File: glbalignle.cpp

package info (click to toggle)
muscle 1%3A3.8.1551-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, buster
  • size: 1,512 kB
  • sloc: cpp: 27,031; xml: 230; makefile: 38; sh: 10
file content (435 lines) | stat: -rw-r--r-- 10,474 bytes parent folder | download | duplicates (13)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
#include "muscle.h"
#include "profile.h"
#include "pwpath.h"

#define	OCC	1

struct DP_MEMORY
	{
	unsigned uLength;
	SCORE *GapOpenA;
	SCORE *GapOpenB;
	SCORE *GapCloseA;
	SCORE *GapCloseB;
	SCORE *MPrev;
	SCORE *MCurr;
	SCORE *MWork;
	SCORE *DPrev;
	SCORE *DCurr;
	SCORE *DWork;
	SCORE **ScoreMxB;
#if	OCC
	FCOUNT *OccA;
	FCOUNT *OccB;
#endif
	unsigned **SortOrderA;
	unsigned *uDeletePos;
	FCOUNT **FreqsA;
	int **TraceBack;
	};

static struct DP_MEMORY DPM;

static void AllocDPMem(unsigned uLengthA, unsigned uLengthB)
	{
// Max prefix length
	unsigned uLength = (uLengthA > uLengthB ? uLengthA : uLengthB) + 1;
	if (uLength < DPM.uLength)
		return;

// Add 256 to allow for future expansion and
// round up to next multiple of 32.
	uLength += 256;
	uLength += 32 - uLength%32;

	const unsigned uOldLength = DPM.uLength;
	if (uOldLength > 0)
		{
		for (unsigned i = 0; i < uOldLength; ++i)
			{
			delete[] DPM.TraceBack[i];
			delete[] DPM.FreqsA[i];
			delete[] DPM.SortOrderA[i];
			}
		for (unsigned n = 0; n < 20; ++n)
			delete[] DPM.ScoreMxB[n];

		delete[] DPM.MPrev;
		delete[] DPM.MCurr;
		delete[] DPM.MWork;
		delete[] DPM.DPrev;
		delete[] DPM.DCurr;
		delete[] DPM.DWork;
		delete[] DPM.uDeletePos;
		delete[] DPM.GapOpenA;
		delete[] DPM.GapOpenB;
		delete[] DPM.GapCloseA;
		delete[] DPM.GapCloseB;
		delete[] DPM.SortOrderA;
		delete[] DPM.FreqsA;
		delete[] DPM.ScoreMxB;
		delete[] DPM.TraceBack;
#if	OCC
		delete[] DPM.OccA;
		delete[] DPM.OccB;
#endif
		}

	DPM.uLength = uLength;

	DPM.GapOpenA = new SCORE[uLength];
	DPM.GapOpenB = new SCORE[uLength];
	DPM.GapCloseA = new SCORE[uLength];
	DPM.GapCloseB = new SCORE[uLength];
#if	OCC
	DPM.OccA = new FCOUNT[uLength];
	DPM.OccB = new FCOUNT[uLength];
#endif

	DPM.SortOrderA = new unsigned*[uLength];
	DPM.FreqsA = new FCOUNT*[uLength];
	DPM.ScoreMxB = new SCORE*[20];
	DPM.MPrev = new SCORE[uLength];
	DPM.MCurr = new SCORE[uLength];
	DPM.MWork = new SCORE[uLength];

	DPM.DPrev = new SCORE[uLength];
	DPM.DCurr = new SCORE[uLength];
	DPM.DWork = new SCORE[uLength];
	DPM.uDeletePos = new unsigned[uLength];

	DPM.TraceBack = new int*[uLength];

	for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
		DPM.ScoreMxB[uLetter] = new SCORE[uLength];

	for (unsigned i = 0; i < uLength; ++i)
		{
		DPM.SortOrderA[i] = new unsigned[20];
		DPM.FreqsA[i] = new FCOUNT[20];
		DPM.TraceBack[i] = new int[uLength];
		}
	}

