8 #define USE_PENALTY_EX 0
9 #define FASTMATCHCALC 1
12 static float **impmtx = NULL;
13 #if 1 // tditeration to naiveQscore_imp de tsukawareru.
14 float imp_match_out_scQ( int i1, int j1 )
16 // fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
17 // fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
18 return( impmtx[i1][j1] );
22 static void imp_match_out_veadQ( float *imp, int i1, int lgth2 )
25 float *pt = impmtx[i1];
30 float *pt = impmtx[i1];
31 for( j=0; j<lgth2; j++ )
35 static void imp_match_out_vead_tateQ( float *imp, int j1, int lgth1 )
38 for( i=0; i<lgth1; i++ )
39 *imp++ += impmtx[i][j1];
42 #if 1 // tbfast.c kara yobareru.
43 void imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
45 int i, j, k1, k2, tmpint, start1, start2, end1, end2;
46 static int impalloclen = 0;
50 static char *nocount1 = NULL;
51 static char *nocount2 = NULL;
54 if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
56 if( impmtx ) FreeFloatMtx( impmtx );
57 if( nocount1 ) free( nocount1 );
58 if( nocount2 ) free( nocount2 );
59 impalloclen = MAX( lgth1, lgth2 ) + 2;
60 impmtx = AllocateFloatMtx( impalloclen, impalloclen );
61 nocount1 = AllocateCharVec( impalloclen );
62 nocount2 = AllocateCharVec( impalloclen );
65 for( i=0; i<lgth1; i++ )
67 for( j=0; j<clus1; j++ )
68 if( seq1[j][i] == '-' ) break;
69 if( j != clus1 ) nocount1[i] = 1;
72 for( i=0; i<lgth2; i++ )
74 for( j=0; j<clus2; j++ )
75 if( seq2[j][i] == '-' ) break;
76 if( j != clus2 ) nocount2[i] = 1;
81 fprintf( stderr, "nocount2 =\n" );
82 for( i = 0; i<impalloclen; i++ )
84 fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
91 fprintf( stderr, "eff1 in _init_strict = \n" );
92 for( i=0; i<clus1; i++ )
93 fprintf( stderr, "eff1[] = %f\n", eff1[i] );
94 for( i=0; i<clus2; i++ )
95 fprintf( stderr, "eff2[] = %f\n", eff2[i] );
98 for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
100 effijx = fastathreshold;
101 for( i=0; i<clus1; i++ )
103 for( j=0; j<clus2; j++ )
105 effij = (float)( eff1[i] * eff2[j] * effijx );
106 tmpptr = localhom[i][j];
109 // fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
110 // fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
111 // fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
112 // fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
117 if( *pt++ != '-' ) tmpint++;
118 if( tmpint == tmpptr->start1 ) break;
120 start1 = pt - seq1[i] - 1;
122 if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
128 // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
129 if( tmpint == tmpptr->end1 ) break;
130 if( *pt++ != '-' ) tmpint++;
132 end1 = pt - seq1[i] - 0;
136 // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
137 if( *pt++ != '-' ) tmpint++;
138 if( tmpint == tmpptr->end1 ) break;
140 end1 = pt - seq1[i] - 1;
148 if( *pt++ != '-' ) tmpint++;
149 if( tmpint == tmpptr->start2 ) break;
151 start2 = pt - seq2[j] - 1;
152 if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
158 if( tmpint == tmpptr->end2 ) break;
159 if( *pt++ != '-' ) tmpint++;
161 end2 = pt - seq2[j] - 0;
165 if( *pt++ != '-' ) tmpint++;
166 if( tmpint == tmpptr->end2 ) break;
168 end2 = pt - seq2[j] - 1;
171 // fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
172 // fprintf( stderr, "step 0\n" );
173 if( end1 - start1 != end2 - start2 )
175 // fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
179 k1 = start1; k2 = start2;
182 while( *pt1 && *pt2 )
184 if( *pt1 != '-' && *pt2 != '-' )
186 // ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃðդ·¤Æ²¼¤µ¤¤¡£
187 // impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
188 // impmtx[k1][k2] += tmpptr->importance * effij;
189 impmtx[k1][k2] += tmpptr->fimportance * effij;
190 // fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
