static TLS int reccycle = 0;
-static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+static void match_calc_add( double **scoringmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
int j, k, l;
- float scarr[26];
- float **cpmxpd = floatwork;
+// double scarr[26];
+ double **cpmxpd = doublework;
int **cpmxpdn = intwork;
int count = 0;
- float *matchpt;
- float **cpmxpdpt;
+ double *matchpt;
+ double **cpmxpdpt;
int **cpmxpdnpt;
int cpkd;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
+ if( initialize )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ count = 0;
+ for( l=0; l<nalphabets; l++ )
+ {
+ if( cpmx2[j][l] )
+ {
+ cpmxpd[j][count] = cpmx2[j][l];
+ cpmxpdn[j][count] = l;
+ count++;
+ }
+ }
+ cpmxpdn[j][count] = -1;
+ }
+ }
+
+ for( l=0; l<nalphabets; l++ )
+ {
+ scarr[l] = 0.0;
+ for( k=0; k<nalphabets; k++ )
+ {
+// scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ scarr[l] += scoringmtx[k][l] * cpmx1[i1][k];
+ }
+ }
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïdoublework¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+ {
+ double *fpt, **fptpt, *fpt2;
+ int *ipt, **iptpt;
+ fpt2 = match;
+ iptpt = cpmxpdn;
+ fptpt = cpmxpd;
+ while( lgth2-- )
+ {
+ *fpt2 = 0.0;
+ ipt=*iptpt,fpt=*fptpt;
+ while( *ipt > -1 )
+ *fpt2 += scarr[*ipt++] * *fpt++;
+ fpt2++,iptpt++,fptpt++;
+ }
+ }
+ for( j=0; j<lgth2; j++ )
+ {
+ match[j] = 0.0;
+ for( k=0; cpmxpdn[j][k]>-1; k++ )
+ match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+ }
+#else
+ matchpt = match;
+ cpmxpdnpt = cpmxpdn;
+ cpmxpdpt = cpmxpd;
+ while( lgth2-- )
+ {
+// *matchpt = 0.0; // add dakara
+ for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
+ *matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
+ matchpt++;
+ cpmxpdnpt++;
+ cpmxpdpt++;
+ }
+#endif
+ free( scarr );
+}
+static void match_calc( double **n_dynamicmtx, double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
+{
+ int j, k, l;
+// double scarr[26];
+ double **cpmxpd = doublework;
+ int **cpmxpdn = intwork;
+ int count = 0;
+ double *matchpt;
+ double **cpmxpdpt;
+ int **cpmxpdnpt;
+ int cpkd;
+ double *scarr;
+ scarr = calloc( nalphabets, sizeof( double ) );
if( initialize )
{
for( j=0; j<lgth2; j++ )
{
count = 0;
- for( l=0; l<26; l++ )
+ for( l=0; l<nalphabets; l++ )
{
if( cpmx2[j][l] )
{
}
}
- for( l=0; l<26; l++ )
+ for( l=0; l<nalphabets; l++ )
{
scarr[l] = 0.0;
- for( k=0; k<26; k++ )
+ for( k=0; k<nalphabets; k++ )
{
- scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+// scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+ scarr[l] += n_dynamicmtx[k][l] * cpmx1[i1][k];
}
}
-#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤\ad¤Ïdoublework¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
{
- float *fpt, **fptpt, *fpt2;
+ double *fpt, **fptpt, *fpt2;
int *ipt, **iptpt;
fpt2 = match;
iptpt = cpmxpdn;
cpmxpdpt++;
}
#endif
+ free( scarr );
}
-static float Atracking( float *lasthorizontalw, float *lastverticalw,
+static double Atracking( double *lasthorizontalw, double *lastverticalw,
char **seq1, char **seq2,
char **mseq1, char **mseq2,
int **ijp, int icyc, int jcyc,
int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
char *gaptable1, *gt1bk;
char *gaptable2, *gt2bk;
- float wm;
+ double wm;
lgth1 = ien-ist+1;
lgth2 = jen-jst+1;
return( 0.0 );
}
-static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, float **gapinfo, int headgp, int tailgp )
+static double MSalignmm_tanni( double **n_dynamicmtx, int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, double **cpmx1, double **cpmx2, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, double **gapinfo, int headgp, int tailgp, double headgapfreq1_g, double headgapfreq2_g )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
register int i, j;
int ll1, ll2;
int lasti, lastj;
- float wm = 0.0; /* int ?????? */
- float g;
- float *currentw, *previousw;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
#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
- float mi, *m;
+ double mi, *m;
int **ijp;
int mpi, *mp;
- float *w1, *w2;
- float *initverticalw; /* kufuu sureba iranai */
- float *lastverticalw; /* kufuu sureba iranai */
+ double *w1, *w2;
+ double *initverticalw; /* kufuu sureba iranai */
+ double *lastverticalw; /* kufuu sureba iranai */
int **intwork;
- float **floatwork;
+ double **doublework;
int **intmtx;
int lgth1, lgth2;
- float *ogcp1;
- float *fgcp1;
- float *ogcp2;
- float *fgcp2;
+ double *ogcp1;
+ double *fgcp1;
+ double *ogcp2;
+ double *fgcp2;
+ double *gapfreq1f;
+ double *gapfreq2f;
// char **aseq1;
// char **aseq2;
// char **aseq1bk, **aseq2bk;
+ double headgapfreq1;
+ double headgapfreq2;
ogcp1 = gapinfo[0] + ist;
fgcp1 = gapinfo[1] + ist;
ogcp2 = gapinfo[2] + jst;
fgcp2 = gapinfo[3] + jst;
+ gapfreq1f = gapinfo[4] + ist;
+ gapfreq2f = gapinfo[5] + jst;
+
+ if( ist > 0 ) headgapfreq1 = gapfreq1f[-1];
+ else headgapfreq1 = headgapfreq1_g;
+ if( jst > 0 ) headgapfreq2 = gapfreq2f[-1];
+ else headgapfreq2 = headgapfreq2_g;
#if STOREWM
char ttt1[10000], ttt2[10000];
m = AllocateFloatVec( ll2+2 );
mp = AllocateIntVec( ll2+2 );
- floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 );
- intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 );
+ doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets+1 );
+ intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets+1 );
intmtx = AllocateIntMtx( ll1+1, ll2+1 );
currentw = w1;
previousw = w2;
- match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 );
if( headgp || ist != 0 )
{
for( i=1; i<lgth1+1; i++ )
{
- initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2f[0] ) ;
}
}
if( headgp || jst != 0 )
{
