#define FASTMATCHCALC 1
#if 0
-static void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+static void st_OpeningGapCount( double *ogcp, int clus, char **seq, double *eff, int len )
{
int i, j, gc, gb;
- float feff;
+ double feff;
for( i=0; i<len; i++ ) ogcp[i] = 0.0;
for( j=0; j<clus; j++ )
{
- feff = (float)eff[j];
+ feff = (double)eff[j];
gc = 0;
for( i=0; i<len; i++ )
{
}
}
-static void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+static void st_FinalGapCount( double *fgcp, int clus, char **seq, double *eff, int len )
{
int i, j, gc, gb;
- float feff;
+ double feff;
for( i=0; i<len; i++ ) fgcp[i] = 0.0;
for( j=0; j<clus; j++ )
{
- feff = (float)eff[j];
+ feff = (double)eff[j];
gc = ( seq[j][0] == '-' );
for( i=1; i<len+1; i++ )
{
static TLS int impalloclen = 0;
-static TLS float **impmtx = NULL;
-float part_imp_match_out_sc( int i1, int j1 )
+static TLS double **impmtx = NULL;
+double part_imp_match_out_sc( int i1, int j1 )
{
// fprintf( stderr, "impalloclen = %d\n", impalloclen );
// fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
return( impmtx[i1+start1][j1+start2] );
#endif
}
-static void part_imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
+static void part_imp_match_out_vead_gapmap( double *imp, int i1, int lgth2, int start2, int *gapmap2 )
{
#if FASTMACHCALC
- float *pt = imp;
+ double *pt = imp;
int *gapmappt = gapmap2;
while( lgth2-- )
*pt++ += impmtx[i1][start2+*gapmappt++];
#endif
}
-static void part_imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int start1, int *gapmap1 )
+static void part_imp_match_out_vead_tate_gapmap( double *imp, int j1, int lgth1, int start1, int *gapmap1 )
{
#if FASTMACHCALC
- float *pt = imp;
+ double *pt = imp;
int *gapmappt = gapmap1;
while( lgth1-- )
*pt++ = impmtx[start1+*gapmappt++][j1];
#endif
}
-void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore )
+#if 1
+void part_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;
- double effij, effijx, effij_kozo;
- char *pt, *pt1, *pt2;
- 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;
+
return;
}
- if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
+ 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+100, impalloclen+100 );
+ impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+// nocount1 = AllocateCharVec( impalloclen );
+// nocount2 = AllocateCharVec( impalloclen );
}
-
-#if 0
- fprintf( stderr, "eff1 in _init_strict = \n" );
- for( i=0; i<clus1; i++ )
- fprintf( stderr, "eff1[] = %f\n", eff1[i] );
- for( i=0; i<clus2; i++ )
- fprintf( stderr, "eff2[] = %f\n", eff2[i] );
-#endif
-
- for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
- impmtx[i][j] = 0.0;
- effijx = 1.0 * fastathreshold;
- for( i=0; i<clus1; i++ )
- {
- for( j=0; j<clus2; j++ )
- {
- effij = eff1[i] * eff2[j] * effijx;
- effij_kozo = 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 = (int)( pt - seq1[i] ) - 1;
-
- if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
- else
- {
-#if MACHIGAI
- while( *pt != 0 )
- {
- if( tmpint == tmpptr->end1 ) break;
- if( *pt++ != '-' ) tmpint++;
- }
- end1 = (int)( pt - seq1[i] ) - 1;
-#else
- while( *pt != 0 )
- {
-// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
- if( *pt++ != '-' ) tmpint++;
- if( tmpint == tmpptr->end1 ) break;
- }
- end1 = (int)( pt - seq1[i] ) - 1;
-#endif
- }
-
- pt = seq2[j];
- tmpint = -1;
- while( *pt != 0 )
- {
- if( *pt++ != '-' ) tmpint++;
- if( tmpint == tmpptr->start2 ) break;
- }
- start2 = (int)( pt - seq2[j] ) - 1;
- if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
- else
- {
-#if MACHIGAI
- while( *pt != 0 )
- {
- if( tmpint == tmpptr->end2 ) break;
- if( *pt++ != '-' ) tmpint++;
- }
- end2 = (int)( pt - seq2[j] ) - 1;
+ fillimp( impmtx, imp, clus1, clus2, lgth1, lgth2, seq1, seq2, eff1, eff2, eff1_kozo, eff2_kozo, localhom, swaplist, forscore, orinum1, orinum2 );
+}
#else
- while( *pt != 0 )
- {
- if( *pt++ != '-' ) tmpint++;
- if( tmpint == tmpptr->end2 ) break;
- }
- end2 = (int)( pt - seq2[j] ) - 1;
-#endif
- }
-// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
-// fprintf( stderr, "step 0\n" );
- if( end1 - start1 != end2 - start2 )
- {
-// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
- }
-
- k1 = start1; k2 = start2;
- pt1 = seq1[i] + k1;
- pt2 = seq2[j] + k2;
- while( *pt1 && *pt2 )
- {
- if( *pt1 != '-' && *pt2 != '-' )
- {
-// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤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, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
-// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
- k1++; k2++;
- pt1++; pt2++;
- }
- else if( *pt1 != '-' && *pt2 == '-' )
- {
-// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
- k2++; pt2++;