191 // fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
192 // fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
196 else if( *pt1 != '-' && *pt2 == '-' )
198 // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
201 else if( *pt1 == '-' && *pt2 != '-' )
203 // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
206 else if( *pt1 == '-' && *pt2 == '-' )
208 // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
212 if( k1 > end1 || k2 > end2 ) break;
215 while( k1 <= end1 && k2 <= end2 )
217 fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
218 if( !nocount1[k1] && !nocount2[k2] )
220 impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold;
221 fprintf( stderr, "marked\n" );
224 fprintf( stderr, "no count\n" );
228 tmpptr = tmpptr->next;
233 if( clus1 == 1 && clus2 == 6 )
235 fprintf( stderr, "\n" );
236 fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
237 fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
238 fprintf( stderr, "impmtx = \n" );
239 for( k2=0; k2<lgth2; k2++ )
240 fprintf( stderr, "%6.3f ", (double)k2 );
241 fprintf( stderr, "\n" );
242 for( k1=0; k1<lgth1; k1++ )
244 fprintf( stderr, "%d ", k1 );
245 for( k2=0; k2<3; k2++ )
246 fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
247 fprintf( stderr, "\n" );
256 static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
261 float **cpmxpd = floatwork;
262 int **cpmxpdn = intwork;
263 float *matchpt, *cpmxpdpt, **cpmxpdptpt;
264 int *cpmxpdnpt, **cpmxpdnptpt;
268 for( j=0; j<lgth2; j++ )
271 for( l=0; l<26; l++ )
275 cpmxpd[j][count] = cpmx2[l][j];
276 cpmxpdn[j][count] = l;
280 cpmxpdn[j][count] = -1;
285 for( l=0; l<26; l++ )
288 for( j=0; j<26; j++ )
289 scarr[l] += n_dis[j][l] * cpmx1[j][i1];
292 cpmxpdnptpt = cpmxpdn;
297 cpmxpdnpt = *cpmxpdnptpt++;
298 cpmxpdpt = *cpmxpdptpt++;
299 while( *cpmxpdnpt>-1 )
300 *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
307 float **cpmxpd = floatwork;
308 int **cpmxpdn = intwork;
313 for( j=0; j<lgth2; j++ )
316 for( l=0; l<26; l++ )
320 cpmxpd[count][j] = cpmx2[l][j];
321 cpmxpdn[count][j] = l;
325 cpmxpdn[count][j] = -1;
328 for( l=0; l<26; l++ )
331 for( k=0; k<26; k++ )
332 scarr[l] += n_dis[k][l] * cpmx1[k][i1];
334 for( j=0; j<lgth2; j++ )
337 for( k=0; cpmxpdn[k][j]>-1; k++ )
338 match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
343 static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
344 char **seq1, char **seq2,
345 char **mseq1, char **mseq2,
346 float **cpmx1, float **cpmx2,
347 short **ijp, int icyc, int jcyc )
349 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
351 char *gaptable1, *gt1bk;
352 char *gaptable2, *gt2bk;
353 lgth1 = strlen( seq1[0] );
354 lgth2 = strlen( seq2[0] );
355 gt1bk = AllocateCharVec( lgth1+lgth2+1 );
356 gt2bk = AllocateCharVec( lgth1+lgth2+1 );
359 for( i=0; i<lgth1; i++ )
361 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
369 wm = lastverticalw[0];
370 for( i=0; i<lgth1; i++ )
372 if( lastverticalw[i] >= wm )
374 wm = lastverticalw[i];
375 iin = i; jin = lgth2-1;
376 ijp[lgth1][lgth2] = +( lgth1 - i );
379 for( j=0; j<lgth2; j++ )
381 if( lasthorizontalw[j] >= wm )
383 wm = lasthorizontalw[j];
384 iin = lgth1-1; jin = j;
385 ijp[lgth1][lgth2] = -( lgth2 - j );
390 for( i=0; i<lgth1+1; i++ )
394 for( j=0; j<lgth2+1; j++ )
396 ijp[0][j] = -( j + 1 );
399 gaptable1 = gt1bk + lgth1+lgth2;
401 gaptable2 = gt2bk + lgth1+lgth2;
404 iin = lgth1; jin = lgth2;
406 for( k=0; k<=lgth1+lgth2; k++ )
408 if( ijp[iin][jin] < 0 )
410 ifi = iin-1; jfi = jin+ijp[iin][jin];
412 else if( ijp[iin][jin] > 0 )
414 ifi = iin-ijp[iin][jin]; jfi = jin-1;
418 ifi = iin-1; jfi = jin-1;
434 if( iin == lgth1 || jin == lgth2 )
438 *impwmpt += imp_match_out_scQ( iin, jin );
440 // fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
442 if( iin <= 0 || jin <= 0 ) break;