for( j=1; j<lgth2+1; j++ )
{
- currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1f[0] ) ;
}
}
for( j=1; j<lgth2+1; ++j )
{
- m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;;
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2f[j-1]; mp[j] = 0;;
}
lastverticalw[0] = currentw[lgth2-1];
previousw[0] = initverticalw[i-1];
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[0] = initverticalw[i];
- mi = previousw[0] + ogcp2[1];
+ mi = previousw[0] + ogcp2[1] * gapfreq1f[i-1];
mpi = 0;
ijppt = ijp[i] + 1;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
- g = mi + fgcp2[j-1];
+ g = mi + fgcp2[j-1] * gapfreq1f[i];
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
wm = g;
*ijppt = -( j - mpi );
}
- g = *prept + ogcp2[j];
+ g = *prept + ogcp2[j] * gapfreq1f[i-1];
if( g >= mi )
{
mi = g;
mi += fpenalty_ex;
#endif
- g = *mjpt + fgcp1[i-1];
+ g = *mjpt + fgcp1[i-1] * gapfreq2f[j];
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
wm = g;
*ijppt = +( i - *mpjpt );
}
- g = *prept + ogcp1[i];
+ g = *prept + ogcp1[i] * gapfreq2f[j-1];
if( g >= *mjpt )
{
*mjpt = g;
FreeIntVec( mp );
- FreeFloatMtx( floatwork );
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
FreeIntMtx( intmtx );
}
static void freearrays_rec1(
- float *w1, float *w2, float *initverticalw, float *lastverticalw,
- float *midw, float *midm, float *midn,
+ double *w1, double *w2, double *initverticalw, double *lastverticalw,
+ double *midw, double *midm, double *midn,
int *jumpbacki, int *jumpbackj, int *jumpforwi, int *jumpforwj, int *jumpdummi, int *jumpdummj,
- float *m, int *mp,
- float **floatwork, int **intwork
+ double *m, int *mp,
+ double **doublework, int **intwork
#if STOREWM
- , float **WMMTX, float **WMMTX2
+ , double **WMMTX, double **WMMTX2
#endif
)
{
FreeFloatVec( m );
FreeIntVec( mp );
- FreeFloatMtx( floatwork );
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
#if STOREWM
#endif
}
-static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, int depth, float **gapinfo, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+static double MSalignmm_rec( double **n_dynamicmtx, int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, double **cpmx1, double **cpmx2, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, int depth, double **gapinfo, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp, double headgapfreq1_g, double headgapfreq2_g )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
int alnlen;
- float value = 0.0;
+ double value = 0.0;
register int i, j;
char **aseq1, **aseq2;
int ll1, ll2, l, len;
int lasti, lastj, imid;
int jmid = 0; // by D.Mathog, a guess
- float wm = 0.0; /* int ?????? */
- float g;
- float *currentw, *previousw;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
#if USE_PENALTY_EX
- float fpenalty_ex = (float)penalty_ex;
+ double fpenalty_ex = (double)penalty_ex;
#endif
- float *wtmp;
+ double *wtmp;
// short *ijppt;
int *mpjpt;
// short **ijp;
int *mp;
int mpi;
- float *mjpt, *prept, *curpt;
- float mi;
- float *m;
- float *w1, *w2;
-// float *match;
- float *initverticalw; /* kufuu sureba iranai */
- float *lastverticalw; /* kufuu sureba iranai */
+ double *mjpt, *prept, *curpt;
+ double mi;
+ double *m;
+ double *w1, *w2;
+// double *match;
+ double *initverticalw; /* kufuu sureba iranai */
+ double *lastverticalw; /* kufuu sureba iranai */
int **intwork;
- float **floatwork;
+ double **doublework;
// short **shortmtx;
#if STOREWM
- float **WMMTX;
- float **WMMTX2;
+ double **WMMTX;
+ double **WMMTX2;
#endif
- float *midw;
- float *midm;
- float *midn;
+ double *midw;
+ double *midm;
+ double *midn;
int lgth1, lgth2;
- float maxwm;
+ double maxwm;
int *jumpforwi;
int *jumpforwj;
int *jumpbacki;
int jumpi, jumpj = 0; // by D.Mathog, a guess
char *gaps;
int ijpi, ijpj;
- float *ogcp1;
- float *fgcp1;
- float *ogcp2;
- float *fgcp2;
- float firstm;
+ double *ogcp1;
+ double *fgcp1;
+ double *ogcp2;
+ double *fgcp2;
+ double firstm;
int firstmp;
#if STOREWM
static TLS char ttt1[50000];
static TLS char ttt2[50000];
#endif
+ double *gapfreq1f;
+ double *gapfreq2f;
+ double headgapfreq1;
+ double headgapfreq2;
#if 0
int nglen1, nglen2;
fgcp1 = gapinfo[1] + ist;
ogcp2 = gapinfo[2] + jst;
fgcp2 = gapinfo[3] + jst;
+ gapfreq1f = gapinfo[4] + ist;
+ gapfreq2f = gapinfo[5] + jst;
+
+ if( ist > 0 ) headgapfreq1 = gapfreq1f[-1];
+ else headgapfreq1 = headgapfreq1_g;
+ if( jst > 0 ) headgapfreq2 = gapfreq2f[-1];
+ else headgapfreq2 = headgapfreq2_g;
depth++;
reccycle++;
{
mseq2[i][0] = 0;
for( j=0; j<lgth1; j++ )
- strcat( mseq2[i], "-" );
+// strcat( mseq2[i], "-" );
+ strcat( mseq2[i], newgapstr );
}
// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
{
// fprintf( stderr, "==== Going to _tanni\n" );
- value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, gapinfo, headgp, tailgp );
+ value = MSalignmm_tanni( n_dynamicmtx, icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, gapinfo, headgp, tailgp, headgapfreq1_g, headgapfreq2_g );
#if MEMSAVE
mp = AllocateIntVec( ll2+2 );
gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
- 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 );
#if DEBUG
fprintf( stderr, "succeeded\n" );
currentw = w1;
previousw = w2;
- match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 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] * gapfreq2f[0] ) ;
}
for( j=1; j<lgth2+1; j++ )
{
- currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+ currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1f[0]) ;
}
#if STOREWM
for( j=1; j<lgth2+1; ++j )
{
- m[j] = currentw[j-1] + ogcp1[1];
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2f[j-1];
// m[j] = currentw[j-1];
