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suboptalign11.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: 13.8 KB

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1	#include "mltaln.h"
2	#include "dp.h"
3
4	#define DEBUG 0
5	#define DEBUG2 0
6	#define XXXXXXX 0
7	#define USE_PENALTY_EX 1
8
9	typedef struct _shuryoten
10	{
11	int i;
12	int j;
13	float wm;
14	struct _shuryoten *next;
15	struct _shuryoten *prev;
16	} Shuryoten;
17
18
19	static int localstop;
20
21	static int compshuryo( Shuryoten s1_arg, Shuryoten s2_arg )
22	{
23	Shuryoten s1 = (Shuryoten )s1_arg;
24	Shuryoten s2 = (Shuryoten )s2_arg;
25	if ( s1->wm > s2->wm ) return( -1 );
26	else if ( s1->wm < s2->wm ) return( 1 );
27	else return( 0 );
28	}
29
30	static void match_calc( float match, char s1, char *s2, int i1, int lgth2 )
31	{
32	int j;
33
34	for( j=0; j<lgth2; j++ )
35	match[j] = amino_dis[(int)(s1)[i1]][(int)(s2)[j]];
36	}
37
38	static float gentracking( int **used,
39	char seq1, char seq2,
40	char mseq1, char mseq2,
41	float cpmx1, float cpmx2,
42	int ijpi, int ijpj, int off1pt, int off2pt, int endi, int endj )
43	{
44	int l, iin, jin, lgth1, lgth2, k, limk;
45	int ifi=0, jfi=0;
46	// char gap[] = "-";
47	char *gap;
48	gap = newgapstr;
49	static char res1 = NULL, res2 = NULL;
50	char mspt1, mspt2;
51	if( res1 == NULL )
52	{
53	res1 = (char *)calloc( N, sizeof( char ) );
54	res2 = (char *)calloc( N, sizeof( char ) );
55	}
56
57	lgth1 = strlen( seq1[0] );
58	lgth2 = strlen( seq2[0] );
59
60	mspt1 = res1 + lgth1+lgth2;
61	*mspt1 = 0;
62	mspt2 = res2 + lgth1+lgth2;
63	*mspt2 = 0;
64	iin = endi; jin = endj;
65
66	limk = lgth1+lgth2;
67	if( used[iin][jin] ) return( -1.0 );
68	for( k=0; k<=limk; k++ )
69	{
70	ifi = ( ijpi[iin][jin] );
71	jfi = ( ijpj[iin][jin] );
72
73	if( used[ifi][jfi] ) return( -1.0 );
74
75	l = iin - ifi;
76	while( --l )
77	{
78	*--mspt1 = seq1[0][ifi+l];
79	--mspt2 = gap;
80	k++;
81	}
82	l= jin - jfi;
83	while( --l )
84	{
85	--mspt1 = gap;
86	*--mspt2 = seq2[0][jfi+l];
87	k++;
88	}
89
90	if( iin <= 0 \|\| jin <= 0 ) break;
91	*--mspt1 = seq1[0][ifi];
92	*--mspt2 = seq2[0][jfi];
93	if( ijpi[ifi][jfi] == localstop ) break;
94	if( ijpj[ifi][jfi] == localstop ) break;
95	k++;
96	iin = ifi; jin = jfi;
97	}
98	if( ifi == -1 ) off1pt = 0; else off1pt = ifi;
99	if( jfi == -1 ) off2pt = 0; else off2pt = jfi;
100
101	// fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
102
103	iin = endi; jin = endj;
104	limk = lgth1+lgth2;
105	for( k=0; k<=limk; k++ )
106	{
107	ifi = ( ijpi[iin][jin] );
108	jfi = ( ijpj[iin][jin] );
109
110	used[ifi][jfi] = 1;
111	if( iin <= 0 \|\| jin <= 0 ) break;
112	if( ijpi[ifi][jfi] == localstop ) break;
113	if( ijpj[ifi][jfi] == localstop ) break;
114
115	k++;
116	iin = ifi; jin = jfi;
117	}
118
119
120	strcpy( mseq1[0], mspt1 );
121	strcpy( mseq2[0], mspt2 );
122
123	fprintf( stderr, "mseq1=%s\nmseq2=%s\n", mspt1, mspt2 );
124
125	return( 0.0 );
126	}
127
128
129	float suboptalign11( char seq1, char seq2, int alloclen, int off1pt, int off2pt, LocalHom *lhmpt )
130	/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
