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 double wm;
14 struct _shuryoten *next;
15 struct _shuryoten *prev;
16 } Shuryoten;
17
18
19 static int localstop;
20
compshuryo(Shuryoten * s1_arg,Shuryoten * s2_arg)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
match_calc(double * match,char ** s1,char ** s2,int i1,int lgth2)30 static void match_calc( double *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
gentracking(int ** used,char ** seq1,char ** seq2,char ** mseq1,char ** mseq2,double ** cpmx1,double ** cpmx2,int ** ijpi,int ** ijpj,int * off1pt,int * off2pt,int endi,int endj)38 static double gentracking( int **used,
39 char **seq1, char **seq2,
40 char **mseq1, char **mseq2,
41 double **cpmx1, double **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
suboptalign11(char ** seq1,char ** seq2,int alloclen,int * off1pt,int * off2pt,LocalHom * lhmpt)129 double 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 double wm = 0.0; // by D.Mathog,
139 double g;
140 double *currentw, *previousw;
141 #if 1
142 double *wtmp;
143 int *ijpipt;
144 int *ijpjpt;
145 double *mjpt, *Mjpt, *prept, *curpt;
146 int *mpjpt, *Mpjpt;
147 #endif
148 static double mi, *m;
149 static double Mi, *largeM;
150 static int **ijpi;
151 static int **ijpj;
152 static int mpi, *mp;
153 static int Mpi, *Mp;
154 static double *w1, *w2;
155 // static double *match;
156 static double *initverticalw; /* kufuu sureba iranai */
157 static double *lastverticalw; /* kufuu sureba iranai */
158 static char **mseq1;
159 static char **mseq2;
160 static double **cpmx1;
161 static double **cpmx2;
162 static int **intwork;
163 static double **doublework;
164 static int orlgth1 = 0, orlgth2 = 0;
165 double maxwm;
166 double tbk;
167 int tbki, tbkj;
168 int endali, endalj;
169 // double localthr = 0.0;
170 // double localthr2 = 0.0;
171 double fpenalty = (double)penalty;
172 double fpenalty_OP = (double)penalty_OP;
173 double fpenalty_ex = (double)penalty_ex;
174 // double fpenalty_EX = (double)penalty_EX;
175 double foffset = (double)offset;
176 double localthr = -foffset;
177 double localthr2 = -foffset;
178 static Shuryoten *shuryo = NULL;
179 int numshuryo;
180 double minshuryowm = 0.0; // by D.Mathog
181 int minshuryopos = 0; // by D.Mathog
182 double 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( doublework );
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( nalphabets, ll1+2 );
260 cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
261
262 doublework = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
263 intwork = AllocateIntMtx( nalphabets, 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
679