#define OUTGAP0TRY 0
#define DEBUG 0
#define XXXXXXX 0
-#define USE_PENALTY_EX 0
+#define USE_PENALTY_EX 1
#define FASTMATCHCALC 1
+#define SLOW 0
-static TLS float **impmtx = NULL;
+static TLS double **impmtx = NULL;
static TLS int impalloclen = 0;
-float imp_match_out_sc( int i1, int j1 )
+double 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 0
+static void imp_match_out_vead_gapmap( double *imp, int i1, int lgth2, int *gapmap2 )
{
#if FASTMATCHCALC
- float *pt = impmtx[i1];
+ double *pt = impmtx[i1];
int *gapmappt = gapmap2;
while( lgth2-- )
*imp++ += pt[*gapmappt++];
#else
int j;
- float *pt = impmtx[i1];
+ double *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 )
+static void imp_match_out_vead_tate_gapmap( double *imp, int j1, int lgth1, int *gapmap1 )
{
#if FASTMATCHCALC
int *gapmappt = gapmap1;
*imp++ += impmtx[gapmap1[i]][j1];
#endif
}
+#endif
-static void imp_match_out_vead( float *imp, int i1, int lgth2 )
+static void imp_match_out_vead( double *imp, int i1, int lgth2 )
{
#if FASTMATCHCALC
- float *pt = impmtx[i1];
+ double *pt = impmtx[i1];
while( lgth2-- )
*imp++ += *pt++;
#else
int j;
- float *pt = impmtx[i1];
+ double *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 )
+static void imp_match_out_vead_tate( double *imp, int j1, int lgth1 )
{
int i;
for( i=0; i<lgth1; i++ )
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 )
+void imp_match_init_strict( double *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, char *swaplist, int forscore, int *orinum1, int *orinum2 )
{
- 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;
+// int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+// double effij;
+// double 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;
+// 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 );
+// 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;
+// nocount1 = AllocateCharVec( impalloclen );
+// nocount2 = AllocateCharVec( impalloclen );
}
-#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] );
+ fillimp( impmtx, imp, clus1, clus2, lgth1, lgth2, seq1, seq2, eff1, eff2, eff1_kozo, eff2_kozo, localhom, swaplist, forscore, orinum1, orinum2 );
}
-#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++ )
+static void match_calc_del( int **which, double ***matrices, double *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, int mid, int nmask, int *mask1, int *mask2 )
+{
+// osoi!
+ int i, j, k, m;
+ int c1, c2;
+// fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
+// fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
+// fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
+// for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+// {
+// if( flip ) reporterr( "in match_calc_slow, which[%d][%d] = %d\n", j, i, which[j][i] );
+// else reporterr( "in match_calc_slow, which[%d][%d] = %d\n", i, j, which[i][j] );
+// }
+ for( k=0; k<lgth2; k++ )
{
- 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++ )
+ for( m=0; m<nmask; m++ )
{
- fprintf( stderr, "%d ", k1 );
- for( k2=0; k2<30; k2++ )
- fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
- fprintf( stderr, "\n" );
+ i = mask1[m];
+ j = mask2[m];
+// reporterr( "Deleting %d-%d (c=%d)\n", i, j, mid );
+// if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
+ c1 = amino_n[(unsigned int)seq1[i][i1]];
+ c2 = amino_n[(unsigned int)seq2[j][k]];
+// reporterr( "k=%d, c1=%d, c2=%d, seq1[i][i1]=%c, seq2[%d][%d]=%c\n", k, c1, c2, seq1[i][i1], j, k, seq2[j][k] );
+ if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
+ if( c1 < 0 || c2 < 0 ) continue;
+// fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
+// fprintf( stderr, "match[k] = %f -> ", match[k], mid );
+ match[k] -= matrices[mid][c1][c2] * eff1[i] * eff2[j];
+// fprintf( stderr, "match[k] = %f (mid=%d)\n", match[k], mid );
}
-// exit( 1 );
}
-#endif
+// fprintf( stderr, "done\n" );
+ return;
}
-#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++ )
+#if SLOW
+static void match_calc_slow( int **which, double ***matrices, double *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, double **doublework, int **intwork, int initialize, int flip )
+{
+// osoi!