mp[j] = 0;
}
w1, w2, initverticalw, lastverticalw, midw, midm, midn,
jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
m, mp,
- floatwork, intwork
+ doublework, intwork
#if STOREWM
, WMMTX, WMMTX2
#endif
previousw[0] = initverticalw[i-1];
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[0] = initverticalw[i];
m[0] = ogcp1[i];
#endif
if( i == imid ) midm[0] = m[0];
- mi = previousw[0] + ogcp2[1];
+ mi = previousw[0] + ogcp2[1] * gapfreq1f[i-1];
// mi = previousw[0];
mpi = 0;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
- g = mi + fgcp2[j-1];
+ g = mi + fgcp2[j-1] * gapfreq1f[i];
// g = mi + fpenalty;
#if 0
fprintf( stderr, "%5.0f?", g );
wm = g;
// *ijppt = -( j - mpi );
}
- g = *prept + ogcp2[j];
+ g = *prept + ogcp2[j] * gapfreq1f[i-1];
// g = *prept;
if( g >= mi )
{
mi += fpenalty_ex;
#endif
- g = *mjpt + fgcp1[i-1];
+ g = *mjpt + fgcp1[i-1] * gapfreq2f[j];
// g = *mjpt + fpenalty;
#if 0
fprintf( stderr, "%5.0f?", g );
}
- g = *prept + ogcp1[i];
+ g = *prept + ogcp1[i] * gapfreq2f[j-1];
// g = *prept;
if( g >= *mjpt )
{
// gyakudp
- match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+ match_calc( n_dynamicmtx, initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, doublework, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, doublework, intwork, 1 );
for( i=0; i<lgth1-1; i++ )
{
- initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
-// initverticalw[i] += fpenalty;
+// initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ initverticalw[i] += ( fgcp1[lgth1-1] * gapfreq2f[lgth2] + ogcp1[i+1] * gapfreq2f[lgth2-1] );
}
for( j=0; j<lgth2-1; j++ )
{
- currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
-// currentw[j] += fpenalty;
+// currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ currentw[j] += ( fgcp2[lgth2-1] * gapfreq1f[lgth1] + ogcp2[j+1] * gapfreq1f[lgth1-1] );
}
#if STOREWM
+#if 0
for( j=lgth2-1; j>0; --j )
{
m[j-1] = currentw[j] + fgcp2[lgth2-2];
// m[j-1] = currentw[j];
mp[j] = lgth1-1;
}
+#else
+ for( j=lgth2-1; j>-1; --j )
+ {
+ m[j] = currentw[j+1] + fgcp1[lgth1-2] * gapfreq2f[j+1];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+#endif
// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
// m[lgth2-1] ha irunoka?
w1, w2, initverticalw, lastverticalw, midw, midm, midn,
jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
m, mp,
- floatwork, intwork
+ doublework, intwork
#if STOREWM
, WMMTX, WMMTX2
#endif
currentw = wtmp;
previousw[lgth2-1] = initverticalw[i+1];
// match_calc( currentw, seq1, seq2, i, lgth2 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[lgth2-1] = initverticalw[i];
// WMMTX2[i][lgth2] += m[lgth2];
// fprintf( stderr, "m[] = %f\n", m[lgth2] );
- mi = previousw[lgth2-1] + fgcp2[lgth2-2];
+ mi = previousw[lgth2-1] + fgcp2[lgth2-2] * gapfreq1f[i+1];
// mi = previousw[lgth2-1];
mpi = lgth2 - 1;
ijpi = i+1;
ijpj = j+1;
- g = mi + ogcp2[j+1];
+ g = mi + ogcp2[j+1] * gapfreq1f[i];
// g = mi + fpenalty;
if( g > wm )
{
ijpi = i+1;
}
- g = *prept + fgcp2[j];
+ g = *prept + fgcp2[j] * gapfreq1f[i+1];
// g = *prept;
if( g >= mi )
{
#endif
// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
- g = *mjpt + ogcp1[i+1];
+ g = *mjpt + ogcp1[i+1] * gapfreq2f[j];
// g = *mjpt + fpenalty;
if( g > wm )
{
}
// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
- g = *prept + fgcp1[i];
+ g = *prept + fgcp1[i] * gapfreq2f[j+1];
// g = *prept;
if( g >= *mjpt )
{
w1, w2, initverticalw, lastverticalw, midw, midm, midn,
jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
m, mp,
- floatwork, intwork
+ doublework, intwork
#if STOREWM
, WMMTX, WMMTX2
#endif
// fprintf( stderr, "==== calling myself (first)\n" );
- value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp ); // chudan mada
+ value = MSalignmm_rec( n_dynamicmtx, icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp, headgapfreq1_g, headgapfreq2_g ); // chudan mada
#if 0
fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
// fprintf( stderr, "l=%d\n", l );
if( l > 0 )
{
- for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+// for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
for( i=0; i<icyc; i++ )
{
strcat( mseq1[i], gaps );
// fprintf( stderr, "l=%d\n", l );
if( l > 0 )
{
- for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+// for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
for( i=0; i<icyc; i++ )
{
strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
#endif
- value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp ); // chudan mada
+ value += MSalignmm_rec( n_dynamicmtx, icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp, headgapfreq1_g, headgapfreq2_g ); // chudan mada
#if 0
fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
}
static void freearrays(
- float *ogcp1,
- float *ogcp2,
- float *fgcp1,
- float *fgcp2,
- float **cpmx1,
- float **cpmx2,
- float **gapinfo,
+ double *ogcp1,
+ double *ogcp2,
+ double *fgcp1,
+ double *fgcp2,
+ double **cpmx1,
+ double **cpmx2,
+ double *gapfreq1f,
+ double *gapfreq2f,
+ double **gapinfo,
char **mseq1,
char **mseq2
)
FreeFloatVec( fgcp2 );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
+ FreeFloatVec( gapfreq1f );
+ FreeFloatVec( gapfreq2f );
free( (void *)gapinfo );
FreeCharMtx( mseq1 );
FreeCharMtx( mseq2 );
}
-float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, 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;
int i, j;
int ll1, ll2;
int lgth1, lgth2;
- float wm = 0.0; /* int ?????? */
+ double wm = 0.0; /* int ?????? */
char **mseq1;
char **mseq2;
- float *ogcp1;
- float *ogcp2;
- float *fgcp1;
- float *fgcp2;
- float **cpmx1;
- float **cpmx2;
- float **gapinfo;
- float fpenalty = (float)penalty;