131	{
132	int k;
133	static int **used;
134	register int i, j;
135	int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
136	int lgth1, lgth2;
137	int resultlen;
138	float wm = 0.0; // by D.Mathog,
139	float g;
140	float currentw, previousw;
141	#if 1
142	float *wtmp;
143	int *ijpipt;
144	int *ijpjpt;
145	float mjpt, Mjpt, prept, curpt;
146	int mpjpt, Mpjpt;
147	#endif
148	static float mi, *m;
149	static float Mi, *largeM;
150	static int **ijpi;
151	static int **ijpj;
152	static int mpi, *mp;
153	static int Mpi, *Mp;
154	static float w1, w2;
155	// static float *match;
156	static float initverticalw; / kufuu sureba iranai */
157	static float lastverticalw; / kufuu sureba iranai */
158	static char **mseq1;
159	static char **mseq2;
160	static float **cpmx1;
161	static float **cpmx2;
162	static int **intwork;
163	static float **floatwork;
164	static int orlgth1 = 0, orlgth2 = 0;
165	float maxwm;
166	float tbk;
167	int tbki, tbkj;
168	int endali, endalj;
169	// float localthr = 0.0;
170	// float localthr2 = 0.0;
171	float fpenalty = (float)penalty;
172	float fpenalty_OP = (float)penalty_OP;
173	float fpenalty_ex = (float)penalty_ex;
174	// float fpenalty_EX = (float)penalty_EX;
175	float foffset = (float)offset;
176	float localthr = -foffset;
177	float localthr2 = -foffset;
178	static Shuryoten *shuryo = NULL;
179	int numshuryo;
180	float minshuryowm = 0.0; // by D.Mathog
181	int minshuryopos = 0; // by D.Mathog
182	float resf;
183
184
185	// fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
186
187	fprintf( stderr, "in suboptalign11\n" );
188	if( !shuryo )
189	{
190	shuryo = (Shuryoten *)calloc( 100, sizeof( Shuryoten ) );
191	}
192	for( i=0; i<100; i++ )
193	{
194	shuryo[i].i = -1;
195	shuryo[i].j = -1;
196	shuryo[i].wm = 0.0;
197	}
198	numshuryo = 0;
199
200	if( orlgth1 == 0 )
201	{
202	}
203
204
205	lgth1 = strlen( seq1[0] );
206	lgth2 = strlen( seq2[0] );
207
208	fprintf( stderr, "in suboptalign11 step 1\n" );
209
210	if( lgth1 > orlgth1 \|\| lgth2 > orlgth2 )
211	{
212	int ll1, ll2;
213
214	fprintf( stderr, "in suboptalign11 step 1.3\n" );
215	if( orlgth1 > 0 && orlgth2 > 0 )
216	{
217	fprintf( stderr, "in suboptalign11 step 1.4\n" );
218	FreeFloatVec( w1 );
219	FreeFloatVec( w2 );
220	// FreeFloatVec( match );
221	FreeFloatVec( initverticalw );
222	FreeFloatVec( lastverticalw );
223	fprintf( stderr, "in suboptalign11 step 1.5\n" );
224
225	FreeFloatVec( m );
226	FreeIntVec( mp );
227	FreeFloatVec( largeM );
228	FreeIntVec( Mp );
229	fprintf( stderr, "in suboptalign11 step 1.6\n" );
230
231
232	FreeFloatMtx( cpmx1 );
233	FreeFloatMtx( cpmx2 );
234
235	fprintf( stderr, "in suboptalign11 step 1.7\n" );
236	FreeFloatMtx( floatwork );
237	FreeIntMtx( intwork );
238	}
239
240	ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
241	ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
242
243	#if DEBUG
244	fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
245	#endif
246
247	w1 = AllocateFloatVec( ll2+2 );
248	w2 = AllocateFloatVec( ll2+2 );
249	// match = AllocateFloatVec( ll2+2 );
250
251	initverticalw = AllocateFloatVec( ll1+2 );