446 iin = ifi; jin = jfi;
449 for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
450 for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
456 static float Atracking( float *lasthorizontalw, float *lastverticalw,
457 char **seq1, char **seq2,
458 char **mseq1, char **mseq2,
459 float **cpmx1, float **cpmx2,
460 short **ijp, int icyc, int jcyc )
462 int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
464 char *gaptable1, *gt1bk;
465 char *gaptable2, *gt2bk;
466 lgth1 = strlen( seq1[0] );
467 lgth2 = strlen( seq2[0] );
469 gt1bk = AllocateCharVec( lgth1+lgth2+1 );
470 gt2bk = AllocateCharVec( lgth1+lgth2+1 );
473 for( i=0; i<lgth1; i++ )
475 fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
483 wm = lastverticalw[0];
484 for( i=0; i<lgth1; i++ )
486 if( lastverticalw[i] >= wm )
488 wm = lastverticalw[i];
489 iin = i; jin = lgth2-1;
490 ijp[lgth1][lgth2] = +( lgth1 - i );
493 for( j=0; j<lgth2; j++ )
495 if( lasthorizontalw[j] >= wm )
497 wm = lasthorizontalw[j];
498 iin = lgth1-1; jin = j;
499 ijp[lgth1][lgth2] = -( lgth2 - j );
504 for( i=0; i<lgth1+1; i++ )
508 for( j=0; j<lgth2+1; j++ )
510 ijp[0][j] = -( j + 1 );
513 gaptable1 = gt1bk + lgth1+lgth2;
515 gaptable2 = gt2bk + lgth1+lgth2;
518 iin = lgth1; jin = lgth2;
519 for( k=0; k<=lgth1+lgth2; k++ )
521 if( ijp[iin][jin] < 0 )
523 ifi = iin-1; jfi = jin+ijp[iin][jin];
525 else if( ijp[iin][jin] > 0 )
527 ifi = iin-ijp[iin][jin]; jfi = jin-1;
531 ifi = iin-1; jfi = jin-1;
547 if( iin <= 0 || jin <= 0 ) break;
551 iin = ifi; jin = jfi;
554 for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
555 for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
563 float Q__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2 )
564 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
568 int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
571 float wm = 0.0; /* int ?????? */
573 float *currentw, *previousw;
574 // float fpenalty = (float)penalty;
576 float fpenalty_ex = (float)penalty_ex;
581 float *mjpt, *prept, *curpt;
587 static float *w1, *w2;
589 static float *initverticalw; /* kufuu sureba iranai */
590 static float *lastverticalw; /* kufuu sureba iranai */
602 static float *ogcp1g;
603 static float *ogcp2g;
604 static float *fgcp1g;
605 static float *fgcp2g;
606 static float *og_h_dg_n1_p;
607 static float *og_h_dg_n2_p;
608 static float *fg_h_dg_n1_p;
609 static float *fg_h_dg_n2_p;
610 static float *og_t_fg_h_dg_n1_p;
611 static float *og_t_fg_h_dg_n2_p;
612 static float *fg_t_og_h_dg_n1_p;
613 static float *fg_t_og_h_dg_n2_p;
614 static float *gapz_n1;
615 static float *gapz_n2;
616 static float **cpmx1;
617 static float **cpmx2;
618 static int **intwork;
619 static float **floatwork;
620 static int orlgth1 = 0, orlgth2 = 0;
621 float fpenalty = (float)penalty;
623 float *fg_t_og_h_dg_n2_p_pt;
624 float *og_t_fg_h_dg_n2_p_pt;
625 float *og_h_dg_n2_p_pt;
626 float *fg_h_dg_n2_p_pt;
631 float fg_t_og_h_dg_n1_p_va;
632 float og_t_fg_h_dg_n1_p_va;
633 float og_h_dg_n1_p_va;
634 float fg_h_dg_n1_p_va;
644 fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] );
645 fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
649 mseq1 = AllocateCharMtx( njob, 0 );
650 mseq2 = AllocateCharMtx( njob, 0 );
654 lgth1 = strlen( seq1[0] );
655 lgth2 = strlen( seq2[0] );
657 if( lgth1 == 0 || lgth2 == 0 )
659 fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
663 if( lgth1 > orlgth1 || lgth2 > orlgth2 )
667 if( orlgth1 > 0 && orlgth2 > 0 )
671 FreeFloatVec( match );
672 FreeFloatVec( initverticalw );
673 FreeFloatVec( lastverticalw );
680 FreeFloatVec( digf1 );
681 FreeFloatVec( digf2 );
682 FreeFloatVec( diaf1 );
683 FreeFloatVec( diaf2 );
684 FreeFloatVec( gapz1 );
685 FreeFloatVec( gapz2 );
686 FreeFloatVec( gapf1 );