+ int i, j, k;
+ int c1, c2;
+ int mid;
+// fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
+// fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
+// fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
+// for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+// {
+// if( flip ) reporterr( "in match_calc_slow, which[%d][%d] = %d\n", j, i, which[j][i] );
+// else reporterr( "in match_calc_slow, which[%d][%d] = %d\n", i, j, which[i][j] );
+// }
+ for( k=0; k<lgth2; k++ )
{
- for( j=0; j<clus2; j++ )
- if( seq2[j][i] == '-' ) break;
- if( j != clus2 ) nocount2[i] = 1;
- else nocount2[i] = 0;
+ match[k] = 0.0;
+ for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+ {
+ if( flip ) mid = which[j][i];
+ else mid = which[i][j];
+// if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
+ c1 = amino_n[(unsigned int)seq1[i][i1]];
+ c2 = amino_n[(unsigned int)seq2[j][k]];
+ if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
+ if( c1 < 0 || c2 < 0 ) continue;
+// fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
+ if( flip )
+ match[k] += matrices[mid][c1][c2] * eff1[i] * eff2[j];
+ else
+ match[k] += matrices[mid][c1][c2] * eff1[i] * eff2[j];
+// fprintf( stderr, "match[k] = %f (which=%d)\n", match[k], mid );
+ }
}
+// fprintf( stderr, "done\n" );
+ return;
+}
+#endif
-#if 0
-fprintf( stderr, "nocount2 =\n" );
-for( i = 0; i<impalloclen; i++ )
+static void fillzero( double *s, int l )
{
- fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+ while( l-- ) *s++ = 0.0;
}
-#endif
- for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
- impmtx[i][j] = 0;
- for( i=0; i<clus1; i++ )
+static void match_calc_add( double **scoreingmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+// fprintf( stderr, "\nmatch_calc... %d", i1 );
+ int j, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ double *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ int *cpmxpdnpt, **cpmxpdnptpt;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+ if( initialize )
{
- fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
- for( j=0; j<clus2; j++ )
+ int count = 0;
+ for( j=0; j<lgth2; 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 )
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
{
- do
+ if( cpmx2[l][j] )
{
- 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++;
- }
+ cpmxpd[j][count] = cpmx2[l][j];
+ cpmxpdn[j][count] = l;
+ count++;
}
- while( dif-- );
}
- else
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ {
+ for( l=0; l<nalphabets; l++ )
+ {
+ scarr[l] = 0.0;
+ for( j=0; j<nalphabets; j++ )
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+// scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ scarr[l] += scoreingmtx[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++;
+ }
+ }
+ free( scarr );
+// fprintf( stderr, "done\n" );
+#else
+ int j, k, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+// simple
+ if( initialize )
+ {
+ int count = 0;
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
{
- do
+ if( cpmx2[l][j] )
{
- 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++;
- }
+ cpmxpd[count][j] = cpmx2[l][j];
+ cpmxpdn[count][j] = l;
+ count++;
}
- while( dif++ );
}
+ cpmxpdn[count][j] = -1;
}
}
-#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++ )
+ for( l=0; l<nalphabets; l++ )
{
- fprintf( stderr, "%d", k1 );
- for( k2=0; k2<lgth2; k2++ )
- fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
- fprintf( stderr, "\n" );
+ scarr[l] = 0.0;
+ for( k=0; k<nalphabets; k++ )
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+ scarr[l] += scoreingmtx[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];
+ }
+ free( scarr );
#endif
}
-#endif
-
-static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+static void match_calc( double **n_dynamicmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
#if FASTMATCHCALC
+// fprintf( stderr, "\nmatch_calc... %d", i1 );
int j, l;
- float scarr[26];
- float **cpmxpd = floatwork;
+// double scarr[26];
+ double **cpmxpd = doublework;
int **cpmxpdn = intwork;
- float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+ double *matchpt, *cpmxpdpt, **cpmxpdptpt;
int *cpmxpdnpt, **cpmxpdnptpt;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
if( initialize )
{
int count = 0;
for( j=0; j<lgth2; j++ )
{
count = 0;
- for( l=0; l<26; l++ )
+ for( l=0; l<nalphabets; l++ )
{
if( cpmx2[l][j] )
{
}
{
- for( l=0; l<26; l++ )
+ for( l=0; l<nalphabets; l++ )
{
scarr[l] = 0.0;
- for( j=0; j<26; j++ )
+ for( j=0; j<nalphabets; j++ )
// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
- scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+// scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ scarr[l] += n_dynamicmtx[j][l] * cpmx1[j][i1];
}
matchpt = match;
cpmxpdnptpt = cpmxpdn;
matchpt++;
}
}
+ free( scarr );
+// fprintf( stderr, "done\n" );
#else
int j, k, l;
- float scarr[26];
- float **cpmxpd = floatwork;
+// double scarr[26];
+ double **cpmxpd = doublework;
int **cpmxpdn = intwork;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
// simple
if( initialize )
{
for( j=0; j<lgth2; j++ )
{
count = 0;
- for( l=0; l<26; l++ )
+ for( l=0; l<nalphabets; l++ )
{
if( cpmx2[l][j] )
{
cpmxpdn[count][j] = -1;
}
}
- for( l=0; l<26; l++ )
+ for( l=0; l<nalphabets; l++ )
{
scarr[l] = 0.0;
- for( k=0; k<26; k++ )
- scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+ for( k=0; k<nalphabets; k++ )
// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+ scarr[l] += n_dynamicmtx[k][l] * cpmx1[k][i1];
}
for( j=0; j<lgth2; j++ )
{
for( k=0; cpmxpdn[k][j]>-1; k++ )
match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
}
+ free( scarr );
#endif
}
-static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw,
