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nwsmall.cpp

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Last change on this file was 10390, checked in by aboeckma, 12 years ago
added muscle sourcles amd makefile
File size: 15.8 KB

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1	#include "muscle.h"
2	#include <math.h>
3	#include "pwpath.h"
4	#include "profile.h"
5	#include <stdio.h>
6
7	// NW small memory
8
9	#define TRACE 0
10
11	#if TRACE
12	extern bool g_bKeepSimpleDP;
13	extern SCORE *g_DPM;
14	extern SCORE *g_DPD;
15	extern SCORE *g_DPI;
16	extern char *g_TBM;
17	extern char *g_TBD;
18	extern char *g_TBI;
19	#endif
20
21	#if TRACE
22	#define ALLOC_TRACE() \
23	const SCORE UNINIT = MINUS_INFINITY; \
24	const size_t LM = uPrefixCountA*uPrefixCountB; \
25	\
26	SCORE *DPM_ = new SCORE[LM]; \
27	SCORE *DPD_ = new SCORE[LM]; \
28	SCORE *DPI_ = new SCORE[LM]; \
29	\
30	char *TBM_ = new char[LM]; \
31	char *TBD_ = new char[LM]; \
32	char *TBI_ = new char[LM]; \
33	\
34	memset(TBM_, '?', LM); \
35	memset(TBD_, '?', LM); \
36	memset(TBI_, '?', LM); \
37	\
38	for (unsigned i = 0; i <= uLengthA; ++i) \
39	for (unsigned j = 0; j <= uLengthB; ++j) \
40	{ \
41	DPM(i, j) = UNINIT; \
42	DPD(i, j) = UNINIT; \
43	DPI(i, j) = UNINIT; \
44	}
45	#else
46	#define ALLOC_TRACE()
47	#endif
48
49	#if TRACE
50	#define SetDPM(i, j, x) DPM(i, j) = x
51	#define SetDPD(i, j, x) DPD(i, j) = x
52	#define SetDPI(i, j, x) DPI(i, j) = x
53	#define SetTBM(i, j, x) TBM(i, j) = x
54	#define SetTBD(i, j, x) TBD(i, j) = x
55	#define SetTBI(i, j, x) TBI(i, j) = x
56	#else
57	#define SetDPM(i, j, x) /* empty */
58	#define SetDPD(i, j, x) /* empty */
59	#define SetDPI(i, j, x) /* empty */
60	#define SetTBM(i, j, x) /* empty */
61	#define SetTBD(i, j, x) /* empty */
62	#define SetTBI(i, j, x) /* empty */
63	#endif
64
65	#define RECURSE_D(i, j) \
66	{ \
67	SCORE DD = DRow[j] + e; \
68	SCORE MD = MPrev[j] + PA[i-1].m_scoreGapOpen;\
69	if (DD > MD) \
70	{ \
71	DRow[j] = DD; \
72	SetTBD(i, j, 'D'); \
73	} \
74	else \
75	{ \
76	DRow[j] = MD; \
77	/* SetBitTBD(TB, i, j, 'M'); */ \
78	TBRow[j] &= ~BIT_xD; \
79	TBRow[j] \|= BIT_MD; \
80	SetTBD(i, j, 'M'); \
81	} \
82	SetDPD(i, j, DRow[j]); \
83	}
84
85	#define RECURSE_D_ATerm(j) RECURSE_D(uLengthA, j)
86	#define RECURSE_D_BTerm(j) RECURSE_D(i, uLengthB)
87
88	#define RECURSE_I(i, j) \
89	{ \
90	Iij += e; \
91	SCORE MI = MCurr[j-1] + PB[j-1].m_scoreGapOpen;\
92	if (MI >= Iij) \
93	{ \
94	Iij = MI; \
95	/* SetBitTBI(TB, i, j, 'M'); */ \
96	TBRow[j] &= ~BIT_xI; \
97	TBRow[j] \|= BIT_MI; \
98	SetTBI(i, j, 'M'); \
99	} \
100	else \
101	SetTBI(i, j, 'I'); \
102	SetDPI(i, j, Iij); \
103	}
104
105	#define RECURSE_I_ATerm(j) RECURSE_I(uLengthA, j)
106	#define RECURSE_I_BTerm(j) RECURSE_I(i, uLengthB)
