| #include "mltaln.h" |
| #include "dp.h" |
| |
| #define MACHIGAI 0 |
| #define OUTGAP0TRY 1 |
| #define DEBUG 0 |
| #define XXXXXXX 0 |
| #define USE_PENALTY_EX 0 |
| #define FASTMATCHCALC 1 |
| |
| static float **impmtx = NULL; |
| |
| #if 0 // by D.Mathog |
| static float countnocountxx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int offset2 ) |
| { |
| // return( 0.0 ); |
| float gclose; |
| float gmatch; |
| Gappat *pat1bk = pat1; |
| Gappat *pat2bk = pat2; |
| |
| gmatch = 0.0; |
| for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0 |
| { |
| if( pat2->len + offset2 == offset1 ) |
| { |
| gmatch = diaf1 * pat2->freq; |
| } |
| } |
| for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) // excl. len=0 |
| { |
| for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0 |
| { |
| if( pat1->len + offset1 == pat2->len + offset2 ) |
| { |
| gmatch += pat1->freq * pat2->freq; |
| // if( r ) fprintf( stderr, "match1!!, len=%d, gmatch=%f * %f\n", pat2->len, pat1->freq, pat2->freq ); |
| } |
| } |
| } |
| return( gmatch ); |
| } |
| #endif |
| |
| static float countnocountmatchx( Gappat *pat1, Gappat *pat2, int offset1, int offset2, int r ) |
| { |
| Gappat *pat1bk = pat1; |
| Gappat *pat2bk = pat2; |
| float val = 0.0; |
| // pat1[][0] ha total gap. |
| for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) |
| { |
| for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) |
| { |
| if( pat1->len + offset1 == pat2->len + offset2 ) |
| { |
| val += pat1->freq * pat2->freq; |
| if( r ) fprintf( stderr, "y %d-%d, len=%d,%d, val = %f\n", (int)(pat1-pat1bk), (int)(pat2-pat2bk), pat1->len, pat2->len, val ); // 070405 |
| // if( r ) fprintf( stderr, "y %d-%d, len=%d,%d, val = %f\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len, val ); |
| } |
| } |
| } |
| if( r ) fprintf( stderr, "nocountmatch=%f\n", val ); |
| return( val ); |
| } |
| |
| #if 0 // by D.Mathog |
| static float countnocountmatch( Gappat *pat1, Gappat *pat2, int r ) |
| { |
| // return( 0.0 ); |
| Gappat *pat1bk = pat1; |
| Gappat *pat2bk = pat2; |
| float val = 0.0; |
| // pat1[][0] ha total gap. |
| for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) |
| { |
| // if( r ) fprintf( stderr, "b %d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len ); |
| for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) |
| { |
| if( pat1->len == pat2->len ) |
| { |
| // if( r ) fprintf( stderr, " x%d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len ); |
| val += pat1->freq * pat2->freq; |
| // if( r ) fprintf( stderr, "y %d-%d, val = %f\n", pat1-pat1bk, pat2-pat2bk,val ); |
| // if( r ) fprintf( stderr, "z tsugi, %d-%d, len=%d,%d\n", pat1-pat1bk+1, pat2-pat2bk+1, (pat1+1)->len, (pat2+1)->len ); |
| } |
| // if( r ) fprintf( stderr, "a %d-%d, len=%d,%d\n", pat1-pat1bk, pat2-pat2bk, pat1->len, pat2->len ); |
| } |
| } |
| // fprintf( stderr, "nocountmatch=%f\n", val ); |
| return( val ); |
| } |
| #endif |
| |
| static float countnocountx( Gappat *pat1, float diaf1, Gappat *pat2, int offset1, int r ) |
| { |
| // return( 0.0 ); |
| float gmatch; |
| Gappat *pat1bk = pat1; |
| Gappat *pat2bk = pat2; |
| |
| gmatch = 0.0; |
| for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0 |
| { |
| if( pat2->len == offset1 ) |
| { |
| gmatch = diaf1 * pat2->freq; |
| // if( r ) fprintf( stderr, "match0!!, len=%d, gmatch=%f * %f\n", pat2->len, diaf1, pat2->freq ); |
| } |
| } |
| for( pat1=pat1bk+1; pat1->len != 0; pat1++ ) // excl. len=0 |
| { |
| for( pat2=pat2bk+1; pat2->len != 0; pat2++ ) // excl. len=0 |
| { |
| if( pat1->len + offset1 == pat2->len ) |
| { |
| gmatch += pat1->freq * pat2->freq; |
| // if( r ) fprintf( stderr, "match1!!, len=%d, gmatch=%f * %f\n", pat2->len, pat1->freq, pat2->freq ); |
| } |
| } |
| } |
| return( gmatch ); |
| } |
| |
| #if 0 // by D.Mathog |
| static float countnocount( Gappat *pat1, Gappat *pat2, int offset1, int offset2 ) //osoi |
| { |
| // return( 0.0 ); |
| Gappat *pat1bk = pat1; |
| Gappat *pat2bk = pat2; |
| float val = 0.0; |
| // pat1[][0] ha total gap. |
| for( pat1=pat1bk+1; pat1->len != -1; pat1++ ) |
| { |
| for( pat2=pat2bk+1; pat2->len != -1; pat2++ ) |
| { |
| if( pat1->len+offset1 == pat2->len+offset2 ) |
| { |
| val += pat1->freq * pat2->freq; |
| } |
| } |
| } |
| // fprintf( stderr, "nocount=%f\n", val ); |
| return( val ); |
| } |
| #endif |
| |
| |
| |
| #if 1 // tditeration |
| float imp_match_out_scH( int i1, int j1 ) |
| { |
| // fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold ); |
| // fprintf( stderr, "val = %f\n", impmtx[i1][j1] ); |
| return( impmtx[i1][j1] ); |
| } |
| #endif |
| |
| static void imp_match_out_veadH( float *imp, int i1, int lgth2 ) |
| { |
| #if FASTMATCHCALC |
| float *pt = impmtx[i1]; |
| while( lgth2-- ) |
| *imp++ += *pt++; |
| #else |
| int j; |
| float *pt = impmtx[i1]; |
| for( j=0; j<lgth2; j++ ) |
| *imp++ += pt[j]; |
| #endif |
| } |
| static void imp_match_out_vead_tateH( float *imp, int j1, int lgth1 ) |
| { |