- }
- else if( *pt1 == '-' && *pt2 != '-' )
- {
-// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
- k1++; pt1++;
- }
- else if( *pt1 == '-' && *pt2 == '-' )
- {
-// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
- k1++; pt1++;
- k2++; pt2++;
- }
- if( k1 > end1 || k2 > end2 ) break;
- }
- tmpptr = tmpptr->next;
- }
- }
- }
-#if 0
- fprintf( stderr, "impmtx = \n" );
- for( k2=0; k2<lgth2; k2++ )
- fprintf( stderr, "%6.3f ", (double)k2 );
- fprintf( stderr, "\n" );
- for( k1=0; k1<lgth1; k1++ )
- {
- fprintf( stderr, "%d", k1 );
- for( k2=0; k2<lgth2; k2++ )
- fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
- fprintf( stderr, "\n" );
- }
- exit( 1 );
#endif
-}
void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
}
-void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
-{
- int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
- static TLS int impalloclen = 0;
- char *pt;
- static TLS char *nocount1 = NULL;
- static TLS char *nocount2 = NULL;
-
- if( impalloclen < lgth1 || impalloclen < lgth2 )
- {
- if( impmtx ) FreeFloatMtx( impmtx );
- if( nocount1 ) free( nocount1 );
- if( nocount2 ) free( nocount2 );
- impalloclen = MAX( lgth1, lgth2 ) + 2;
- impmtx = AllocateFloatMtx( impalloclen, impalloclen );
- nocount1 = AllocateCharVec( impalloclen );
- nocount2 = AllocateCharVec( impalloclen );
- impalloclen -= 2;
- }
- for( i=0; i<lgth1; i++ )
- {
- for( j=0; j<clus1; j++ )
- if( seq1[j][i] == '-' ) break;
- if( j != clus1 ) nocount1[i] = 1;
- else nocount1[i] = 0;
- }
- for( i=0; i<lgth2; i++ )
- {
- for( j=0; j<clus2; j++ )
- if( seq2[j][i] == '-' ) break;
- if( j != clus2 ) nocount2[i] = 1;
- else nocount2[i] = 0;
- }
-#if 0
-fprintf( stderr, "nocount2 =\n" );
-for( i = 0; i<impalloclen; i++ )
+static void match_calc( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
- fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
-}
-#endif
-
- for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
- impmtx[i][j] = 0.0;
- for( i=0; i<clus1; i++ )
+#if FASTMATCHCALC
+ 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_consweight_multi[j][l] * cpmx1[j][i1];
+// scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+ }
+ matchpt = match;
+ cpmxpdnptpt = cpmxpdn;
+ cpmxpdptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *matchpt = 0.0;
+ cpmxpdnpt = *cpmxpdnptpt++;
+ cpmxpdpt = *cpmxpdptpt++;
+ while( *cpmxpdnpt>-1 )
+ *matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+ matchpt++;
+ }
+ }
+ free( scarr );
+#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_consweight_multi[k][l] * cpmx1[k][i1];
+// scarr[l] += n_dis[k][l] * cpmx1[k][i1];
}
- exit( 1 );
+ 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 match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+
+static void fillzero( double *s, int l )
+{
+ while( l-- ) *s++ = 0.0;
+}
+
+
+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( m=0; m<nmask; m++ )
+ {
+ 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[(int)seq1[i][i1]];
+ c2 = amino_n[(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 );
+ }
+ }
+// fprintf( stderr, "done\n" );
+ return;
+}
+
+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;
- 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++ )
- scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+ 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;
+// *matchpt = 0.0;
cpmxpdnpt = *cpmxpdnptpt++;
cpmxpdpt = *cpmxpdptpt++;
while( *cpmxpdnpt>-1 )
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;
- // simple
+ 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<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] += scoreingmtx[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 start1, int end1, int start2, int end2,
- int *gapmap1, int *gapmap2 )
+ int *gapmap1, int *gapmap2,
+ int *warpis, int *warpjs, int warpbase )
{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
// char gap[] = "-";
char *gap;
- float wm;
+ double wm;
gap = newgapstr;
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[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 )
+ if( ifi == -warpbase && jfi == -warpbase )
{
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = seq1[i][ifi+l];
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = *gap;
- k++;
+ l = iin;
+ while( --l >= 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin;
+ while( --l >= 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][l];
+ k++;
+ }
+ break;
}
- l= jin - jfi;
- while( --l )
+ else
{
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = *gap;
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = seq2[j][jfi+l];
- k++;
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
}
if( iin != lgth1 && jin != lgth2 ) // ??
