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phy3.cpp

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Last change on this file was 10390, checked in by aboeckma, 11 years ago
added muscle sourcles amd makefile
File size: 13.4 KB

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1	#include "muscle.h"
2	#include "tree.h"
3	#include "edgelist.h"
4
5	#define TRACE 0
6
7	struct EdgeInfo
8	{
9	EdgeInfo()
10	{
11	m_bSet = false;
12	}
13	// Is data in this structure valid (i.e, has been set)?
14	bool m_bSet;
15
16	// Node at start of this edge
17	unsigned m_uNode1;
18
19	// Node at end of this edge
20	unsigned m_uNode2;
21
22	// Maximum distance from Node2 to a leaf
23	double m_dMaxDistToLeaf;
24
25	// Sum of distances from Node2 to all leaves under Node2
26	double m_dTotalDistToLeaves;
27
28	// Next node on path from Node2 to most distant leaf
29	unsigned m_uMaxStep;
30
31	// Most distant leaf from Node2 (used for debugging only)
32	unsigned m_uMostDistantLeaf;
33
34	// Number of leaves under Node2
35	unsigned m_uLeafCount;
36	};
37
38	static void RootByMidLongestSpan(const Tree &tree, EdgeInfo **EIs,
39	unsigned ptruNode1, unsigned ptruNode2,
40	double ptrdLength1, double ptrdLength2);
41	static void RootByMinAvgLeafDist(const Tree &tree, EdgeInfo **EIs,
42	unsigned ptruNode1, unsigned ptruNode2,
43	double ptrdLength1, double ptrdLength2);
44
45	static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
46	{
47	Log("Node1 Node2 MaxDist TotDist MostDist LeafCount Step\n");
48	Log("----- ----- ------- ------- -------- --------- ----\n");
49	// 12345 12345 1234567 1234567 12345678 123456789
50
51	for (unsigned uNode = 0; uNode < uNodeCount; ++uNode)
52	for (unsigned uNeighbor = 0; uNeighbor < 3; ++uNeighbor)
53	{
54	const EdgeInfo &EI = EIs[uNode][uNeighbor];
55	if (!EI.m_bSet)
56	continue;
57	Log("%5u %5u %7.3g %7.3g %8u %9u",
58	EI.m_uNode1,
59	EI.m_uNode2,
60	EI.m_dMaxDistToLeaf,
61	EI.m_dTotalDistToLeaves,
62	EI.m_uMostDistantLeaf,
63	EI.m_uLeafCount);
64	if (NULL_NEIGHBOR != EI.m_uMaxStep)
65	Log(" %4u", EI.m_uMaxStep);
66	Log("\n");
67	}
68	}
69
70	static void CalcInfo(const Tree &tree, unsigned uNode1, unsigned uNode2, EdgeInfo **EIs)
71	{
72	const unsigned uNeighborIndex = tree.GetNeighborSubscript(uNode1, uNode2);
73	EdgeInfo &EI = EIs[uNode1][uNeighborIndex];
74	EI.m_uNode1 = uNode1;
75	EI.m_uNode2 = uNode2;
76
77	if (tree.IsLeaf(uNode2))
78	{
79	EI.m_dMaxDistToLeaf = 0;
80	EI.m_dTotalDistToLeaves = 0;
81	EI.m_uMaxStep = NULL_NEIGHBOR;
82	EI.m_uMostDistantLeaf = uNode2;
83	EI.m_uLeafCount = 1;
84	EI.m_bSet = true;
85	return;
86	}
87
88	double dMaxDistToLeaf = -1e29;
89	double dTotalDistToLeaves = 0.0;
90	unsigned uLeafCount = 0;
91	unsigned uMostDistantLeaf = NULL_NEIGHBOR;