107
108	#define RECURSE_M(i, j) \
109	{ \
110	SCORE DM = DRow[j] + PA[i-1].m_scoreGapClose; \
111	SCORE IM = Iij + PB[j-1].m_scoreGapClose; \
112	SCORE MM = MCurr[j]; \
113	TB[i+1][j+1] &= ~BIT_xM; \
114	if (MM >= DM && MM >= IM) \
115	{ \
116	MNext[j+1] += MM; \
117	SetDPM(i+1, j+1, MNext[j+1]); \
118	SetTBM(i+1, j+1, 'M'); \
119	/* SetBitTBM(TB, i+1, j+1, 'M'); */ \
120	TB[i+1][j+1] \|= BIT_MM; \
121	} \
122	else if (DM >= MM && DM >= IM) \
123	{ \
124	MNext[j+1] += DM; \
125	SetDPM(i+1, j+1, MNext[j+1]); \
126	SetTBM(i+1, j+1, 'D'); \
127	/* SetBitTBM(TB, i+1, j+1, 'D'); */ \
128	TB[i+1][j+1] \|= BIT_DM; \
129	} \
130	else \
131	{ \
132	assert(IM >= MM && IM >= DM); \
133	MNext[j+1] += IM; \
134	SetDPM(i+1, j+1, MNext[j+1]); \
135	SetTBM(i+1, j+1, 'I'); \
136	/* SetBitTBM(TB, i+1, j+1, 'I'); */ \
137	TB[i+1][j+1] \|= BIT_IM; \
138	} \
139	}
140
141	#if TRACE
142	static bool LocalEq(BASETYPE b1, BASETYPE b2)
143	{
144	if (b1 < -100000 && b2 < -100000)
145	return true;
146	double diff = fabs(b1 - b2);
147	if (diff < 0.0001)
148	return true;
149	double sum = fabs(b1) + fabs(b2);
150	return diff/sum < 0.005;
151	}
152
153	static char Get_M_Char(char Bits)
154	{
155	switch (Bits & BIT_xM)
156	{
157	case BIT_MM:
158	return 'M';
159	case BIT_DM:
160	return 'D';
161	case BIT_IM:
162	return 'I';
163	}
164	Quit("Huh?");
165	return '?';
166	}
167
168	static char Get_D_Char(char Bits)
169	{
170	return (Bits & BIT_xD) ? 'M' : 'D';
171	}
172
173	static char Get_I_Char(char Bits)
174	{
175	return (Bits & BIT_xI) ? 'M' : 'I';
176	}
177
178	static bool DPEq(char c, SCORE g_DP, SCORE DPD_,
179	unsigned uPrefixCountA, unsigned uPrefixCountB)
180	{
181	SCORE *DPM_ = g_DP;
182	for (unsigned i = 0; i < uPrefixCountA; ++i)
183	for (unsigned j = 0; j < uPrefixCountB; ++j)
184	if (!LocalEq(DPM(i, j), DPD(i, j)))
185	{
186	Log("*DPDIFF* DP%c(%d, %d) Simple = %.2g, Fast = %.2g\n",
187	c, i, j, DPM(i, j), DPD(i, j));
188	return false;
189	}
190	return true;
191	}
192
193	static bool CompareTB(char *TB, char TBM_, char TBD_, char TBI_,
194	unsigned uPrefixCountA, unsigned uPrefixCountB)
195	{
196	SCORE *DPM_ = g_DPM;
197	bool Eq = true;
198	for (unsigned i = 0; i < uPrefixCountA; ++i)
199	for (unsigned j = 0; j < uPrefixCountB; ++j)
200	{
201	char c1 = TBM(i, j);
202	char c2 = Get_M_Char(TB[i][j]);
203	if (c1 != '?' && c1 != c2 && DPM(i, j) > -100000)
204	{
205	Log("TBM(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
206	Eq = false;
207	goto D;
208	}
209	}
210
211	D:
212	SCORE *DPD_ = g_DPD;
213	for (unsigned i = 0; i < uPrefixCountA; ++i)
214	for (unsigned j = 0; j < uPrefixCountB; ++j)
215	{
216	char c1 = TBD(i, j);
217	char c2 = Get_D_Char(TB[i][j]);
218	if (c1 != '?' && c1 != c2 && DPD(i, j) > -100000)
219	{