252	lastverticalw = AllocateFloatVec( ll1+2 );
253
254	m = AllocateFloatVec( ll2+2 );
255	mp = AllocateIntVec( ll2+2 );
256	largeM = AllocateFloatVec( ll2+2 );
257	Mp = AllocateIntVec( ll2+2 );
258
259	cpmx1 = AllocateFloatMtx( 26, ll1+2 );
260	cpmx2 = AllocateFloatMtx( 26, ll2+2 );
261
262	floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
263	intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
264
265	mseq1 = AllocateCharMtx( njob, ll1+ll2 );
266	mseq2 = AllocateCharMtx( njob, ll1+ll2 );
267
268	#if DEBUG
269	fprintf( stderr, "succeeded\n" );
270	#endif
271
272	orlgth1 = ll1 - 100;
273	orlgth2 = ll2 - 100;
274	}
275	fprintf( stderr, "in suboptalign11 step 1.6\n" );
276
277
278
279	fprintf( stderr, "in suboptalign11 step 2\n" );
280
281	if( orlgth1 > commonAlloc1 \|\| orlgth2 > commonAlloc2 )
282	{
283	int ll1, ll2;
284
285	if( commonAlloc1 && commonAlloc2 )
286	{
287	FreeIntMtx( commonIP );
288	FreeIntMtx( commonJP );
289	FreeIntMtx( used );
290	}
291
292	ll1 = MAX( orlgth1, commonAlloc1 );
293	ll2 = MAX( orlgth2, commonAlloc2 );
294
295	#if DEBUG
296	fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
297	#endif
298
299	used = AllocateIntMtx( ll1+10, ll2+10 );
300	commonIP = AllocateIntMtx( ll1+10, ll2+10 );
301	commonJP = AllocateIntMtx( ll1+10, ll2+10 );
302
303	#if DEBUG
304	fprintf( stderr, "succeeded\n\n" );
305	#endif
306
307	commonAlloc1 = ll1;
308	commonAlloc2 = ll2;
309	}
310	ijpi = commonIP;
311	ijpj = commonJP;
312
313
314	#if 0
315	for( i=0; i<lgth1; i++ )
316	fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
317	#endif
318
319	fprintf( stderr, "in suboptalign11 step 3\n" );
320	currentw = w1;
321	previousw = w2;
322
323	match_calc( initverticalw, seq2, seq1, 0, lgth1 );
324
325	match_calc( currentw, seq1, seq2, 0, lgth2 );
326
327
328	lasti = lgth2+1;
329	for( j=1; j<lasti; ++j )
330	{
331	m[j] = currentw[j-1]; mp[j] = 0;
332	largeM[j] = currentw[j-1]; Mp[j] = 0;
333	}
334
335	lastverticalw[0] = currentw[lgth2-1];
336
337
338	#if 0
339	fprintf( stderr, "currentw = \n" );
340	for( i=0; i<lgth1+1; i++ )
341	{
342	fprintf( stderr, "%5.2f ", currentw[i] );
343	}
344	fprintf( stderr, "\n" );
345	fprintf( stderr, "initverticalw = \n" );
346	for( i=0; i<lgth2+1; i++ )
347	{
348	fprintf( stderr, "%5.2f ", initverticalw[i] );
349	}
350	fprintf( stderr, "\n" );
351	#endif
352	#if DEBUG2
353	fprintf( stderr, "\n" );
354	fprintf( stderr, " " );
355	for( j=0; j<lgth2+1; j++ )
356	fprintf( stderr, "%c ", seq2[0][j] );
357	fprintf( stderr, "\n" );
358	#endif
359
360	localstop = lgth1+lgth2+1;
361	maxwm = -999.9;
362	endali = endalj = 0;
363	#if DEBUG2
364	fprintf( stderr, "\n" );
365	fprintf( stderr, "%c ", seq1[0][0] );
366
367	for( j=0; j<lgth2+1; j++ )
368	fprintf( stderr, "%5.0f ", currentw[j] );
369	fprintf( stderr, "\n" );
370	#endif
371
372	lasti = lgth1+1;
373	for( i=1; i<lasti; i++ )
374	{
375	wtmp = previousw;
376	previousw = currentw;
377	currentw = wtmp;
378
379	previousw[0] = initverticalw[i-1];
380
381	match_calc( currentw, seq1, seq2, i, lgth2 );
382	#if DEBUG2
383	fprintf( stderr, "%c ", seq1[0][i] );