| int i; |
| for( i=0; i<lgth1; i++ ) |
| *imp++ += impmtx[i][j1]; |
| } |
| |
| #if 1 // tbfast.c kara yobareru. |
| void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore ) |
| { |
| int i, j, k1, k2, tmpint, start1, start2, end1, end2; |
| static int impalloclen = 0; |
| float effij; |
| double effijx; |
| char *pt, *pt1, *pt2; |
| static char *nocount1 = NULL; |
| static char *nocount2 = NULL; |
| LocalHom *tmpptr; |
| |
| if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 ) |
| { |
| if( impmtx ) FreeFloatMtx( impmtx ); |
| if( nocount1 ) free( nocount1 ); |
| if( nocount2 ) free( nocount2 ); |
| impalloclen = MAX( lgth1, lgth2 ) + 2; |
| impmtx = AllocateFloatMtx( impalloclen, impalloclen ); |
| nocount1 = AllocateCharVec( impalloclen ); |
| nocount2 = AllocateCharVec( impalloclen ); |
| } |
| |
| for( i=0; i<lgth1; i++ ) |
| { |
| for( j=0; j<clus1; j++ ) |
| if( seq1[j][i] == '-' ) break; |
| if( j != clus1 ) nocount1[i] = 1; |
| else nocount1[i] = 0; |
| } |
| for( i=0; i<lgth2; i++ ) |
| { |
| for( j=0; j<clus2; j++ ) |
| if( seq2[j][i] == '-' ) break; |
| if( j != clus2 ) nocount2[i] = 1; |
| else nocount2[i] = 0; |
| } |
| |
| #if 0 |
| fprintf( stderr, "nocount2 =\n" ); |
| for( i = 0; i<impalloclen; i++ ) |
| { |
| fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] ); |
| } |
| #endif |
| |
| |
| |
| #if 0 |
| fprintf( stderr, "eff1 in _init_strict = \n" ); |
| for( i=0; i<clus1; i++ ) |
| fprintf( stderr, "eff1[] = %f\n", eff1[i] ); |
| for( i=0; i<clus2; i++ ) |
| fprintf( stderr, "eff2[] = %f\n", eff2[i] ); |
| #endif |
| |
| for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ ) |
| impmtx[i][j] = 0.0; |
| effijx = fastathreshold; |
| for( i=0; i<clus1; i++ ) |
| { |
| for( j=0; j<clus2; j++ ) |
| { |
| effij = (float)( eff1[i] * eff2[j] * effijx ); |
| tmpptr = localhom[i][j]; |
| while( tmpptr ) |
| { |
| // fprintf( stderr, "start1 = %d\n", tmpptr->start1 ); |
| // fprintf( stderr, "end1 = %d\n", tmpptr->end1 ); |
| // fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] ); |
| // fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] ); |
| pt = seq1[i]; |
| tmpint = -1; |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == tmpptr->start1 ) break; |
| } |
| start1 = pt - seq1[i] - 1; |
| |
| if( tmpptr->start1 == tmpptr->end1 ) end1 = start1; |
| else |
| { |
| #if MACHIGAI |
| while( *pt != 0 ) |
| { |
| // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] ); |
| if( tmpint == tmpptr->end1 ) break; |
| if( *pt++ != '-' ) tmpint++; |
| } |
| end1 = pt - seq1[i] - 0; |
| #else |
| while( *pt != 0 ) |
| { |
| // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] ); |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == tmpptr->end1 ) break; |
| } |
| end1 = pt - seq1[i] - 1; |
| #endif |
| } |
| |
| pt = seq2[j]; |
| tmpint = -1; |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == tmpptr->start2 ) break; |
| } |
| start2 = pt - seq2[j] - 1; |
| if( tmpptr->start2 == tmpptr->end2 ) end2 = start2; |
| else |
| { |
| #if MACHIGAI |
| while( *pt != 0 ) |
| { |
| if( tmpint == tmpptr->end2 ) break; |
| if( *pt++ != '-' ) tmpint++; |
| } |
| end2 = pt - seq2[j] - 0; |
| #else |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == tmpptr->end2 ) break; |
| } |
| end2 = pt - seq2[j] - 1; |
| #endif |
| } |
| // 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] ); |
| // fprintf( stderr, "step 0\n" ); |
| if( end1 - start1 != end2 - start2 ) |
| { |
| // fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 ); |
| } |
| |
| #if 1 |
| k1 = start1; k2 = start2; |
| pt1 = seq1[i] + k1; |
| pt2 = seq2[j] + k2; |
| while( *pt1 && *pt2 ) |
| { |
| if( *pt1 != '-' && *pt2 != '-' ) |
| { |
| // ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃðդ·¤Æ²¼¤µ¤¤¡£ |
| // impmtx[k1][k2] += tmpptr->wimportance * fastathreshold; |
| // impmtx[k1][k2] += tmpptr->importance * effij; |
| impmtx[k1][k2] += tmpptr->fimportance * effij; |
| // fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij ); |
| // fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 ); |
| // fprintf( stderr, "%d (%c) - %d (%c) - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij ); |
| k1++; k2++; |
| pt1++; pt2++; |
| } |
| else if( *pt1 != '-' && *pt2 == '-' ) |
| { |
| // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 ); |
| k2++; pt2++; |
| } |
| else if( *pt1 == '-' && *pt2 != '-' ) |
| { |
| // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 ); |
| k1++; pt1++; |
| } |
| else if( *pt1 == '-' && *pt2 == '-' ) |
| { |
| // fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 ); |
| k1++; pt1++; |
| k2++; pt2++; |
| } |
| if( k1 > end1 || k2 > end2 ) break; |
| } |
| #else |
| while( k1 <= end1 && k2 <= end2 ) |
| { |
| fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 ); |
| if( !nocount1[k1] && !nocount2[k2] ) |
| { |
| impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j] * fastathreshold; |
| fprintf( stderr, "marked\n" ); |
| } |
| else |
