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glbalignla.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: 10.2 KB

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1	#include "muscle.h"
2	#include "profile.h"
3	#include "pwpath.h"
4
5	#define OCC 1
6
7	struct DP_MEMORY
8	{
9	unsigned uLength;
10	SCORE *GapOpenA;
11	SCORE *GapOpenB;
12	SCORE *GapCloseA;
13	SCORE *GapCloseB;
14	SCORE *MPrev;
15	SCORE *MCurr;
16	SCORE *MWork;
17	SCORE *DPrev;
18	SCORE *DCurr;
19	SCORE *DWork;
20	SCORE **ScoreMxB;
21	#if OCC
22	FCOUNT *OccA;
23	FCOUNT *OccB;
24	#endif
25	unsigned **SortOrderA;
26	unsigned *uDeletePos;
27	FCOUNT **FreqsA;
28	int **TraceBack;
29	};
30
31	static struct DP_MEMORY DPM;
32
33	static void AllocDPMem(unsigned uLengthA, unsigned uLengthB)
34	{
35	// Max prefix length
36	unsigned uLength = (uLengthA > uLengthB ? uLengthA : uLengthB) + 1;
37	if (uLength < DPM.uLength)
38	return;
39
40	// Add 256 to allow for future expansion and
41	// round up to next multiple of 32.
42	uLength += 256;
43	uLength += 32 - uLength%32;
44
45	const unsigned uOldLength = DPM.uLength;
46	if (uOldLength > 0)
47	{
48	for (unsigned i = 0; i < uOldLength; ++i)
49	{
50	delete[] DPM.TraceBack[i];
51	delete[] DPM.FreqsA[i];
52	delete[] DPM.SortOrderA[i];
53	}
54	for (unsigned n = 0; n < 20; ++n)
55	delete[] DPM.ScoreMxB[n];
56
57	delete[] DPM.MPrev;
58	delete[] DPM.MCurr;
59	delete[] DPM.MWork;
60	delete[] DPM.DPrev;
61	delete[] DPM.DCurr;
62	delete[] DPM.DWork;
63	delete[] DPM.uDeletePos;
64	delete[] DPM.GapOpenA;
65	delete[] DPM.GapOpenB;
66	delete[] DPM.GapCloseA;
67	delete[] DPM.GapCloseB;
68	delete[] DPM.SortOrderA;
69	delete[] DPM.FreqsA;
70	delete[] DPM.ScoreMxB;
71	delete[] DPM.TraceBack;
72	#if OCC
73	delete[] DPM.OccA;
74	delete[] DPM.OccB;
75	#endif
76	}
77
78	DPM.uLength = uLength;
79
80	DPM.GapOpenA = new SCORE[uLength];
81	DPM.GapOpenB = new SCORE[uLength];
82	DPM.GapCloseA = new SCORE[uLength];
83	DPM.GapCloseB = new SCORE[uLength];
84	#if OCC
85	DPM.OccA = new FCOUNT[uLength];
86	DPM.OccB = new FCOUNT[uLength];
87	#endif
88
89	DPM.SortOrderA = new unsigned*[uLength];
90	DPM.FreqsA = new FCOUNT*[uLength];
91	DPM.ScoreMxB = new SCORE*[20];
92	DPM.MPrev = new SCORE[uLength];
93	DPM.MCurr = new SCORE[uLength];
94	DPM.MWork = new SCORE[uLength];
95
96	DPM.DPrev = new SCORE[uLength];
97	DPM.DCurr = new SCORE[uLength];
98	DPM.DWork = new SCORE[uLength];
99	DPM.uDeletePos = new unsigned[uLength];
100
101	DPM.TraceBack = new int*[uLength];
102
103	for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
104	DPM.ScoreMxB[uLetter] = new SCORE[uLength];
105
106	for (unsigned i = 0; i < uLength; ++i)
107	{
108	DPM.SortOrderA[i] = new unsigned[20];
109	DPM.FreqsA[i] = new FCOUNT[20];
110	DPM.TraceBack[i] = new int[uLength];
111	}
112	}
113
114	SCORE GlobalAlignLA(const ProfPos PA, unsigned uLengthA, const ProfPos PB,