+static void Atracking_localhom( double *impwmpt, double *lasthorizontalw, double *lastverticalw,
char **seq1, char **seq2,
char **mseq1, char **mseq2,
- float **cpmx1, float **cpmx2,
- int **ijp, int icyc, int jcyc )
+ int **ijp, int icyc, int jcyc,
+ int *warpis, int *warpjs, int warpbase,
+ int *ngap1, int *ngap2, int reuseprofiles )
{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
- float wm;
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+ double wm;
char *gaptable1, *gt1bk;
char *gaptable2, *gt2bk;
lgth1 = strlen( seq1[0] );
*gaptable1 = 0;
gaptable2 = gt2bk + lgth1+lgth2;
*gaptable2 = 0;
+ *ngap1 = *ngap2 = 0;
iin = lgth1; jin = lgth2;
+ limk = lgth1+lgth2 + 1;
*impwmpt = 0.0;
- for( k=0; k<=lgth1+lgth2; k++ )
+ for( k=0; k<limk; k++ )
{
- if( ijp[iin][jin] < 0 )
+ if( ijp[iin][jin] >= warpbase )
+ {
+ ifi = warpis[ijp[iin][jin]-warpbase];
+ jfi = warpjs[ijp[iin][jin]-warpbase];
+ }
+ else if( ijp[iin][jin] < 0 )
{
ifi = iin-1; jfi = jin+ijp[iin][jin];
}
{
ifi = iin-1; jfi = jin-1;
}
- l = iin - ifi;
- while( --l )
+ if( ifi == -warpbase && jfi == -warpbase )
{
- *--gaptable1 = 'o';
- *--gaptable2 = '-';
- k++;
+ l = iin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ *ngap2 = 1;
+ }
+ l= jin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ *ngap1 = 1;
+ }
+ break;
}
- l= jin - jfi;
- while( --l )
+ else
{
- *--gaptable1 = '-';
- *--gaptable2 = 'o';
- k++;
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ *ngap2 = 1;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ *ngap1 = 1;
+ }
}
if( iin == lgth1 || jin == lgth2 )
;
else
{
- *impwmpt += imp_match_out_sc( iin, jin );
+ *impwmpt += (double)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] );
}
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 );
+ if( *ngap1 || !reuseprofiles )
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+
+ if( *ngap2 || !reuseprofiles )
+ 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,
+
+static double Atracking( double *lasthorizontalw, double *lastverticalw,
char **seq1, char **seq2,
char **mseq1, char **mseq2,
- float **cpmx1, float **cpmx2,
int **ijp, int icyc, int jcyc,
- int *gapmap1, int *gapmap2 )
+ int tailgp,
+ int *warpis, int *warpjs, int warpbase,
+ int *ngap1, int *ngap2, int reuseprofiles )
{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
- float wm;
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+ double 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 );
}
#endif
- if( outgap == 1 )
+ if( tailgp == 1 )
;
else
{
gaptable2 = gt2bk + lgth1+lgth2;
*gaptable2 = 0;
+ *ngap1 = *ngap2 = 0;
iin = lgth1; jin = lgth2;
- *impwmpt = 0.0;
- for( k=0; k<=lgth1+lgth2; k++ )
+ limk = lgth1+lgth2 + 1;
+ for( k=0; k<limk; k++ )
{
- if( ijp[iin][jin] < 0 )
+ if( ijp[iin][jin] >= warpbase )
+ {
+ ifi = warpis[ijp[iin][jin]-warpbase];
+ jfi = warpjs[ijp[iin][jin]-warpbase];
+ }
+ else if( ijp[iin][jin] < 0 )
{
ifi = iin-1; jfi = jin+ijp[iin][jin];
}
{
ifi = iin-1; jfi = jin-1;
}
- l = iin - ifi;
- while( --l )
- {
- *--gaptable1 = 'o';
- *--gaptable2 = '-';
- k++;
- }
- l= jin - jfi;
- while( --l )
+
+ if( ifi == -warpbase && jfi == -warpbase )
{
- *--gaptable1 = '-';
- *--gaptable2 = 'o';
- k++;
+ l = iin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ *ngap2=1;
+ }
+ l= jin;
+ while( --l >= 0 )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ *ngap1=1;
+ }
+ break;
}
- 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] );
+ l = iin - ifi;
+ while( --l )
+ {
+ *--gaptable1 = 'o';
+ *--gaptable2 = '-';
+ k++;
+ *ngap2=1;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ *--gaptable1 = '-';
+ *--gaptable2 = 'o';
+ k++;
+ *ngap1=1;
+ }
}
if( iin <= 0 || jin <= 0 ) break;
- *--gaptable1 = '-';
- *--gaptable2 = '-';
+ *--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 );
+
+// reporterr( "gaptable1=%s\n", gaptable1 );
+// reporterr( "gaptable2=%s\n", gaptable2 );
+
+
+ if( *ngap1 || !reuseprofiles )
+ for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+
+ if( *ngap2 || !reuseprofiles )
+ for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
free( gt1bk );
free( gt2bk );
+
+ return( 0.0 );
}
-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 )
+
+double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp, int firstmem, int calledbyfulltreebase )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
- 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] );
+ int reuseprofiles;
+ static TLS int previousfirstlen; // 2016/Feb/1 // MEMBER NO CHECK GA HITSUYOU!!!!
+ static TLS int previousicyc; // 2016/Feb/1 // MEMBER NO CHECK GA HITSUYOU!!!!
+ static TLS int previousfirstmem;
+ static TLS int previouscall;
+ int ngap1, ngap2;
+// int k;
+ register int i, j;
+ int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+ int lgth1, lgth2;
+ int resultlen;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
+// double fpenalty = (double)penalty;
+#if USE_PENALTY_EX
+ double fpenalty_ex = (double)penalty_ex;
+#endif
+#if 1
+ double *wtmp;
+ int *ijppt;
+ double *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ static TLS double mi, *m;
+ static TLS int **ijp;
+ static TLS int mpi, *mp;
+ static TLS double *w1, *w2;
+ static TLS double *match;
+ static TLS double *initverticalw; /* kufuu sureba iranai */
+ static TLS double *lastverticalw; /* kufuu sureba iranai */
+ static TLS char **mseq1;
+ static TLS char **mseq2;
+ static TLS char **mseq;
+ static TLS double *ogcp1, *ogcp1o;
+ static TLS double *ogcp2;
+ static TLS double *fgcp1, *fgcp1o;
+ static TLS double *fgcp2;
+ static TLS double **cpmx1;
+ static TLS double **cpmx2;
+ static TLS int **intwork;
+ static TLS double **doublework;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ static TLS double *gapfreq1;
+ static TLS double *gapfreq2;
+ double fpenalty = (double)penalty;
