2], 1);
CU_ASSERT_EQUAL(tree.left_sib[1], 0);
CU_ASSERT_EQUAL(tree.left_sib[0], TSK_NULL);
CU_ASSERT_EQUAL(tree.num_children[u], 4);

u = 8;
ret = tsk_tree_get_num_samples(&tree, u, &num_samples);
Expand All @@ -3953,6 +3988,7 @@ test_single_nonbinary_tree_iter(void)
CU_ASSERT_EQUAL(tree.right_child[u], 5);
CU_ASSERT_EQUAL(tree.left_sib[5], 4);
CU_ASSERT_EQUAL(tree.left_sib[4], TSK_NULL);
CU_ASSERT_EQUAL(tree.num_children[u], 2);

u = 9;
ret = tsk_tree_get_num_samples(&tree, u, &num_samples);
Expand All @@ -3962,6 +3998,7 @@ test_single_nonbinary_tree_iter(void)
CU_ASSERT_EQUAL(tree.left_sib[8], 7);
CU_ASSERT_EQUAL(tree.left_sib[7], 6);
CU_ASSERT_EQUAL(tree.left_sib[6], TSK_NULL);
CU_ASSERT_EQUAL(tree.num_children[u], 3);

CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&tree), 1);
CU_ASSERT_EQUAL(tsk_tree_get_left_root(&tree), 9);
Expand Down Expand Up @@ -5196,6 +5233,31 @@ test_tsk_treeseq_bad_records(void)
tsk_table_collection_free(&tables);
}

static void
test_num_children_multi_tree(void)
{
int ret;
tsk_treeseq_t ts;
tsk_tree_t t;

tsk_treeseq_from_text(
&ts, 10, unary_ex_nodes, unary_ex_edges, NULL, NULL, NULL, NULL, NULL, 0);

ret = tsk_tree_init(&t, &ts, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_tree_next(&t));
CU_ASSERT_EQUAL(t.num_children[8], 2);

CU_ASSERT_TRUE(tsk_tree_next(&t));
CU_ASSERT_EQUAL(t.num_children[8], 1);

CU_ASSERT_TRUE(tsk_tree_next(&t));
CU_ASSERT_EQUAL(t.num_children[8], 0);

tsk_tree_free(&t);
tsk_treeseq_free(&ts);
}

/*=======================================================
* Diff iter tests.
*======================================================*/
Expand Down Expand Up @@ -5474,6 +5536,8 @@ test_virtual_root_properties(void)

CU_ASSERT_FALSE(tsk_tree_is_sample(&t, t.virtual_root));

CU_ASSERT_EQUAL(tsk_tree_get_num_roots(&t), 1);

tsk_tree_free(&t);
tsk_treeseq_free(&ts);
}
Expand Down Expand Up @@ -7747,6 +7811,7 @@ main(int argc, char **argv)
test_simplify_keep_input_roots_multi_tree },
{ "test_left_to_right_multi_tree", test_left_to_right_multi_tree },
{ "test_gappy_multi_tree", test_gappy_multi_tree },
{ "test_num_children_multi_tree", test_num_children_multi_tree },

{ "test_tsk_treeseq_bad_records", test_tsk_treeseq_bad_records },

Expand Down
21 changes: 11 additions & 10 deletions c/tskit/trees.c
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Expand Up @@ -3466,8 +3466,10 @@ tsk_tree_init(tsk_tree_t *self, const tsk_treeseq_t *tree_sequence, tsk_flags_t
self->right_child = tsk_malloc(N * sizeof(*self->right_child));
self->left_sib = tsk_malloc(N * sizeof(*self->left_sib));
self->right_sib = tsk_malloc(N * sizeof(*self->right_sib));
self->num_children = tsk_calloc(N, sizeof(*self->num_children));
if (self->parent == NULL || self->left_child == NULL || self->right_child == NULL
|| self->left_sib == NULL || self->right_sib == NULL) {
|| self->left_sib == NULL || self->right_sib == NULL
|| self->num_children == NULL) {
goto out;
}
if (!(self->options & TSK_NO_SAMPLE_COUNTS)) {
Expand Down Expand Up @@ -3532,6 +3534,7 @@ tsk_tree_free(tsk_tree_t *self)
tsk_safe_free(self->left_sample);
tsk_safe_free(self->right_sample);
tsk_safe_free(self->next_sample);
tsk_safe_free(self->num_children);
return 0;
}

Expand Down Expand Up @@ -3680,6 +3683,7 @@ tsk_tree_copy(const tsk_tree_t *self, tsk_tree_t *dest, tsk_flags_t options)
tsk_memcpy(dest->right_child, self->right_child, N * sizeof(*self->right_child));
tsk_memcpy(dest->left_sib, self->left_sib, N * sizeof(*self->left_sib));
tsk_memcpy(dest->right_sib, self->right_sib, N * sizeof(*self->right_sib));
tsk_memcpy(dest->num_children, self->num_children, N * sizeof(*self->num_children));
if (!(dest->options & TSK_NO_SAMPLE_COUNTS)) {
if (self->options & TSK_NO_SAMPLE_COUNTS) {
ret = TSK_ERR_UNSUPPORTED_OPERATION;
Expand Down Expand Up @@ -3878,15 +3882,7 @@ tsk_tree_get_right_root(const tsk_tree_t *self)
tsk_size_t
tsk_tree_get_num_roots(const tsk_tree_t *self)
{
const tsk_id_t *restrict right_sib = self->right_sib;
const tsk_id_t *restrict left_child = self->left_child;
tsk_size_t num_roots = 0;
tsk_id_t u;

for (u = left_child[self->virtual_root]; u != TSK_NULL; u = right_sib[u]) {
num_roots++;
}
return num_roots;
return self->num_children[self->virtual_root];
}

int TSK_WARN_UNUSED
Expand Down Expand Up @@ -4200,6 +4196,7 @@ tsk_tree_remove_branch(
tsk_id_t *restrict right_child = self->right_child;
tsk_id_t *restrict left_sib = self->left_sib;
tsk_id_t *restrict right_sib = self->right_sib;
tsk_size_t *restrict num_children = self->num_children;
tsk_id_t lsib = left_sib[c];
tsk_id_t rsib = right_sib[c];