92	unsigned uMaxStep = NULL_NEIGHBOR;
93
94	const unsigned uNeighborCount = tree.GetNeighborCount(uNode2);
95	for (unsigned uSub = 0; uSub < uNeighborCount; ++uSub)
96	{
97	const unsigned uNode3 = tree.GetNeighbor(uNode2, uSub);
98	if (uNode3 == uNode1)
99	continue;
100	const EdgeInfo &EINext = EIs[uNode2][uSub];
101	if (!EINext.m_bSet)
102	Quit("CalcInfo: internal error, dist %u->%u not known",
103	uNode2, uNode3);
104
105
106	uLeafCount += EINext.m_uLeafCount;
107
108	const double dEdgeLength = tree.GetEdgeLength(uNode2, uNode3);
109	const double dTotalDist = EINext.m_dTotalDistToLeaves +
110	EINext.m_uLeafCount*dEdgeLength;
111	dTotalDistToLeaves += dTotalDist;
112
113	const double dDist = EINext.m_dMaxDistToLeaf + dEdgeLength;
114	if (dDist > dMaxDistToLeaf)
115	{
116	dMaxDistToLeaf = dDist;
117	uMostDistantLeaf = EINext.m_uMostDistantLeaf;
118	uMaxStep = uNode3;
119	}
120	}
121	if (NULL_NEIGHBOR == uMaxStep \|\| NULL_NEIGHBOR == uMostDistantLeaf \|\|
122	0 == uLeafCount)
123	Quit("CalcInfo: internal error 2");
124
125	const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
126	EI.m_dMaxDistToLeaf = dMaxDistToLeaf;
127	EI.m_dTotalDistToLeaves = dTotalDistToLeaves;
128	EI.m_uMaxStep = uMaxStep;
129	EI.m_uMostDistantLeaf = uMostDistantLeaf;
130	EI.m_uLeafCount = uLeafCount;
131	EI.m_bSet = true;
132	}
133
134	static bool Known(const Tree &tree, EdgeInfo **EIs, unsigned uNodeFrom,
135	unsigned uNodeTo)
136	{
137	const unsigned uSub = tree.GetNeighborSubscript(uNodeFrom, uNodeTo);
138	return EIs[uNodeFrom][uSub].m_bSet;
139	}
140
141	static bool AllKnownOut(const Tree &tree, EdgeInfo **EIs, unsigned uNodeFrom,
142	unsigned uNodeTo)
143	{
144	const unsigned uNeighborCount = tree.GetNeighborCount(uNodeTo);
145	for (unsigned uSub = 0; uSub < uNeighborCount; ++uSub)
146	{
147	unsigned uNeighborIndex = tree.GetNeighbor(uNodeTo, uSub);
148	if (uNeighborIndex == uNodeFrom)
149	continue;
150	if (!EIs[uNodeTo][uSub].m_bSet)
151	return false;
152	}
153	return true;
154	}
155
156	void FindRoot(const Tree &tree, unsigned ptruNode1, unsigned ptruNode2,
157	double ptrdLength1, double ptrdLength2,
158	ROOT RootMethod)
159	{
160	#if TRACE
161	tree.LogMe();
162	#endif
163	if (tree.IsRooted())
164	Quit("FindRoot: tree already rooted");
165
166	const unsigned uNodeCount = tree.GetNodeCount();
167	const unsigned uLeafCount = tree.GetLeafCount();
168
169	if (uNodeCount < 2)
170	Quit("Root: don't support trees with < 2 edges");
171
172	EdgeInfo *EIs = new EdgeInfo [uNodeCount];
173	for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
174	EIs[uNodeIndex] = new EdgeInfo[3];
175
176	EdgeList Edges;
177	for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
178	if (tree.IsLeaf(uNodeIndex))
179	{