{
- *impwmpt += part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
+ *impwmpt += (double)part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
// fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
}
if( iin <= 0 || jin <= 0 ) break;
- for( i=0; i<icyc; i++ )
+ for( i=0; i<icyc; i++ )
*--mseq1[i] = seq1[i][ifi];
- for( j=0; j<jcyc; j++ )
+ for( j=0; j<jcyc; j++ )
*--mseq2[j] = seq2[j][jfi];
k++;
iin = ifi; jin = jfi;
}
}
-static float Atracking( 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 **ijp, int icyc, int jcyc,
+ int *warpis, int *warpjs, int warpbase )
{
- int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk;
+ int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk, limk;
// char gap[] = "-";
char *gap;
gap = newgapstr;
- float wm = 0.0;
+ double wm = 0.0;
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
}
iin = lgth1; jin = lgth2;
lastk = lgth1+lgth2;
- for( k=0; k<=lastk; 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 )
+ if( ifi == -warpbase && jfi == -warpbase )
{
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = seq1[i][ifi+l];
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = *gap;
- k++;
+ l = iin;
+ while( --l >= 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin;
+ while( --l >= 0 )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][l];
+ k++;
+ }
+ break;
}
- l= jin - jfi;
- while( --l )
+ else
{
- for( i=0; i<icyc; i++ )
- *--mseq1[i] = *gap;
- for( j=0; j<jcyc; j++ )
- *--mseq2[j] = seq2[j][jfi+l];
- k++;
+ l = iin - ifi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = seq1[i][ifi+l];
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = *gap;
+ k++;
+ }
+ l= jin - jfi;
+ while( --l )
+ {
+ for( i=0; i<icyc; i++ )
+ *--mseq1[i] = *gap;
+ for( j=0; j<jcyc; j++ )
+ *--mseq2[j] = seq2[j][jfi+l];
+ k++;
+ }
}
+
if( iin <= 0 || jin <= 0 ) break;
for( i=0; i<icyc; i++ )
*--mseq1[i] = seq1[i][ifi];
return( 0.0 );
}
-float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
+double partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
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;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
#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 double *ogcp1;
+ static TLS double *ogcp2;
+ static TLS double *fgcp1;
+ static TLS double *fgcp2;
+ static TLS double **cpmx1;
+ static TLS double **cpmx2;
+ static TLS double *gapfreq1;
+ static TLS double *gapfreq2;
static TLS int **intwork;
- static TLS float **floatwork;
+ static TLS double **doublework;
static TLS int orlgth1 = 0, orlgth2 = 0;
- float fpenalty = (float)penalty;
+ double fpenalty = (double)penalty;
+ double fpenalty_shift = (double)penalty_shift;
#if USE_PENALTY_EX
- float fpenalty_ex = (float)penalty_ex;
+ double fpenalty_ex = (double)penalty_ex;
#endif
- float *fgcp2pt;
- float *ogcp2pt;
- float fgcp1va;
- float ogcp1va;
+ 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;
if( seq1 == NULL )
orlgth1 = 0;
orlgth2 = 0;
- part_imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+ part_imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
free( mseq1 );
free( mseq2 );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
- FreeFloatMtx( floatwork );
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
}
}
return( 0.0 );
}
+// fprintf( stderr, "IN partA__align\n" );
+
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
#if 1
- if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
- if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
+// if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
+// if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
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 )
+ {
+ if( outgap == 0 )
+ {
+ fprintf( stderr, "At present, outgap 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" );
for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
- FreeFloatMtx( floatwork );
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
}
fgcp1 = 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 );
+
+ gapfreq1 = AllocateFloatVec( ll1+2 );
+ gapfreq2 = AllocateFloatVec( ll2+2 );
#if FASTMATCHCALC
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
+ doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets );
#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
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( 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;
}
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 - 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] ) * 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++ )
previousw = w2;
- match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+ match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
if( localhom )
part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