| fprintf( stderr, "no count\n" ); |
| k1++; k2++; |
| } |
| #endif |
| tmpptr = tmpptr->next; |
| } |
| } |
| } |
| #if 0 |
| if( clus1 == 1 && clus2 == 6 ) |
| { |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "seq1[0] = %s\n", seq1[0] ); |
| fprintf( stderr, "seq2[0] = %s\n", seq2[0] ); |
| fprintf( stderr, "impmtx = \n" ); |
| for( k2=0; k2<lgth2; k2++ ) |
| fprintf( stderr, "%6.3f ", (double)k2 ); |
| fprintf( stderr, "\n" ); |
| for( k1=0; k1<lgth1; k1++ ) |
| { |
| fprintf( stderr, "%d ", k1 ); |
| for( k2=0; k2<3; k2++ ) |
| fprintf( stderr, "%2.1f ", impmtx[k1][k2] ); |
| fprintf( stderr, "\n" ); |
| } |
| exit( 1 ); |
| } |
| #endif |
| } |
| #endif |
| |
| |
| static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize ) |
| { |
| #if FASTMATCHCALC |
| int j, l; |
| float scarr[26]; |
| float **cpmxpd = floatwork; |
| int **cpmxpdn = intwork; |
| float *matchpt, *cpmxpdpt, **cpmxpdptpt; |
| int *cpmxpdnpt, **cpmxpdnptpt; |
| if( initialize ) |
| { |
| int count = 0; |
| for( j=0; j<lgth2; j++ ) |
| { |
| count = 0; |
| for( l=0; l<26; l++ ) |
| { |
| if( cpmx2[l][j] ) |
| { |
| cpmxpd[j][count] = cpmx2[l][j]; |
| cpmxpdn[j][count] = l; |
| count++; |
| } |
| } |
| cpmxpdn[j][count] = -1; |
| } |
| } |
| |
| { |
| for( l=0; l<26; l++ ) |
| { |
| scarr[l] = 0.0; |
| for( j=0; j<26; j++ ) |
| scarr[l] += n_dis[j][l] * cpmx1[j][i1]; |
| } |
| matchpt = match; |
| cpmxpdnptpt = cpmxpdn; |
| cpmxpdptpt = cpmxpd; |
| while( lgth2-- ) |
| { |
| *matchpt = 0.0; |
| cpmxpdnpt = *cpmxpdnptpt++; |
| cpmxpdpt = *cpmxpdptpt++; |
| while( *cpmxpdnpt>-1 ) |
| *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++; |
| matchpt++; |
| } |
| } |
| #else |
| int j, k, l; |
| float scarr[26]; |
| float **cpmxpd = floatwork; |
| int **cpmxpdn = intwork; |
| // simple |
| if( initialize ) |
| { |
| int count = 0; |
| for( j=0; j<lgth2; j++ ) |
| { |
| count = 0; |
| for( l=0; l<26; l++ ) |
| { |
| if( cpmx2[l][j] ) |
| { |
| cpmxpd[count][j] = cpmx2[l][j]; |
| cpmxpdn[count][j] = l; |
| count++; |
| } |
| } |
| cpmxpdn[count][j] = -1; |
| } |
| } |
| for( l=0; l<26; l++ ) |
| { |
| scarr[l] = 0.0; |
| for( k=0; k<26; k++ ) |
| scarr[l] += n_dis[k][l] * cpmx1[k][i1]; |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| match[j] = 0.0; |
| for( k=0; cpmxpdn[k][j]>-1; k++ ) |
| match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j]; |
| } |
| #endif |
| } |
| |
| static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw, |
| char **seq1, char **seq2, |
| char **mseq1, char **mseq2, |
| float **cpmx1, float **cpmx2, |
| int **ijp, int icyc, int jcyc ) |
| { |
| int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k; |
| float wm; |
| char *gaptable1, *gt1bk; |
| char *gaptable2, *gt2bk; |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| gt1bk = AllocateCharVec( lgth1+lgth2+1 ); |
| gt2bk = AllocateCharVec( lgth1+lgth2+1 ); |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] ); |
| } |
| #endif |
| |
| if( outgap == 1 ) |
| ; |
| else |
| { |
| wm = lastverticalw[0]; |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( lastverticalw[i] >= wm ) |
| { |
| wm = lastverticalw[i]; |
| iin = i; jin = lgth2-1; |
| ijp[lgth1][lgth2] = +( lgth1 - i ); |
| } |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| if( lasthorizontalw[j] >= wm ) |
| { |
| wm = lasthorizontalw[j]; |
| iin = lgth1-1; jin = j; |
| ijp[lgth1][lgth2] = -( lgth2 - j ); |
| } |
| } |
| } |
| |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| ijp[i][0] = i + 1; |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| ijp[0][j] = -( j + 1 ); |
| } |
| |
| gaptable1 = gt1bk + lgth1+lgth2; |
| *gaptable1 = 0; |
| gaptable2 = gt2bk + lgth1+lgth2; |
| *gaptable2 = 0; |
| |
| iin = lgth1; jin = lgth2; |
| *impwmpt = 0.0; |
| for( k=0; k<=lgth1+lgth2; k++ ) |
| { |
| if( ijp[iin][jin] < 0 ) |
| { |
| ifi = iin-1; jfi = jin+ijp[iin][jin]; |
| } |
| else if( ijp[iin][jin] > 0 ) |
| { |
| ifi = iin-ijp[iin][jin]; jfi = jin-1; |
| } |
| else |
| { |
| ifi = iin-1; jfi = jin-1; |
| } |
| l = iin - ifi; |
| while( --l ) |
| { |
| *--gaptable1 = 'o'; |
| *--gaptable2 = '-'; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| *--gaptable1 = '-'; |
| *--gaptable2 = 'o'; |
| k++; |
| } |
| if( iin == lgth1 || jin == lgth2 ) |
| ; |
| else |
| { |
| *impwmpt += imp_match_out_scH( iin, jin ); |
| |
| // fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] ); |
| } |
| if( iin <= 0 || jin <= 0 ) break; |
| *--gaptable1 = 'o'; |
| *--gaptable2 = 'o'; |
| k++; |
| iin = ifi; jin = jfi; |
| } |
| |
| for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 ); |
| for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 ); |
| |
| free( gt1bk ); |
| free( gt2bk ); |
| } |
| |
| static float Atracking( float *lasthorizontalw, float *lastverticalw, |
| char **seq1, char **seq2, |
| char **mseq1, char **mseq2, |
| float **cpmx1, float **cpmx2, |
| int **ijp, int icyc, int jcyc ) |
| { |
| int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k; |
