+++ /dev/null
-#include "mltaln.h"
-#include "dp.h"
-
-#define MACHIGAI 0
-#define OUTGAP0TRY 0
-#define DEBUG 0
-#define XXXXXXX 0
-#define USE_PENALTY_EX 0
-#define FASTMATCHCALC 1
-
-
-static TLS float **impmtx = NULL;
-static TLS int impalloclen = 0;
-float imp_match_out_sc( 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] );
-}
-static void imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
-{
-#if FASTMATCHCALC
- float *pt = impmtx[i1];
- int *gapmappt = gapmap2;
- while( lgth2-- )
- *imp++ += pt[*gapmappt++];
-#else
- int j;
- float *pt = impmtx[i1];
- for( j=0; j<lgth2; j++ )
- *imp++ += pt[gapmap2[j]];
-#endif
-}
-
-
-static void imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int *gapmap1 )
-{
-#if FASTMATCHCALC
- int *gapmappt = gapmap1;
- while( lgth1-- )
- *imp++ += impmtx[*gapmappt++][j1];
-#else
- int i;
- for( i=0; i<lgth1; i++ )
- *imp++ += impmtx[gapmap1[i]][j1];
-#endif
-}
-
-static void imp_match_out_vead( 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_tate( float *imp, int j1, int lgth1 )
-{
- int i;
- for( i=0; i<lgth1; i++ )
- *imp++ += impmtx[i][j1];
-}
-
-void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *pair )
-{
- foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, pair );
-}
-
-
-void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore )
-{
- int i, j, k1, k2, tmpint, start1, start2, end1, end2;
- float effij;
- float effij_kozo;
- double effijx;
- char *pt, *pt1, *pt2;
- static TLS char *nocount1 = NULL;
- static TLS char *nocount2 = NULL;
- LocalHom *tmpptr;
-
- if( seq1 == NULL )
- {
- if( impmtx ) FreeFloatMtx( impmtx );
- impmtx = NULL;
- if( nocount1 ) free( nocount1 );
- nocount1 = NULL;
- if( nocount2 ) free( nocount2 );
- nocount2 = NULL;
-
- return;
- }
-
- 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 );
- effij_kozo = (float)( eff1_kozo[i] * eff2_kozo[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¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
-// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
-// impmtx[k1][k2] += tmpptr->importance * effij;
-// impmtx[k1][k2] += tmpptr->fimportance * effij;
- if( tmpptr->korh == 'k' )
- impmtx[k1][k2] += tmpptr->fimportance * effij_kozo;
- else
- 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 == 1 )
- {
- fprintf( stderr, "writing impmtx\n" );
- 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<30; k2++ )
- fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
- fprintf( stderr, "\n" );
- }
-// exit( 1 );
- }
-#endif
-}
-
-#if 0
-void 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 TLS int impalloclen = 0;
- char *pt;
- int allgap;
- static TLS char *nocount1 = NULL;
- static TLS char *nocount2 = NULL;
-
- 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
-
- for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
- impmtx[i][j] = 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" );
- }
-#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];
- scarr[l] += n_dis_consweight_multi[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 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_sc( 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 void Atracking_localhom_gapmap( 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 *gapmap1, int *gapmap2 )
-{
- 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_sc( gapmap1[iin], gapmap2[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 = '-';
- *--gaptable2 = '-';
- 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 tailgp )
-{
- 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( tailgp == 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 A__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, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
-/* 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 TLS float mi, *m;
- static TLS int **ijp;
- static TLS int mpi, *mp;
- static TLS float *w1, *w2;
- static TLS float *match;
- static TLS float *initverticalw; /* kufuu sureba iranai */
- static TLS float *lastverticalw; /* kufuu sureba iranai */
- static TLS char **mseq1;
- static TLS char **mseq2;
- static TLS char **mseq;
- static TLS float *ogcp1;
- static TLS float *ogcp2;
- static TLS float *fgcp1;
- static TLS float *fgcp2;
- static TLS float **cpmx1;
- static TLS float **cpmx2;
- static TLS int **intwork;
- static TLS float **floatwork;
- static TLS int orlgth1 = 0, orlgth2 = 0;
- float fpenalty = (float)penalty;
- float *fgcp2pt;
- float *ogcp2pt;
- float fgcp1va;
- float ogcp1va;
-
-
- if( seq1 == NULL )
- {
- if( orlgth1 )
- {
-// fprintf( stderr, "## Freeing local arrays in A__align\n" );
- orlgth1 = 0;
- orlgth2 = 0;
-
- imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
-
- free( mseq1 );
- free( mseq2 );
- 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 );
-
- }
- else
- {
-// fprintf( stderr, "## Not allocated\n" );
- }
- return( 0.0 );
- }
-
- lgth1 = strlen( seq1[0] );
- lgth2 = strlen( seq2[0] );
-#if 1
- if( lgth1 == 0 || lgth2 == 0 )
- {
- fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
- }
- if( lgth1 == 0 && lgth2 == 0 )
- return( 0.0 );
-
- if( lgth1 == 0 )
- {
- for( i=0; i<icyc; i++ )
- {
- j = lgth2;
- seq1[i][j] = 0;
- while( j ) seq1[i][--j] = '-';
-// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
- }
- return( 0.0 );
- }
-
- if( lgth2 == 0 )
- {
- for( i=0; i<jcyc; i++ )
- {
- j = lgth1;
