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MSalign11.c

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Last change on this file was 10371, checked in by aboeckma, 11 years ago
updated mafft version. Added extensions (no svn ignore, yet)
File size: 13.0 KB

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1	#include "mltaln.h"
2	#include "dp.h"
3
4	#define DEBUG 0
5	#define XXXXXXX 0
6	#define USE_PENALTY_EX 0
7
8	static void extendmseq( char mseq1, char mseq2, char seq1, char seq2, int i, int j, int prevhiti, int prevhitj )
9	{
10	// char gap[] = "-";
11	char *gap;
12	gap = newgapstr;
13	int l;
14
15	fprintf( stderr, "i=%d, prevhiti=%d\n", i, prevhiti );
16	fprintf( stderr, "j=%d, prevhitj=%d\n", j, prevhitj );
17	l = prevhiti - i - 1;
18	fprintf( stderr, "l=%d\n", l );
19	while( l>0 )
20	{
21	*--mseq1[0] = seq1[0][i+l--];
22	--mseq2[0] = gap;
23	}
24	l= prevhitj - j - 1;
25	fprintf( stderr, "l=%d\n", l );
26	while( l>0 )
27	{
28	--mseq1[0] = gap;
29	*--mseq2[0] = seq2[0][j+l--];
30	}
31	if( i < 0 \|\| j < 0 ) return;
32	*--mseq1[0] = seq1[0][i];
33	*--mseq2[0] = seq2[0][j];
34	fprintf( stderr, "added %c to mseq1, mseq1 = %s \n", seq1[0][i], mseq1[0] );
35	fprintf( stderr, "added %c to mseq2, mseq2 = %s \n", seq2[0][j], mseq2[0] );
36	}
37
38	static void match_calc( float match, char s1, char *s2, int i1, int lgth2 )
39	{
40	char tmpc = s1[0][i1];
41	char *seq2 = s2[0];
42
43	while( lgth2-- )
44	match++ = amino_dis[(int)tmpc][(int)seq2++];
45	}
46
47	static float Atracking( float lasthorizontalw, float lastverticalw,
48	char seq1, char seq2,
49	char mseq1, char mseq2,
50	float cpmx1, float cpmx2,
51	int **ijp )
52	{
53	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
54	// char gap[] = "-";
55	char *gap;
56	gap = newgapstr;
57	lgth1 = strlen( seq1[0] );
58	lgth2 = strlen( seq2[0] );
59
60
61	#if 0
62	for( i=0; i<lgth1; i++ )
63	{
64	fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
65	}
66	#endif
67
68	for( i=0; i<lgth1+1; i++ )
69	{
70	ijp[i][0] = i + 1;
71	}
72	for( j=0; j<lgth2+1; j++ )
73	{
74	ijp[0][j] = -( j + 1 );
75	}
76
77
78	mseq1[0] += lgth1+lgth2;
79	*mseq1[0] = 0;
80	mseq2[0] += lgth1+lgth2;
81	*mseq2[0] = 0;
82	iin = lgth1; jin = lgth2;
83	limk = lgth1+lgth2 + 1;
84	for( k=0; k<limk; k++ )
85	{
86	if( ijp[iin][jin] < 0 )
87	{
88	ifi = iin-1; jfi = jin+ijp[iin][jin];
89	}
90	else if( ijp[iin][jin] > 0 )
91	{
92	ifi = iin-ijp[iin][jin]; jfi = jin-1;
93	}
94	else
95	{
96	ifi = iin-1; jfi = jin-1;
97	}
98	l = iin - ifi;
99	while( --l )
100	{
101	*--mseq1[0] = seq1[0][ifi+l];
102	--mseq2[0] = gap;
103	k++;
104	}
105	l= jin - jfi;
106	while( --l )
107	{
108	--mseq1[0] = gap;
109	*--mseq2[0] = seq2[0][jfi+l];
110	k++;
111	}
112	if( iin <= 0 \|\| jin <= 0 ) break;
113	*--mseq1[0] = seq1[0][ifi];
114	*--mseq2[0] = seq2[0][jfi];
115	k++;
116	iin = ifi; jin = jfi;
117	}
118	return( 0.0 );
119	}
120
121	void backdp( float *WMMTX, float wmmax, float maxinw, float maxinh, int lgth1, int lgth2, int alloclen, float w1, float w2, float initverticalw, float m, int mp, int iin, int jin, char seq1, char seq2, char mseq1, char mseq2 )