SCORE GlobalAlignLE(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
	SetTermGaps(PA, uLengthA);
	SetTermGaps(PB, uLengthB);

	const unsigned uPrefixCountA = uLengthA + 1;
	const unsigned uPrefixCountB = uLengthB + 1;

	AllocDPMem(uLengthA, uLengthB);

	SCORE *GapOpenA = DPM.GapOpenA;
	SCORE *GapOpenB = DPM.GapOpenB;
	SCORE *GapCloseA = DPM.GapCloseA;
	SCORE *GapCloseB = DPM.GapCloseB;

	unsigned **SortOrderA = DPM.SortOrderA;
	FCOUNT **FreqsA = DPM.FreqsA;
	SCORE **ScoreMxB = DPM.ScoreMxB;
	SCORE *MPrev = DPM.MPrev;
	SCORE *MCurr = DPM.MCurr;
	SCORE *MWork = DPM.MWork;

	SCORE *DPrev = DPM.DPrev;
	SCORE *DCurr = DPM.DCurr;
	SCORE *DWork = DPM.DWork;

#if	OCC
	FCOUNT *OccA = DPM.OccA;
	FCOUNT *OccB = DPM.OccB;
#endif

	unsigned *uDeletePos = DPM.uDeletePos;

	int **TraceBack = DPM.TraceBack;

	for (unsigned i = 0; i < uLengthA; ++i)
		{
		GapOpenA[i] = PA[i].m_scoreGapOpen;
		GapCloseA[i] = PA[i].m_scoreGapClose;
#if	OCC
		OccA[i] = PA[i].m_fOcc;
#endif

		for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
			{
			SortOrderA[i][uLetter] = PA[i].m_uSortOrder[uLetter];
			FreqsA[i][uLetter] = PA[i].m_fcCounts[uLetter];
			}
		}

	for (unsigned j = 0; j < uLengthB; ++j)
		{
		GapOpenB[j] = PB[j].m_scoreGapOpen;
		GapCloseB[j] = PB[j].m_scoreGapClose;
#if	OCC
		OccB[j] = PB[j].m_fOcc;
#endif
		}

	for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
		{
		for (unsigned j = 0; j < uLengthB; ++j)
			ScoreMxB[uLetter][j] = PB[j].m_AAScores[uLetter];
		}

	for (unsigned i = 0; i < uPrefixCountA; ++i)
		memset(TraceBack[i], 0, uPrefixCountB*sizeof(int));

// Special case for i=0
	unsigned **ptrSortOrderA = SortOrderA;
	FCOUNT **ptrFreqsA = FreqsA;
	assert(ptrSortOrderA == &(SortOrderA[0]));
	assert(ptrFreqsA == &(FreqsA[0]));
	TraceBack[0][0] = 0;

	SCORE scoreSum = 0;
	unsigned *ptrSortOrderAi = SortOrderA[0];
	const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 20;
	FCOUNT *ptrFreqsAi = FreqsA[0];
	for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
		{
		const unsigned uLetter = *ptrSortOrderAi;
		const FCOUNT fcLetter = ptrFreqsAi[uLetter];
		if (0 == fcLetter)
			break;
		scoreSum += fcLetter*ScoreMxB[uLetter][0];
		}
	if (0 == scoreSum)
		MPrev[0] = -2.5;
	else
		{
#if	OCC
		MPrev[0] = (logf(scoreSum) - g_scoreCenter)*OccA[0]*OccB[0];
#else
		MPrev[0] = (logf(scoreSum) - g_scoreCenter);
#endif
		}