| float wm; |
| char *gaptable1, *gt1bk; |
| char *gaptable2, *gt2bk; |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| gt1bk = AllocateCharVec( lgth1+lgth2+1 ); |
| gt2bk = AllocateCharVec( lgth1+lgth2+1 ); |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| { |
| fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] ); |
| } |
| #endif |
| |
| if( outgap == 1 ) |
| ; |
| else |
| { |
| wm = lastverticalw[0]; |
| for( i=0; i<lgth1; i++ ) |
| { |
| if( lastverticalw[i] >= wm ) |
| { |
| wm = lastverticalw[i]; |
| iin = i; jin = lgth2-1; |
| ijp[lgth1][lgth2] = +( lgth1 - i ); |
| } |
| } |
| for( j=0; j<lgth2; j++ ) |
| { |
| if( lasthorizontalw[j] >= wm ) |
| { |
| wm = lasthorizontalw[j]; |
| iin = lgth1-1; jin = j; |
| ijp[lgth1][lgth2] = -( lgth2 - j ); |
| } |
| } |
| } |
| |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| ijp[i][0] = i + 1; |
| } |
| for( j=0; j<lgth2+1; j++ ) |
| { |
| ijp[0][j] = -( j + 1 ); |
| } |
| |
| gaptable1 = gt1bk + lgth1+lgth2; |
| *gaptable1 = 0; |
| gaptable2 = gt2bk + lgth1+lgth2; |
| *gaptable2 = 0; |
| |
| iin = lgth1; jin = lgth2; |
| for( k=0; k<=lgth1+lgth2; k++ ) |
| { |
| if( ijp[iin][jin] < 0 ) |
| { |
| ifi = iin-1; jfi = jin+ijp[iin][jin]; |
| } |
| else if( ijp[iin][jin] > 0 ) |
| { |
| ifi = iin-ijp[iin][jin]; jfi = jin-1; |
| } |
| else |
| { |
| ifi = iin-1; jfi = jin-1; |
| } |
| l = iin - ifi; |
| while( --l ) |
| { |
| *--gaptable1 = 'o'; |
| *--gaptable2 = '-'; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| *--gaptable1 = '-'; |
| *--gaptable2 = 'o'; |
| k++; |
| } |
| if( iin <= 0 || jin <= 0 ) break; |
| *--gaptable1 = 'o'; |
| *--gaptable2 = 'o'; |
| k++; |
| iin = ifi; jin = jfi; |
| } |
| |
| for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 ); |
| for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 ); |
| |
| free( gt1bk ); |
| free( gt2bk ); |
| |
| return( 0.0 ); |
| } |
| |
| float H__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 ) |
| /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */ |
| { |
| // int k; |
| register int i, j; |
| int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */ |
| int lgth1, lgth2; |
| int resultlen; |
| float wm = 0.0; /* int ?????? */ |
| float g; |
| float *currentw, *previousw; |
| // float fpenalty = (float)penalty; |
| #if USE_PENALTY_EX |
| float fpenalty_ex = (float)penalty_ex; |
| #endif |
| #if 1 |
| float *wtmp; |
| int *ijppt; |
| float *mjpt, *prept, *curpt; |
| int *mpjpt; |
| #endif |
| static float mi, *m; |
| static int **ijp; |
| static int mpi, *mp; |
| static float *w1, *w2; |
| static float *match; |
| static float *initverticalw; /* kufuu sureba iranai */ |
| static float *lastverticalw; /* kufuu sureba iranai */ |
| static char **mseq1; |
| static char **mseq2; |
| static char **mseq; |
| static Gappat **gappat1; |
| static Gappat **gappat2; |
| static float *digf1; |
| static float *digf2; |
| static float *diaf1; |
| static float *diaf2; |
| static float *gapz1; |
| static float *gapz2; |
| static float *gapf1; |
| static float *gapf2; |
| static float *ogcp1g; |
| static float *ogcp2g; |
| static float *fgcp1g; |
| static float *fgcp2g; |
| static float *ogcp1; |
| static float *ogcp2; |
| static float *fgcp1; |
| static float *fgcp2; |
| static float **cpmx1; |
| static float **cpmx2; |
| static int **intwork; |
| static float **floatwork; |
| static int orlgth1 = 0, orlgth2 = 0; |
| float fpenalty = (float)penalty; |
| float tmppenal; |
| float cumpenal; |
| float *fgcp2pt; |
| float *ogcp2pt; |
| float fgcp1va; |
| float ogcp1va; |
| int maegap; |
| |
| |
| |
| #if 0 |
| fprintf( stderr, "#### eff in SA+++align\n" ); |
| fprintf( stderr, "#### seq1[0] = %s\n", seq1[0] ); |
| fprintf( stderr, "#### strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) ); |
| for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] ); |
| #endif |
| if( orlgth1 == 0 ) |
| { |
| mseq1 = AllocateCharMtx( njob, 0 ); |
| mseq2 = AllocateCharMtx( njob, 0 ); |
| } |
| |
| |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| #if 0 |
| if( lgth1 == 0 || lgth2 == 0 ) |
| { |
| fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 ); |
| } |
| #endif |
| |
| if( lgth1 > orlgth1 || lgth2 > orlgth2 ) |
| { |
| int ll1, ll2; |
| |
| if( orlgth1 > 0 && orlgth2 > 0 ) |
| { |
| FreeFloatVec( w1 ); |
| FreeFloatVec( w2 ); |
| FreeFloatVec( match ); |
| FreeFloatVec( initverticalw ); |
| FreeFloatVec( lastverticalw ); |
| |
| FreeFloatVec( m ); |
| FreeIntVec( mp ); |
| |
| FreeCharMtx( mseq ); |
| |
| free( gappat1 ); |
| free( gappat2 ); |
| FreeFloatVec( digf1 ); |
| FreeFloatVec( digf2 ); |
| FreeFloatVec( diaf1 ); |
| FreeFloatVec( diaf2 ); |
| FreeFloatVec( gapz1 ); |
| FreeFloatVec( gapz2 ); |
| FreeFloatVec( gapf1 ); |
| FreeFloatVec( gapf2 ); |
| FreeFloatVec( ogcp1 ); |
| FreeFloatVec( ogcp2 ); |
| FreeFloatVec( fgcp1 ); |
| FreeFloatVec( fgcp2 ); |
| FreeFloatVec( ogcp1g ); |
| FreeFloatVec( ogcp2g ); |
| FreeFloatVec( fgcp1g ); |