384	fprintf( stderr, "%5.0f ", currentw[0] );
385	#endif
386
387	#if XXXXXXX
388	fprintf( stderr, "\n" );
389	fprintf( stderr, "i=%d\n", i );
390	fprintf( stderr, "currentw = \n" );
391	for( j=0; j<lgth2; j++ )
392	{
393	fprintf( stderr, "%5.2f ", currentw[j] );
394	}
395	fprintf( stderr, "\n" );
396	#endif
397	#if XXXXXXX
398	fprintf( stderr, "\n" );
399	fprintf( stderr, "i=%d\n", i );
400	fprintf( stderr, "currentw = \n" );
401	for( j=0; j<lgth2; j++ )
402	{
403	fprintf( stderr, "%5.2f ", currentw[j] );
404	}
405	fprintf( stderr, "\n" );
406	#endif
407	currentw[0] = initverticalw[i];
408
409	mi = previousw[0]; mpi = 0;
410	Mi = previousw[0]; Mpi = 0;
411
412	#if 0
413	if( mi < localthr ) mi = localthr2;
414	#endif
415
416	ijpipt = ijpi[i] + 1;
417	ijpjpt = ijpj[i] + 1;
418	mjpt = m + 1;
419	Mjpt = largeM + 1;
420	prept = previousw;
421	curpt = currentw + 1;
422	mpjpt = mp + 1;
423	Mpjpt = Mp + 1;
424	tbk = -999999.9;
425	tbki = 0;
426	tbkj = 0;
427	lastj = lgth2+1;
428	for( j=1; j<lastj; j++ )
429	{
430	wm = *prept;
431	*ijpipt = i-1;
432	*ijpjpt = j-1;
433
434
435	// fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
436	// fprintf( stderr, "wm=%f\n", wm );
437	#if 0
438	fprintf( stderr, "%5.0f->", wm );
439	#endif
440	g = mi + fpenalty;
441	#if 0
442	fprintf( stderr, "%5.0f?", g );
443	#endif
444	if( g > wm )
445	{
446	wm = g;
447	// *ijpipt = i - 1;
448	*ijpjpt = mpi;
449	}
450	g = *prept;
451	if( g > mi )
452	{
453	mi = g;
454	mpi = j-1;
455	}
456
457	#if USE_PENALTY_EX
458	mi += fpenalty_ex;
459	#endif
460
461	#if 0
462	fprintf( stderr, "%5.0f->", wm );
463	#endif
464	g = *mjpt + fpenalty;
465	#if 0
466	fprintf( stderr, "m%5.0f?", g );
467	#endif
468	if( g > wm )
469	{
470	wm = g;
471	ijpipt = mpjpt;
472	// *ijpjpt = j - 1;
473	}
474	g = *prept;
475	if( g > *mjpt )
476	{
477	*mjpt = g;
478	*mpjpt = i-1;
479	}
480	#if USE_PENALTY_EX
481	*mjpt += fpenalty_ex;
482	#endif
483
484
485	g = tbk + fpenalty_OP;
486	// g = tbk;
487	if( g > wm )
488	{
489	wm = g;
490	*ijpipt = tbki;
491	*ijpjpt = tbkj;
492	// fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, ijpipt, ijpjpt );
493	}
494	g = Mi;
495	if( g > tbk )
496	{
497	tbk = g;
498	tbki = i-1;
499	tbkj = Mpi;
500	}
501	g = *Mjpt;
502	if( g > tbk )
503	{
504	tbk = g;
505	tbki = *Mpjpt;
506	tbkj = j-1;
507	}
508	// tbk += fpenalty_EX;// + foffset;
509
510	g = *prept;
511	if( g > *Mjpt )
512	{
513	*Mjpt = g;
514	*Mpjpt = i-1;
515	}
516	// *Mjpt += fpenalty_EX;// + foffset;
517
518	g = *prept;
519	if( g > Mi )
520	{
521	Mi = g;
522	Mpi = j-1;
523	}
524	// Mi += fpenalty_EX;// + foffset;
525
526
527	// fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, mjpt );
528	// fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(ijpipt)], seq2[0][abs(ijpjpt)] );
529
530
531	if( maxwm < wm )
532	{
533	maxwm = wm;
534	endali = i;
535	endalj = j;
536	}
537
538	#if 1
539	if( numshuryo < 100 )
540	{
541	shuryo[numshuryo].i = i;
542	shuryo[numshuryo].j = j;
543	shuryo[numshuryo].wm = wm;
544
545	if( minshuryowm > wm )
546	{
547	minshuryowm = wm;
548	minshuryopos = numshuryo;