220	Log("TBD(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
221	Eq = false;
222	goto I;
223	}
224	}
225	I:
226	SCORE *DPI_ = g_DPI;
227	for (unsigned i = 0; i < uPrefixCountA; ++i)
228	for (unsigned j = 0; j < uPrefixCountB; ++j)
229	{
230	char c1 = TBI(i, j);
231	char c2 = Get_I_Char(TB[i][j]);
232	if (c1 != '?' && c1 != c2 && DPI(i, j) > -100000)
233	{
234	Log("TBI(%d, %d) Simple = %c, NW = %c\n", i, j, c1, c2);
235	Eq = false;
236	goto Done;
237	}
238	}
239	Done:
240	if (Eq)
241	Log("TB success\n");
242	return Eq;
243	}
244
245	static const char *LocalScoreToStr(SCORE s)
246	{
247	static char str[16];
248	if (s < -100000)
249	return " *";
250	sprintf(str, "%6.1f", s);
251	return str;
252	}
253
254	static void LogDP(const SCORE DPM_, const ProfPos PA, const ProfPos *PB,
255	unsigned uPrefixCountA, unsigned uPrefixCountB)
256	{
257	Log(" ");
258	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
259	{
260	char c = ' ';
261	if (uPrefixLengthB > 0)
262	c = ConsensusChar(PB[uPrefixLengthB - 1]);
263	Log(" %4u:%c", uPrefixLengthB, c);
264	}
265	Log("\n");
266	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
267	{
268	char c = ' ';
269	if (uPrefixLengthA > 0)
270	c = ConsensusChar(PA[uPrefixLengthA - 1]);
271	Log("%4u:%c ", uPrefixLengthA, c);
272	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
273	Log(" %s", LocalScoreToStr(DPM(uPrefixLengthA, uPrefixLengthB)));
274	Log("\n");
275	}
276	}
277
278	static void LogBitTB(char *TB, const ProfPos PA, const ProfPos *PB,
279	unsigned uPrefixCountA, unsigned uPrefixCountB)
280	{
281	Log(" ");
282	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
283	{
284	char c = ' ';
285	if (uPrefixLengthB > 0)
286	c = ConsensusChar(PB[uPrefixLengthB - 1]);
287	Log(" %4u:%c", uPrefixLengthB, c);
288	}
289	Log("\n");
290	Log("Bit TBM:\n");
291	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
292	{
293	char c = ' ';
294	if (uPrefixLengthA > 0)
295	c = ConsensusChar(PA[uPrefixLengthA - 1]);
296	Log("%4u:%c ", uPrefixLengthA, c);
297	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
298	{
299	char c = Get_M_Char(TB[uPrefixLengthA][uPrefixLengthB]);
300	Log(" %6c", c);
301	}
302	Log("\n");
303	}
304
305	Log("\n");
306	Log("Bit TBD:\n");
307	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
308	{
309	char c = ' ';
310	if (uPrefixLengthA > 0)
311	c = ConsensusChar(PA[uPrefixLengthA - 1]);
312	Log("%4u:%c ", uPrefixLengthA, c);
313	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
314	{
315	char c = Get_D_Char(TB[uPrefixLengthA][uPrefixLengthB]);
316	Log(" %6c", c);
317	}
318	Log("\n");
319	}
320
321	Log("\n");
322	Log("Bit TBI:\n");
323	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
324	{
325	char c = ' ';
326	if (uPrefixLengthA > 0)