+ double *ogcp1;
+ double *ogcp2;
+ double *fgcp1;
+ double *fgcp2;
+ double **cpmx1;
+ double **cpmx2;
+ double **gapinfo;
+ double fpenalty = (double)penalty;
+ double *gapfreq1f;
+ double *gapfreq2f;
int nglen1, nglen2;
+ double headgapfreq1;
+ double headgapfreq2;
#if 0
fprintf( stderr, "eff in SA+++align\n" );
mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
- gapinfo = AllocateFloatMtx( 4, 0 );
+ gapinfo = AllocateFloatMtx( 6, 0 );
ogcp1 = AllocateFloatVec( ll1+2 );
ogcp2 = AllocateFloatVec( ll2+2 );
fgcp1 = AllocateFloatVec( ll1+2 );
fgcp2 = AllocateFloatVec( ll2+2 );
- cpmx1 = AllocateFloatMtx( ll1+2, 27 );
- cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+ cpmx1 = AllocateFloatMtx( ll1+2, nalphabets+1 );
+ cpmx2 = AllocateFloatMtx( ll2+2, nalphabets+1 );
+
+ gapfreq1f = AllocateFloatVec( ll1+2 ); // must be filled with 0.0
+ gapfreq2f = AllocateFloatVec( ll2+2 ); // must be filled with 0.0
for( i=0; i<icyc; i++ )
{
new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap2 );
new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
+ outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
+ outgapcount( gapfreq1f+lgth1, icyc, egap1, eff1 );
+ outgapcount( gapfreq2f+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;
+ gapfreq1f[lgth1] = 0.0;
+ gapfreq2f[lgth2] = 0.0;
+ }
+
+ if( legacygapcost == 0 )
+ {
+ gapcountf( gapfreq1f, seq1, icyc, eff1, lgth1 );
+ gapcountf( gapfreq2f, seq2, jcyc, eff2, lgth2 );
+ for( i=0; i<lgth1+1; i++ ) gapfreq1f[i] = 1.0 - gapfreq1f[i];
+ for( i=0; i<lgth2+1; i++ ) gapfreq2f[i] = 1.0 - gapfreq2f[i];
+ headgapfreq1 = 1.0 - headgapfreq1;
+ headgapfreq2 = 1.0 - headgapfreq2;
+ }
+ else
+ {
+ for( i=0; i<lgth1+1; i++ ) gapfreq1f[i] = 1.0;
+ for( i=0; i<lgth2+1; i++ ) gapfreq2f[i] = 1.0;
+ headgapfreq1 = 1.0;
+ headgapfreq2 = 1.0;
}
#if 1
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 * ( gapfreq1f[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1f[i] );
// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[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 * ( gapfreq2f[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2f[i] );
// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
}
#else
gapinfo[1] = fgcp1;
gapinfo[2] = ogcp2;
gapinfo[3] = fgcp2;
+ gapinfo[4] = gapfreq1f;
+ gapinfo[5] = gapfreq2f;
#endif
#if 0
fflush( stdout );
#endif
- wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, lgth1, lgth2, mseq1, mseq2, 0, gapinfo, chudanpt, chudanref, chudanres, headgp, tailgp );
+ wm = MSalignmm_rec( n_dynamicmtx, icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, lgth1, lgth2, mseq1, mseq2, 0, gapinfo, chudanpt, chudanref, chudanres, headgp, tailgp, headgapfreq1, headgapfreq2 );
#ifdef enablemultithread
if( chudanres && *chudanres )
{
// fprintf( stderr, "\n\n## CHUUDAN!!! relay\n" );
*chudanres = 1;
- freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapinfo, mseq1, mseq2 );
+ freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapfreq1f, gapfreq2f, gapinfo, mseq1, mseq2 );
return( -1.0 );
}
#endif
-#if DEBUG
+#if 0
+ fprintf( stderr, "\n" );
fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+ fprintf( stderr, "\n" );
#endif
// fprintf( stderr, "wm = %f\n", wm );
}
- freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapinfo, mseq1, mseq2 );
+ freearrays( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1, cpmx2, gapfreq1f, gapfreq2f, gapinfo, mseq1, mseq2 );
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
}
}
+#if 0
+ fprintf( stderr, "\n" );
+ 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] );
+ fprintf( stderr, "\n" );
+#endif
+
+ return( wm );
+}
+
+// -------------------------------
+// variousdist
+// -------------------------------
+
+static void fillzero( double *s, int l )
+{
+ while( l-- ) *s++ = 0.0;
+}
+
+static double MSalignmm_tanni_variousdist( double ***matrices, int icyc, int jcyc, char **seq1, char **seq2, double ***cpmx1s, double ***cpmx2s, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, double **gapinfo, int headgp, int tailgp, double headgapfreq1_g, double headgapfreq2_g )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ register int i, j, c;
+ int ll1, ll2;
+ int lasti, lastj;
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
+#if USE_PENALTY_EX
+ double fpenalty_ex = (double)penalty_ex;
+#endif
+#if 1
+ double *wtmp;
+ int *ijppt;
+ double *mjpt, *prept, *curpt;
+ int *mpjpt;
+#endif
+ double mi, *m;
+ int **ijp;
+ int mpi, *mp;
+ double *w1, *w2;
+ double *initverticalw; /* kufuu sureba iranai */
+ double *lastverticalw; /* kufuu sureba iranai */
+ int ***intwork;
+ double ***doublework;
+ int **intmtx;
+ int lgth1, lgth2;
+ double *ogcp1;
+ double *fgcp1;
+ double *ogcp2;
+ double *fgcp2;
+ double *gapfreq1f;
+ double *gapfreq2f;
+// char **aseq1;
+// char **aseq2;
+// char **aseq1bk, **aseq2bk;
+ double headgapfreq1;
+ double headgapfreq2;
+
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+ gapfreq1f = gapinfo[4] + ist;
+ gapfreq2f = gapinfo[5] + jst;
+
+ if( ist > 0 ) headgapfreq1 = gapfreq1f[-1];
+ else headgapfreq1 = headgapfreq1_g;
+ if( jst > 0 ) headgapfreq2 = gapfreq2f[-1];
+ else headgapfreq2 = headgapfreq2_g;
+
+#if STOREWM
+ char ttt1[10000], ttt2[10000];
+#endif
+
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+#if STOREWM
+ strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+ strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+ fprintf( stderr, "ttt1 = %s\n", ttt1 );
+ fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+#if 0
+ fprintf( stderr, "in _tanni ist,ien = %d,%d, fulllen1=%d\n", ist, ien, fulllen1 );
+ fprintf( stderr, "in _tanni jst,jen = %d,%d, fulllen2=%d\n", jst, jen, fulllen2 );