549	}
550	numshuryo++;
551	}
552	else
553	{
554	if( wm > minshuryowm )
555	{
556	shuryo[minshuryopos].i = i;
557	shuryo[minshuryopos].j = j;
558	shuryo[minshuryopos].wm = wm;
559	minshuryowm = wm;
560	for( k=0; k<100; k++ ) // muda
561	{
562	if( shuryo[k].wm < minshuryowm )
563	{
564	minshuryowm = shuryo[k].wm;
565	minshuryopos = k;
566	break;
567	}
568	}
569	}
570	}
571	#endif
572	#if 1
573	if( wm < localthr )
574	{
575	// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
576	*ijpipt = localstop;
577	// *ijpjpt = localstop;
578	wm = localthr2;
579	}
580	#endif
581	#if 0
582	fprintf( stderr, "%5.0f ", *curpt );
583	#endif
584	#if DEBUG2
585	fprintf( stderr, "%5.0f ", wm );
586	// fprintf( stderr, "%c-%c ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], ijppt, localstop );
587	#endif
588
589	*curpt += wm;
590	ijpipt++;
591	ijpjpt++;
592	mjpt++;
593	Mjpt++;
594	prept++;
595	mpjpt++;
596	Mpjpt++;
597	curpt++;
598	}
599	#if DEBUG2
600	fprintf( stderr, "\n" );
601	#endif
602
603	lastverticalw[i] = currentw[lgth2-1];
604	}
605
606	for( k=0; k<100; k++ )
607	{
608	fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
609	}
610
611
612	#if 1
613	fprintf( stderr, "maxwm = %f\n", maxwm );
614	fprintf( stderr, "endali = %d\n", endali );
615	fprintf( stderr, "endalj = %d\n", endalj );
616	#endif
617
618	qsort( shuryo, 100, sizeof( Shuryoten ), (int (*)())compshuryo );
619	for( k=0; k<100; k++ )
620	{
621	fprintf( stderr, "shuryo[%d].i,j,wm = %d,%d,%f\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
622	}
623
624
625	lasti = lgth1+1;
626	for( i=0; i<lasti; i++ )
627	{
628	ijpi[i][0] = localstop;
629	ijpj[i][0] = localstop;
630	}
631	lastj = lgth2+1;
632	for( j=0; j<lastj; j++ )
633	{
634	ijpi[0][j] = localstop;
635	ijpj[0][j] = localstop;
636	}
637
638	for( i=0; i<lasti; i++ ) for( j=0; j<lastj; j++ ) used[i][j] = 0;
639
640	for( k=0; k<numshuryo; k++ )
641	{
642	if( shuryo[k].wm < shuryo[0].wm * 0.3 ) break;
643	fprintf( stderr, "k=%d, shuryo[k].i,j,wm=%d,%d,%f go\n", k, shuryo[k].i, shuryo[k].j, shuryo[k].wm );
644	resf = gentracking( used, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, shuryo[k].i, shuryo[k].j );
645	if( resf == -1.0 ) continue;
646	putlocalhom3( mseq1[0], mseq2[0], lhmpt, off1pt, off2pt, (int)shuryo[k].wm, strlen( mseq1[0] ) );
647	#if 0
648	fprintf( stderr, "\n" );
649	fprintf( stderr, ">\n%s\n", mseq1[0] );
650	fprintf( stderr, ">\n%s\n", mseq2[0] );
651	#endif
652	}
653	for( i=0; i<20; i++ )
654	{
655	for( j=0; j<20; j++ )
656	{
657	fprintf( stderr, "%2d ", used[i][j] );
658	}
659	fprintf( stderr, "\n" );
660	}
661
662
663	// fprintf( stderr, "### impmatch = %f\n", *impmatch );
664
665	resultlen = strlen( mseq1[0] );
666	if( alloclen < resultlen \|\| resultlen > N )
667	{
668	fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
669	ErrorExit( "LENGTH OVER!\n" );
670	}
671
672
673
674
675
676	return( wm );
677	}
678

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source: tags/arb-6.0/GDE/MAFFT/mafft-7.055-with-extensions/core/suboptalign11.c

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