+ double fpenalty_shift = (double)penalty_shift;
+ double *fgcp2pt;
+ double *ogcp2pt;
+ double fgcp1va;
+ double ogcp1va;
+ double *gf2pt;
+ double *gf2ptpre;
+ double gf1va;
+ double gf1vapre;
+ double headgapfreq1;
+ double headgapfreq2;
+
+ int *warpis = NULL;
+ int *warpjs = NULL;
+ int *warpi = NULL;
+ int *warpj = NULL;
+ int *prevwarpi = NULL;
+ int *prevwarpj = NULL;
+ double *wmrecords = NULL;
+ double *prevwmrecords = NULL;
+ int warpn = 0;
+ int warpbase;
+ double curm = 0.0;
+ double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+ int *warpipt, *warpjpt;
+
+// for( i=0; i<icyc; i++ ) fprintf( stderr, "%s, %f\n", seq1[i], eff1[i] );
+// for( i=0; i<jcyc; i++ ) fprintf( stderr, "%s, %f\n", seq2[i], eff2[i] );
- 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( seq1 == NULL )
{
if( orlgth1 )
{
orlgth1 = 0;
orlgth2 = 0;
- imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+ imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
free( mseq1 );
free( mseq2 );
FreeCharMtx( mseq );
FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp1o );
FreeFloatVec( ogcp2 );
FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp1o );
FreeFloatVec( fgcp2 );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
- FreeFloatMtx( floatwork );
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
}
return( 0.0 );
}
+
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
-#if 1
+#if 0
if( lgth1 == 0 || lgth2 == 0 )
{
fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
}
+#endif
if( lgth1 == 0 && lgth2 == 0 )
return( 0.0 );
{
j = lgth2;
seq1[i][j] = 0;
- while( j ) seq1[i][--j] = '-';
+ while( j ) seq1[i][--j] = *newgapstr;
// fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
}
return( 0.0 );
{
j = lgth1;
seq2[i][j] = 0;
- while( j ) seq2[i][--j] = '-';
+ while( j ) seq2[i][--j] = *newgapstr;
// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
}
return( 0.0 );
}
-#endif
+
+ warpbase = lgth1 + lgth2;
+ warpis = NULL;
+ warpjs = NULL;
+ warpn = 0;
+
+
+
+ if( trywarp )
+ {
+// fprintf( stderr, "IN A__align, penalty_shift = %d\n", penalty_shift );
+ if( headgp == 0 || tailgp == 0 )
+ {
+ fprintf( stderr, "At present, headgp and tailgp must be 1 to allow shift.\n" );
+ exit( 1 );
+ }
+ wmrecords = AllocateFloatVec( lgth2+1 );
+ warpi = AllocateIntVec( lgth2+1 );
+ warpj = AllocateIntVec( lgth2+1 );
+ prevwmrecords = AllocateFloatVec( lgth2+1 );
+ prevwarpi = AllocateIntVec( lgth2+1 );
+ prevwarpj = AllocateIntVec( lgth2+1 );
+ for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
+ }
#if 0
{
int ll1, ll2;
+
if( orlgth1 > 0 && orlgth2 > 0 )
{
FreeFloatVec( w1 );
FreeCharMtx( mseq );
FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp1o );
FreeFloatVec( ogcp2 );
FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp1o );
FreeFloatVec( fgcp2 );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
- FreeFloatMtx( floatwork );
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
}
mseq = AllocateCharMtx( njob, ll1+ll2 );
ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp1o = AllocateFloatVec( ll1+2 );
ogcp2 = AllocateFloatVec( ll2+2 );
fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp1o = AllocateFloatVec( ll1+2 );
fgcp2 = AllocateFloatVec( ll2+2 );
- cpmx1 = AllocateFloatMtx( 26, ll1+2 );
- cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+ cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
+ cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
+ previousfirstlen = -1;
+ previousicyc = -1;
+
+ gapfreq1 = AllocateFloatVec( ll1+2 );
+ gapfreq2 = AllocateFloatVec( ll2+2 );
#if FASTMATCHCALC
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+ doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets+1 );
#else
- floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
- intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
+ doublework = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
+ intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
#endif
#if DEBUG
#if 0
{
- float t = 0.0;
+ double 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 );
+ if( calledbyfulltreebase && previouscall && firstmem >= 0 && firstmem == previousfirstmem && lgth1 == previousfirstlen && nthread == 0 && icyc == previousicyc+1 ) // mouhitotsu jouken ga iru. firstmem >= 0 && firstmem == previousfirstmem && calledbytreebase && prevcalledbytreebase
+ reuseprofiles = 1;
+ else
+ reuseprofiles = 0;
+
+
+ if( reuseprofiles )
+ {
+// reporterr( "r" );
+ cpmx_calc_add( seq1, cpmx1, eff1, lgth1, icyc );
+ }
+ else
+ {
+// reporterr( "n" );
+ 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( ogcp1o, icyc, seq1, eff1, lgth1, sgap1 );
+ new_FinalGapCount( fgcp1o, icyc, seq1, eff1, lgth1, egap1 );
+
new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
- new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+
+ outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
+ outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
+ outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
+ outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
}
else
{
- st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+ if( reuseprofiles )
+ {
+ st_OpeningGapAdd( ogcp1o, icyc, seq1, eff1, lgth1 );
+ st_FinalGapAdd( fgcp1o, icyc, seq1, eff1, lgth1 );
+ }
+ else
+ {
+ st_OpeningGapCount( ogcp1o, icyc, seq1, eff1, lgth1 );
+ st_FinalGapCount( fgcp1o, 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 );
+
+ headgapfreq1 = 0.0;
+ headgapfreq2 = 0.0;
+ gapfreq1[lgth1] = 0.0;
+ gapfreq2[lgth2] = 0.0;
}
+ if( legacygapcost == 0 )
+ {
+ if( reuseprofiles )
+ gapcountadd( gapfreq1, seq1, icyc, eff1, lgth1 );
+ else
+ gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
+
+ gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
+
