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
|
#include <catch.hpp>
#include <terraces/subtree_extraction.hpp>
#include "../lib/trees_impl.hpp"
#include "../lib/validation.hpp"
namespace terraces {
namespace tests {
using std::vector;
TEST_CASE("subtree extraction: full data", "[subtree_extraction]") {
tree t{{none, 4, 5, none}, {2, none, none, 0}, {4, 6, 1, none}, {4, none, none, 1},
{0, 2, 3, none}, {0, none, none, 2}, {2, none, none, 3}};
bitmatrix bm{4, 1};
for (index row = 0; row < bm.rows(); ++row) {
bm.set(row, 0, true);
}
auto t2 = subtrees(t, bm)[0];
check_rooted_tree(t);
check_rooted_tree(t2);
vector<index> exp_pre{0, 1, 2, 3, 4, 5, 6};
vector<index> exp_post{3, 4, 2, 5, 1, 6, 0};
auto res_pre = preorder(t2);
auto res_post = postorder(t2);
CHECK(t2[3].taxon() == 3);
CHECK(t2[4].taxon() == 0);
CHECK(t2[5].taxon() == 1);
CHECK(t2[6].taxon() == 2);
CHECK(is_isomorphic_unrooted(t, t2));
CHECK(exp_pre == res_pre);
CHECK(exp_post == res_post);
}
TEST_CASE("subtree extraction: example", "[subtree_extraction]") {
tree t{{none, 4, 5, none}, {2, none, none, 0}, {4, 6, 1, none}, {4, none, none, 1},
{0, 2, 3, none}, {0, none, none, 2}, {2, none, none, 3}};
bitmatrix bm{4, 2};
bm.set(0, 0, true);
bm.set(0, 1, true);
bm.set(1, 0, true);
bm.set(2, 0, true);
bm.set(2, 1, true);
bm.set(3, 1, true);
auto trees = subtrees(t, bm);
auto t1 = trees[0];
auto t2 = trees[1];
vector<index> exp_pre1{0, 1, 2, 3, 4};
vector<index> exp_pre2{0, 1, 2, 3, 4};
vector<index> exp_post1{2, 3, 1, 4, 0};
vector<index> exp_post2{2, 3, 1, 4, 0};
CHECK(t1[2].taxon() == 0);
CHECK(t1[3].taxon() == 1);
CHECK(t1[4].taxon() == 2);
CHECK(t2[2].taxon() == 3);
CHECK(t2[3].taxon() == 0);
CHECK(t2[4].taxon() == 2);
CHECK(exp_pre1 == preorder(trees[0]));
CHECK(exp_pre2 == preorder(trees[1]));
CHECK(exp_post1 == postorder(trees[0]));
CHECK(exp_post2 == postorder(trees[1]));
}
TEST_CASE("subtree extraction: moved root", "[subtree_extraction]") {
std::stringstream mss{"5 1\n1 1\n1 2\n1 3\n0 4\n0 5"};
auto matrix = parse_bitmatrix(mss);
auto to_str = [&](const tree& t) {
std::stringstream ss;
ss << as_newick(t, matrix.names);
return ss.str();
};
auto t1 = parse_nwk("((4,5),(1,(2,3)));", matrix.indices);
auto t2 = parse_nwk("((((1,2),3),4),5);", matrix.indices);
auto t3 = parse_nwk("(4,((1,5),(2,3)));", matrix.indices);
auto t4 = parse_nwk("(4,((2,3),(1,5)));", matrix.indices);
auto t5 = parse_nwk("(5,((3,(1,4)),2));", matrix.indices);
auto st1 = subtrees(t1, matrix.matrix)[0];
auto st2 = subtrees(t2, matrix.matrix)[0];
auto st3 = subtrees(t3, matrix.matrix)[0];
auto st4 = subtrees(t4, matrix.matrix)[0];
auto st5 = subtrees(t5, matrix.matrix)[0];
CHECK(to_str(st1) == "(1,(2,3));");
CHECK(to_str(st2) == "((1,2),3);");
CHECK(to_str(st3) == "(1,(2,3));");
CHECK(to_str(st4) == "((2,3),1);");
CHECK(to_str(st5) == "((3,1),2);");
}
} // namespace tests
} // namespace terraces
|