327	c = ConsensusChar(PA[uPrefixLengthA - 1]);
328	Log("%4u:%c ", uPrefixLengthA, c);
329	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
330	{
331	char c = Get_I_Char(TB[uPrefixLengthA][uPrefixLengthB]);
332	Log(" %6c", c);
333	}
334	Log("\n");
335	}
336	}
337
338	static void ListTB(char TBM_, const ProfPos PA, const ProfPos *PB,
339	unsigned uPrefixCountA, unsigned uPrefixCountB)
340	{
341	Log(" ");
342	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
343	{
344	char c = ' ';
345	if (uPrefixLengthB > 0)
346	c = ConsensusChar(PB[uPrefixLengthB - 1]);
347	Log(" %4u:%c", uPrefixLengthB, c);
348	}
349	Log("\n");
350	for (unsigned uPrefixLengthA = 0; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
351	{
352	char c = ' ';
353	if (uPrefixLengthA > 0)
354	c = ConsensusChar(PA[uPrefixLengthA - 1]);
355	Log("%4u:%c ", uPrefixLengthA, c);
356	for (unsigned uPrefixLengthB = 0; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
357	{
358	char c = TBM(uPrefixLengthA, uPrefixLengthB);
359	Log(" %6c", c);
360	}
361	Log("\n");
362	}
363	}
364
365	static const char *BitsToStr(char Bits)
366	{
367	static char Str[9];
368
369	sprintf(Str, "%cM %cD %cI",
370	Get_M_Char(Bits),
371	Get_D_Char(Bits),
372	Get_I_Char(Bits));
373	}
374	#endif // TRACE
375
376	static inline void SetBitTBM(char **TB, unsigned i, unsigned j, char c)
377	{
378	char Bit;
379	switch (c)
380	{
381	case 'M':
382	Bit = BIT_MM;
383	break;
384	case 'D':
385	Bit = BIT_DM;
386	break;
387	case 'I':
388	Bit = BIT_IM;
389	break;
390	default:
391	Quit("Huh?!");
392	}
393	TB[i][j] &= ~BIT_xM;
394	TB[i][j] \|= Bit;
395	}
396
397	static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c)
398	{
399	char Bit;
400	switch (c)
401	{
402	case 'M':
403	Bit = BIT_MD;
404	break;
405	case 'D':
406	Bit = BIT_DD;
407	break;
408	default:
409	Quit("Huh?!");
410	}
411	TB[i][j] &= ~BIT_xD;
412	TB[i][j] \|= Bit;
413	}
414
415	static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c)
416	{
417	char Bit;
418	switch (c)
419	{
420	case 'M':
421	Bit = BIT_MI;
422	break;
423	case 'I':
424	Bit = BIT_II;
425	break;
426	default:
427	Quit("Huh?!");
428	}
429	TB[i][j] &= ~BIT_xI;
430	TB[i][j] \|= Bit;
431	}
432
433	#if TRACE
434	#define LogMatrices() \
435	{ \
436	Log("Bit DPM:\n"); \
437	LogDP(DPM_, PA, PB, uPrefixCountA, uPrefixCountB); \
438	Log("Bit DPD:\n"); \
439	LogDP(DPD_, PA, PB, uPrefixCountA, uPrefixCountB); \
440	Log("Bit DPI:\n"); \
441	LogDP(DPI_, PA, PB, uPrefixCountA, uPrefixCountB); \
442	Log("Bit TB:\n"); \
443	LogBitTB(TB, PA, PB, uPrefixCountA, uPrefixCountB); \
444	bool Same; \
445	Same = DPEq('M', g_DPM, DPM_, uPrefixCountA, uPrefixCountB);\
446	if (Same) \
447	Log("DPM success\n"); \
448	Same = DPEq('D', g_DPD, DPD_, uPrefixCountA, uPrefixCountB);\