+ for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
+ for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
+ headgapfreq1 = 1.0 - headgapfreq1;
+ headgapfreq2 = 1.0 - headgapfreq2;
+ }
+ else
+ {
+ for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
+ for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
+ headgapfreq1 = 1.0;
+ headgapfreq2 = 1.0;
+ }
+
+#if 0
+ fprintf( stderr, "\ngapfreq1[] =" );
+ for( i=0; i<lgth1; i++ ) fprintf( stderr, "%5.2f ", gapfreq1[i] );
+ fprintf( stderr, "\n" );
+
+ fprintf( stderr, "\ngapfreq2[] =" );
+ for( i=0; i<lgth2; i++ ) fprintf( stderr, "%5.2f ", gapfreq2[i] );
+ fprintf( stderr, "\n" );
+#endif
+
+
for( i=0; i<lgth1; i++ )
{
- ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
- fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1o[i] ) * fpenalty * ( gapfreq1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1o[i] ) * fpenalty * ( gapfreq1[i] );
}
+
for( i=0; i<lgth2; i++ )
{
- ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
- fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
}
#if 0
for( i=0; i<lgth1; i++ )
currentw = w1;
previousw = w2;
- match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
if( localhom )
imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
- match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, 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 );
+ imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
#endif
{
for( i=1; i<lgth1+1; i++ )
{
- initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
}
for( j=1; j<lgth2+1; j++ )
{
- currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+// currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
}
}
#if OUTGAP0TRY
else
{
+ fprintf( stderr, "offset = %d\n", offset );
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
+#if 0
+ fprintf( stderr, "\n " );
+ for( j=0; j<lgth2+1; j++ ) fprintf( stderr, " %c ", seq2[0][j] );
+ fprintf( stderr, "\n%c ", seq1[0][0] );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
for( j=1; j<lgth2+1; ++j )
{
- m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+// m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
}
if( lgth2 == 0 )
lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
lastverticalw[0] = currentw[lgth2-1];
if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
previousw[0] = initverticalw[i-1];
- match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+ match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
#endif
currentw[0] = initverticalw[i];
-
- mi = previousw[0] + ogcp2[1]; mpi = 0;
+#if 0
+ fprintf( stderr, "%c ", seq1[0][i] );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// mi = previousw[0] + ogcp2[1]; mpi = 0;
+ mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
ijppt = ijp[i] + 1;
mjpt = m + 1;
prept = previousw;
ogcp2pt = ogcp2 + 1;
fgcp1va = fgcp1[i-1];
ogcp1va = ogcp1[i];
- lastj = lgth2+1;
+ gf1va = gapfreq1[i];
+ gf1vapre = gapfreq1[i-1];
+ gf2pt = gapfreq2+1;
+ gf2ptpre = gapfreq2;
+
+ if( trywarp )
+ {
+ prevwmrecordspt = prevwmrecords;
+ wmrecordspt = wmrecords+1;
+ wmrecords1pt = wmrecords;
+ warpipt = warpi + 1;
+ warpjpt = warpj + 1;
+ }
+
+
for( j=1; j<lastj; j++ )
{
#ifdef xxxenablemultithread
*ijppt = 0;
#if 0
+ fprintf( stderr, "\n i=%d, j=%d %c, %c", i, j, seq1[0][i], seq2[0][j] );
fprintf( stderr, "%5.0f->", wm );
+ fprintf( stderr, "%5.0f? (penal=%5.2f)", g=mi+*fgcp2pt*(1.0-gapfreq1[i]), *fgcp2pt*(1.0-gapfreq1[i]) );
#endif
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( (g=mi+*fgcp2pt) > wm )
+ if( (g=mi+*fgcp2pt*gf1va) > wm )
{
wm = g;
*ijppt = -( j - mpi );
+// fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );
}
- if( (g=*prept+*ogcp2pt) >= mi )
+ if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
{
mi = g;
mpi = j-1;
#endif
#if 0
- fprintf( stderr, "%5.0f?", g );
+ fprintf( stderr, "%5.0f->", wm );
+ fprintf( stderr, "%5.0f? (penal=%5.2f)", g=*mjpt+fgcp1va*(1.0-gapfreq2[j]), fgcp1va*(1.0-gapfreq2[j]) );
#endif
- if( (g=*mjpt+fgcp1va) > wm )
+ if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
+// fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );
}
- if( (g=*prept+ogcp1va) >= *mjpt )
+ if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
{
*mjpt = g;
*mpjpt = i-1;
m[j] += fpenalty_ex;
#endif
+
+ if( trywarp )
+ {
+#if USE_PENALTY_EX
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
+#else
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
+#endif
+ {
+// fprintf( stderr, "WARP!!\n" );
+ if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
+ {
+ *ijppt = warpbase + warpn - 1;
+ }
+ else
+ {
+ *ijppt = warpbase + warpn;
+ warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
+ warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
+ warpis[warpn] = prevwarpi[j-1];
+ warpjs[warpn] = prevwarpj[j-1];
+ warpn++;
+ }
+ wm = g;
+ }
+
#if 0
- fprintf( stderr, "%5.0f ", wm );
+ fprintf( stderr, "%5.0f ", wm );
#endif
+ curm = *curpt + wm;
+
+ if( *wmrecords1pt > *wmrecordspt )
+ {
+ *wmrecordspt = *wmrecords1pt;
+ *warpipt = *(warpipt-1);
+ *warpjpt = *(warpjpt-1);
+ }
+ if( curm > *wmrecordspt )
+ {
+ *wmrecordspt = curm;
+ *warpipt = i;
+ *warpjpt = j;
+ }
+ wmrecordspt++;
+ wmrecords1pt++;
+ warpipt++;
+ warpjpt++;
+ }
+
*curpt++ += wm;
ijppt++;
mjpt++;
mpjpt++;
fgcp2pt++;
ogcp2pt++;
+ gf2ptpre++;
+ gf2pt++;
}
lastverticalw[i] = currentw[lgth2-1];
+
+ if( trywarp )
+ {
+ fltncpy( prevwmrecords, wmrecords, lastj );
+ intncpy( prevwarpi, warpi, lastj );
+ intncpy( prevwarpj, warpj, lastj );
+ }
}
-// fprintf( stderr, "wm = %f\n", wm );
+ if( trywarp )
+ {
+// fprintf( stderr, "wm = %f\n", wm );
+// fprintf( stderr, "warpn = %d\n", warpn );
+ free( wmrecords );
+ free( prevwmrecords );
+ free( warpi );
+ free( warpj );
+ free( prevwarpi );