115	unsigned uLengthB, PWPath &Path)
116	{
117	const unsigned uPrefixCountA = uLengthA + 1;
118	const unsigned uPrefixCountB = uLengthB + 1;
119
120	AllocDPMem(uLengthA, uLengthB);
121
122	SCORE *GapOpenA = DPM.GapOpenA;
123	SCORE *GapOpenB = DPM.GapOpenB;
124	SCORE *GapCloseA = DPM.GapCloseA;
125	SCORE *GapCloseB = DPM.GapCloseB;
126
127	unsigned **SortOrderA = DPM.SortOrderA;
128	FCOUNT **FreqsA = DPM.FreqsA;
129	SCORE **ScoreMxB = DPM.ScoreMxB;
130	SCORE *MPrev = DPM.MPrev;
131	SCORE *MCurr = DPM.MCurr;
132	SCORE *MWork = DPM.MWork;
133
134	SCORE *DPrev = DPM.DPrev;
135	SCORE *DCurr = DPM.DCurr;
136	SCORE *DWork = DPM.DWork;
137
138	#if OCC
139	FCOUNT *OccA = DPM.OccA;
140	FCOUNT *OccB = DPM.OccB;
141	#endif
142
143	unsigned *uDeletePos = DPM.uDeletePos;
144
145	int **TraceBack = DPM.TraceBack;
146
147	for (unsigned i = 0; i < uLengthA; ++i)
148	{
149	GapOpenA[i] = PA[i].m_scoreGapOpen;
150	GapCloseA[i] = PA[i].m_scoreGapClose;
151	#if OCC
152	OccA[i] = PA[i].m_fOcc;
153	#endif
154
155	for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
156	{
157	SortOrderA[i][uLetter] = PA[i].m_uSortOrder[uLetter];
158	FreqsA[i][uLetter] = PA[i].m_fcCounts[uLetter];
159	}
160	}
161
162	for (unsigned j = 0; j < uLengthB; ++j)
163	{
164	GapOpenB[j] = PB[j].m_scoreGapOpen;
165	GapCloseB[j] = PB[j].m_scoreGapClose;
166	#if OCC
167	OccB[j] = PB[j].m_fOcc;
168	#endif
169	}
170
171	for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
172	{
173	for (unsigned j = 0; j < uLengthB; ++j)
174	ScoreMxB[uLetter][j] = PB[j].m_AAScores[uLetter];
175	}
176
177	for (unsigned i = 0; i < uPrefixCountA; ++i)
178	memset(TraceBack[i], 0, uPrefixCountB*sizeof(int));
179
180	// Special case for i=0
181	unsigned **ptrSortOrderA = SortOrderA;
182	FCOUNT **ptrFreqsA = FreqsA;
183	assert(ptrSortOrderA == &(SortOrderA[0]));
184	assert(ptrFreqsA == &(FreqsA[0]));
185	TraceBack[0][0] = 0;
186
187	SCORE scoreSum = 0;
188	unsigned *ptrSortOrderAi = SortOrderA[0];
189	const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 20;
190	FCOUNT *ptrFreqsAi = FreqsA[0];
191	for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
192	{
193	const unsigned uLetter = *ptrSortOrderAi;
194	const FCOUNT fcLetter = ptrFreqsAi[uLetter];
195	if (0 == fcLetter)
196	break;
197	scoreSum += fcLetter*ScoreMxB[uLetter][0];
198	}
199	if (0 == scoreSum)
200	MPrev[0] = -2.5;
201	else
202	{
203	#if OCC
204	MPrev[0] = (logf(scoreSum) - g_scoreCenter)OccA[0]OccB[0];
205	#else
206	MPrev[0] = (logf(scoreSum) - g_scoreCenter);
207	#endif
208	}
209
210	// D(0,0) is -infinity (requires I->D).
211	DPrev[0] = MINUS_INFINITY;
212
213	for (unsigned j = 1; j < uLengthB; ++j)
214	{
215	// Only way to get M(0, j) looks like this:
216	// A ----X
217	// B XXXXX
218	// 0 j
219	// So gap-open at j=0, gap-close at j-1.