| FreeFloatVec( fgcp2g ); |
| |
| |
| FreeFloatMtx( cpmx1 ); |
| FreeFloatMtx( cpmx2 ); |
| |
| FreeFloatMtx( floatwork ); |
| FreeIntMtx( intwork ); |
| } |
| |
| ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100; |
| ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100; |
| |
| #if DEBUG |
| fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 ); |
| #endif |
| |
| w1 = AllocateFloatVec( ll2+2 ); |
| w2 = AllocateFloatVec( ll2+2 ); |
| match = AllocateFloatVec( ll2+2 ); |
| |
| initverticalw = AllocateFloatVec( ll1+2 ); |
| lastverticalw = AllocateFloatVec( ll1+2 ); |
| |
| m = AllocateFloatVec( ll2+2 ); |
| mp = AllocateIntVec( ll2+2 ); |
| |
| mseq = AllocateCharMtx( njob, ll1+ll2 ); |
| |
| digf1 = AllocateFloatVec( ll1+2 ); |
| digf2 = AllocateFloatVec( ll2+2 ); |
| diaf1 = AllocateFloatVec( ll1+2 ); |
| diaf2 = AllocateFloatVec( ll2+2 ); |
| gappat1 = (Gappat **)calloc( ll1+2, sizeof( Gappat * ) ); |
| gappat2 = (Gappat **)calloc( ll2+2, sizeof( Gappat * ) ); |
| gapz1 = AllocateFloatVec( ll1+2 ); |
| gapz2 = AllocateFloatVec( ll2+2 ); |
| gapf1 = AllocateFloatVec( ll1+2 ); |
| gapf2 = AllocateFloatVec( ll2+2 ); |
| ogcp1 = AllocateFloatVec( ll1+2 ); |
| ogcp2 = AllocateFloatVec( ll2+2 ); |
| fgcp1 = AllocateFloatVec( ll1+2 ); |
| fgcp2 = AllocateFloatVec( ll2+2 ); |
| ogcp1g = AllocateFloatVec( ll1+2 ); |
| ogcp2g = AllocateFloatVec( ll2+2 ); |
| fgcp1g = AllocateFloatVec( ll1+2 ); |
| fgcp2g = AllocateFloatVec( ll2+2 ); |
| |
| cpmx1 = AllocateFloatMtx( 26, ll1+2 ); |
| cpmx2 = AllocateFloatMtx( 26, ll2+2 ); |
| |
| #if FASTMATCHCALC |
| floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); |
| intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 ); |
| #else |
| floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); |
| intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); |
| #endif |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n" ); |
| #endif |
| |
| orlgth1 = ll1 - 100; |
| orlgth2 = ll2 - 100; |
| } |
| |
| |
| for( i=0; i<icyc; i++ ) |
| { |
| mseq1[i] = mseq[i]; |
| seq1[i][lgth1] = 0; |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| mseq2[j] = mseq[icyc+j]; |
| seq2[j][lgth2] = 0; |
| } |
| |
| |
| if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 ) |
| { |
| int ll1, ll2; |
| |
| if( commonAlloc1 && commonAlloc2 ) |
| { |
| FreeIntMtx( commonIP ); |
| } |
| |
| ll1 = MAX( orlgth1, commonAlloc1 ); |
| ll2 = MAX( orlgth2, commonAlloc2 ); |
| |
| #if DEBUG |
| fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 ); |
| #endif |
| |
| commonIP = AllocateIntMtx( ll1+10, ll2+10 ); |
| |
| #if DEBUG |
| fprintf( stderr, "succeeded\n\n" ); |
| #endif |
| |
| commonAlloc1 = ll1; |
| commonAlloc2 = ll2; |
| } |
| ijp = commonIP; |
| |
| #if 0 |
| { |
| float t = 0.0; |
| for( i=0; i<icyc; i++ ) |
| t += eff1[i]; |
| fprintf( stderr, "## totaleff = %f\n", t ); |
| } |
| #endif |
| |
| cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); |
| cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc ); |
| |
| if( sgap1 ) |
| { |
| new_OpeningGapCount_zure( ogcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 ); |
| new_OpeningGapCount_zure( ogcp2g, jcyc, seq2, eff2, lgth2, sgap2, egap1 ); |
| new_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1, sgap1, egap1 ); |
| new_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2, sgap1, egap2 ); |
| getdigapfreq_part( digf1, icyc, seq1, eff1, lgth1, sgap1, egap1 ); // sgap1 ha iranai ? |
| getdigapfreq_part( digf2, jcyc, seq2, eff2, lgth2, sgap2, egap2 ); // sgap1 ha iranai ? |
| getdiaminofreq_part( diaf1, icyc, seq1, eff1, lgth1, sgap1, egap1 ); // sgap1 ha iranai ? |
| getdiaminofreq_part( diaf2, jcyc, seq2, eff2, lgth2, sgap1, egap2 ); // sgap1 ha iranai ? |
| getgapfreq( gapf1, icyc, seq1, eff1, lgth1 ); // atode |
| getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 ); // atode |
| getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 ); // atode |
| getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 ); // atode |
| } |
| else |
| { |
| st_OpeningGapCount( ogcp1g, icyc, seq1, eff1, lgth1 ); |
| st_OpeningGapCount( ogcp2g, jcyc, seq2, eff2, lgth2 ); |
| st_FinalGapCount_zure( fgcp1g, icyc, seq1, eff1, lgth1 ); |
| st_FinalGapCount_zure( fgcp2g, jcyc, seq2, eff2, lgth2 ); |
| st_getGapPattern( gappat1, icyc, seq1, eff1, lgth1 ); |
| st_getGapPattern( gappat2, jcyc, seq2, eff2, lgth2 ); |
| getdigapfreq_st( digf1, icyc, seq1, eff1, lgth1 ); |
| getdigapfreq_st( digf2, jcyc, seq2, eff2, lgth2 ); |
| getdiaminofreq_x( diaf1, icyc, seq1, eff1, lgth1 ); |
| getdiaminofreq_x( diaf2, jcyc, seq2, eff2, lgth2 ); |
| getgapfreq( gapf1, icyc, seq1, eff1, lgth1 ); |
| getgapfreq( gapf2, jcyc, seq2, eff2, lgth2 ); |
| getgapfreq_zure( gapz1, icyc, seq1, eff1, lgth1 ); |
| getgapfreq_zure( gapz2, jcyc, seq2, eff2, lgth2 ); |
| } |
| |
| #if 0 |
| for( i=0; i<lgth1; i++ ) |
| fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] ); |
| #endif |
| |
| currentw = w1; |
