| #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 |
| |
| #if 0 |
| static void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len ) |
| { |
| int i, j, gc, gb; |
| float feff; |
| |
| for( i=0; i<len; i++ ) ogcp[i] = 0.0; |
| for( j=0; j<clus; j++ ) |
| { |
| feff = (float)eff[j]; |
| gc = 0; |
| for( i=0; i<len; i++ ) |
| { |
| gb = gc; |
| gc = ( seq[j][i] == '-' ); |
| { |
| if( !gb * gc ) ogcp[i] += feff; |
| } |
| } |
| } |
| } |
| |
| static void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len ) |
| { |
| int i, j, gc, gb; |
| float feff; |
| |
| for( i=0; i<len; i++ ) fgcp[i] = 0.0; |
| for( j=0; j<clus; j++ ) |
| { |
| feff = (float)eff[j]; |
| gc = ( seq[j][0] == '-' ); |
| for( i=1; i<len+1; i++ ) |
| { |
| gb = gc; |
| gc = ( seq[j][i] == '-' ); |
| { |
| if( gb * !gc ) fgcp[i-1] += feff; |
| } |
| } |
| } |
| } |
| #endif |
| |
| |
| |
| |
| |
| static int impalloclen = 0; |
| static float **impmtx = NULL; |
| float part_imp_match_out_sc( int i1, int j1 ) |
| { |
| // fprintf( stderr, "impalloclen = %d\n", impalloclen ); |
| // fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] ); |
| return( impmtx[i1][j1] ); |
| #if 0 |
| if( i1 == l1 || j1 == l2 ) return( 0.0 ); |
| return( impmtx[i1+start1][j1+start2] ); |
| #endif |
| } |
| static void part_imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int start2, int *gapmap2 ) |
| { |
| #if FASTMACHCALC |
| float *pt = imp; |
| int *gapmappt = gapmap2; |
| while( lgth2-- ) |
| *pt++ += impmtx[i1][start2+*gapmappt++]; |
| #else |
| int j; |
| for( j=0; j<lgth2; j++ ) |
| { |
| imp[j] += impmtx[i1][start2+gapmap2[j]]; |
| } |
| #endif |
| } |
| |
| static void part_imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int start1, int *gapmap1 ) |
| { |
| #if FASTMACHCALC |
| float *pt = imp; |
| int *gapmappt = gapmap1; |
| while( lgth1-- ) |
| *pt++ = impmtx[start1+*gapmappt++][j1]; |
| #else |
| int i; |
| for( i=0; i<lgth1; i++ ) |
| { |
| imp[i] += impmtx[start1+gapmap1[i]][j1]; |
| } |
| #endif |
| } |
| |
| void part_imp_match_init_strict( 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; |
| double effij, effijx; |
| char *pt, *pt1, *pt2; |
| LocalHom *tmpptr; |
| |
| if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 ) |
| { |
| if( impmtx ) FreeFloatMtx( impmtx ); |
| impalloclen = MAX( lgth1, lgth2 ) + 2; |
| impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 ); |
| } |
| |
| |
| #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 = 1.0 * fastathreshold; |
| for( i=0; i<clus1; i++ ) |
| { |
| for( j=0; j<clus2; j++ ) |
| { |
| effij = 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 = (int)( pt - seq1[i] ) - 1; |
| |
| if( tmpptr->start1 == tmpptr->end1 ) end1 = start1; |
| else |
| { |
| #if MACHIGAI |
| while( *pt != 0 ) |
| { |
| if( tmpint == tmpptr->end1 ) break; |
| if( *pt++ != '-' ) tmpint++; |
| } |
| end1 = (int)( pt - seq1[i] ) - 1; |
| #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 = (int)( pt - seq1[i] ) - 1; |
| #endif |
| } |
| |
| pt = seq2[j]; |
| tmpint = -1; |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == tmpptr->start2 ) break; |
| } |
| start2 = (int)( 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 = (int)( pt - seq2[j] ) - 1; |
| #else |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == tmpptr->end2 ) break; |
| } |
| end2 = (int)( 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 ); |
| } |
| |
| 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, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen ); |
| // fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 ); |
| 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; |
| } |
| tmpptr = tmpptr->next; |
| } |
| } |
| } |
| #if 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<lgth2; k2++ ) |
| fprintf( stderr, "%2.1f ", impmtx[k1][k2] ); |
| fprintf( stderr, "\n" ); |
| } |
| exit( 1 ); |
| #endif |
| } |
| |
| |
| void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair ) |
| { |
| foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair ); |
| } |
| |
| |
| void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom ) |
| { |
| int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2; |
| static int impalloclen = 0; |
| char *pt; |
| static char *nocount1 = NULL; |
| static char *nocount2 = NULL; |
| |
| if( impalloclen < lgth1 || impalloclen < lgth2 ) |
| { |
| 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 ); |
| impalloclen -= 2; |
| } |
| |
| 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 |
| |
| for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ ) |
| impmtx[i][j] = 0.0; |
| for( i=0; i<clus1; i++ ) |
| { |
| fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] ); |
| for( j=0; j<clus2; j++ ) |
| { |
| fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 ); |
| fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 ); |
| fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] ); |
| pt = seq1[i]; |
| tmpint = -1; |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == localhom[i][j]->start1 ) break; |
| } |
| start1 = pt - seq1[i] - 1; |
| |
| while( *pt != 0 ) |
| { |
| // fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] ); |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == localhom[i][j]->end1 ) break; |
| } |
| end1 = pt - seq1[i] - 1; |
| |
| pt = seq2[j]; |
| tmpint = -1; |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == localhom[i][j]->start2 ) break; |
| } |
| start2 = pt - seq2[j] - 1; |
| while( *pt != 0 ) |
| { |
| if( *pt++ != '-' ) tmpint++; |
| if( tmpint == localhom[i][j]->end2 ) break; |
| } |
| end2 = pt - seq2[j] - 1; |
| // fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 ); |
| k1 = start1; |
| k2 = start2; |
| fprintf( stderr, "step 0\n" ); |
| while( k1 <= end1 && k2 <= end2 ) |
| { |
| #if 0 |
| if( !nocount1[k1] && !nocount2[k2] ) |
| impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j]; |
| k1++; k2++; |
| #else |
| if( !nocount1[k1] && !nocount2[k2] ) |
| impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j]; |
| k1++; k2++; |
| #endif |
| } |
| |
| dif = ( end1 - start1 ) - ( end2 - start2 ); |
| fprintf( stderr, "dif = %d\n", dif ); |
| if( dif > 0 ) |
| { |
| do |
| { |
| fprintf( stderr, "dif = %d\n", dif ); |
| k1 = start1; |
| k2 = start2 - dif; |
| while( k1 <= end1 && k2 <= end2 ) |
| { |
| if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] ) |
| impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j]; |
| k1++; k2++; |
| } |
| } |
| while( dif-- ); |
| } |
| else |
| { |
| do |
| { |
| k1 = start1 + dif; |
| k2 = start2; |
| while( k1 <= end1 ) |
| { |
| if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] ) |
| impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j]; |
| k1++; k2++; |
| } |
| } |
| while( dif++ ); |
| } |
| } |
| } |
| #if 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<lgth2; k2++ ) |
| fprintf( stderr, "%6.3f ", impmtx[k1][k2] ); |
| fprintf( stderr, "\n" ); |
| } |
| exit( 1 ); |
| #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_consweight_multi[j][l] * cpmx1[j][i1]; |
| // 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_consweight_multi[k][l] * cpmx1[k][i1]; |
| // 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 start1, int end1, int start2, int end2, |
| int *gapmap1, int *gapmap2 ) |
| { |
| int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k; |
| char gap[] = "-"; |
| float wm; |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| #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 ); |
| } |
| |
| for( i=0; i<icyc; i++ ) |
| { |
| mseq1[i] += lgth1+lgth2; |
| *mseq1[i] = 0; |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| mseq2[j] += lgth1+lgth2; |
| *mseq2[j] = 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 ) |
| { |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = seq1[i][ifi+l]; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = *gap; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = *gap; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = seq2[j][jfi+l]; |
| k++; |
| } |
| if( iin != lgth1 && jin != lgth2 ) // ?? |
| { |
| *impwmpt += part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 ); |
| // 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; |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = seq1[i][ifi]; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = seq2[j][jfi]; |
| k++; |
| iin = ifi; jin = jfi; |
| } |
| } |
| 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, lastk; |
| char gap[] = "-"; |
| float wm = 0.0; |
| lgth1 = strlen( seq1[0] ); |
| lgth2 = strlen( seq2[0] ); |
| |
| #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 ); |
| } |
| |
| for( i=0; i<icyc; i++ ) |
| { |
| mseq1[i] += lgth1+lgth2; |
| *mseq1[i] = 0; |
| } |
| for( j=0; j<jcyc; j++ ) |
| { |
| mseq2[j] += lgth1+lgth2; |
| *mseq2[j] = 0; |
| } |
| iin = lgth1; jin = lgth2; |
| lastk = lgth1+lgth2; |
| for( k=0; k<=lastk; 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 ) |
| { |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = seq1[i][ifi+l]; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = *gap; |
| k++; |
| } |
| l= jin - jfi; |
| while( --l ) |
| { |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = *gap; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = seq2[j][jfi+l]; |
| k++; |
| } |
| if( iin <= 0 || jin <= 0 ) break; |