// D(0,0) is -infinity (requires I->D).
	DPrev[0] = MINUS_INFINITY;

	for (unsigned j = 1; j < uLengthB; ++j)
		{
	// Only way to get M(0, j) looks like this:
	//		A	----X
	//		B	XXXXX
	//			0   j
	// So gap-open at j=0, gap-close at j-1.
		SCORE scoreSum = 0;
		unsigned *ptrSortOrderAi = SortOrderA[0];
		const unsigned *ptrSortOrderAEnd = ptrSortOrderAi + 20;
		FCOUNT *ptrFreqsAi = FreqsA[0];
		for (; ptrSortOrderAi != ptrSortOrderAEnd; ++ptrSortOrderAi)
			{
			const unsigned uLetter = *ptrSortOrderAi;
			const FCOUNT fcLetter = ptrFreqsAi[uLetter];
			if (0 == fcLetter)
				break;
			scoreSum += fcLetter*ScoreMxB[uLetter][j];
			}
		if (0 == scoreSum)
			MPrev[j] = -2.5;
		else
			{
#if	OCC
			MPrev[j] = (logf(scoreSum) - g_scoreCenter)*OccA[0]*OccB[j] +
			  GapOpenB[0] + GapCloseB[j-1];
#else
			MPrev[j] = (logf(scoreSum) - g_scoreCenter) +
			  GapOpenB[0] + GapCloseB[j-1];
#endif
			}
		TraceBack[0][j] = -(int) j;

	// Assume no D->I transitions, then can't be a delete if only
	// one letter from A.
		DPrev[j] = MINUS_INFINITY;
		}

	SCORE IPrev_j_1;
	for (unsigned i = 1; i < uLengthA; ++i)
		{
		++ptrSortOrderA;
		++ptrFreqsA;
		assert(ptrSortOrderA == &(SortOrderA[i]));
		assert(ptrFreqsA == &(FreqsA[i]));

		SCORE *ptrMCurr_j = MCurr;
		memset(ptrMCurr_j, 0, uLengthB*sizeof(SCORE));
		const FCOUNT *FreqsAi = *ptrFreqsA;

		const unsigned *SortOrderAi = *ptrSortOrderA;
		const unsigned *ptrSortOrderAiEnd = SortOrderAi + 20;
		const SCORE *ptrMCurrMax = MCurr + uLengthB;
		for (const unsigned *ptrSortOrderAi = SortOrderAi;
		  ptrSortOrderAi != ptrSortOrderAiEnd;
		  ++ptrSortOrderAi)
			{
			const unsigned uLetter = *ptrSortOrderAi;
			SCORE *NSBR_Letter = ScoreMxB[uLetter];
			const FCOUNT fcLetter = FreqsAi[uLetter];
			if (0 == fcLetter)
				break;
			SCORE *ptrNSBR = NSBR_Letter;
			for (SCORE *ptrMCurr = MCurr; ptrMCurr != ptrMCurrMax; ++ptrMCurr)
				*ptrMCurr += fcLetter*(*ptrNSBR++);
			}

#if	OCC
		const FCOUNT OccAi = OccA[i];
#endif
		for (unsigned j = 0; j < uLengthB; ++j)
			{
			if (MCurr[j] == 0)
				MCurr[j] = -2.5;
			else
#if	OCC
				MCurr[j] = (logf(MCurr[j]) - g_scoreCenter)*OccAi*OccB[j];
#else
				MCurr[j] = (logf(MCurr[j]) - g_scoreCenter);
#endif
			}

		ptrMCurr_j = MCurr;
		unsigned *ptrDeletePos = uDeletePos;

	// Special case for j=0
	// Only way to get M(i, 0) looks like this:
	//			0   i
	//		A	XXXXX
	//		B	----X
	// So gap-open at i=0, gap-close at i-1.
		assert(ptrMCurr_j == &(MCurr[0]));
		*ptrMCurr_j += GapOpenA[0] + GapCloseA[i-1];

		++ptrMCurr_j;

		int *ptrTraceBack_ij = TraceBack[i];
		*ptrTraceBack_ij++ = (int) i;

		SCORE *ptrMPrev_j = MPrev;
		SCORE *ptrDPrev = DPrev;
		SCORE d = *ptrDPrev;
		SCORE DNew = *ptrMPrev_j + GapOpenA[i];
		if (DNew > d)
			{
			d = DNew;
			*ptrDeletePos = i;
			}