122	{
123	register int i, j;
124	int prevhiti, prevhitj;
125	// int lasti, lastj;
126	float g;
127	float fpenalty = (float)penalty;
128	#if USE_PENALTY_EX
129	float fpenalty_ex = (float)penalty_ex;
130	#endif
131	float currentw, previousw, *wtmp;
132	float mi;
133	int mpi;
134	int *mpjpt;
135	float mjpt, prept, *curpt;
136	float wm = 0.0;
137	float forwwm;
138
139	currentw = w1;
140	previousw = w2;
141
142	match_calc( initverticalw, seq2, seq1, lgth2-1, lgth1 );
143	match_calc( currentw, seq1, seq2, lgth1-1, lgth2 );
144
145
146	prevhiti = iin;
147	prevhitj = jin;
148	fprintf( stderr, "prevhiti = %d, lgth1 = %d\n", prevhiti, lgth1 );
149	fprintf( stderr, "prevhitj = %d, lgth2 = %d\n", prevhitj, lgth2 );
150	extendmseq( mseq1, mseq2, seq1, seq2, prevhiti, prevhitj, lgth1, lgth2 );
151
152	for( i=0; i<lgth1-1; i++ )
153	{
154	initverticalw[i] += fpenalty;
155	WMMTX[i][lgth2-1] += fpenalty;
156	}
157	for( j=0; j<lgth2-1; j++ )
158	{
159	currentw[j] += fpenalty;
160	WMMTX[lgth1-1][j] += fpenalty;
161	}
162
163
164	#if 0
165	fprintf( stderr, "initverticalw = \n" );
166	for( i=0; i<lgth1; i++ )
167	fprintf( stderr, "% 8.2f", initverticalw[i] );
168	fprintf( stderr, "\n" );
169	fprintf( stderr, "currentw = \n" );
170	for( i=0; i<lgth2; i++ )
171	fprintf( stderr, "% 8.2f", currentw[i] );
172	fprintf( stderr, "\n" );
173	#endif
174
175	for( j=lgth2-1; j>0; --j )
176	{
177	m[j-1] = currentw[j];
178	mp[j] = 0; // iranai
179	}
180
181	for( j=0; j<lgth2; j++ ) m[j] = 0.0;
182	//m[lgth2-1] ga, irunoka iranainoka irahai.
183
184	for( i=lgth1-2; i>-1; i-- )
185	{
186	wtmp = previousw;
187	previousw = currentw;
188	currentw = wtmp;
189
190	previousw[lgth2-1] = initverticalw[i+1];
191
192	match_calc( currentw, seq1, seq2, i, lgth2 );
193
194	#if 0
195	fprintf( stderr, "i=%d, currentw = \n", i );
196	for( j=0; j<lgth2; j++ ) fprintf( stderr, "% 8.2f", currentw[j] );
197	fprintf( stderr, "\n" );
198	#endif
199
200	currentw[lgth2-1] = initverticalw[i];
201
202	mi = previousw[lgth2-1];
203	mpi = lgth2-1; //iranai
204
205
206	mjpt = m + lgth2 - 2;
207	prept = previousw + lgth2 - 1;
208	curpt = currentw + lgth2 - 2;
209	mpjpt = mp + lgth2 - 2;
210
211	for( j=lgth2-2; j>-1; j-- )
212	{
213
214	// fprintf( stderr, "i,j=%d,%d %c-%c ", i, j, seq1[0][i], seq2[0][j] );
215	wm = *prept;
216	g = mi + fpenalty;
217	#if 0
218	fprintf( stderr, "%5.0f?", g );
219	#endif
220	if( g > wm )
221	{
222	wm = g;
223	}
224	g = *prept;
225	if( g >= mi )
226	{
227	mi = g;
228	mpi = j+1; //iranai
229	}
230	#if USE_PENALTY_EX
231	mi += fpenalty_ex;
232	#endif
233
234	g = *mjpt + fpenalty;
235	#if 0
236	fprintf( stderr, "%5.0f?", g );
237	#endif
238	if( g > wm )
239	{
240	wm = g;
241	}
242	g = *prept;
243	if( g >= *mjpt )
244	{
245	*mjpt = g;
246	*mpjpt = i-1; //iranai
247	}
248	#if USE_PENALTY_EX
249	m[j] += fpenalty_ex;
250	#endif
251
252	#if 0
253	fprintf( stderr, "curpt = %5.0f \n", curpt );