| previousw = w2; |
| |
| match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 ); |
| if( localhom ) |
| imp_match_out_vead_tateH( initverticalw, 0, lgth1 ); // 060306 |
| |
| match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 ); |
| if( localhom ) |
| imp_match_out_veadH( currentw, 0, lgth2 ); // 060306 |
| |
| |
| #if 0 // -> tbfast.c |
| if( localhom ) |
| imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 ); |
| |
| #endif |
| |
| if( outgap == 1 ) |
| { |
| // if( g ) fprintf( stderr, "init-match penal1=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] ); |
| // initverticalw[0] += g; |
| // currentw[0] += g; |
| |
| // if( g ) fprintf( stderr, "init-match penal2=%f, %c-%c\n", g, seq1[0][0], seq2[0][0] ); |
| // initverticalw[0] += g; |
| // currentw[0] += g; |
| |
| for( i=1; i<lgth1+1; i++ ) |
| { |
| // initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ; |
| |
| tmppenal = 0.0; |
| // tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapz2[0])*(1.0-ogcp1g[0]+0.0) + gapz2[0]*(1.0-digf1[0] - diaf1[0]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-0.0)*(1.0-ogcp1g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada |
| // tmppenal = 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-0.0) * (1.0-diaf1[0]) + 0.0 ) * 0.5 * fpenalty; // 0. |
| // tmppenal -= ( (1.0-gapf2[j-1]) * ogcp1g[i] + gapf2[j-1] ) * 0.5 * fpenalty; |
| // fprintf( stderr, "0,0<-%d,%d, tmppenal 1 = %f\n", i, 0, tmppenal ); |
| initverticalw[i] += tmppenal; |
| |
| tmppenal = diaf1[i] * ( 1.0 - gapf2[0] ) * fpenalty; |
| if( gappat1[i][0].freq ) |
| { |
| tmppenal += ( gappat1[i][0].freq ) * ( 1.0 - gapf2[0] ) * fpenalty; |
| tmppenal -= ( countnocountx( gappat2[0], diaf2[0], gappat1[i], i, 1 ) ) * fpenalty; |
| } |
| // tmppenal = ( (1.0-gapf2[j])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[j]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapz2[1])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapz2[1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapf2[0])*(1.0-fgcp1g[i]+ogcp1g[i]) + gapf2[0]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-gapf2[0]) * (1.0-diaf1[i]) + gapf2[0] ) * 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-gapf2[j]) * fgcp1g[i] + gapf2[j] ) * 0.5 * fpenalty; |
| initverticalw[i] += tmppenal; |
| // fprintf( stderr, "0,0<-%d,%d, tmppenal 2 = %f, cumpenal=%f, fgcp1g[i]=%f, ogcp1g[i]=%f\n", i, 0, tmppenal, cumpenal, fgcp1g[i], ogcp1g[i] ); |
| |
| } |
| cumpenal = 0.0; |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| // currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ; |
| |
| tmppenal = 0.0; |
| // tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[j]+fgcp2g[j]) + gapf1[i-1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapz1[0])*(1.0-ogcp2g[0]+0.0) + gapz1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-0.0)*(1.0-ogcp2g[0]+0.0) + 0.0*(1.0-0.0-0.0) ) * 0.5 * fpenalty; // mada |
| // tmppenal = 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-0.0) * (1.0-diaf2[0]) + 0.0 ) * 0.5 * fpenalty; // 0. |
| // tmppenal -= ( (1.0-gapf1[0]) * fgcp2g[j] + gapf1[0] ) * 0.5 * fpenalty; |
| // fprintf( stderr, "0,0<-%d,%d, tmppenal 3 = %f\n", 0, j, tmppenal ); |
| currentw[j] += tmppenal; |
| |
| tmppenal = diaf2[j] * ( 1.0 - gapf1[0] ) * fpenalty; |
| if( gappat2[j][0].freq ) |
| { |
| tmppenal += ( gappat2[j][0].freq ) * ( 1.0 - gapf1[0] ) * fpenalty; |
| tmppenal -= ( countnocountx( gappat1[0], diaf1[0], gappat2[j], j, 1 ) ) * fpenalty; |
| } |
| // tmppenal = ( (1.0-gapf1[i])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[i]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapz1[1])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapz1[1]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapf1[0])*(1.0-fgcp2g[j]+ogcp2g[j]) + gapf1[0]*(1.0-digf2[j]-diaf2[j]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-gapf1[0]) * (1.0-diaf2[j]) + gapf1[0] ) * 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-gapf1[0]) * ogcp2g[j] + gapf1[i-1] ) * 0.5 * fpenalty; |
| // fprintf( stderr, "0,0<-%d,%d, tmppenal 4 = %f\n", 0, j, tmppenal ); |
| currentw[j] += tmppenal; |
| } |
| } |
| #if OUTGAP0TRY |
| else |
| { |
| for( j=1; j<lgth2+1; j++ ) |
| currentw[j] -= offset * j / 2.0; |
| for( i=1; i<lgth1+1; i++ ) |
| initverticalw[i] -= offset * i / 2.0; |
| } |
| #endif |
| |
| m[0] = 0.0; // iranai |
| for( j=1; j<lgth2+1; ++j ) |
| { |
| // m[j] = currentw[j-1] + ogcp1[1]; |
| mp[j] = 0; |
| |
| tmppenal = 0.0; |
| // tmppenal = ( (1.0-gapz2[j])*(1.0-ogcp1g[1]+fgcp1g[1]) + gapz2[j]*(1.0-digf1[1]-diaf1[1]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[1]+fgcp1g[1]) + gapf2[j-1]*(1.0-digf1[1]-diaf1[1]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapf2[j-1])*(1.0-ogcp1g[i]+fgcp1g[i]) + gapf2[j-1]*(1.0-digf1[i]-diaf1[i]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-0.0) * (1.0-0.0) + 0.0 ) * 0.5 * fpenalty; |
| // tmppenal -= ( (1.0-gapf2[-1]) * (1.0-diaf1[0]) + gapf2[-1] ) * 0.5 * fpenalty; |