| for( i=0; i<icyc; i++ ) |
| *--mseq1[i] = seq1[i][ifi]; |
| for( j=0; j<jcyc; j++ ) |
| *--mseq2[j] = seq2[j][jfi]; |
| k++; |
| iin = ifi; jin = jfi; |
| } |
| return( 0.0 ); |
| } |
| |
| float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, 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; |
| #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 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; |
| #if USE_PENALTY_EX |
| float fpenalty_ex = (float)penalty_ex; |
| #endif |
| float *fgcp2pt; |
| float *ogcp2pt; |
| float fgcp1va; |
| float ogcp1va; |
| |
| |
| |
| #if 0 |
| fprintf( stderr, "eff in SA+++align\n" ); |
| 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( 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 ); |
| |
| FreeFloatVec( ogcp1 ); |
| FreeFloatVec( ogcp2 ); |
| FreeFloatVec( fgcp1 ); |
| FreeFloatVec( fgcp2 ); |
| |
| |
| 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 ); |
| |
| ogcp1 = AllocateFloatVec( ll1+2 ); |
| ogcp2 = AllocateFloatVec( ll2+2 ); |
| fgcp1 = AllocateFloatVec( ll1+2 ); |
| fgcp2 = 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, 26 ); |
| #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]; |
| for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j]; |
| |
| |
| 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; |
| |
| cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc ); |
| cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc ); |
| |
| if( sgap1 ) |
| { |
| new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 ); |
| new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 ); |
| new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 ); |
| new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 ); |
| } |
| else |
| { |
| st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 ); |
| st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 ); |
| st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 ); |
| st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 ); |
| } |
| |
| for( i=0; i<lgth1; i++ ) |
| { |
| ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty; |
| fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty; |
| } |
| for( i=0; i<lgth2; i++ ) |
| { |
| ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty; |
| fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty; |
| } |
| #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 ) |
| part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 ); |
| |
| |
| match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 ); |
| if( localhom ) |
| part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 ); |
| #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 ) |
| { |
| for( i=1; i<lgth1+1; i++ ) |
| { |
| initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ; |
| } |
| for( j=1; j<lgth2+1; j++ ) |
| { |
| currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ; |
| } |
| } |
| #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 |
| |
| for( j=1; j<lgth2+1; ++j ) |
| { |
| m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0; |
| } |
| |
| lastverticalw[0] = currentw[lgth2-1]; |
| |
| if( outgap ) lasti = lgth1+1; else lasti = lgth1; |
| lastj = lgth2+1; |
| |
| #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 ); |
| // imp_match_out_vead( currentw, i, lgth2 ); |
| part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 ); |
| } |
| #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]; 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]; |
| for( j=1; j<lastj; j++ ) |
| { |
| wm = *prept; |
| *ijppt = 0; |
| |
| #if 0 |
| fprintf( stderr, "%5.0f->", wm ); |
| #endif |
| g = mi + *fgcp2pt; |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( g > wm ) |
| { |
| wm = g; |
| *ijppt = -( j - mpi ); |
| } |
| g = *prept + *ogcp2pt; |
| if( g >= mi ) |
| { |
| mi = g; |
| mpi = j-1; |
| } |
| #if USE_PENALTY_EX |
| mi += fpenalty_ex; |
| #endif |
| |
| g = *mjpt + fgcp1va; |
| #if 0 |
| fprintf( stderr, "%5.0f?", g ); |
| #endif |
| if( g > wm ) |
| { |
| wm = g; |
| *ijppt = +( i - *mpjpt ); |
| } |
| g = *prept + ogcp1va; |
| if( g >= *mjpt ) |
| { |
| *mjpt = g; |
| *mpjpt = i-1; |
| } |
| #if USE_PENALTY_EX |
| m[j] += fpenalty_ex; |
| #endif |
| |
| #if 0 |
| fprintf( stderr, "%5.0f ", wm ); |
| #endif |
| *curpt += wm; |
| ijppt++; |
| mjpt++; |
| prept++; |
| mpjpt++; |
| curpt++; |
| fgcp2pt++; |
| ogcp2pt++; |
| } |
| lastverticalw[i] = currentw[lgth2-1]; |
| } |
| |
| #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, start1, end1, start2, end2, gapmap1, gapmap2 ); |
| } |
| 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] ); |
| */ |
| |
| |
| return( wm ); |
| } |
| |