180	unsigned uParent = tree.GetNeighbor1(uNodeIndex);
181	Edges.Add(uParent, uNodeIndex);
182	}
183
184	#if TRACE
185	Log("Edges: ");
186	Edges.LogMe();
187	#endif
188
189	// Main loop: iterate until all distances known
190	double dAllMaxDist = -1e20;
191	unsigned uMaxFrom = NULL_NEIGHBOR;
192	unsigned uMaxTo = NULL_NEIGHBOR;
193	for (;;)
194	{
195	EdgeList NextEdges;
196
197	#if TRACE
198	Log("\nTop of main loop\n");
199	Log("Edges: ");
200	Edges.LogMe();
201	Log("MDs:\n");
202	ListEIs(EIs, uNodeCount);
203	#endif
204
205	// For all edges
206	const unsigned uEdgeCount = Edges.GetCount();
207	if (0 == uEdgeCount)
208	break;
209	for (unsigned n = 0; n < uEdgeCount; ++n)
210	{
211	unsigned uNodeFrom;
212	unsigned uNodeTo;
213	Edges.GetEdge(n, &uNodeFrom, &uNodeTo);
214
215	CalcInfo(tree, uNodeFrom, uNodeTo, EIs);
216	#if TRACE
217	Log("Edge %u -> %u\n", uNodeFrom, uNodeTo);
218	#endif
219	const unsigned uNeighborCount = tree.GetNeighborCount(uNodeFrom);
220	for (unsigned i = 0; i < uNeighborCount; ++i)
221	{
222	const unsigned uNeighborIndex = tree.GetNeighbor(uNodeFrom, i);
223	if (!Known(tree, EIs, uNeighborIndex, uNodeFrom) &&
224	AllKnownOut(tree, EIs, uNeighborIndex, uNodeFrom))
225	NextEdges.Add(uNeighborIndex, uNodeFrom);
226	}
227	}
228	Edges.Copy(NextEdges);
229	}
230
231	#if TRACE
232	ListEIs(EIs, uNodeCount);
233	#endif
234
235	switch (RootMethod)
236	{
237	case ROOT_MidLongestSpan:
238	RootByMidLongestSpan(tree, EIs, ptruNode1, ptruNode2,
239	ptrdLength1, ptrdLength2);
240	break;
241
242	case ROOT_MinAvgLeafDist:
243	RootByMinAvgLeafDist(tree, EIs, ptruNode1, ptruNode2,
244	ptrdLength1, ptrdLength2);
245	break;
246
247	default:
248	Quit("Invalid RootMethod=%d", RootMethod);
249	}
250
251	for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
252	delete[] EIs[uNodeIndex];
253	delete[] EIs;
254	}
255
256	static void RootByMidLongestSpan(const Tree &tree, EdgeInfo **EIs,
257	unsigned ptruNode1, unsigned ptruNode2,
258	double ptrdLength1, double ptrdLength2)
259	{
260	const unsigned uNodeCount = tree.GetNodeCount();
261
262	unsigned uLeaf1 = NULL_NEIGHBOR;
263	unsigned uMostDistantLeaf = NULL_NEIGHBOR;
264	double dMaxDist = -VERY_LARGE_DOUBLE;
265	for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
266	{
267	if (!tree.IsLeaf(uNodeIndex))
268	continue;
269
270	const unsigned uNode2 = tree.GetNeighbor1(uNodeIndex);
271	if (NULL_NEIGHBOR == uNode2)
272	Quit("RootByMidLongestSpan: internal error 0");
273	const double dEdgeLength = tree.GetEdgeLength(uNodeIndex, uNode2);
274	const EdgeInfo &EI = EIs[uNodeIndex][0];
275	if (!EI.m_bSet)
276	Quit("RootByMidLongestSpan: internal error 1");
277	if (EI.m_uNode1 != uNodeIndex \|\| EI.m_uNode2 != uNode2)
278	Quit("RootByMidLongestSpan: internal error 2");