687 FreeFloatVec( gapf2 );
688 FreeFloatVec( ogcp1g );
689 FreeFloatVec( ogcp2g );
690 FreeFloatVec( fgcp1g );
691 FreeFloatVec( fgcp2g );
692 FreeFloatVec( og_h_dg_n1_p );
693 FreeFloatVec( og_h_dg_n2_p );
694 FreeFloatVec( fg_h_dg_n1_p );
695 FreeFloatVec( fg_h_dg_n2_p );
696 FreeFloatVec( og_t_fg_h_dg_n1_p );
697 FreeFloatVec( og_t_fg_h_dg_n2_p );
698 FreeFloatVec( fg_t_og_h_dg_n1_p );
699 FreeFloatVec( fg_t_og_h_dg_n2_p );
700 FreeFloatVec( gapz_n1 );
701 FreeFloatVec( gapz_n2 );
703 FreeFloatMtx( cpmx1 );
704 FreeFloatMtx( cpmx2 );
706 FreeFloatMtx( floatwork );
707 FreeIntMtx( intwork );
710 ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
711 ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
714 fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
717 w1 = AllocateFloatVec( ll2+2 );
718 w2 = AllocateFloatVec( ll2+2 );
719 match = AllocateFloatVec( ll2+2 );
721 initverticalw = AllocateFloatVec( ll1+2 );
722 lastverticalw = AllocateFloatVec( ll1+2 );
724 m = AllocateFloatVec( ll2+2 );
725 mp = AllocateIntVec( ll2+2 );
727 mseq = AllocateCharMtx( njob, ll1+ll2 );
729 digf1 = AllocateFloatVec( ll1+2 );
730 digf2 = AllocateFloatVec( ll2+2 );
731 diaf1 = AllocateFloatVec( ll1+2 );
732 diaf2 = AllocateFloatVec( ll2+2 );
733 gapz1 = AllocateFloatVec( ll1+2 );
734 gapz2 = AllocateFloatVec( ll2+2 );
735 gapf1 = AllocateFloatVec( ll1+2 );
736 gapf2 = AllocateFloatVec( ll2+2 );
737 ogcp1g = AllocateFloatVec( ll1+2 );
738 ogcp2g = AllocateFloatVec( ll2+2 );
739 fgcp1g = AllocateFloatVec( ll1+2 );
740 fgcp2g = AllocateFloatVec( ll2+2 );
741 og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
742 og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
743 fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
744 fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
745 og_t_fg_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
746 og_t_fg_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
747 fg_t_og_h_dg_n1_p = AllocateFloatVec( ll1 + 2 );
748 fg_t_og_h_dg_n2_p = AllocateFloatVec( ll2 + 2 );
749 gapz_n1 = AllocateFloatVec( ll1+2 );
750 gapz_n2 = AllocateFloatVec( ll2+2 );
752 cpmx1 = AllocateFloatMtx( 26, ll1+2 );
753 cpmx2 = AllocateFloatMtx( 26, ll2+2 );
754 fprintf( stderr, "ll2 = %d\n", ll2 );
757 floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
758 intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
760 floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
761 intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
765 fprintf( stderr, "succeeded\n" );
773 for( i=0; i<icyc; i++ )
778 for( j=0; j<jcyc; j++ )
780 mseq2[j] = mseq[icyc+j];
785 if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
789 if( commonAlloc1 && commonAlloc2 )
791 FreeShortMtx( commonIP );
794 ll1 = MAX( orlgth1, commonAlloc1 );
795 ll2 = MAX( orlgth2, commonAlloc2 );
798 fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
801 commonIP = AllocateShortMtx( ll1+10, ll2+10 );
804 fprintf( stderr, "succeeded\n\n" );
815 for( i=0; i<icyc; i++ )
817 fprintf( stderr, "## totaleff = %f\n", t );
821 cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
822 cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
826 new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
827 new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
828 new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 );
829 new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
830 getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
831 getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
832 getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 );
833 getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 );
834 getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
835 getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