+ fprintf( stderr, "in _tanni seq1[0] = %-*.*s\n", ien-ist+1, ien-ist+1, seq1[0]+ist );
+ fprintf( stderr, "in _tanni seq2[0] = %-*.*s\n", jen-jst+1, jen-jst+1, seq2[0]+jst );
+#endif
+
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+// aseq1 = AllocateCharMtx( icyc, 0 );
+// aseq2 = AllocateCharMtx( jcyc, 0 );
+// aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+// aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+// for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+// for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+
+ doublework = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets+1 );
+ intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets+1 );
+
+
+ intmtx = AllocateIntMtx( ll1+1, ll2+1 );
+
+ ijp = intmtx;
+
+ currentw = w1;
+ previousw = w2;
+
+#if 0
+ match_calc( n_dynamicmtx, initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 );
+#else
+ fillzero( initverticalw, lgth1 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], initverticalw, cpmx2s[c]+jst, cpmx1s[c]+ist, 0, lgth1, doublework[c], intwork[c], 1 );
+
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], currentw, cpmx1s[c]+ist, cpmx2s[c]+jst, 0, lgth2, doublework[c], intwork[c], 1 );
+#endif
+
+ if( headgp || ist != 0 )
+ {
+ for( i=1; i<lgth1+1; i++ )
+ {
+ initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2f[0] ) ;
+ }
+ }
+ if( headgp || jst != 0 )
+ {
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1f[0] ) ;
+ }
+ }
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2f[j-1]; mp[j] = 0;;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+
+
+ if( tailgp || jen != fulllen2-1 ) lasti = lgth1+1; else lasti = lgth1;
+// if( 1 ) lasti = lgth1+1; else lasti = lgth1;
+ for( i=1; i<lasti; i++ )
+ {
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+#if 0
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], currentw, cpmx1s[c]+ist, cpmx2s[c]+jst, i, lgth2, doublework[c], intwork[c], 0 );
+#endif
+ currentw[0] = initverticalw[i];
+
+ mi = previousw[0] + ogcp2[1] * gapfreq1f[i-1];
+ mpi = 0;
+
+ ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+// if( tailgp && jen != fulllen2-1 ) lastj = lgth2+1; else lastj = lgth2;
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+ wm = *prept;
+ *ijppt = 0;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fgcp2[j-1] * gapfreq1f[i];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = -( j - mpi );
+ }
+ g = *prept + ogcp2[j] * gapfreq1f[i-1];
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1[i-1] * gapfreq2f[j];
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+ *ijppt = +( i - *mpjpt );
+ }
+ g = *prept + ogcp1[i] * gapfreq2f[j-1];
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+
+ ijppt++;
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+ }
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+ Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, ist, ien, jst, jen, fulllen1, fulllen2, tailgp );
+#if 0
+ fprintf( stderr, "res in _tanni mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "res in _tanni mseq2[0] = %s\n", mseq2[0] );
+#endif
+
+// for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+// for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+// fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+// fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+
+ FreeFloatCub( doublework );
+ FreeIntCub( intwork );
+
+ FreeIntMtx( intmtx );
+
+
+// FreeCharMtx( aseq1bk );
+// FreeCharMtx( aseq2bk );
+
+// free( aseq1 );
+// free( aseq2 );
+
+ return( wm );
+
+}
+
+static void freearrays_rec1_variousdist(
+ double *w1, double *w2, double *initverticalw, double *lastverticalw,
+ double *midw, double *midm, double *midn,
+ int *jumpbacki, int *jumpbackj, int *jumpforwi, int *jumpforwj, int *jumpdummi, int *jumpdummj,
+ double *m, int *mp,
+ double ***doublework, int ***intwork
+#if STOREWM
+ , double **WMMTX, double **WMMTX2
+#endif
+)
+{
+
+ FreeFloatVec( w1 );
+ FreeFloatVec( w2 );
+ FreeFloatVec( initverticalw );
+ FreeFloatVec( lastverticalw );
+ FreeFloatVec( midw );
+ FreeFloatVec( midm );
+ FreeFloatVec( midn );
+
+ FreeIntVec( jumpbacki );
+ FreeIntVec( jumpbackj );
+ FreeIntVec( jumpforwi );
+ FreeIntVec( jumpforwj );
+ FreeIntVec( jumpdummi );
+ FreeIntVec( jumpdummj );
+
+ FreeFloatVec( m );
+ FreeIntVec( mp );
+
+ FreeFloatCub( doublework );
+ FreeIntCub( intwork );
+
+#if STOREWM
+ FreeFloatMtx( WMMTX );
+ FreeFloatMtx( WMMTX2 );
+#endif
+}
+
+static double MSalignmm_rec_variousdist( double ***matrices, int icyc, int jcyc, char **seq1, char **seq2, double ***cpmx1s, double ***cpmx2s, int ist, int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, int depth, double **gapinfo, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp, double headgapfreq1_g, double headgapfreq2_g )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+// int k;
+ int alnlen;
+ double value = 0.0;
+ register int i, j, c;
+ char **aseq1, **aseq2;
+ int ll1, ll2, l, len;
+ int lasti, lastj, imid;
+ int jmid = 0; // by D.Mathog, a guess
+ double wm = 0.0; /* int ?????? */
+ double g;
+ double *currentw, *previousw;
+#if USE_PENALTY_EX
+ double fpenalty_ex = (double)penalty_ex;
+#endif
+ double *wtmp;
+// short *ijppt;
+ int *mpjpt;
+// short **ijp;
+ int *mp;
+ int mpi;
+ double *mjpt, *prept, *curpt;
+ double mi;
+ double *m;
+ double *w1, *w2;
+// double *match;
+ double *initverticalw; /* kufuu sureba iranai */
+ double *lastverticalw; /* kufuu sureba iranai */
+ int ***intwork;
+ double ***doublework;
+// short **shortmtx;
+#if STOREWM
+ double **WMMTX;
+ double **WMMTX2;
+#endif
+ double *midw;
+ double *midm;