254	#endif
255
256	// forwwm = wm + MIN( maxinw[i], maxinh[j] );
257	forwwm = wm + MIN( maxinw[i], maxinh[j] );
258	WMMTX[i][j] = forwwm;
259	if( forwwm == wmmax && i<prevhiti && j<prevhitj )
260	{
261	fprintf( stderr, "hit!\n" );
262	extendmseq( mseq1, mseq2, seq1, seq2, i, j, prevhiti, prevhitj );
263	if( forwwm == wmmax )
264	{
265	*--mseq1[0] = 'u';
266	*--mseq2[0] = 'u';
267	}
268	prevhiti = i;
269	prevhitj = j;
270	}
271	*curpt += wm;
272
273	mjpt--;
274	prept--;
275	mpjpt--;
276	curpt--;
277	}
278	}
279	extendmseq( mseq1, mseq2, seq1, seq2, -1, -1, prevhiti, prevhitj );
280	}
281
282
283	float MSalign11( char seq1, char seq2, int alloclen )
284	/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
285	{
286	// int k;
287	register int i, j;
288	int lasti, lastj;
289	int iin = 0, jin = 0; // by Mathog, a guess
290	int lgth1, lgth2;
291	int resultlen;
292	float wm = 0.0; /* int ?????? */
293	float g;
294	float currentw, previousw;
295	float fpenalty = (float)penalty;
296	#if USE_PENALTY_EX
297	float fpenalty_ex = (float)penalty_ex;
298	#endif
299	float maxinw = NULL, maxinwpt = NULL; // by D.Mathog, guess
300	float *maxinh = NULL; // by D.Mathog, guess
301	#if 1
302	float wmmax;
303	float *wtmp;
304	int *ijppt;
305	float mjpt, prept, *curpt;
306	int *mpjpt;
307	#endif
308	static float mi, *m;
309	static int **ijp;
310	static int mpi, *mp;
311	static float w1, w2;
312	static float *match;
313	static float initverticalw; / kufuu sureba iranai */
314	static float lastverticalw; / kufuu sureba iranai */
315	static char **mseq1;
316	static char **mseq2;
317	static char **mseq;
318	static float **cpmx1;
319	static float **cpmx2;
320	static int **intwork;
321	static float **WMMTX;
322	static float **floatwork;
323	static int orlgth1 = 0, orlgth2 = 0;
324
325	if( orlgth1 == 0 )
326	{
327	mseq1 = AllocateCharMtx( njob, 0 );
328	mseq2 = AllocateCharMtx( njob, 0 );
329	}
330
331
332	lgth1 = strlen( seq1[0] );
333	lgth2 = strlen( seq2[0] );
334
335	if( lgth1 > orlgth1 \|\| lgth2 > orlgth2 )
336	{
337	int ll1, ll2;
338
339	if( orlgth1 > 0 && orlgth2 > 0 )
340	{
341	FreeFloatVec( w1 );
342	FreeFloatVec( w2 );
343	FreeFloatVec( match );
344	FreeFloatVec( initverticalw );
345	FreeFloatVec( lastverticalw );
346	FreeFloatVec( maxinw );
347	FreeFloatVec( maxinh );
348
349	FreeFloatVec( m );
350	FreeIntVec( mp );
351
352	FreeCharMtx( mseq );
353
354
355	FreeFloatMtx( cpmx1 );
356	FreeFloatMtx( cpmx2 );
357
358	FreeFloatMtx( floatwork );
359	FreeIntMtx( intwork );
360	}
361
362	ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
363	ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
364
365	#if DEBUG
366	fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
367	#endif
368
369	w1 = AllocateFloatVec( ll2+2 );
370	w2 = AllocateFloatVec( ll2+2 );
371	match = AllocateFloatVec( ll2+2 );
372
373	initverticalw = AllocateFloatVec( ll1+2 );
374	lastverticalw = AllocateFloatVec( ll1+2 );
375	maxinw = AllocateFloatVec( ll1+2 );
376
377