836 getgapfreq_zure_part( gapz1, icyc, seq1, eff1, lgth1, sgap1 );
837 getgapfreq_zure_part( gapz2, jcyc, seq2, eff2, lgth2, sgap1 );
841 st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 );
842 st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 );
843 st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 );
844 st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 );
845 getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 );
846 getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 );
847 getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 );
848 getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 );
849 getgapfreq( gapf1, icyc, seq1, eff1, lgth1 );
850 getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 );
851 getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 );
852 getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 );
857 // fprintf( stderr, "lgth2 = %d\n", lgth2 );
858 for( i=0; i<lastj; i++ )
860 og_h_dg_n2_p[i] = ( 1.0-ogcp2g[i]-digf2[i] ) * fpenalty * 0.5;
861 fg_h_dg_n2_p[i] = ( 1.0-fgcp2g[i]-digf2[i] ) * fpenalty * 0.5;
862 og_t_fg_h_dg_n2_p[i] = (1.0-ogcp2g[i]+fgcp2g[i]-digf2[i]) * 0.5 * fpenalty;
863 fg_t_og_h_dg_n2_p[i] = (1.0-fgcp2g[i]+ogcp2g[i]-digf2[i]) * 0.5 * fpenalty;
864 gapz_n2[i] = (1.0-gapz2[i]);
867 for( i=0; i<lastj; i++ )
869 og_h_dg_n1_p[i] = ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
870 fg_h_dg_n1_p[i] = ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
871 og_t_fg_h_dg_n1_p[i] = (1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) * 0.5 * fpenalty;
872 fg_t_og_h_dg_n1_p[i] = (1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) * 0.5 * fpenalty;
873 gapz_n1[i] = (1.0-gapz1[i]);
879 for( i=0; i<lgth1; i++ )
880 fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
886 match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
888 imp_match_out_vead_tateQ( initverticalw, 0, lgth1 ); // 060306
890 match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
892 imp_match_out_veadQ( currentw, 0, lgth2 ); // 060306
897 imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
908 // g += ogcp1g[0] * og_h_dg_n2_p[0];
909 g += ogcp1g[0] * ( 1.0-ogcp2g[0]-digf2[0] ) * fpenalty * 0.5;
910 // if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
912 // g += ogcp2g[0] * og_h_dg_n1_p[0];
913 g += ogcp2g[0] * ( 1.0-ogcp1g[0]-digf1[0] ) * fpenalty * 0.5;
914 // if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] );
916 // g += fgcp1g[0] * fg_h_dg_n2_p[0];
917 g += fgcp1g[0] * ( 1.0-fgcp2g[0]-digf2[0] ) * fpenalty * 0.5;
918 // if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
920 // g += fgcp2g[0] * fg_h_dg_n1_p[0];
921 g += fgcp2g[0] * ( 1.0-fgcp1g[0]-digf1[0] ) * fpenalty * 0.5;
922 // if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
925 initverticalw[0] += g;
928 for( i=1; i<lgth1+1; i++ )
930 // tmppenal = gapz_n2[0]*og_t_fg_h_dg_n1_p[0];
931 tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+fgcp1g[0]-digf1[0]) ) * 0.5 * fpenalty; // mada
932 initverticalw[i] += tmppenal;
934 // tmppenal = gapz_n2[1]*fg_t_og_h_dg_n1_p[i];
935 tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
936 initverticalw[i] += tmppenal;
939 for( j=1; j<lgth2+1; j++ )
941 // tmppenal = gapz_n1[0]*og_t_fg_h_dg_n2_p[0];
942 tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+fgcp2g[0]-digf2[0]) ) * 0.5 * fpenalty; // mada
943 currentw[j] += tmppenal;
945 // tmppenal = gapz_n1[1]*fg_t_og_h_dg_n2_p[j];
946 tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
947 currentw[j] += tmppenal;
953 for( j=1; j<lgth2+1; j++ )
954 currentw[j] -= offset * j / 2.0;
955 for( i=1; i<lgth1+1; i++ )
956 initverticalw[i] -= offset * i / 2.0;
960 m[0] = 0.0; // iranai
961 for( j=1; j<lgth2+1; ++j )
964 m[j] = currentw[j-1] + 10000 * fpenalty; //iinoka?
