TEST_F(PhyloTreeTest, PrefixCoding) {
vector<PhyloTreeNode*> nodes1 = Fasta::readFastaFile("tests/aligned.fasta");
PhyloTree t;
t.setEvolutionModel(new Kimura(10.0));
t.buildRandomTree(nodes1);
double lh1 = t.logLikelihood();
ASSERT_LT(lh1, 0.0);
string prefixCoded = PhyloTreeNode::prefixRepresentation(t.getRoot());
vector<PhyloTreeNode*> nodes2 = Fasta::readFastaFile("tests/aligned.fasta");
PhyloTree t2 = PhyloTree::decodePrefixNotation(nodes2, prefixCoded, new Kimura(10.0));
double lh2 = t.logLikelihood();
ASSERT_DOUBLE_EQ(lh1, lh2);
}
TEST_F(PhyloTreeTest, RandomTree) {
vector<PhyloTreeNode*> leaves;
unsigned int n = 30;
for (unsigned int i = 0; i < n; i++) {
leaves.push_back(new PhyloTreeNode());
}
PhyloTree t;
t.buildRandomTree(leaves);
ASSERT_LT(log2(n), t.height()); // |tree| must be ≥ log₂(n)
ASSERT_GE(n+1, t.height()); // |tree| must be ≤ n+1
ASSERT_TRUE(t.getRoot()->isRoot()); // there should be a parentless root node
// all leaves should now have a parent
for (unsigned int i = 0; i < n; i++) {
ASSERT_TRUE(!leaves.at(i)->isRoot());
}
}