+ free( prevwarpj );
+ }
#if OUTGAP0TRY
if( !outgap )
*/
if( localhom )
{
- Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles );
}
else
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, tailgp );
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles );
+
+// reporterr( "reuseprofiles after Atracking = %d\n", reuseprofiles );
+
+ if( warpis ) free( warpis );
+ if( warpjs ) free( warpjs );
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
}
- for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
- for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+ if( ngap1 || !reuseprofiles )
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ if( ngap2 || !reuseprofiles )
+ 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] );
for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
#endif
-// fprintf( stderr, "wm = %f\n", wm );
+// fprintf( stdout, "firstmem=%d, icyc=%d, jcyc=%d, wm = %f\n", firstmem, icyc, jcyc, wm );
+
+// fprintf( stderr, "lgth1 = %d\n", lgth1 );
+// fprintf( stderr, "-> %d\n", strlen( seq1[0] ) );
+ previousfirstlen = lgth1;
+ previousfirstmem = firstmem;
+ previousicyc = icyc;
+ previouscall = calledbyfulltreebase;
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 )
+double A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, int *gapmap1, int *gapmap2 )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
+ fprintf( stderr, "Unexpected error. Please contact kazutaka.katoh@aist.go.jp\n" );
+ exit( 1 );
+}
+
+
+double A__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *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 */
+ register int i, j, c;
+ int ngap1, ngap2;
+ 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;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
+// double fpenalty = (double)penalty;
#if USE_PENALTY_EX
- float fpenalty_ex = (float)penalty_ex;
+ double fpenalty_ex = (double)penalty_ex;
#endif
#if 1
- float *wtmp;
+ double *wtmp;
int *ijppt;
- float *mjpt, *prept, *curpt;
+ double *mjpt, *prept, *curpt;
int *mpjpt;
#endif
- static TLS float mi, *m;
+ static TLS double 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 double *w1, *w2;
+ static TLS double *match;
+ static TLS double *initverticalw; /* kufuu sureba iranai */
+ static TLS double *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 double *ogcp1;
+ static TLS double *ogcp2;
+ static TLS double *fgcp1;
+ static TLS double *fgcp2;
+ static TLS double ***cpmx1s;
+ static TLS double ***cpmx2s;
+ static TLS int ***intwork;
+ static TLS double ***doublework;
static TLS int orlgth1 = 0, orlgth2 = 0;
- float *fgcp2pt;
- float *ogcp2pt;
- float fgcp1va;
- float ogcp1va;
+ static TLS double *gapfreq1;
+ static TLS double *gapfreq2;
+ double fpenalty = (double)penalty;
+ double fpenalty_shift = (double)penalty_shift;
+ double *fgcp2pt;
+ double *ogcp2pt;
+ double fgcp1va;
+ double ogcp1va;
+ double *gf2pt;
+ double *gf2ptpre;
+ double gf1va;
+ double gf1vapre;
+ double headgapfreq1;
+ double headgapfreq2;
+
+ int *warpis = NULL;
+ int *warpjs = NULL;
+ int *warpi = NULL;
+ int *warpj = NULL;
+ int *prevwarpi = NULL;
+ int *prevwarpj = NULL;
+ double *wmrecords = NULL;
+ double *prevwmrecords = NULL;
+ int warpn = 0;
+ int warpbase;
+ double curm = 0.0;
+ double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+ int *warpipt, *warpjpt;
+ int *nmask, **masklist1, **masklist2;
-#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 )
+ if( seq1 == NULL )
{
- mseq1 = AllocateCharMtx( njob, 0 );
- mseq2 = AllocateCharMtx( njob, 0 );
+ 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, NULL, 0, NULL, NULL );
+
+ 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 );
+
+
+ FreeFloatCub( cpmx1s );
+ FreeFloatCub( cpmx2s );
+
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatCub( doublework );
+ FreeIntCub( intwork );
+
+ }
+ else
+ {
+// fprintf( stderr, "## Not allocated\n" );
+ }
+ return( 0.0 );
}
+#if SLOW
+ nmask = calloc( maxdistclass, sizeof( int ) );
+#else
+ masklist1 = AllocateIntMtx( maxdistclass, 0 );
+ masklist2 = AllocateIntMtx( maxdistclass, 0 );
+ nmask = calloc( maxdistclass, sizeof( int ) );
+
+ for( c=0; c<maxdistclass; c++ )
+ {
+ for( i=0; i<icyc; i++ ) for( j=0; j<jcyc; j++ )
+ {
+ if( eff1s[c][i] * eff2s[c][j] != 0.0 )
+ {
+
+ if( c != which[i][j] )
+ {
+ masklist1[c] = realloc( masklist1[c], sizeof( int ) * (nmask[c]+1) );
+ masklist2[c] = realloc( masklist2[c], sizeof( int ) * (nmask[c]+1) );
+
+ masklist1[c][nmask[c]] = i;
+ masklist2[c][nmask[c]] = j;
+ nmask[c]++;
+ }
+ }
+ }
+ }
+ for( c=0; c<maxdistclass; c++ ) if( nmask[c] ) break;
+ if( c<maxdistclass ) reporterr( "Found a complex grouping. This step may be a bit slow.\n" );
+#endif
+
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 );
+ fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ }
+#endif
+ 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] = *newgapstr;
+// 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] = *newgapstr;
+// fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+ }
+ return( 0.0 );
+ }
+
+ warpbase = lgth1 + lgth2;
+ warpis = NULL;
+ warpjs = NULL;
+ warpn = 0;
+
+ if( trywarp )
+ {
+// fprintf( stderr, "In A__align_variousdist !!!!!\n" );
+ if( headgp == 0 || tailgp == 0 )
+ {
+ fprintf( stderr, "At present, headgp and tailgp must be 1.\n" );
+ exit( 1 );
+ }
+ wmrecords = AllocateFloatVec( lgth2+1 );
+ warpi = AllocateIntVec( lgth2+1 );
+ warpj = AllocateIntVec( lgth2+1 );
+ prevwmrecords = AllocateFloatVec( lgth2+1 );
+ prevwarpi = AllocateIntVec( lgth2+1 );
+ prevwarpj = AllocateIntVec( lgth2+1 );
+ for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
+ for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
+ for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
}
+