220	SCORE scoreSum = 0;
221	unsigned *ptrSortOrderAi = SortOrderA[0];
222	const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 20;
223	FCOUNT *ptrFreqsAi = FreqsA[0];
224	for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
225	{
226	const unsigned uLetter = *ptrSortOrderAi;
227	const FCOUNT fcLetter = ptrFreqsAi[uLetter];
228	if (0 == fcLetter)
229	break;
230	scoreSum += fcLetter*ScoreMxB[uLetter][j];
231	}
232	if (0 == scoreSum)
233	MPrev[j] = -2.5;
234	else
235	{
236	#if OCC
237	MPrev[j] = (logf(scoreSum) - g_scoreCenter)OccA[0]OccB[j] +
238	GapOpenB[0] + GapCloseB[j-1];
239	#else
240	MPrev[j] = (logf(scoreSum) - g_scoreCenter) +
241	GapOpenB[0] + GapCloseB[j-1];
242	#endif
243	}
244	TraceBack[0][j] = -(int) j;
245
246	// Assume no D->I transitions, then can't be a delete if only
247	// one letter from A.
248	DPrev[j] = MINUS_INFINITY;
249	}
250
251	SCORE IPrev_j_1;
252	for (unsigned i = 1; i < uLengthA; ++i)
253	{
254	++ptrSortOrderA;
255	++ptrFreqsA;
256	assert(ptrSortOrderA == &(SortOrderA[i]));
257	assert(ptrFreqsA == &(FreqsA[i]));
258
259	SCORE *ptrMCurr_j = MCurr;
260	memset(ptrMCurr_j, 0, uLengthB*sizeof(SCORE));
261	const FCOUNT FreqsAi = ptrFreqsA;
262
263	const unsigned SortOrderAi = ptrSortOrderA;
264	const unsigned *ptrSortOrderAiEnd = SortOrderAi + 20;
265	const SCORE *ptrMCurrMax = MCurr + uLengthB;
266	for (const unsigned *ptrSortOrderAi = SortOrderAi;
267	ptrSortOrderAi != ptrSortOrderAiEnd;
268	++ptrSortOrderAi)
269	{
270	const unsigned uLetter = *ptrSortOrderAi;
271	SCORE *NSBR_Letter = ScoreMxB[uLetter];
272	const FCOUNT fcLetter = FreqsAi[uLetter];
273	if (0 == fcLetter)
274	break;
275	SCORE *ptrNSBR = NSBR_Letter;
276	for (SCORE *ptrMCurr = MCurr; ptrMCurr != ptrMCurrMax; ++ptrMCurr)
277	ptrMCurr += fcLetter(*ptrNSBR++);
278	}
279
280	#if OCC
281	const FCOUNT OccAi = OccA[i];
282	#endif
283	for (unsigned j = 0; j < uLengthB; ++j)
284	{
285	if (MCurr[j] == 0)
286	MCurr[j] = -2.5;
287	else
288	#if OCC
289	MCurr[j] = (logf(MCurr[j]) - g_scoreCenter)OccAiOccB[j];
290	#else
291	MCurr[j] = (logf(MCurr[j]) - g_scoreCenter);
292	#endif
293	}
294
295	ptrMCurr_j = MCurr;
296	unsigned *ptrDeletePos = uDeletePos;
297
298	// Special case for j=0
299	// Only way to get M(i, 0) looks like this:
300	// 0 i
301	// A XXXXX
302	// B ----X
303	// So gap-open at i=0, gap-close at i-1.