+ double *midn;
+ int lgth1, lgth2;
+ double maxwm;
+ int *jumpforwi;
+ int *jumpforwj;
+ int *jumpbacki;
+ int *jumpbackj;
+ int *jumpdummi; //muda
+ int *jumpdummj = NULL; // by D.Mathog, a guess
+ int jumpi, jumpj = 0; // by D.Mathog, a guess
+ char *gaps;
+ int ijpi, ijpj;
+ double *ogcp1;
+ double *fgcp1;
+ double *ogcp2;
+ double *fgcp2;
+ double firstm;
+ int firstmp;
+#if STOREWM
+ static TLS char ttt1[50000];
+ static TLS char ttt2[50000];
+#endif
+ double *gapfreq1f;
+ double *gapfreq2f;
+ double headgapfreq1;
+ double headgapfreq2;
+
+#if 0
+ int nglen1, nglen2;
+ nglen1 = seqlen( seq1[0] );
+ nglen2 = seqlen( seq2[0] );
+#endif
+
+// fprintf( stderr, "fulllen1 = %d, fulllen2 = %d, headgp = %d, tailgp = %d\n", fulllen1, fulllen2, headgp, tailgp );
+
+ ogcp1 = gapinfo[0] + ist;
+ fgcp1 = gapinfo[1] + ist;
+ ogcp2 = gapinfo[2] + jst;
+ fgcp2 = gapinfo[3] + jst;
+ gapfreq1f = gapinfo[4] + ist;
+ gapfreq2f = gapinfo[5] + jst;
+
+ if( ist > 0 ) headgapfreq1 = gapfreq1f[-1];
+ else headgapfreq1 = headgapfreq1_g;
+ if( jst > 0 ) headgapfreq2 = gapfreq2f[-1];
+ else headgapfreq2 = headgapfreq2_g;
+
+ depth++;
+ reccycle++;
+
+ lgth1 = ien-ist+1;
+ lgth2 = jen-jst+1;
+
+// if( lgth1 < 5 )
+// fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
+// if( lgth2 < 5 )
+// fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
+//
+
+
+#if STOREWM
+ fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+ strncpy( ttt1, seq1[0]+ist, lgth1 );
+ strncpy( ttt2, seq2[0]+jst, lgth2 );
+ ttt1[lgth1] = 0;
+ ttt2[lgth2] = 0;
+ fprintf( stderr, "seq1 = %s\n", ttt1 );
+ fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+ if( lgth2 <= 0 ) // lgth1 <= 0 ha?
+ {
+// fprintf( stderr, "\n\n==== jimei\n\n" );
+// exit( 1 );
+ for( i=0; i<icyc; i++ )
+ {
+ strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+ mseq1[i][lgth1] = 0;
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ mseq2[i][0] = 0;
+ for( j=0; j<lgth1; j++ )
+// strcat( mseq2[i], "-" );
+ strcat( mseq2[i], newgapstr );
+ }
+
+// fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+// fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+ return( 0.0 );
+ }
+
+#if MEMSAVE
+ aseq1 = AllocateCharMtx( icyc, 0 );
+ aseq2 = AllocateCharMtx( jcyc, 0 );
+ for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
+ for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
+#else
+ aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+ aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+#endif
+
+// fprintf( stderr, "####(s) seq1[0] (%d) = \n%-*.*s\n (a%d-a%d)\n", depth, ien-ist+1, ien-ist+1, seq1[0]+ist, ist, ien );
+// fprintf( stderr, "####(s) seq2[0] (%d) = \n%-*.*s\n (b%d-b%d)\n", depth, jen-jst+1, jen-jst+1, seq2[0]+jst, jst, jen );
+
+// if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai
+// if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
+ if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
+ {
+// fprintf( stderr, "==== Going to _tanni\n" );
+
+ value = MSalignmm_tanni_variousdist( matrices, icyc, jcyc, seq1, seq2, cpmx1s, cpmx2s, ist, ien, jst, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, gapinfo, headgp, tailgp, headgapfreq1_g, headgapfreq2_g );
+
+
+#if MEMSAVE
+ free( aseq1 );
+ free( aseq2 );
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+ FreeCharMtx( aseq1 );
+ FreeCharMtx( aseq2 );
+#endif
+
+// fprintf( stderr, "value = %f\n", value );
+
+ return( value );
+ }
+// fprintf( stderr, "Trying to divide the mtx\n" );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+// fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+ w1 = AllocateFloatVec( ll2+2 );
+ w2 = AllocateFloatVec( ll2+2 );
+// match = AllocateFloatVec( ll2+2 );
+ midw = AllocateFloatVec( ll2+2 );
+ midn = AllocateFloatVec( ll2+2 );
+ midm = AllocateFloatVec( ll2+2 );
+ jumpbacki = AllocateIntVec( ll2+2 );
+ jumpbackj = AllocateIntVec( ll2+2 );
+ jumpforwi = AllocateIntVec( ll2+2 );
+ jumpforwj = AllocateIntVec( ll2+2 );
+ jumpdummi = AllocateIntVec( ll2+2 );
+ jumpdummj = AllocateIntVec( ll2+2 );
+
+ initverticalw = AllocateFloatVec( ll1+2 );
+ lastverticalw = AllocateFloatVec( ll1+2 );
+
+ m = AllocateFloatVec( ll2+2 );
+ mp = AllocateIntVec( ll2+2 );
+ gaps = AllocateCharVec( MAX( ll1, 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
+
+#if STOREWM
+ WMMTX = AllocateFloatMtx( ll1, ll2 );
+ WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+ shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+ fprintf( stderr, "succeeded\n\n" );
+#endif
+
+ ijp = shortmtx;
+#endif
+
+ currentw = w1;
+ previousw = w2;
+
+#if 0
+ match_calc( n_dynamicmtx, initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 );
+#else
+ fillzero( initverticalw, lgth1 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], initverticalw, cpmx2s[c]+jst, cpmx1s[c]+ist, 0, lgth1, doublework[c], intwork[c], 1 );
+
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], currentw, cpmx1s[c]+ist, cpmx2s[c]+jst, 0, lgth2, doublework[c], intwork[c], 1 );
+#endif
+
+
+ for( i=1; i<lgth1+1; i++ )
+ {
+// initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+ initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2f[0] ) ;
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1f[0]) ;
+ }
+
+#if STOREWM
+ WMMTX[0][0] = initverticalw[0];
+ for( i=1; i<lgth1+1; i++ )
+ {
+ WMMTX[i][0] = initverticalw[i];
+ }
+ for( j=1; j<lgth2+1; j++ )
+ {
+ WMMTX[0][j] = currentw[j];
+ }
+#endif
+
+
+ for( j=1; j<lgth2+1; ++j )
+ {
+ m[j] = currentw[j-1] + ogcp1[1] * gapfreq2f[j-1];
+// m[j] = currentw[j-1];
+ mp[j] = 0;
+ }
+
+ lastverticalw[0] = currentw[lgth2-1];
+
+ imid = lgth1 * 0.5;
+
+ jumpi = 0; // atode kawaru.