+#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( fgcp2 );
- FreeFloatMtx( cpmx1 );
- FreeFloatMtx( cpmx2 );
+ FreeFloatCub( cpmx1s );
+ FreeFloatCub( cpmx2s );
- FreeFloatMtx( floatwork );
- FreeIntMtx( intwork );
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatCub( doublework );
+ FreeIntCub( intwork );
}
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
fgcp1 = AllocateFloatVec( ll1+2 );
fgcp2 = AllocateFloatVec( ll2+2 );
- cpmx1 = AllocateFloatMtx( 26, ll1+2 );
- cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+ cpmx1s = AllocateFloatCub( maxdistclass, nalphabets, ll1+2 );
+ cpmx2s = AllocateFloatCub( maxdistclass, nalphabets, 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
+ gapfreq1 = AllocateFloatVec( ll1+2 );
+ gapfreq2 = AllocateFloatVec( ll2+2 );
+
+ doublework = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
+ intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets+1 );
#if DEBUG
fprintf( stderr, "succeeded\n" );
}
ijp = commonIP;
- cpmx_calc_new( seq1, cpmx1, eff1, strlen( seq1[0] ), icyc );
- cpmx_calc_new( seq2, cpmx2, eff2, strlen( seq2[0] ), jcyc );
+#if 0
+ {
+ double t = 0.0;
+ for( i=0; i<icyc; i++ )
+ t += eff1[i];
+ fprintf( stderr, "## totaleff = %f\n", t );
+ }
+#endif
+
+#if SLOW
+#else
+// cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+// cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ cpmx_calc_new( seq1, cpmx1s[c], eff1s[c], lgth1, icyc );
+ cpmx_calc_new( seq2, cpmx2s[c], eff2s[c], lgth2, jcyc );
+ }
+#endif
+
+ 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 );
+ outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
+ outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
+ outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
+ outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
+ }
+ 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 );
+ headgapfreq1 = 0.0;
+ headgapfreq2 = 0.0;
+ gapfreq1[lgth1] = 0.0;
+ gapfreq2[lgth2] = 0.0;
+ }
+
+ if( legacygapcost == 0 )
+ {
+ gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
+ gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
+ for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
+ for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
+ headgapfreq1 = 1.0 - headgapfreq1;
+ headgapfreq2 = 1.0 - headgapfreq2;
+ }
+ else
+ {
+ for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
+ for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
+ headgapfreq1 = 1.0;
+ headgapfreq2 = 1.0;
+ }
- 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 );
+#if 0
+ fprintf( stderr, "\ngapfreq1[] =" );
+ for( i=0; i<lgth1; i++ ) fprintf( stderr, "%5.2f ", gapfreq1[i] );
+ fprintf( stderr, "\n" );
+
+ fprintf( stderr, "\ngapfreq2[] =" );
+ for( i=0; i<lgth2; i++ ) fprintf( stderr, "%5.2f ", gapfreq2[i] );
+ fprintf( stderr, "\n" );
+#endif
+
for( i=0; i<lgth1; i++ )
{
- ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
- fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
}
+
for( i=0; i<lgth2; i++ )
{
- ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
- fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
}
#if 0
for( i=0; i<lgth1; i++ )
currentw = w1;
previousw = w2;
+// for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+// for( j=0; j<jcyc; j++ ) fprintf( stderr, "seq2[j] = %s\n", seq2[j] );
+
+#if SLOW
+ match_calc_slow( which, matrices, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, *doublework, *intwork, 1, 1 );
+#else
+ fillzero( initverticalw, lgth1 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+// fprintf( stderr, "c=%d matrices[c][W][W] = %f\n", c, matrices[c][amino_n['W']][amino_n['W']] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "seq1[i] = %c, cpmx1s[c][3][%d] = %f\n", seq1[0][i], i, cpmx1s[c][3][i] );
+// for( i=0; i<lgth2; i++ ) fprintf( stderr, "seq2[i] = %c, cpmx2s[c][3][%d] = %f\n", seq2[0][i], i, cpmx2s[c][3][i] );
+ match_calc_add( matrices[c], initverticalw, cpmx2s[c], cpmx1s[c], 0, lgth1, doublework[c], intwork[c], 1 );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "c=%d, %d - %f\n", c, i, initverticalw[i] );
+ if( nmask[c] ) match_calc_del( which, matrices, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, c, nmask[c], masklist2[c], masklist1[c] );
+ }
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
+#endif
+
+// exit( 1 );
- match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
if( localhom )
- imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0], lgth1, gapmap1 ); // 060306
+ imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
+#if SLOW
+ match_calc_slow( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, *doublework, *intwork, 1, 0 );
+// for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
+// exit( 1 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], 0, lgth2, doublework[c], intwork[c], 1 );
+ if( nmask[c] ) match_calc_del( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, c, nmask[c], masklist1[c], masklist2[c] );
+ }
+// for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
+// exit( 1 );
+#endif
- match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
if( localhom )
- imp_match_out_vead_gapmap( currentw, gapmap1[0], lgth2, gapmap2 ); // 060306
+ 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 );
+ imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
#endif
- if( 1 ) // tsuneni outgap=1
+ if( headgp == 1 )
{
for( i=1; i<lgth1+1; i++ )
{
- initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
}
for( j=1; j<lgth2+1; j++ )
{
- currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+// currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
}
}
#if OUTGAP0TRY
else
{
+ fprintf( stderr, "offset = %d\n", offset );
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
+#if 0