- match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
if( localhom )
part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
#if 0 // -> tbfast.c
{
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
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;;
}
lastverticalw[0] = currentw[lgth2-1];
previousw[0] = initverticalw[i-1];
- match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
-#if XXXXXXX
+ match_calc( currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
+#if 0
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
-fprintf( stderr, "currentw = \n" );
+fprintf( stderr, "currentw before imp = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
// imp_match_out_vead( currentw, i, lgth2 );
part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
}
-#if XXXXXXX
-fprintf( stderr, "\n" );
+#if 0
+fprintf( stderr, "specificity = 0\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
currentw[0] = initverticalw[i];
- mi = previousw[0] + ogcp2[1]; mpi = 0;
+// mi = previousw[0] + ogcp2[1]; mpi = 0;
+ mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
ijppt = ijp[i] + 1;
mjpt = m + 1;
ogcp2pt = ogcp2+1;
fgcp1va = fgcp1[i-1];
ogcp1va = ogcp1[i];
+ 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
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
- g = mi + *fgcp2pt;
-#if 0
- fprintf( stderr, "%5.0f?", g );
-#endif
- if( g > wm )
+// g = mi + *fgcp2pt * gapfreq1[i];
+ if( (g = mi + *fgcp2pt * gf1va) > wm )
{
wm = g;
*ijppt = -( j - mpi );
}
- g = *prept + *ogcp2pt;
- if( g >= mi )
+// g = *prept + *ogcp2pt * gapfreq1[i-1];
+ 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 );
-#endif
- if( g > wm )
+// g = *mjpt + fgcp1va * gapfreq2[j];
+ if( (g = *mjpt + fgcp1va * *gf2pt) > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
}
- g = *prept + ogcp1va;
- if( g >= *mjpt )
+// g = *prept + ogcp1va * gapfreq2[j-1];
+ 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
+ {
+// fprintf( stderr, "WARP in partA__align\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;
+ }
+ 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 );
curpt++;
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( localhom )
{
- Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
+ Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2, warpis, warpjs, warpbase );
}
else
- Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
+
+ if( warpis ) free( warpis );
+ if( warpjs ) free( warpjs );
// fprintf( stderr, "### impmatch = %f\n", *impmatch );
return( wm );
}
+double partA__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, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j, c;
+ 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;
+#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;
+ static TLS double *ogcp2;
+ static TLS double *fgcp1;
+ static TLS double *fgcp2;
+ static TLS double ***cpmx1s;
+ static TLS double ***cpmx2s;
+ static TLS double *gapfreq1;
+ static TLS double *gapfreq2;
+ static TLS int ***intwork;
+ static TLS double ***doublework;
+ static TLS int orlgth1 = 0, orlgth2 = 0;
+ double fpenalty = (double)penalty;
+ double fpenalty_shift = (double)penalty_shift;
+#if USE_PENALTY_EX
+ double fpenalty_ex = (double)penalty_ex;
+#endif
+ 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( seq1 == NULL )
+ {
+ if( orlgth1 )
+ {
+// fprintf( stderr, "## Freeing local arrays in A__align\n" );
+ orlgth1 = 0;
+ orlgth2 = 0;
+
+ part_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 );
+ }
+
+ 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" );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+#if 1
+// if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
+// if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
+
+ 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 );
+ }
+#endif
+
+ warpbase = lgth1 + lgth2;
+ warpis = NULL;
+ warpjs = NULL;
+ warpn = 0;
+
+
+ if( trywarp )
+ {
+// fprintf( stderr, "IN partA__align_variousdist\n" );
+ if( outgap == 0 )
+ {
+ fprintf( stderr, "At present, outgap 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
+ 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 );
+ }
+
+
+
+
+ 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 );
+
+
+ FreeFloatCub( cpmx1s );
+ FreeFloatCub( cpmx2s );
+
+ FreeFloatVec( gapfreq1 );
+ FreeFloatVec( gapfreq2 );
+
+ FreeFloatCub( doublework );
+ FreeIntCub( 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 );
+
+ cpmx1s = AllocateFloatCub( maxdistclass, nalphabets, ll1+2 );
+ cpmx2s = AllocateFloatCub( maxdistclass, nalphabets, ll2+2 );
+
+ gapfreq1 = AllocateFloatVec( ll1+2 );
+ gapfreq2 = AllocateFloatVec( ll2+2 );
+
+ doublework = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
+ intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n" );
+#endif
+