+ lasti = lgth1+1;
+#if STOREWM
+ for( i=1; i<lasti; i++ )
+#else
+ for( i=1; i<=imid; i++ )
+#endif
+ {
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! zenhan\n" );
+ *chudanres = 1;
+ freearrays_rec1_variousdist
+ (
+ w1, w2, initverticalw, lastverticalw, midw, midm, midn,
+ jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
+ m, mp,
+ doublework, intwork
+#if STOREWM
+ , WMMTX, WMMTX2
+#endif
+ );
+ freearrays_rec2( gaps, aseq1, aseq2 );
+ return( -1.0 );
+ }
+#endif
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+
+ previousw[0] = initverticalw[i-1];
+
+#if 0
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], currentw, cpmx1s[c]+ist, cpmx2s[c]+jst, i, lgth2, doublework[c], intwork[c], 0 );
+#endif
+ currentw[0] = initverticalw[i];
+
+ m[0] = ogcp1[i];
+#if STOREM
+ WMMTX2[i][0] = m[0];
+#endif
+ if( i == imid ) midm[0] = m[0];
+
+ mi = previousw[0] + ogcp2[1] * gapfreq1f[i-1];
+// mi = previousw[0];
+ mpi = 0;
+
+
+// ijppt = ijp[i] + 1;
+ mjpt = m + 1;
+ prept = previousw;
+ curpt = currentw + 1;
+ mpjpt = mp + 1;
+
+
+ lastj = lgth2+1;
+ for( j=1; j<lastj; j++ )
+ {
+
+ wm = *prept;
+
+#if 0
+ fprintf( stderr, "%5.0f->", wm );
+#endif
+ g = mi + fgcp2[j-1] * gapfreq1f[i];
+// g = mi + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = -( j - mpi );
+ }
+ g = *prept + ogcp2[j] * gapfreq1f[i-1];
+// g = *prept;
+ if( g >= mi )
+ {
+ mi = g;
+ mpi = j-1;
+ }
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+ g = *mjpt + fgcp1[i-1] * gapfreq2f[j];
+// g = *mjpt + fpenalty;
+#if 0
+ fprintf( stderr, "%5.0f?", g );
+#endif
+ if( g > wm )
+ {
+ wm = g;
+// *ijppt = +( i - *mpjpt );
+ }
+
+
+ g = *prept + ogcp1[i] * gapfreq2f[j-1];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i-1;
+ }
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+#if 0
+ fprintf( stderr, "%5.0f ", wm );
+#endif
+ *curpt += wm;
+
+#if STOREWM
+ WMMTX[i][j] = *curpt;
+ WMMTX2[i][j] = *mjpt;
+#endif
+
+ if( i == imid ) //muda
+ {
+ jumpbackj[j] = *mpjpt; // muda atode matomeru
+ jumpbacki[j] = mpi; // muda atode matomeru
+// fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+// fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+ midw[j] = *curpt;
+ midm[j] = *mjpt;
+ midn[j] = mi;
+ }
+
+// fprintf( stderr, "m[%d] = %f\n", j, m[j] );
+ mjpt++;
+ prept++;
+ mpjpt++;
+ curpt++;
+
+ }
+ lastverticalw[i] = currentw[lgth2-1];
+
+#if STOREWM
+ WMMTX2[i][lgth2] = m[lgth2-1];
+#endif
+
+#if 0 // ue
+ if( i == imid )
+ {
+ for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+ for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+ }
+#endif
+ }
+// for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "WMMTX2 = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+ fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+#if 0
+ match_calc( n_dynamicmtx, initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, doublework, intwork, 1 );
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, doublework, intwork, 1 );
+#else
+ fillzero( initverticalw, lgth1 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], initverticalw, cpmx2s[c]+jst, cpmx1s[c]+ist, lgth2-1, lgth1, doublework[c], intwork[c], 1 );
+
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], currentw, cpmx1s[c]+ist, cpmx2s[c]+jst, lgth1-1, lgth2, doublework[c], intwork[c], 1 );
+#endif
+
+ for( i=0; i<lgth1-1; i++ )
+ {
+// initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ initverticalw[i] += ( fgcp1[lgth1-1] * gapfreq2f[lgth2] + ogcp1[i+1] * gapfreq2f[lgth2-1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+// currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ currentw[j] += ( fgcp2[lgth2-1] * gapfreq1f[lgth1] + ogcp2[j+1] * gapfreq1f[lgth1-1] );
+ }
+
+#if STOREWM
+ for( i=0; i<lgth1-1; i++ )
+ {
+ WMMTX[i][lgth2-1] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
+ fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+ }
+ for( j=0; j<lgth2-1; j++ )
+ {
+ WMMTX[lgth1-1][j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
+ fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+ }
+#endif
+
+
+
+
+
+
+#if 0
+ for( j=lgth2-1; j>0; --j )
+ {
+ m[j-1] = currentw[j] + fgcp2[lgth2-2];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+#else
+ for( j=lgth2-1; j>-1; --j )
+ {
+ m[j] = currentw[j+1] + fgcp1[lgth1-2] * gapfreq2f[j+1];
+// m[j-1] = currentw[j];
+ mp[j] = lgth1-1;
+ }
+#endif
+
+// for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+ // m[lgth2-1] ha irunoka?