378	m = AllocateFloatVec( ll2+2 );
379	mp = AllocateIntVec( ll2+2 );
380	maxinh = AllocateFloatVec( ll2+2 );
381
382	mseq = AllocateCharMtx( njob, ll1+ll2 );
383
384	cpmx1 = AllocateFloatMtx( 26, ll1+2 );
385	cpmx2 = AllocateFloatMtx( 26, ll2+2 );
386
387	floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
388	intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
389
390	#if DEBUG
391	fprintf( stderr, "succeeded\n" );
392	#endif
393
394	orlgth1 = ll1 - 100;
395	orlgth2 = ll2 - 100;
396	}
397
398
399	mseq1[0] = mseq[0];
400	mseq2[0] = mseq[1];
401
402
403	if( orlgth1 > commonAlloc1 \|\| orlgth2 > commonAlloc2 )
404	{
405	int ll1, ll2;
406
407	if( commonAlloc1 && commonAlloc2 )
408	{
409	FreeIntMtx( commonIP );
410	FreeFloatMtx( WMMTX );
411	}
412
413	ll1 = MAX( orlgth1, commonAlloc1 );
414	ll2 = MAX( orlgth2, commonAlloc2 );
415
416	#if DEBUG
417	fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
418	#endif
419
420	commonIP = AllocateIntMtx( ll1+10, ll2+10 );
421	WMMTX = AllocateFloatMtx( ll1+10, ll2+10 );
422
423	#if DEBUG
424	fprintf( stderr, "succeeded\n\n" );
425	#endif
426
427	commonAlloc1 = ll1;
428	commonAlloc2 = ll2;
429	}
430	ijp = commonIP;
431
432
433	#if 0
434	for( i=0; i<lgth1; i++ )
435	fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
436	#endif
437
438	currentw = w1;
439	previousw = w2;
440
441	match_calc( initverticalw, seq2, seq1, 0, lgth1 );
442
443
444	match_calc( currentw, seq1, seq2, 0, lgth2 );
445
446	WMMTX[0][0] = initverticalw[0];
447
448	maxinh[0] = initverticalw[0];
449	for( i=1; i<lgth1+1; i++ )
450	{
451	initverticalw[i] += fpenalty;
452	WMMTX[i][0] = initverticalw[i];
453	if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
454	}
455	maxinw[0] = currentw[0];
456	for( j=1; j<lgth2+1; j++ )
457	{
458	currentw[j] += fpenalty;
459	WMMTX[0][j] = currentw[j];
460	if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
461	}
462
463	for( j=1; j<lgth2+1; ++j )
464	{
465	m[j] = currentw[j-1]; mp[j] = 0;
466	}
467
468	lastverticalw[0] = currentw[lgth2-1];
469
470	lasti = lgth1+1;
471
472	for( i=1; i<lasti; i++ )
473	{
474	wtmp = previousw;
475	previousw = currentw;
476	currentw = wtmp;
477
478	previousw[0] = initverticalw[i-1];
479
480	match_calc( currentw, seq1, seq2, i, lgth2 );
481
482	currentw[0] = initverticalw[i];
483
484	mi = previousw[0]; mpi = 0;
485
486	maxinwpt = maxinw + i;
487	*maxinwpt = currentw[0];
488
489	fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
490
491	ijppt = ijp[i] + 1;
492	mjpt = m + 1;
493	prept = previousw;
494	curpt = currentw + 1;
495	mpjpt = mp + 1;
496	lastj = lgth2+1;
497
498	for( j=1; j<lastj; j++ )
499	{
500	wm = *prept;
501	*ijppt = 0;
502
503	#if 0
504	fprintf( stderr, "%5.0f->", wm );
505	#endif
506	g = mi + fpenalty;
507	#if 0
508	fprintf( stderr, "%5.0f?", g );
509	#endif
510	if( g > wm )
511	{
512	wm = g;
513	*ijppt = -( j - mpi );
514	}
515	g = *prept;
516	if( g >= mi )
517	{
518	mi = g;
519	mpi = j-1;
520	}
521	#if USE_PENALTY_EX
522	mi += fpenalty_ex;
523	#endif
524