449	if (Same) \
450	Log("DPD success\n"); \
451	Same = DPEq('I', g_DPI, DPI_, uPrefixCountA, uPrefixCountB);\
452	if (Same) \
453	Log("DPI success\n"); \
454	CompareTB(TB, g_TBM, g_TBD, g_TBI, uPrefixCountA, uPrefixCountB);\
455	}
456	#else
457	#define LogMatrices() /* empty */
458	#endif
459
460	static unsigned uCachePrefixCountB;
461	static unsigned uCachePrefixCountA;
462	static SCORE *CacheMCurr;
463	static SCORE *CacheMNext;
464	static SCORE *CacheMPrev;
465	static SCORE *CacheDRow;
466	static char **CacheTB;
467
468	static void AllocCache(unsigned uPrefixCountA, unsigned uPrefixCountB)
469	{
470	if (uPrefixCountA <= uCachePrefixCountA && uPrefixCountB <= uCachePrefixCountB)
471	return;
472
473	delete[] CacheMCurr;
474	delete[] CacheMNext;
475	delete[] CacheMPrev;
476	delete[] CacheDRow;
477	for (unsigned i = 0; i < uCachePrefixCountA; ++i)
478	delete[] CacheTB[i];
479	delete[] CacheTB;
480
481	uCachePrefixCountA = uPrefixCountA + 1024;
482	uCachePrefixCountB = uPrefixCountB + 1024;
483
484	CacheMCurr = new SCORE[uCachePrefixCountB];
485	CacheMNext = new SCORE[uCachePrefixCountB];
486	CacheMPrev = new SCORE[uCachePrefixCountB];
487	CacheDRow = new SCORE[uCachePrefixCountB];
488
489	CacheTB = new char *[uCachePrefixCountA];
490	for (unsigned i = 0; i < uCachePrefixCountA; ++i)
491	CacheTB[i] = new char [uCachePrefixCountB];
492	}
493
494	SCORE NWSmall(const ProfPos PA, unsigned uLengthA, const ProfPos PB,
495	unsigned uLengthB, PWPath &Path)
496	{
497	if (0 == uLengthB \|\| 0 == uLengthA )
498	Quit("Internal error, NWSmall: length=0");
499
500	SetTermGaps(PA, uLengthA);
501	SetTermGaps(PB, uLengthB);
502
503	const unsigned uPrefixCountA = uLengthA + 1;
504	const unsigned uPrefixCountB = uLengthB + 1;
505	const SCORE e = g_scoreGapExtend;
506
507	ALLOC_TRACE()
508
509	AllocCache(uPrefixCountA, uPrefixCountB);
510
511	SCORE *MCurr = CacheMCurr;
512	SCORE *MNext = CacheMNext;
513	SCORE *MPrev = CacheMPrev;
514	SCORE *DRow = CacheDRow;
515
516	char **TB = CacheTB;
517	for (unsigned i = 0; i < uPrefixCountA; ++i)
518	memset(TB[i], 0, uPrefixCountB);
519
520	SCORE Iij = MINUS_INFINITY;
521	SetDPI(0, 0, Iij);
522
523	Iij = PB[0].m_scoreGapOpen;
524	SetDPI(0, 1, Iij);
525
526	for (unsigned j = 2; j <= uLengthB; ++j)
527	{
528	Iij += e;
529	SetDPI(0, j, Iij);
530	SetTBI(0, j, 'I');
531	}
532
533	for (unsigned j = 0; j <= uLengthB; ++j)
534	{
535	DRow[j] = MINUS_INFINITY;
536	SetDPD(0, j, DRow[j]);
537	SetTBD(0, j, 'D');
538	}
539
540	MPrev[0] = 0;
541	SetDPM(0, 0, MPrev[0]);
542	for (unsigned j = 1; j <= uLengthB; ++j)
543	{
544	MPrev[j] = MINUS_INFINITY;
545	SetDPM(0, j, MPrev[j]);
546	}
547
548	MCurr[0] = MINUS_INFINITY;
549	SetDPM(1, 0, MCurr[0]);
550
551	MCurr[1] = ScoreProfPos2(PA[0], PB[0]);