Expand All @@ -4216,6 +4213,7 @@ tsk_tree_remove_branch(
parent[c] = TSK_NULL;
left_sib[c] = TSK_NULL;
right_sib[c] = TSK_NULL;
num_children[p]--;
}

static inline void
Expand All @@ -4226,6 +4224,7 @@ tsk_tree_insert_branch(
tsk_id_t *restrict right_child = self->right_child;
tsk_id_t *restrict left_sib = self->left_sib;
tsk_id_t *restrict right_sib = self->right_sib;
tsk_size_t *restrict num_children = self->num_children;
tsk_id_t u;

parent[c] = p;
Expand All @@ -4240,6 +4239,7 @@ tsk_tree_insert_branch(
right_sib[c] = TSK_NULL;
}
right_child[p] = c;
num_children[p]++;
}

static inline void
Expand Down Expand Up @@ -4590,6 +4590,7 @@ tsk_tree_clear(tsk_tree_t *self)
tsk_memset(self->right_child, 0xff, N * sizeof(*self->right_child));
tsk_memset(self->left_sib, 0xff, N * sizeof(*self->left_sib));
tsk_memset(self->right_sib, 0xff, N * sizeof(*self->right_sib));
tsk_memset(self->num_children, 0, N * sizeof(*self->num_children));

if (sample_counts) {
tsk_memset(self->num_samples, 0, N * sizeof(*self->num_samples));
Expand Down
4 changes: 4 additions & 0 deletions c/tskit/trees.h
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,10 @@ typedef struct {
``TSK_NULL`` if node u has no siblings to its right.
*/
tsk_id_t *right_sib;
/**
@brief The number of children of node u is num_children[u].
*/
tsk_size_t *num_children;
/**
@brief The total number of edges defining the topology of this tree.
This is equal to the number of tree sequence edges that intersect with
Expand Down
2 changes: 2 additions & 0 deletions python/tests/__init__.py
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Expand Up @@ -42,6 +42,7 @@ def __init__(self, num_nodes):
self.right_child = [tskit.NULL for _ in range(num_nodes)]
self.left_sib = [tskit.NULL for _ in range(num_nodes)]
self.right_sib = [tskit.NULL for _ in range(num_nodes)]
self.num_children = [0 for _ in range(num_nodes)]
self.left = 0
self.right = 0
self.index = -1
Expand Down Expand Up @@ -220,6 +221,7 @@ def trees(self):
pt.right_child[:] = rtt.right_child
pt.left_sib[:] = rtt.left_sib
pt.right_sib[:] = rtt.right_sib
pt.num_children[:] = rtt.num_children
pt.left_root = rtt.left_child[-1]
pt.left = left
pt.right = right
Expand Down
13 changes: 13 additions & 0 deletions python/tests/test_utilities.py
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Expand Up @@ -23,6 +23,7 @@
Tests for the various testing utilities.
"""
import msprime
import numpy as np
import pytest

import tests.tsutil as tsutil
Expand Down Expand Up @@ -181,3 +182,15 @@ def test_sort_individuals(self):
tables.individuals.add_row(parents=[0], metadata=b"1")
with pytest.raises(ValueError, match="Individual pedigree has cycles"):
tsutil.sort_individual_table(tables)


class TestQuintuplyLinkedTrees:
def test_branch_operations_num_children(self):
qlt = tsutil.QuintuplyLinkedTree(3)
assert np.sum(qlt.num_children) == 0
qlt.insert_branch(2, 0)
assert qlt.num_children[2] == 1
assert np.sum(qlt.num_children) == 1

qlt.remove_branch(2, 0)
assert qlt.num_children[2] == 0
8 changes: 6 additions & 2 deletions python/tests/tsutil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1228,15 +1228,17 @@ def __init__(self, n, root_threshold=1):
self.right_sib = np.zeros(n + 1, dtype=np.int32) - 1
self.num_samples = np.zeros(n + 1, dtype=np.int32)
self.num_edges = 0
self.num_children = np.zeros(n + 1, dtype=np.int32)

def __str__(self):
s = "id\tparent\tlchild\trchild\tlsib\trsib\tnsamp\n"
s = "id\tparent\tlchild\trchild\tlsib\trsib\tnsamp\tnchild\n"
for j in range(len(self.parent)):
s += (
f"{j}\t{self.parent[j]}\t"
f"{self.left_child[j]}\t{self.right_child[j]}\t"
f"{self.left_sib[j]}\t{self.right_sib[j]}\t"
f"{self.num_samples[j]}\n"
f"{self.num_samples[j]}\t"
f"{self.num_children[j]}\n"
)
return s

Expand All @@ -1262,6 +1264,7 @@ def remove_branch(self, p, c):
self.parent[c] = -1
self.left_sib[c] = -1
self.right_sib[c] = -1
self.num_children[p] -= 1

def insert_branch(self, p, c):
assert self.parent[c] == -1, "contradictory edges"
Expand All @@ -1276,6 +1279,7 @@ def insert_branch(self, p, c):
self.left_sib[c] = u
self.right_sib[c] = -1
self.right_child[p] = c
self.num_children[p] += 1

def is_potential_root(self, u):
return self.num_samples[u] >= self.root_threshold
Expand Down