967 lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
969 lastverticalw[0] = currentw[lgth2-1];
971 if( outgap ) lasti = lgth1+1; else lasti = lgth1;
974 fprintf( stderr, "currentw = \n" );
975 for( i=0; i<lgth1+1; i++ )
977 fprintf( stderr, "%5.2f ", currentw[i] );
979 fprintf( stderr, "\n" );
980 fprintf( stderr, "initverticalw = \n" );
981 for( i=0; i<lgth2+1; i++ )
983 fprintf( stderr, "%5.2f ", initverticalw[i] );
985 fprintf( stderr, "\n" );
986 fprintf( stderr, "fcgp\n" );
987 for( i=0; i<lgth1; i++ )
988 fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
989 for( i=0; i<lgth2; i++ )
990 fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
993 for( i=1; i<lasti; i++ )
996 previousw = currentw;
999 previousw[0] = initverticalw[i-1];
1001 match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
1003 fprintf( stderr, "\n" );
1004 fprintf( stderr, "i=%d\n", i );
1005 fprintf( stderr, "currentw = \n" );
1006 for( j=0; j<lgth2; j++ )
1008 fprintf( stderr, "%5.2f ", currentw[j] );
1010 fprintf( stderr, "\n" );
1014 // fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
1016 imp_match_out_veadQ( currentw, i, lgth2 );
1018 imp_match_out_veadQ( currentw, i, lgth2 );
1022 fprintf( stderr, "\n" );
1023 fprintf( stderr, "i=%d\n", i );
1024 fprintf( stderr, "currentw = \n" );
1025 for( j=0; j<lgth2; j++ )
1027 fprintf( stderr, "%5.2f ", currentw[j] );
1029 fprintf( stderr, "\n" );
1031 currentw[0] = initverticalw[i];
1034 mi = previousw[0] + 10000 * fpenalty;
1039 curpt = currentw + 1;
1041 fg_t_og_h_dg_n2_p_pt = fg_t_og_h_dg_n2_p + 1;
1042 og_t_fg_h_dg_n2_p_pt = og_t_fg_h_dg_n2_p + 1;
1043 og_h_dg_n2_p_pt = og_h_dg_n2_p + 1;
1044 fg_h_dg_n2_p_pt = fg_h_dg_n2_p + 1;
1045 gapz_n2_pt0 = gapz_n2 + 1;
1046 gapz_n2_pt1 = gapz_n2 + 2;
1047 fgcp2pt = fgcp2g + 1;
1048 ogcp2pt = ogcp2g + 1;
1050 fg_t_og_h_dg_n1_p_va = fg_t_og_h_dg_n1_p[i];
1051 og_t_fg_h_dg_n1_p_va = og_t_fg_h_dg_n1_p[i];
1052 og_h_dg_n1_p_va = og_h_dg_n1_p[i];
1053 fg_h_dg_n1_p_va = fg_h_dg_n1_p[i];
1054 gapz_n1_va0 = gapz_n1[i];
1055 gapz_n1_va1 = gapz_n1[i+1];
1056 fgcp1va = fgcp1g[i];
1057 ogcp1va = ogcp1g[i];
1060 for( j=1; j<lastj; j++ )
1064 // g = ogcp1va * *og_h_dg_n2_p_pt;
1065 // g = ogcp1g[i] * og_h_dg_n2_p[j];
1066 g = ogcp1g[i] * ( 1.0-ogcp2g[j]-digf2[j] ) * fpenalty * 0.5;
1067 // if( g && i==j ) fprintf( stderr, "match penal1=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
1070 // g = *ogcp2pt * og_h_dg_n1_p_va;
1071 // g = ogcp2g[j] * og_h_dg_n1_p[i];
1072 g = ogcp2g[j] * ( 1.0-ogcp1g[i]-digf1[i] ) * fpenalty * 0.5;
1073 // if( g && i==j ) fprintf( stderr, "match penal2=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
1076 // g = fgcp1va * *fg_h_dg_n2_p_pt;
1077 // g = fgcp1g[i] * fg_h_dg_n2_p[j];
1078 g = fgcp1g[i] * ( 1.0-fgcp2g[j]-digf2[j] ) * fpenalty * 0.5;
1079 // if( g && i==j ) fprintf( stderr, "match penal3=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
1082 // g = *fgcp2pt * fg_h_dg_n1_p_va;
1083 // g = fgcp2g[j] * fg_h_dg_n1_p[i];