279	const double dSpanLength = dEdgeLength + EI.m_dMaxDistToLeaf;
280	if (dSpanLength > dMaxDist)
281	{
282	dMaxDist = dSpanLength;
283	uLeaf1 = uNodeIndex;
284	uMostDistantLeaf = EI.m_uMostDistantLeaf;
285	}
286	}
287
288	if (NULL_NEIGHBOR == uLeaf1)
289	Quit("RootByMidLongestSpan: internal error 3");
290
291	const double dTreeHeight = dMaxDist/2.0;
292	unsigned uNode1 = uLeaf1;
293	unsigned uNode2 = tree.GetNeighbor1(uLeaf1);
294	double dAccumSpanLength = 0;
295
296	#if TRACE
297	Log("RootByMidLongestSpan: span=%u", uLeaf1);
298	#endif
299
300	for (;;)
301	{
302	const double dEdgeLength = tree.GetEdgeLength(uNode1, uNode2);
303	#if TRACE
304	Log("->%u(%g;%g)", uNode2, dEdgeLength, dAccumSpanLength);
305	#endif
306	if (dAccumSpanLength + dEdgeLength >= dTreeHeight)
307	{
308	*ptruNode1 = uNode1;
309	*ptruNode2 = uNode2;
310	*ptrdLength1 = dTreeHeight - dAccumSpanLength;
311	ptrdLength2 = dEdgeLength - ptrdLength1;
312	#if TRACE
313	{
314	const EdgeInfo &EI = EIs[uLeaf1][0];
315	Log("...\n");
316	Log("Midpoint: Leaf1=%u Leaf2=%u Node1=%u Node2=%u Length1=%g Length2=%g\n",
317	uLeaf1, EI.m_uMostDistantLeaf, ptruNode1, ptruNode2, ptrdLength1, ptrdLength2);
318	}
319	#endif
320	return;
321	}
322
323	if (tree.IsLeaf(uNode2))
324	Quit("RootByMidLongestSpan: internal error 4");
325
326	dAccumSpanLength += dEdgeLength;
327	const unsigned uSub = tree.GetNeighborSubscript(uNode1, uNode2);
328	const EdgeInfo &EI = EIs[uNode1][uSub];
329	if (!EI.m_bSet)
330	Quit("RootByMidLongestSpan: internal error 5");
331
332	uNode1 = uNode2;
333	uNode2 = EI.m_uMaxStep;
334	}
335	}
336
337	/***
338	Root by balancing average distance to leaves.
339	The root is a point p such that the average
340	distance to leaves to the left of p is the
341	same as the to the right.
342
343	This is the method used by CLUSTALW, which
344	was originally used in PROFILEWEIGHT:
345
346	Thompson et al. (1994) CABIOS (10) 1, 19-29.
347	***/
348
349	static void RootByMinAvgLeafDist(const Tree &tree, EdgeInfo **EIs,
350	unsigned ptruNode1, unsigned ptruNode2,
351	double ptrdLength1, double ptrdLength2)
352	{
353	const unsigned uNodeCount = tree.GetNodeCount();
354	const unsigned uLeafCount = tree.GetLeafCount();
355	unsigned uNode1 = NULL_NEIGHBOR;
356	unsigned uNode2 = NULL_NEIGHBOR;
357	double dMinHeight = VERY_LARGE_DOUBLE;
358	double dBestLength1 = VERY_LARGE_DOUBLE;
359	double dBestLength2 = VERY_LARGE_DOUBLE;
360
361	for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
362	{
363	const unsigned uNeighborCount = tree.GetNeighborCount(uNodeIndex);
364	for (unsigned uSub = 0; uSub < uNeighborCount; ++uSub)
365	{
366	const unsigned uNeighborIndex = tree.GetNeighbor(uNodeIndex, uSub);
367
368	// Avoid visiting same edge a second time in reversed order.
