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
|
#include <catch.hpp>
#include <iostream>
#include <sstream>
#include <terraces/advanced.hpp>
#include <terraces/errors.hpp>
#include <terraces/parser.hpp>
namespace terraces {
namespace tests {
TEST_CASE("parsing a tree with just a root-node", "[parser]") {
const auto results = parse_new_nwk("foo");
const auto& tree = results.tree;
const auto& names = results.names;
const auto& indices = results.indices;
REQUIRE(tree.size() == 1);
CHECK(tree[0].parent() == none);
CHECK(tree[0].lchild() == none);
CHECK(tree[0].rchild() == none);
CHECK(names[0] == "foo");
CHECK(indices.at("foo") == 0);
}
TEST_CASE("parsing a tree with three leaves and two inner nodes", "[parser]") {
const auto results = parse_new_nwk("((foo,bar)inner, baz)outer");
const auto& tree = results.tree;
const auto& names = results.names;
const auto& indices = results.indices;
REQUIRE(tree.size() == 5);
CHECK(tree[0].parent() == none);
CHECK(tree[0].lchild() == 1);
CHECK(tree[0].rchild() == 4);
CHECK(tree[1].parent() == 0);
CHECK(tree[1].lchild() == 2);
CHECK(tree[1].rchild() == 3);
CHECK(tree[2].parent() == 1);
CHECK(tree[2].lchild() == none);
CHECK(tree[2].rchild() == none);
CHECK(tree[3].parent() == 1);
CHECK(tree[3].lchild() == none);
CHECK(tree[3].rchild() == none);
CHECK(tree[4].parent() == 0);
CHECK(tree[4].lchild() == none);
CHECK(tree[4].rchild() == none);
CHECK(names[0] == "foo");
CHECK(names[1] == "bar");
CHECK(names[2] == "baz");
CHECK(indices.at("foo") == 0);
CHECK(indices.at("bar") == 1);
CHECK(indices.at("baz") == 2);
CHECK(indices.size() == 3);
}
TEST_CASE("parsing a tree with quotes, three leaves and two inner nodes", "[parser]") {
const auto results = parse_new_nwk("((foo,bar)'inner', 'baz')outer");
const auto& tree = results.tree;
const auto& names = results.names;
const auto& indices = results.indices;
REQUIRE(tree.size() == 5);
CHECK(tree[0].parent() == none);
CHECK(tree[0].lchild() == 1);
CHECK(tree[0].rchild() == 4);
CHECK(tree[1].parent() == 0);
CHECK(tree[1].lchild() == 2);
CHECK(tree[1].rchild() == 3);
CHECK(tree[2].parent() == 1);
CHECK(tree[2].lchild() == none);
CHECK(tree[2].rchild() == none);
CHECK(tree[3].parent() == 1);
CHECK(tree[3].lchild() == none);
CHECK(tree[3].rchild() == none);
CHECK(tree[4].parent() == 0);
CHECK(tree[4].lchild() == none);
CHECK(tree[4].rchild() == none);
CHECK(names[0] == "foo");
CHECK(names[1] == "bar");
CHECK(names[2] == "baz");
CHECK(indices.at("foo") == 0);
CHECK(indices.at("bar") == 1);
CHECK(indices.at("baz") == 2);
CHECK(indices.size() == 3);
}
TEST_CASE("parsing an unrooted tree with three leaves", "[parser]") {
const auto results = parse_new_nwk("(foo,bar,'baz')");
auto exp_names = name_map{"foo", "bar", "baz"};
auto exp_tree = tree{{none, 1, 3, none},
{0, none, none, 0},
{3, none, none, 1},
{0, 2, 4, none},
{3, none, none, 2}};
CHECK(results.names == exp_names);
CHECK(results.tree == exp_tree);
}
TEST_CASE("parsing tree with unnecessary parentheses", "[parser]") {
CHECK_THROWS_AS(parse_new_nwk("()"), bad_input_error);
}
TEST_CASE("parsing trees with mismatching parentheses", "[parser]") {
// too many closing parentheses
CHECK_THROWS_AS(parse_new_nwk("((a,b),c))"), bad_input_error);
// too many opening parentheses
CHECK_THROWS_AS(parse_new_nwk("((a,b)"), bad_input_error);
// too many opening parentheses
CHECK_THROWS_AS(parse_new_nwk("((a,b),c"), bad_input_error);
// ternary nodes (simple)
CHECK_THROWS_AS(parse_new_nwk("((a,b,c),a)"), bad_input_error);
// ternary nodes (complex)
CHECK_THROWS_AS(parse_new_nwk("(a,((b,c),((d,e),f),g))"), bad_input_error);
}
TEST_CASE("parsing trees invalid format", "[parser]") {
// inner node names must come after their children.
CHECK_THROWS_AS(parse_new_nwk("a(,)"), bad_input_error);
}
TEST_CASE("parsing trees with unclosed quotes", "[parser]") {
CHECK_THROWS_AS(parse_new_nwk("(('a',''),(('c,),),)"), bad_input_error);
}
TEST_CASE("parsing trees with duplicate taxa", "[parser]") {
CHECK_THROWS_AS(parse_new_nwk("(a,a)"), bad_input_error);
index_map inds{{"a", 0}};
CHECK_THROWS_AS(parse_nwk("(a,a)", inds), bad_input_error);
}
TEST_CASE("parsing a datafile with three species and two cols", "[parser],[data-parser]") {
auto stream = std::istringstream{"3 2\n0 1 foo\n1 1 bar\n1 1 baz\n"};
const auto res = parse_bitmatrix(stream);
const auto& mat = res.matrix;
REQUIRE(mat.cols() == 2);
REQUIRE(mat.rows() == 3);
CHECK(!mat.get(0, 0));
CHECK(mat.get(0, 1));
CHECK(mat.get(1, 0));
CHECK(mat.get(1, 1));
CHECK(mat.get(2, 0));
CHECK(mat.get(2, 1));
CHECK(find_comprehensive_taxon(mat) == 1);
}
TEST_CASE("parsing a datafile with duplicate species", "[parser],[data-parser]") {
auto stream = std::istringstream{"3 2\n1 0 foo\n1 1 bar\n1 1 bar\n"};
CHECK_THROWS_AS(terraces::parse_bitmatrix(stream), bad_input_error);
}
TEST_CASE("parsing a complex datafile", "[parser],[data-parser]") {
auto stream = std::istringstream{"5 3\n"
"0 1 0 foo\n"
"1 1 1 bar\n"
"0 1 0 bla\n"
"1 0 1 blub\n"
"1 1 0 gaehn\n"};
const auto res = terraces::parse_bitmatrix(stream);
const auto& mat = res.matrix;
REQUIRE(mat.cols() == 3);
REQUIRE(mat.rows() == 5);
CHECK(!mat.get(0, 0));
CHECK(mat.get(0, 1));
CHECK(!mat.get(0, 2));
CHECK(mat.get(1, 0));
CHECK(mat.get(1, 1));
CHECK(mat.get(1, 2));
CHECK(!mat.get(2, 0));
CHECK(mat.get(2, 1));
CHECK(!mat.get(2, 2));
CHECK(mat.get(3, 0));
CHECK(!mat.get(3, 1));
CHECK(mat.get(3, 2));
CHECK(mat.get(4, 0));
CHECK(mat.get(4, 1));
CHECK(!mat.get(4, 2));
CHECK(find_comprehensive_taxon(mat) == 1);
}
} // namespace tests
} // namespace terraces
|