+ orlgth1 = ll1 - 100;
+ orlgth2 = ll2 - 100;
+ }
+
+
+ for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
+ for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+
+ if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+ {
+ int ll1, ll2;
+
+ if( commonAlloc1 && commonAlloc2 )
+ {
+ FreeIntMtx( commonIP );
+ }
+
+ ll1 = MAX( orlgth1, commonAlloc1 );
+ ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+ fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+ commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ commonAlloc1 = ll1;
+ commonAlloc2 = ll2;
+ }
+ ijp = commonIP;
+
+// cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+// cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+ 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 );
+ }
+
+ 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;
+ }
+
+ for( i=0; i<lgth1; 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] ) * fpenalty * ( gapfreq2[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[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, doublework, intwork, 1 );
+ fillzero( initverticalw, lgth1 );
+ for( c=0; c<maxdistclass; c++ )
+ {
+ match_calc_add( matrices[c], initverticalw, cpmx2s[c], cpmx1s[c], 0, lgth1, doublework[c], intwork[c], 1 );
+ if( nmask[c] ) match_calc_del( which, matrices, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, c, nmask[c], masklist2[c], masklist1[c] );
+ }
+
+ if( localhom )
+ part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
+
+
+// match_calc( currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
+ 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] );
+ }
+ if( localhom )
+ part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
+#if 0 // -> tbfast.c
+ if( localhom )
+ imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+ if( outgap == 1 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ 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] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
+ }
+ }
+#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;
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ if( outgap ) lasti = lgth1+1; else lasti = lgth1;
+ lastj = lgth2+1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+ fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ )
+ fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ )
+ fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+ for( i=1; i<lasti; i++ )
+ {
+
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! i\n" );
+ *chudanres = 1;
+ if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
+ if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+ return( -1.0 );
+ }
+#endif
+
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+// match_calc( currentw, cpmx1, cpmx2, i, lgth2, doublework, intwork, 0 );
+ 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] );
+ }
+#if 0
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw before imp = \n" );
+for( j=0; j<lgth2; j++ )
+{
+ fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+ if( localhom )
+ {
+// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+// imp_match_out_vead( currentw, i, lgth2 );
+ part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
+ }
+#if 0
+fprintf( stderr, "specificity = %f\n", specificityconsideration );
+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;
+ mi = previousw[0] + ogcp2[1] * gapfreq1[i-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];
+ 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!!! j\n" );
+ *chudanres = 1;
+ if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
+ if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
+ if( nmask ) free( nmask ); nmask = NULL;
+ return( -1.0 );
+ }
+#endif
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+// g = mi + *fgcp2pt * gapfreq1[i];
+ if( (g = mi + *fgcp2pt * gf1va) > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+// g = *prept + *ogcp2pt * gapfreq1[i-1];
+ if( (g = *prept + *ogcp2pt * gf1vapre) >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// g = *mjpt + fgcp1va * gapfreq2[j];
+ if( (g = *mjpt + fgcp1va * *gf2pt) > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+// g = *prept + ogcp1va * gapfreq2[j-1];
+ 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 );
+#endif
+ *curpt += wm;
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ 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 )
+ {
+ 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, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2, warpis, warpjs, warpbase );
+ }
+ else
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
+
+ if( warpis ) free( warpis );
+ if( warpjs ) free( warpjs );
+
+// 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] );
+ */
+
+ 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