示例#1
0
// NeighborJoinD is the same as NeighborJoin but is destructive on the receiver.
//
// It saves a little memory if you have no further use for the distance matrix.
func (dm DistanceMatrix) NeighborJoinD() (u graph.LabeledUndirected, wt []float64) {
	td := make([]float64, len(dm))  // total-distance vector
	nx := make([]graph.NI, len(dm)) // node number corresponding to dist matrix index
	for i := range dm {
		nx[i] = graph.NI(i)
	}

	// closest clusters (min value in dm)
	// return smaller index (j) first
	closest := func() (jMin, iMin int) {
		min := math.Inf(1)
		iMin = -1
		jMin = -1
		for i := 1; i < len(dm); i++ {
			for j := 0; j < i; j++ {
				d := float64(len(dm)-2)*dm[i][j] - td[i] - td[j]
				if d < min {
					min = d
					iMin = i
					jMin = j
				}
			}
		}
		return
	}

	// wt is edge weight from parent (limb length)
	var tree graph.LabeledAdjacencyList
	var nj func(graph.NI)
	nj = func(m graph.NI) { // m is next internal node number
		if len(dm) == 2 {
			wt = make([]float64, 1, m-1)
			wt[0] = dm[0][1]
			tree = make(graph.LabeledAdjacencyList, m)
			n0 := nx[0]
			n1 := nx[1]
			tree[n0] = []graph.Half{{To: n1}}
			tree[n1] = []graph.Half{{To: n0}}
			return
		}
		// compute or recompute TotalDistance
		for k, dk := range dm {
			t := 0.
			for _, d := range dk {
				t += d
			}
			td[k] = t
		}
		d1, d2 := closest()
		Δ := (td[d2] - td[d1]) / float64(len(dm)-2)
		d21 := dm[d2][d1]
		ll2 := .5 * (d21 + Δ)
		ll1 := .5 * (d21 - Δ)
		n1 := nx[d1]
		n2 := nx[d2]

		di1 := dm[d1] // rows in distance matrix
		di2 := dm[d2]

		// replace d1 with mean distance
		for j, dij := range di1 {
			mn := .5 * (dij + di2[j] - d21)
			if j == d1 && mn != 0 {
				panic("uh uh, prolly skip this one...")
			}
			di1[j] = mn
			dm[j][d1] = mn
		}

		// d1 has been replaced, delete d2
		copy(dm[d2:], dm[d2+1:])
		dm = dm[:len(dm)-1]
		for i, di := range dm {
			copy(di[d2:], di[d2+1:])
			dm[i] = di[:len(di)-1]
		}
		nx[d1] = m
		copy(nx[d2:], nx[d2+1:])
		nx = nx[:len(dm)]

		// recurse
		nj(m + 1)

		// join limbs to tree
		wx1 := graph.LI(len(wt))
		wx2 := wx1 + 1
		wt = append(wt, ll1, ll2)
		tree[m] = append(tree[m],
			graph.Half{n1, wx1},
			graph.Half{n2, wx2})
		tree[n1] = append(tree[n1], graph.Half{m, wx1})
		tree[n2] = append(tree[n2], graph.Half{m, wx2})
		return
	}
	nj(graph.NI(len(dm)))
	return graph.LabeledUndirected{tree}, wt
}
示例#2
0
// AdditiveTree constructs an unrooted tree from an additive distance matrix.
//
// DistanceMatrix d must be additive.  Use provably additive matrices or
// use DistanceMatrix.Additive() to verify the additive property.
//
// Result is an unrooted tree, not necessarily binary, as an undirected graph.
// The first len(d) nodes are the leaves represented by the distance matrix.
// Internal nodes follow.
//
// Time complexity is O(n^2) in the number of leaves.
func (d DistanceMatrix) AdditiveTree() (u graph.LabeledUndirected, edgeWts []float64) {
	// interpretation of the presented recursive algorithm.  ideas of
	// things to try:  1: construct result as a parent list rather than
	// a child tree.  2: drop the recursion.  3. make tree always binary.
	t := make(graph.LabeledAdjacencyList, len(d), len(d)+len(d)-2)
	var ap func(int)
	ap = func(n int) {
		if n == 1 {
			edgeWts = []float64{d[0][1]}
			t[0] = []graph.Half{{1, 0}}
			t[1] = []graph.Half{{0, 0}}
			return
		}
		nLen, i, k := d.limbWeightSubMatrix(n)
		x := d[i][n] - nLen
		ap(n - 1)
		// f() finds and returns connection node v.
		// method: df search to find i from k, find connection point on the
		// way out.
		// create connection node v if needed, return v if found, -1 if not.
		var vis graph.Bits
		var f func(n graph.NI) graph.NI
		f = func(n graph.NI) graph.NI {
			if int(n) == i {
				return n
			}
			vis.SetBit(n, 1)
			for tx, to := range t[n] {
				if vis.Bit(to.To) == 1 {
					continue
				}
				p := f(to.To)
				switch {
				case p < 0: // not found yet
					continue
				case x == 0: // p is connection node
					return p
				case x < edgeWts[to.Label]: // new node at dist x from to.To
					// plan is to recycle the existing half edges between
					// n and to.To to go to new node v.  The edge(n, v)
					// gets to keep the recycled edge label with weight
					// reduced by x.  The edge(to.To, v) gets a new edge label
					// with weight x.

					v := graph.NI(len(t))  // new node
					t[n][tx].To = v        // redirect half
					edgeWts[to.Label] -= x // reduce wt

					y := graph.LI(len(edgeWts)) // new label for edge(to.To, v)
					edgeWts = append(edgeWts, x)
					// now find reciprocal half from to.To back to n
					for fx, from := range t[to.To] {
						if from.To == n { // here it is
							// recycle it to go to v now.
							t[to.To][fx] = graph.Half{v, y}
							break
						}
					}
					t = append(t, []graph.Half{{n, to.Label}, {to.To, y}})
					x = 0
					return v
				default: // continue back out
					x -= edgeWts[to.Label]
					return n
				}
			}
			return -1
		}
		vis.Clear()
		v := f(graph.NI(k))
		y := graph.LI(len(edgeWts))
		edgeWts = append(edgeWts, nLen)
		t[n] = []graph.Half{{v, y}}
		t[v] = append(t[v], graph.Half{graph.NI(n), y})
	}
	ap(len(d) - 1)
	return graph.LabeledUndirected{t}, edgeWts
}