func rankMatrix(
domains *inDomains,
matrix *intern.Table,
query intern.Atom,
) []intern.Atom {
r := &rankedAtoms{
atoms: make([]intern.Atom, len(domains.atoms)),
dists: make([]float64, len(domains.atoms)),
}
for i, query2 := range domains.atoms {
r.atoms[i] = query2
r.dists[i] = matrix.Get(query, query2)
}
sort.Sort(r)
return r.atoms
}
func tpsAndTns(
domains *inDomains,
boa *intern.Table,
query intern.Atom,
threshold float64,
) (tps []bool, tns []bool) {
tps = make([]bool, domains.in.Len())
tns = make([]bool, domains.in.Len())
for _, query2 := range domains.atoms {
if boa.Get(query, query2) <= threshold {
tps[query2] = true
} else {
tns[query2] = true
}
}
return
}
func treeClusters(
threshold float64,
dists *intern.Table,
tree *newick.Tree,
) clusters {
if len(tree.Children) == 0 {
if len(tree.Label) > 0 {
return clusters{[]string{tree.Label}}
}
return nil
}
// Compare all pairs in this tree. If all are within the threshold given,
// then add this subtree as a cluster and move on. Otherwise, dig deeper.
within := forNode(tree, func(node1 *newick.Tree) bool {
if len(node1.Label) == 0 {
return true
}
a1 := dists.Atom(node1.Label)
return forNode(tree, func(node2 *newick.Tree) bool {
if len(node2.Label) == 0 {
return true
}
return dists.Get(a1, dists.Atom(node2.Label)) <= threshold
})
})
if within {
cluster := make([]string, 0, 10)
forNode(tree, func(node *newick.Tree) bool {
if len(node.Label) == 0 {
return true
}
cluster = append(cluster, node.Label)
return true
})
return clusters{cluster}
}
clusters := make(clusters, 0, len(tree.Children))
for i := range tree.Children {
clusters = append(
clusters, treeClusters(threshold, dists, &tree.Children[i])...)
}
return clusters
}
func dist(matrix *intern.Table, d1, d2 string) float64 {
return matrix.Get(matrix.Atom(d1), matrix.Atom(d2))
}