304	assert(ptrMCurr_j == &(MCurr[0]));
305	*ptrMCurr_j += GapOpenA[0] + GapCloseA[i-1];
306
307	++ptrMCurr_j;
308
309	int *ptrTraceBack_ij = TraceBack[i];
310	*ptrTraceBack_ij++ = (int) i;
311
312	SCORE *ptrMPrev_j = MPrev;
313	SCORE *ptrDPrev = DPrev;
314	SCORE d = *ptrDPrev;
315	SCORE DNew = *ptrMPrev_j + GapOpenA[i];
316	if (DNew > d)
317	{
318	d = DNew;
319	*ptrDeletePos = i;
320	}
321
322	SCORE *ptrDCurr = DCurr;
323
324	assert(ptrDCurr == &(DCurr[0]));
325	*ptrDCurr = d;
326
327	// Can't have an insert if no letters from B
328	IPrev_j_1 = MINUS_INFINITY;
329
330	unsigned uInsertPos;
331	const SCORE scoreGapOpenAi = GapOpenA[i];
332	const SCORE scoreGapCloseAi_1 = GapCloseA[i-1];
333
334	for (unsigned j = 1; j < uLengthB; ++j)
335	{
336	// Here, MPrev_j is preserved from previous
337	// iteration so with current i,j is M[i-1][j-1]
338	SCORE MPrev_j = *ptrMPrev_j;
339	SCORE INew = MPrev_j + GapOpenB[j];
340	if (INew > IPrev_j_1)
341	{
342	IPrev_j_1 = INew;
343	uInsertPos = j;
344	}
345
346	SCORE scoreMax = MPrev_j;
347
348	assert(ptrDPrev == &(DPrev[j-1]));
349	SCORE scoreD = *ptrDPrev++ + scoreGapCloseAi_1;
350	if (scoreD > scoreMax)
351	{
352	scoreMax = scoreD;
353	assert(ptrDeletePos == &(uDeletePos[j-1]));
354	ptrTraceBack_ij = (int) i - (int) ptrDeletePos;
355	assert(*ptrTraceBack_ij > 0);
356	}
357	++ptrDeletePos;
358
359	SCORE scoreI = IPrev_j_1 + GapCloseB[j-1];
360	if (scoreI > scoreMax)
361	{
362	scoreMax = scoreI;
363	*ptrTraceBack_ij = (int) uInsertPos - (int) j;
364	assert(*ptrTraceBack_ij < 0);
365	}
366
367	assert(ptrSortOrderA == &(SortOrderA[i]));
368	assert(ptrFreqsA == &(FreqsA[i]));
369
370	*ptrMCurr_j += scoreMax;
371	assert(ptrMCurr_j == &(MCurr[j]));
372	++ptrMCurr_j;
373
374	MPrev_j = *(++ptrMPrev_j);
375	assert(ptrDPrev == &(DPrev[j]));
376	SCORE d = *ptrDPrev;
377	SCORE DNew = MPrev_j + scoreGapOpenAi;
378	if (DNew > d)
379	{
380	d = DNew;
381	assert(ptrDeletePos == &uDeletePos[j]);
382	*ptrDeletePos = i;
383	}
384	assert(ptrDCurr + 1 == &(DCurr[j]));
385	*(++ptrDCurr) = d;
386
387	++ptrTraceBack_ij;
388	}
389
390	Rotate(MPrev, MCurr, MWork);
391	Rotate(DPrev, DCurr, DWork);
392	}
393
394	// Special case for i=uLengthA
395	SCORE IPrev = MINUS_INFINITY;
396
397	unsigned uInsertPos;
398
399	for (unsigned j = 1; j < uLengthB; ++j)
400	{
401	SCORE INew = MPrev[j-1] + GapOpenB[j];
402	if (INew > IPrev)
403	{
404	uInsertPos = j;
405	IPrev = INew;
406	}
407	}
408
409	// Special case for i=uLengthA, j=uLengthB
410	SCORE scoreMax = MPrev[uLengthB-1];
411	int iTraceBack = 0;
412
413	SCORE scoreD = DPrev[uLengthB-1] + GapCloseA[uLengthA-1];
414	if (scoreD > scoreMax)
415	{
416	scoreMax = scoreD;
417	iTraceBack = (int) uLengthA - (int) uDeletePos[uLengthB-1];
418	}
419
420	SCORE scoreI = IPrev + GapCloseB[uLengthB-1];
421	if (scoreI > scoreMax)
422	{
423	scoreMax = scoreI;
424	iTraceBack = (int) uInsertPos - (int) uLengthB;
425	}
426
427	TraceBack[uLengthA][uLengthB] = iTraceBack;
428
429	TraceBackToPath(TraceBack, uLengthA, uLengthB, Path);
430
431	return scoreMax;
432	}

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source: branches/stable/GDE/MUSCLE/src/glbalignla.cpp

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