| // if( tmppenal ) fprintf( stderr, "%c=%c, end j tmppenal=%f\n", seq1[0][0], seq2[0][j-1], tmppenal ); |
| m[j] = currentw[j-1] + tmppenal + fpenalty * 10000; |
| // m[j] = currentw[j-1] + ogcp1[1]; |
| } |
| if( lgth2 == 0 ) |
| lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari |
| else |
| lastverticalw[0] = currentw[lgth2-1]; |
| |
| if( outgap ) lasti = lgth1+1; else lasti = lgth1; |
| |
| #if XXXXXXX |
| fprintf( stderr, "currentw = \n" ); |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| fprintf( stderr, "%5.2f ", currentw[i] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "initverticalw = \n" ); |
| for( i=0; i<lgth2+1; i++ ) |
| { |
| fprintf( stderr, "%5.2f ", initverticalw[i] ); |
| } |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "fcgp\n" ); |
| for( i=0; i<lgth1; i++ ) |
| fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] ); |
| for( i=0; i<lgth2; i++ ) |
| fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] ); |
| #endif |
| |
| for( i=1; i<lasti; i++ ) |
| { |
| wtmp = previousw; |
| previousw = currentw; |
| currentw = wtmp; |
| |
| previousw[0] = initverticalw[i-1]; |
| |
| match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 ); |
| #if XXXXXXX |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "i=%d\n", i ); |
| fprintf( stderr, "currentw = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "%5.2f ", currentw[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| if( localhom ) |
| { |
| // fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i ); |
| #if 0 |
| imp_match_out_veadH( currentw, i, lgth2 ); |
| #else |
| imp_match_out_veadH( currentw, i, lgth2 ); |
| #endif |
| } |
| #if XXXXXXX |
| fprintf( stderr, "\n" ); |
| fprintf( stderr, "i=%d\n", i ); |
| fprintf( stderr, "currentw = \n" ); |
| for( j=0; j<lgth2; j++ ) |
| { |
| fprintf( stderr, "%5.2f ", currentw[j] ); |
| } |
| fprintf( stderr, "\n" ); |
| #endif |
| currentw[0] = initverticalw[i]; |
| |
| |
| // mi = previousw[0] + ogcp2[1]; // machigai |
| tmppenal = 0.0; |
| // tmppenal = ( (1.0-gapz1[i])*(1.0-ogcp2g[1]+fgcp2g[1]) + gapz1[i]*(1.0-digf2[1]-diaf2[1]) ) * 0.5 * fpenalty; // mada |
| // tmppenal = ( (1.0-gapf1[i-1])*(1.0-ogcp2g[1]+fgcp2g[1]) + gapf1[i-1]*(1.0-digf2[1]-diaf2[1]) ) * 0.5 * fpenalty; // mada |
| // fprintf( stderr, "%c=%c, end i tmppenal=%f, ogcp2g[1]=%f\n", seq1[0][i-1], seq2[0][0], tmppenal, ogcp2g[1] ); |
| // mi = previousw[0] + tmppenal; |
| mi = previousw[0] + tmppenal + fpenalty * 10000; |
| |
| mpi = 0; |
| ijppt = ijp[i] + 1; |
| mjpt = m + 1; |
| prept = previousw; |
| curpt = currentw + 1; |
| mpjpt = mp + 1; |
| fgcp2pt = fgcp2; |
| ogcp2pt = ogcp2 + 1; |
| fgcp1va = fgcp1[i-1]; |
| ogcp1va = ogcp1[i]; |
| lastj = lgth2+1; |
| for( j=1; j<lastj; j++ ) |
| { |
| wm = *prept; |
| |
| if( gappat2[j][0].freq ) |
| { |
| g = diaf1[i] * gappat2[j][0].freq * fpenalty; |
| // if( seq1[0][i] == 'D' && seq2[0][j] == 'D' ) |
| // if( g ) fprintf( stderr, "match penal1=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] ); |
| wm += g; |
| } |
| |
| if( gappat1[i][0].freq ) |
| { |
| g = diaf2[j] * gappat1[i][0].freq * fpenalty; |
| // if( seq1[0][i] == 'D' && seq2[0][j] == 'D' ) |
| // if( g ) fprintf( stderr, "match penal2=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] ); |
| wm += g; |
| } |
| { |
| g = ( (gappat1[i][0].freq) * (gappat2[j][0].freq) ) * fpenalty; |
| // if( seq1[0][i] == 'D' && seq2[0][j] == 'D' ) |
| // if( g ) fprintf( stderr, "match penal3=%f, %c-%c\n", g/fpenalty, seq1[0][i], seq2[0][j] ); |
| wm += g; |
| } |
| if( 0 ) |
| { |
| maegap = ijp[i-1][j-1]; |
| // if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' ) |
| // fprintf( stderr, "i,j=%d,%d, maegap=%d\n", i, j, maegap ); |
| maegap = 0; |
| |
| if( maegap == 0 ) |
| { |
| g = ( countnocountmatchx( gappat1[i], gappat2[j], 0, 0, 0 ) ) * fpenalty; |
| // if( seq1[0][i] == 'D' && seq2[0][j] == 'D' ) |
| // fprintf( stderr, "kanwa0 %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 1 ) ); |
| } |
| #if 0 // atta houga yoi hazu |
| else if( maegap < 0 ) // i jump |
| { |
| g = ( countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 0 ) ) * fpenalty; |
| if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' ) |
| { |
| fprintf( stderr, "i-jumped, offset1=%d\n", maegap ); |
| fprintf( stderr, "kanwa1 %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 0 ) ); |
| } |
| } |
| else // j jump |
| { |
| g = ( countnocountmatchx( gappat1[i], gappat2[j], maegap, 0, 0 ) ) * fpenalty; |
| if( seq1[0][i] == 'Y' && seq2[0][j] == 'Y' ) |
| { |
| fprintf( stderr, "j-jumped, offset1=%d\n", maegap ); |
| fprintf( stderr, "kanwa2, %c-%c, i,j=%d,%d, g/fpenalty=%f, nocount=%f\n", seq1[0][i], seq2[0][j], i, j, g/fpenalty, countnocountmatchx( gappat1[i], gappat2[j], 0, -maegap, 1 ) ); |
| } |
| } |
| #endif |
| wm -= g; |
| } |
| |
| *ijppt = 0; |
| |
| #if 0 |
| fprintf( stderr, "%5.0f->", wm ); |
| #endif |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| // tmppenal = fpenalty; |