		SCORE *ptrDCurr = DCurr;

		assert(ptrDCurr == &(DCurr[0]));
		*ptrDCurr = d;

	// Can't have an insert if no letters from B
		IPrev_j_1 = MINUS_INFINITY;

		unsigned uInsertPos = 0;
		const SCORE scoreGapOpenAi = GapOpenA[i];
		const SCORE scoreGapCloseAi_1 = GapCloseA[i-1];

		for (unsigned j = 1; j < uLengthB; ++j)
			{
		// Here, MPrev_j is preserved from previous
		// iteration so with current i,j is M[i-1][j-1]
			SCORE MPrev_j = *ptrMPrev_j;
			SCORE INew = MPrev_j + GapOpenB[j];
			if (INew > IPrev_j_1)
				{
				IPrev_j_1 = INew;
				uInsertPos = j;
				}

			SCORE scoreMax = MPrev_j;

			assert(ptrDPrev == &(DPrev[j-1]));
			SCORE scoreD = *ptrDPrev++ + scoreGapCloseAi_1;
			if (scoreD > scoreMax)
				{
				scoreMax = scoreD;
				assert(ptrDeletePos == &(uDeletePos[j-1]));
				*ptrTraceBack_ij = (int) i - (int) *ptrDeletePos;
				assert(*ptrTraceBack_ij > 0);
				}
			++ptrDeletePos;

			SCORE scoreI = IPrev_j_1 + GapCloseB[j-1];
			if (scoreI > scoreMax)
				{
				scoreMax = scoreI;
				*ptrTraceBack_ij = (int) uInsertPos - (int) j;
				assert(*ptrTraceBack_ij < 0);
				}

			assert(ptrSortOrderA == &(SortOrderA[i]));
			assert(ptrFreqsA == &(FreqsA[i]));

			*ptrMCurr_j += scoreMax;
			assert(ptrMCurr_j == &(MCurr[j]));
			++ptrMCurr_j;

			MPrev_j = *(++ptrMPrev_j);
			assert(ptrDPrev == &(DPrev[j]));
			SCORE d = *ptrDPrev;
			SCORE DNew = MPrev_j + scoreGapOpenAi;
			if (DNew > d)
				{
				d = DNew;
				assert(ptrDeletePos == &uDeletePos[j]);
				*ptrDeletePos = i;
				}
			assert(ptrDCurr + 1 == &(DCurr[j]));
			*(++ptrDCurr) = d;

			++ptrTraceBack_ij;
			}

		Rotate(MPrev, MCurr, MWork);
		Rotate(DPrev, DCurr, DWork);
		}

// Special case for i=uLengthA
	SCORE IPrev = MINUS_INFINITY;

	unsigned uInsertPos;

	for (unsigned j = 1; j < uLengthB; ++j)
		{
		SCORE INew = MPrev[j-1] + GapOpenB[j];
		if (INew > IPrev)
			{
			uInsertPos = j;
			IPrev = INew;
			}
		}

// Special case for i=uLengthA, j=uLengthB
	SCORE scoreMax = MPrev[uLengthB-1];
	int iTraceBack = 0;

	SCORE scoreD = DPrev[uLengthB-1] + GapCloseA[uLengthA-1];
	if (scoreD > scoreMax)
		{
		scoreMax = scoreD;
		iTraceBack = (int) uLengthA - (int) uDeletePos[uLengthB-1];
		}

	SCORE scoreI = IPrev + GapCloseB[uLengthB-1];
	if (scoreI > scoreMax)
		{
		scoreMax = scoreI;
		iTraceBack = (int) uInsertPos - (int) uLengthB;
		}

	TraceBack[uLengthA][uLengthB] = iTraceBack;

	TraceBackToPath(TraceBack, uLengthA, uLengthB, Path);

	return scoreMax;
	}