552	SetDPM(1, 1, MCurr[1]);
553	SetBitTBM(TB, 1, 1, 'M');
554	SetTBM(1, 1, 'M');
555
556	for (unsigned j = 2; j <= uLengthB; ++j)
557	{
558	MCurr[j] = ScoreProfPos2(PA[0], PB[j-1]) + PB[0].m_scoreGapOpen +
559	(j - 2)*e + PB[j-2].m_scoreGapClose;
560	SetDPM(1, j, MCurr[j]);
561	SetBitTBM(TB, 1, j, 'I');
562	SetTBM(1, j, 'I');
563	}
564
565	// Main DP loop
566	for (unsigned i = 1; i < uLengthA; ++i)
567	{
568	char *TBRow = TB[i];
569
570	Iij = MINUS_INFINITY;
571	SetDPI(i, 0, Iij);
572
573	DRow[0] = PA[0].m_scoreGapOpen + (i - 1)*e;
574	SetDPD(i, 0, DRow[0]);
575
576	MCurr[0] = MINUS_INFINITY;
577	if (i == 1)
578	{
579	MCurr[1] = ScoreProfPos2(PA[0], PB[0]);
580	SetBitTBM(TB, i, 1, 'M');
581	SetTBM(i, 1, 'M');
582	}
583	else
584	{
585	MCurr[1] = ScoreProfPos2(PA[i-1], PB[0]) + PA[0].m_scoreGapOpen +
586	(i - 2)*e + PA[i-2].m_scoreGapClose;
587	SetBitTBM(TB, i, 1, 'D');
588	SetTBM(i, 1, 'D');
589	}
590	SetDPM(i, 0, MCurr[0]);
591	SetDPM(i, 1, MCurr[1]);
592
593	for (unsigned j = 1; j < uLengthB; ++j)
594	MNext[j+1] = ScoreProfPos2(PA[i], PB[j]);
595
596	for (unsigned j = 1; j < uLengthB; ++j)
597	{
598	RECURSE_D(i, j)
599	RECURSE_I(i, j)
600	RECURSE_M(i, j)
601	}
602	// Special case for j=uLengthB
603	RECURSE_D_BTerm(i)
604	RECURSE_I_BTerm(i)
605
606	// Prev := Curr, Curr := Next, Next := Prev
607	Rotate(MPrev, MCurr, MNext);
608	}
609
610	// Special case for i=uLengthA
611	char *TBRow = TB[uLengthA];
612	MCurr[0] = MINUS_INFINITY;
613	if (uLengthA > 1)
614	MCurr[1] = ScoreProfPos2(PA[uLengthA-1], PB[0]) + (uLengthA - 2)*e +
615	PA[0].m_scoreGapOpen + PA[uLengthA-2].m_scoreGapClose;
616	else
617	MCurr[1] = ScoreProfPos2(PA[uLengthA-1], PB[0]) + PA[0].m_scoreGapOpen +
618	PA[0].m_scoreGapClose;
619	SetBitTBM(TB, uLengthA, 1, 'D');
620	SetTBM(uLengthA, 1, 'D');
621	SetDPM(uLengthA, 0, MCurr[0]);
622	SetDPM(uLengthA, 1, MCurr[1]);
623
624	DRow[0] = MINUS_INFINITY;
625	SetDPD(uLengthA, 0, DRow[0]);
626	for (unsigned j = 1; j <= uLengthB; ++j)
627	RECURSE_D_ATerm(j);
628
629	Iij = MINUS_INFINITY;
630	for (unsigned j = 1; j <= uLengthB; ++j)
631	RECURSE_I_ATerm(j)
632
633	LogMatrices();
634
635	SCORE MAB = MCurr[uLengthB];
636	SCORE DAB = DRow[uLengthB];
637	SCORE IAB = Iij;
638
639	SCORE Score = MAB;
640	char cEdgeType = 'M';
641	if (DAB > Score)
642	{
643	Score = DAB;
644	cEdgeType = 'D';
645	}
646	if (IAB > Score)
647	{
648	Score = IAB;
649	cEdgeType = 'I';
650	}
651
652	#if TRACE
653	Log(" Fast: MAB=%.4g DAB=%.4g IAB=%.4g best=%c\n",
654	MAB, DAB, IAB, cEdgeType);
655	#endif
656
657	BitTraceBack(TB, uLengthA, uLengthB, cEdgeType, Path);
658
659	#if DBEUG
660	Path.Validate();
661	#endif
662
663	return 0;
664	}

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

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