+ fprintf( stderr, "\n " );
+ for( j=0; j<lgth2+1; j++ ) fprintf( stderr, " %c ", seq2[0][j] );
+ fprintf( stderr, "\n%c ", seq1[0][0] );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
for( j=1; j<lgth2+1; ++j )
{
- m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+// m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
}
-
if( lgth2 == 0 )
- lastverticalw[0] = 0.0;
+ lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
else
lastverticalw[0] = currentw[lgth2-1];
- if( 1 ) lasti = lgth1+1; else lasti = lgth1; // tsuneni outgap=1
+ if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
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" );
+ if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
+ if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+ *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 SLOW
+ match_calc_slow( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, *doublework, *intwork, 0, 0 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], i, lgth2, doublework[c], intwork[c], 0 );
+ if( nmask[c] ) match_calc_del( which, matrices, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, c, nmask[c], masklist1[c], masklist2[c] );
+ }
+#endif
+#if 0
+ if( i == 1 )
+ {
+ fprintf( stderr, "\n" );
+ for( j=0; j<lgth2; j++ ) fprintf( stderr, "%d - %f\n", j, currentw[j] );
+ exit( 1 );
+ }
+#endif
+
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
#if 0
imp_match_out_vead( currentw, i, lgth2 );
#else
- imp_match_out_vead_gapmap( currentw, gapmap1[i], lgth2, gapmap2 );
+ imp_match_out_vead( currentw, i, lgth2 );
#endif
}
#if XXXXXXX
#endif
currentw[0] = initverticalw[i];
-
- mi = previousw[0] + ogcp2[1]; mpi = 0;
-
+#if 0
+ fprintf( stderr, "%c ", seq1[0][i] );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "%5.0f ", currentw[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// mi = previousw[0] + ogcp2[1]; mpi = 0;
+ mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
ijppt = ijp[i] + 1;
mjpt = m + 1;
prept = previousw;
ogcp2pt = ogcp2 + 1;
fgcp1va = fgcp1[i-1];
ogcp1va = ogcp1[i];
- lastj = lgth2+1;
+ gf1va = gapfreq1[i];
+ gf1vapre = gapfreq1[i-1];
+ gf2pt = gapfreq2+1;
+ gf2ptpre = gapfreq2;
+
+ if( trywarp )
+ {
+ prevwmrecordspt = prevwmrecords;
+ wmrecordspt = wmrecords+1;
+ wmrecords1pt = wmrecords;
+ warpipt = warpi + 1;
+ warpjpt = warpj + 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" );
+ if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
+ if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+ *chudanres = 1;
+ return( -1.0 );
+ }
+#endif
wm = *prept;
*ijppt = 0;
#if 0
+ fprintf( stderr, "\n i=%d, j=%d %c, %c", i, j, seq1[0][i], seq2[0][j] );
fprintf( stderr, "%5.0f->", wm );
+ fprintf( stderr, "%5.0f? (penal=%5.2f)", g=mi+*fgcp2pt*(1.0-gapfreq1[i]), *fgcp2pt*(1.0-gapfreq1[i]) );
#endif
- g = mi + *fgcp2pt;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
+ if( (g=mi+*fgcp2pt*gf1va) > wm )
{
wm = g;
*ijppt = -( j - mpi );
+// fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );
}
- g = *prept + *ogcp2pt;
- if( g >= mi )
+ if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
{
mi = g;
mpi = j-1;
mi += fpenalty_ex;
#endif
- g = *mjpt + fgcp1va;
#if 0
- fprintf( stderr, "%5.0f?", g );
+ fprintf( stderr, "%5.0f->", wm );
+ fprintf( stderr, "%5.0f? (penal=%5.2f)", g=*mjpt+fgcp1va*(1.0-gapfreq2[j]), fgcp1va*(1.0-gapfreq2[j]) );
#endif
- if( g > wm )
+ if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
+// fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );
}
- g = *prept + ogcp1va;
- if( g >= *mjpt )
+ if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
{
*mjpt = g;
*mpjpt = i-1;
#if USE_PENALTY_EX
m[j] += fpenalty_ex;
#endif
+ if( trywarp )
+ {
+#if USE_PENALTY_EX
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
+#else
+ if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
+#endif
+ {
+ if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
+ {
+ *ijppt = warpbase + warpn - 1;
+ }
+ else
+ {
+ *ijppt = warpbase + warpn;
+ warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
+ warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
+ warpis[warpn] = prevwarpi[j-1];
+ warpjs[warpn] = prevwarpj[j-1];
+ warpn++;
+ }
+ wm = g;
+ }
+ curm = *curpt + wm;
+
+ if( *wmrecords1pt > *wmrecordspt )
+ {
+ *wmrecordspt = *wmrecords1pt;
+ *warpipt = *(warpipt-1);
+ *warpjpt = *(warpjpt-1);
+ }
+ if( curm > *wmrecordspt )
+ {
+ *wmrecordspt = curm;
+ *warpipt = i;
+ *warpjpt = j;
+ }
+ wmrecordspt++;
+ wmrecords1pt++;
+ warpipt++;
+ warpjpt++;
+ }
#if 0
fprintf( stderr, "%5.0f ", wm );
mpjpt++;
fgcp2pt++;
ogcp2pt++;
+ gf2ptpre++;
+ gf2pt++;
+
}
lastverticalw[i] = currentw[lgth2-1];
+
+ if( trywarp )
+ {
+ fltncpy( prevwmrecords, wmrecords, lastj );
+ intncpy( prevwarpi, warpi, lastj );
+ intncpy( prevwarpj, warpj, lastj );
+ }
}
+ if( trywarp )
+ {
+// fprintf( stderr, "wm = %f\n", wm );
+// fprintf( stderr, "warpn = %d\n", warpn );
+ free( wmrecords );
+ free( prevwmrecords );
+ free( warpi );
+ free( warpj );
+ free( prevwarpi );
+ free( prevwarpj );
+ }
+
#if OUTGAP0TRY
if( !outgap )
*/
if( localhom )
{
- Atracking_localhom_gapmap( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, gapmap1, gapmap2 );
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase, &ngap1, &ngap2, 0 );
}
else
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, 1 );
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0 );
+
+ if( warpis ) free( warpis );
+ if( warpjs ) free( warpjs );
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
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 );
+
+ if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
+ if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+
return( wm );
}
-
git://source.jalview.org / jabaws.git / blobdiff