369	if (uNeighborIndex < uNodeIndex)
370	continue;
371
372	const unsigned uSubRev = tree.GetNeighborSubscript(uNeighborIndex, uNodeIndex);
373	if (NULL_NEIGHBOR == uSubRev)
374	Quit("RootByMinAvgLeafDist, internal error 1");
375
376	// Get info for edges Node1->Node2 and Node2->Node1 (reversed)
377	const EdgeInfo &EI = EIs[uNodeIndex][uSub];
378	const EdgeInfo &EIRev = EIs[uNeighborIndex][uSubRev];
379
380	if (EI.m_uNode1 != uNodeIndex \|\| EI.m_uNode2 != uNeighborIndex \|\|
381	EIRev.m_uNode1 != uNeighborIndex \|\| EIRev.m_uNode2 != uNodeIndex)
382	Quit("RootByMinAvgLeafDist, internal error 2");
383	if (!EI.m_bSet)
384	Quit("RootByMinAvgLeafDist, internal error 3");
385	if (uLeafCount != EI.m_uLeafCount + EIRev.m_uLeafCount)
386	Quit("RootByMinAvgLeafDist, internal error 4");
387
388	const double dEdgeLength = tree.GetEdgeLength(uNodeIndex, uNeighborIndex);
389	if (dEdgeLength != tree.GetEdgeLength(uNeighborIndex, uNodeIndex))
390	Quit("RootByMinAvgLeafDist, internal error 5");
391
392	// Consider point p on edge 12 in tree (1=Node, 2=Neighbor).
393	//
394	// ----- ----
395	// \| \|
396	// 1----p--2
397	// \| \|
398	// ----- ----
399	//
400	// Define:
401	// ADLp = average distance to leaves to left of point p.
402	// ADRp = average distance to leaves to right of point p.
403	// L = edge length = distance 12
404	// x = distance 1p
405	// So distance p2 = L - x.
406	// Average distance from p to leaves on left of p is:
407	// ADLp = ADL1 + x
408	// Average distance from p to leaves on right of p is:
409	// ADRp = ADR2 + (L - x)
410	// To be a root, we require these two distances to be equal,
411	// ADLp = ADRp
412	// ADL1 + x = ADR2 + (L - x)
413	// Solving for x,
414	// x = (ADR2 - ADL1 + L)/2
415	// If 0 <= x <= L, we can place the root on edge 12.
416
417	const double ADL1 = EI.m_dTotalDistToLeaves / EI.m_uLeafCount;
418	const double ADR2 = EIRev.m_dTotalDistToLeaves / EIRev.m_uLeafCount;
419
420	const double x = (ADR2 - ADL1 + dEdgeLength)/2.0;
421	if (x >= 0 && x <= dEdgeLength)
422	{
423	const double dLength1 = x;
424	const double dLength2 = dEdgeLength - x;
425	const double dHeight1 = EI.m_dMaxDistToLeaf + dLength1;
426	const double dHeight2 = EIRev.m_dMaxDistToLeaf + dLength2;
427	const double dHeight = dHeight1 >= dHeight2 ? dHeight1 : dHeight2;
428	#if TRACE
429	Log("Candidate root Node1=%u Node2=%u Height=%g\n",
430	uNodeIndex, uNeighborIndex, dHeight);
431	#endif
432	if (dHeight < dMinHeight)
433	{
434	uNode1 = uNodeIndex;
435	uNode2 = uNeighborIndex;
436	dBestLength1 = dLength1;
437	dBestLength2 = dLength2;
438	dMinHeight = dHeight;
439	}
440	}
441	}
442	}
443
444	if (NULL_NEIGHBOR == uNode1 \|\| NULL_NEIGHBOR == uNode2)
445	Quit("RootByMinAvgLeafDist, internal error 6");
446
447	#if TRACE
448	Log("Best root Node1=%u Node2=%u Length1=%g Length2=%g Height=%g\n",
449	uNode1, uNode2, dBestLength1, dBestLength2, dMinHeight);
450	#endif
451
452	*ptruNode1 = uNode1;
453	*ptruNode2 = uNode2;
454	*ptrdLength1 = dBestLength1;
455	*ptrdLength2 = dBestLength2;
456	}
457
458	void FixRoot(Tree &tree, ROOT Method)
459	{
460	if (!tree.IsRooted())
461	Quit("FixRoot: expecting rooted tree");
462
463	// Pseudo-root: keep root assigned by clustering
464	if (ROOT_Pseudo == Method)
465	return;
466
467	tree.UnrootByDeletingRoot();
468	tree.RootUnrootedTree(Method);
469	}

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source: trunk/GDE/MUSCLE/src/phy3.cpp

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