| tmppenal = diaf2[j] * ( 1.0 - gapf1[i] ) * fpenalty; |
| if( gappat2[j][0].freq ) |
| { |
| tmppenal += ( gappat2[j][0].freq ) * ( 1.0 - gapf1[i] ) * fpenalty; |
| // tmppenal -= ( countnocountx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, 0 ) ) * fpenalty; |
| maegap = ijp[i-1][mpi]; |
| maegap = 0; |
| if( maegap == 0 ) |
| { |
| tmppenal -= ( countnocountx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, 0 ) ) * fpenalty; |
| } |
| #if 0 // attahouga yoi hazu |
| else if( maegap < 0 ) // i jump |
| { |
| maegap = -maegap; |
| tmppenal -= ( countnocountxx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1+maegap, 0 ) ) * fpenalty; |
| } |
| else // j jump |
| { |
| tmppenal -= ( countnocountxx( gappat1[i], diaf1[i], gappat2[j], j-mpi-1, maegap ) ) * fpenalty; |
| } |
| #endif |
| } |
| if( (g=mi+tmppenal) > wm ) |
| { |
| // if( seq1[0][i] == 'A' && seq2[0][j] == 'A' ) fprintf( stderr, "jump i start=%f (i,j=%d,%d, *ijppt=%d, digf2[j]=%f, diaf2[j]=%f), %c-%c\n", g-mi, i, j, -(j-mpi), digf2[j], diaf2[j], seq1[0][i], seq2[0][j] ); |
| wm = g; |
| *ijppt = -( j - mpi ); |
| } |
| if( (g=*prept) >= mi ) |
| { |
| // fprintf( stderr, "jump i end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] ); |
| mi = g; |
| mpi = j-1; |
| } |
| else if( j != 1 ) |
| { |
| // mi += ( ogcp2g[j-0] + fgcp2g[j] ) * fpenalty * 0.5; |
| // fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", '=', '=', seq2[0][j-1], seq2[0][j], ogcp2g[j-0] * fpenalty*0.5, fgcp2g[j] * fpenalty*0.5 ); |
| } |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| |
| // tmppenal = fpenalty; |
| tmppenal = diaf1[i] * ( 1.0 - gapf2[j] ) * fpenalty; |
| if( gappat1[i][0].freq ) |
| { |
| tmppenal += ( gappat1[i][0].freq ) * ( 1.0 - gapf2[j] ) * fpenalty; |
| // tmppenal -= ( countnocountx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, 1 ) ) * fpenalty; |
| maegap = ijp[*mpjpt][j-1]; |
| if( maegap == 0 ) |
| { |
| tmppenal -= ( countnocountx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, 1 ) ) * fpenalty; |
| } |
| #if 0 // attahouga yoi hazu |
| else if( maegap > 0 ) // j jump |
| { |
| tmppenal -= ( countnocountxx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1+maegap, 0 ) ) * fpenalty; |
| } |
| else // i jump |
| { |
| maegap = -maegap; |
| tmppenal -= ( countnocountxx( gappat2[j], diaf2[j], gappat1[i], i-*mpjpt-1, maegap ) ) * fpenalty; |
| } |
| #endif |
| } |
| if( (g=*mjpt+tmppenal) > wm ) |
| { |
| // if( seq1[0][i] == 'S' && seq2[0][j] == 'S' ) fprintf( stderr, "jump j start at %d, %d, g=%f, %c-%c\n", i, j, g-*mjpt, seq1[0][i], seq2[0][j] ); |
| wm = g; |
| *ijppt = +( i - *mpjpt ); |
| } |
| if( (g=*prept) >= *mjpt ) |
| { |
| // fprintf( stderr, "jump j end=%f, %c-%c\n", g-*prept, seq1[0][i-1], seq2[0][j-1] ); |
| *mjpt = g; |
| *mpjpt = i-1; |
| } |
| else if( i != 1 ) |
| { |
| // m[j] += ( ogcp1g[i-0] + fgcp1g[i] ) * fpenalty * 0.5; |
| // fprintf( stderr, "%c%c/%c%c exp, og=%f,fg=%f\n", seq1[0][i-1], seq1[0][i], '=', '=', ogcp1g[i-0] * fpenalty*0.5, fgcp1g[i] * fpenalty*0.5 ); |
| } |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "%5.0f ", wm ); |
| #endif |
| *curpt++ += wm; |
| ijppt++; |
| mjpt++; |
| prept++; |
| mpjpt++; |
| fgcp2pt++; |
| ogcp2pt++; |
| } |
| lastverticalw[i] = currentw[lgth2-1]; |
| } |
| |
| // fprintf( stderr, "wm = %f\n", wm ); |
| |
| #if OUTGAP0TRY |
| if( !outgap ) |
| { |
| for( j=1; j<lgth2+1; j++ ) |
| currentw[j] -= offset * ( lgth2 - j ) / 2.0; |
| for( i=1; i<lgth1+1; i++ ) |
| lastverticalw[i] -= offset * ( lgth1 - i / 2.0); |
| } |
| #endif |
| |
| /* |
| fprintf( stderr, "\n" ); |
| for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] ); |
| fprintf( stderr, "#####\n" ); |
| for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] ); |
| fprintf( stderr, "====>" ); |
| for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] ); |
| for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] ); |
| */ |
| if( localhom ) |
| { |
| Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); |
| } |
| else |
| Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc ); |
| |
| // fprintf( stderr, "### impmatch = %f\n", *impmatch ); |
| |
| resultlen = strlen( mseq1[0] ); |
| if( alloclen < resultlen || resultlen > N ) |
| { |
| fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N ); |
| ErrorExit( "LENGTH OVER!\n" ); |
| } |
| |
| |
| for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] ); |
| for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] ); |
| /* |
| fprintf( stderr, "\n" ); |
| for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] ); |
| fprintf( stderr, "#####\n" ); |
| for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] ); |
| */ |
| |
| fprintf( stderr, "wm = %f\n", wm ); |
| |
| for( i=0; i<lgth1+1; i++ ) |
| { |
| free( gappat1[i] ); |
| gappat1[i] = NULL; |
| } |
| for( i=0; i<lgth2+1; i++ ) |
| { |
| free( gappat2[i] ); |
| gappat2[i] = NULL; |
| } |
| |
| return( wm ); |
| } |
| |