525	g = *mjpt + fpenalty;
526	#if 0
527	fprintf( stderr, "%5.0f?", g );
528	#endif
529	if( g > wm )
530	{
531	wm = g;
532	ijppt = +( i - mpjpt );
533	}
534	g = *prept;
535	if( g >= *mjpt )
536	{
537	*mjpt = g;
538	*mpjpt = i-1;
539	}
540	#if USE_PENALTY_EX
541	m[j] += fpenalty_ex;
542	#endif
543
544	#if 0
545	fprintf( stderr, "%5.0f ", wm );
546	#endif
547	*curpt += wm;
548
549	WMMTX[i][j] = *curpt;
550
551
552	if( j<lgth2 && maxinwpt < curpt ) maxinwpt = curpt;
553	if( j<lgth2 && maxinh[j] < curpt ) maxinh[j] = curpt;
554	// fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
555
556	ijppt++;
557	mjpt++;
558	prept++;
559	mpjpt++;
560	curpt++;
561	}
562	lastverticalw[i] = currentw[lgth2-1];
563	}
564
565	wmmax = -999.9;
566	for( i=0; i<lgth1; i++ )
567	{
568	g = lastverticalw[i];
569	if( g > wmmax )
570	{
571	wmmax = g;
572	iin = i;
573	jin = lgth2-1;
574	}
575	}
576	for( j=0; j<lgth2; j++ )
577	{
578	g = currentw[j];
579	if( g > wmmax )
580	{
581	wmmax = g;
582	iin = lgth1-1;
583	jin = j;
584	}
585	}
586
587	for( i=0; i<lgth1; i++ )
588	fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
589	for( j=0; j<lgth2; j++ )
590	fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
591
592	fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
593	if( iin == lgth1 - 1 && jin == lgth2 - 1 )
594	;
595	else
596	wmmax += fpenalty;
597
598	fprintf( stderr, "wmmax = %f\n", wmmax );
599
600	#if 0
601	for( i=0; i<lgth1; i++ )
602	{
603	for( j=0; j<lgth2; j++ )
604	{
605	fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
606	}
607	fprintf( stderr, "\n" );
608	}
609	#endif
610
611	mseq1[0] += lgth1+lgth2;
612	*mseq1[0] = 0;
613	mseq2[0] += lgth1+lgth2;
614	*mseq2[0] = 0;
615
616	backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
617
618	fprintf( stderr, "\n" );
619	#if 1
620	fprintf( stderr, "\n" );
621	fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
622	fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
623	#endif
624
625	#if 0
626	for( i=0; i<lgth1; i++ )
627	{
628	for( j=0; j<lgth2; j++ )
629	{
630	fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
631	}
632	fprintf( stderr, "\n" );
633	}
634	#endif
635
636	mseq1[0] = mseq[0];
637	mseq2[0] = mseq[1];
638	mseq1[0] += lgth1+lgth2;
639	*mseq1[0] = 0;
640	mseq2[0] += lgth1+lgth2;
641	*mseq2[0] = 0;
642
643	Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
644
645
646	resultlen = strlen( mseq1[0] );
647	if( alloclen < resultlen \|\| resultlen > N )
648	{
649	fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
650	ErrorExit( "LENGTH OVER!\n" );
651	}
652
653
654	strcpy( seq1[0], mseq1[0] );
655	strcpy( seq2[0], mseq2[0] );
656	#if 1
657	fprintf( stderr, "\n" );
658	fprintf( stderr, ">\n%s\n", mseq1[0] );
659	fprintf( stderr, ">\n%s\n", mseq2[0] );
660	#endif
661
662
663	return( wm );
664	}
665

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source: branches/stable/GDE/MAFFT/mafft-7.055-with-extensions/core/MSalign11.c

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