- seq2[i][j] = 0;
- while( j ) seq2[i][--j] = '-';
-// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
- }
- return( 0.0 );
- }
-#endif
-
-
-#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] );
- fprintf( stderr, "#### seq2[0] = %s\n", seq2[0] );
- fprintf( stderr, "#### strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
- for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
-#endif
- if( orlgth1 == 0 )
- {
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 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, 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( 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 )
- imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
-
- match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
- if( localhom )
- imp_match_out_vead( 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( headgp == 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;
- }
- if( lgth2 == 0 )
- lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
- else
- lastverticalw[0] = currentw[lgth2-1];
-
- if( tailgp ) 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++ )
- {
-
-#ifdef enablemultithread
-// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
- if( chudanpt && *chudanpt != chudanref )
- {
-// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
- *chudanres = 1;
- return( -1.0 );
- }
-#endif
- 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_vead( currentw, i, lgth2 );
-#else
- imp_match_out_vead( 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]; 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++ )
- {
-#ifdef xxxenablemultithread
-// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
- if( chudanpt && *chudanpt != chudanref )
- {
-// fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
- *chudanres = 1;
- return( -1.0 );
- }
-#endif
- wm = *prept;
- *ijppt = 0;
-
-#if 0
- fprintf( stderr, "%5.0f->", wm );
-#endif
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( (g=mi+*fgcp2pt) > wm )
- {
- wm = g;
- *ijppt = -( j - mpi );
- }
- if( (g=*prept+*ogcp2pt) >= mi )
- {
- mi = g;
- mpi = j-1;
- }
-#if USE_PENALTY_EX
- mi += fpenalty_ex;
-#endif
-
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( (g=*mjpt+fgcp1va) > wm )
- {
- wm = g;
- *ijppt = +( i - *mpjpt );
- }
- if( (g=*prept+ogcp1va) >= *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++;
- 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, tailgp );
-
-// 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] );
-#if 0
- 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] );
-#endif
-
-// fprintf( stderr, "wm = %f\n", wm );
-
- return( wm );
-}
-
-float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 )
-/* 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 TLS float mi, *m;
- static TLS int **ijp;
- static TLS int mpi, *mp;
- static TLS float *w1, *w2;
- static TLS float *match;
- static TLS float *initverticalw; /* kufuu sureba iranai */
- static TLS float *lastverticalw; /* kufuu sureba iranai */
- static TLS char **mseq1;
- static TLS char **mseq2;
- static TLS char **mseq;
- static TLS float *ogcp1;
- static TLS float *ogcp2;
- static TLS float *fgcp1;
- static TLS float *fgcp2;
- static TLS float **cpmx1;
- static TLS float **cpmx2;
- static TLS int **intwork;
- static TLS float **floatwork;
- static TLS int orlgth1 = 0, orlgth2 = 0;
- 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 0
- if( lgth1 == 0 || lgth2 == 0 )
- {
- fprintf( stderr, "WARNING (Aalign_gapmap): 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 );
-
- 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( 27, 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;
-
- cpmx_calc_new( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
- cpmx_calc_new( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
-
- 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] );
- fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
- }
- for( i=0; i<lgth2; i++ )
- {
- ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
- fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
- }
-#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_tate_gapmap( initverticalw, gapmap2[0], lgth1, gapmap1 ); // 060306
-
-
- match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
- if( localhom )
- imp_match_out_vead_gapmap( currentw, gapmap1[0], lgth2, gapmap2 ); // 060306
-#if 0 // -> tbfast.c
- if( localhom )
- imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
-
-#endif
-
- if( 1 ) // tsuneni 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;
- }
-
- if( lgth2 == 0 )
- lastverticalw[0] = 0.0;
- else
- lastverticalw[0] = currentw[lgth2-1];
-
- if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap=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 );
-#if 0
- imp_match_out_vead( currentw, i, lgth2 );
-#else
- imp_match_out_vead_gapmap( currentw, gapmap1[i], lgth2, gapmap2 );
-#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]; 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;
- *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++;
- 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_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
- }
- else
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, 1 );
-
-// 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 );
-
- return( wm );
-}
-
git://source.jalview.org / jabaws.git / blobdiff