1084 g = fgcp2g[j] * ( 1.0-fgcp1g[i]-digf1[i] ) * fpenalty * 0.5;
1085 // if( g && i==j ) fprintf( stderr, "match penal4=%f, %c-%c\n", g, seq1[0][i], seq2[0][j] );
1091 fprintf( stderr, "%5.0f->", wm );
1094 fprintf( stderr, "%5.0f?", g );
1096 // tmppenal = gapz_n1_va1 * *fg_t_og_h_dg_n2_p_pt;
1097 // tmppenal = gapz_n1[i+1] * fg_t_og_h_dg_n2_p[j];
1098 tmppenal = ( (1.0-gapz1[i+1])*(1.0-fgcp2g[j]+ogcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
1099 if( (g=mi+tmppenal) > wm )
1101 // fprintf( stderr, "jump i start=%f (j=%d, fgcp2g[j]=%f, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, j, fgcp2g[j], digf2[j], diaf2[j], seq1[0][i], seq2[0][j] );
1103 *ijppt = -( j - mpi );
1105 // tmppenal = gapz_n1_va0 * *og_t_fg_h_dg_n2_p_pt;
1106 // tmppenal = gapz_n1[i] * og_t_fg_h_dg_n2_p[j];
1107 tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[j]+fgcp2g[j]-digf2[j]) ) * 0.5 * fpenalty; // mada
1108 if( (g=*prept+tmppenal) >= mi )
1110 // fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] );
1116 fprintf( stderr, "%5.0f?", g );
1118 // tmppenal = *gapz_n2_pt1 * fg_t_og_h_dg_n1_p_va;
1119 // tmppenal = gapz_n2[j+1] * fg_t_og_h_dg_n1_p[i];
1120 tmppenal = ( (1.0-gapz2[j+1])*(1.0-fgcp1g[i]+ogcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
1121 if( (g=*mjpt+tmppenal) > wm )
1124 *ijppt = +( i - *mpjpt );
1126 // tmppenal = *gapz_n2_pt0 * og_t_fg_h_dg_n1_p_va;
1127 // tmppenal = gapz_n2[j] * og_t_fg_h_dg_n1_p[i];
1128 tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[i]+fgcp1g[i]-digf1[i]) ) * 0.5 * fpenalty; // mada
1129 if( (g=*prept+tmppenal) >= *mjpt )
1135 fprintf( stderr, "%5.0f ", wm );
1142 fg_t_og_h_dg_n2_p_pt++;
1143 og_t_fg_h_dg_n2_p_pt++;
1151 lastverticalw[i] = currentw[lgth2-1];
1154 // fprintf( stderr, "wm = %f\n", wm );
1159 for( j=1; j<lgth2+1; j++ )
1160 currentw[j] -= offset * ( lgth2 - j ) / 2.0;
1161 for( i=1; i<lgth1+1; i++ )
1162 lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
1167 fprintf( stderr, "\n" );
1168 for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
1169 fprintf( stderr, "#####\n" );
1170 for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
1171 fprintf( stderr, "====>" );
1172 for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
1173 for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
1177 Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1180 Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
1182 // fprintf( stderr, "### impmatch = %f\n", *impmatch );
1184 resultlen = strlen( mseq1[0] );
1185 if( alloclen < resultlen || resultlen > N )
1187 fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
1188 ErrorExit( "LENGTH OVER!\n" );
1192 for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
1193 for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
1195 fprintf( stderr, "\n" );
1196 for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
1197 fprintf( stderr, "#####\n" );
1198 for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
1201 fprintf( stderr, "wm = %f\n", wm );