+
+
+// for( i=lgth1-2; i>=imid; i-- )
+ firstm = -9999999.9;
+// firstmp = lgth1-1;
+ firstmp = lgth1;
+ for( i=lgth1-2; i>-1; i-- )
+ {
+#ifdef enablemultithread
+// fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+ if( chudanpt && *chudanpt != chudanref )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! kouhan\n" );
+ *chudanres = 1;
+ freearrays_rec1_variousdist
+ (
+ w1, w2, initverticalw, lastverticalw, midw, midm, midn,
+ jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
+ m, mp,
+ doublework, intwork
+#if STOREWM
+ , WMMTX, WMMTX2
+#endif
+ );
+ freearrays_rec2( gaps, aseq1, aseq2 );
+ return( -1.0 );
+ }
+#endif
+ wtmp = previousw;
+ previousw = currentw;
+ currentw = wtmp;
+ previousw[lgth2-1] = initverticalw[i+1];
+#if 0
+ match_calc( n_dynamicmtx, currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
+#else
+ fillzero( currentw, lgth2 );
+ for( c=0; c<maxdistclass; c++ )
+ match_calc_add( matrices[c], currentw, cpmx1s[c]+ist, cpmx2s[c]+jst, i, lgth2, doublework[c], intwork[c], 0 );
+#endif
+
+ currentw[lgth2-1] = initverticalw[i];
+
+// m[lgth2] = fgcp1[i];
+// WMMTX2[i][lgth2] += m[lgth2];
+// fprintf( stderr, "m[] = %f\n", m[lgth2] );
+
+ mi = previousw[lgth2-1] + fgcp2[lgth2-2] * gapfreq1f[i+1];
+// mi = previousw[lgth2-1];
+ mpi = lgth2 - 1;
+
+ mjpt = m + lgth2 - 2;
+ prept = previousw + lgth2 - 1;
+ curpt = currentw + lgth2 - 2;
+ mpjpt = mp + lgth2 - 2;
+
+
+ for( j=lgth2-2; j>-1; j-- )
+ {
+ wm = *prept;
+ ijpi = i+1;
+ ijpj = j+1;
+
+ g = mi + ogcp2[j+1] * gapfreq1f[i];
+// g = mi + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpj = mpi;
+ ijpi = i+1;
+ }
+
+ g = *prept + fgcp2[j] * gapfreq1f[i+1];
+// g = *prept;
+ if( g >= mi )
+ {
+// fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+ mi = g;
+ mpi = j + 1;
+ }
+
+#if USE_PENALTY_EX
+ mi += fpenalty_ex;
+#endif
+
+// fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+ g = *mjpt + ogcp1[i+1] * gapfreq2f[j];
+// g = *mjpt + fpenalty;
+ if( g > wm )
+ {
+ wm = g;
+ ijpi = *mpjpt;
+ ijpj = j+1;
+ }
+
+// if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+ g = *prept + fgcp1[i] * gapfreq2f[j+1];
+// g = *prept;
+ if( g >= *mjpt )
+ {
+ *mjpt = g;
+ *mpjpt = i + 1;
+ }
+
+#if USE_PENALTY_EX
+ m[j] += fpenalty_ex;
+#endif
+
+ if( i == jumpi || i == imid - 1 )
+ {
+ jumpforwi[j] = ijpi; //muda
+ jumpforwj[j] = ijpj; //muda
+// fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+// fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+ }
+ if( i == imid ) // muda
+ {
+ midw[j] += wm;
+// midm[j+1] += *mjpt + fpenalty; //??????
+ midm[j+1] += *mjpt; //??????
+ }
+ if( i == imid - 1 )
+ {
+// midn[j] += mi + fpenalty; //????
+ midn[j] += mi; //????
+ }
+#if STOREWM
+ WMMTX[i][j] += wm;
+// WMMTX2[i][j+1] += *mjpt + fpenalty;
+ WMMTX2[i][j+1] += *mjpt;
+#endif
+ *curpt += wm;
+
+ mjpt--;
+ prept--;
+ mpjpt--;
+ curpt--;
+ }
+// fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
+ g = *prept + fgcp1[i];
+ if( firstm < g )
+ {
+ firstm = g;
+ firstmp = i + 1;
+ }
+#if STOREWM
+ WMMTX2[i][j+1] += firstm;
+#endif
+ if( i == imid ) midm[j+1] += firstm;
+
+
+ if( i == imid - 1 )
+ {
+ maxwm = midw[1];
+ jmid = 0;
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ for( j=2; j<lgth2-1; j++ )
+ {
+ wm = midw[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+ for( j=0; j<lgth2+1; j++ )
+ {
+ wm = midm[j];
+ if( wm > maxwm )
+ {
+ jmid = j;
+ maxwm = wm;
+ }
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+ }
+
+// if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+
+// fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+ wm = midw[jmid];
+ jumpi = imid-1;
+ jumpj = jmid-1;
+ if( jmid > 0 && midn[jmid-1] > wm ) //060413
+ {
+ jumpi = imid-1;
+ jumpj = jumpbacki[jmid];
+ wm = midn[jmid-1];
+// fprintf( stderr, "rejump (n)\n" );
+ }
+ if( midm[jmid] > wm )
+ {
+ jumpi = jumpbackj[jmid];
+ jumpj = jmid-1;
+ wm = midm[jmid];
+// fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+ }
+
+
+// fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+// fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "midn = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midn[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midw = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midw[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "midm = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.1f ", midm[j] );
+ }
+ fprintf( stderr, "\n" );
+#endif
+// fprintf( stderr, "maxwm = %f\n", maxwm );
+ }
+ if( i == jumpi ) //saki?
+ {
+// fprintf( stderr, "#### FIRST i=%d, jumpi<imid=%d<%d, ist=%d, ien=%d, firstmp=%d, lgth1=%d\n", i, jumpi, imid, ist, ien, firstmp, lgth1 );
+// fprintf( stderr, "#### mark 1\n" );
+// fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+// fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+
+ if( jmid == 0 )
+ {
+// fprintf( stderr, "#### CHUI2!\n" );
+ jumpj = 0; jmid = 1;
+#if 0 // v6.823 made
+ jumpi = firstmp-1;
+ imid = firstmp;
+#endif
+#if 0
+ jumpi = 0;
+ imid = 1;
+#else
+// if( 1 || firstmp > 100 ) // naze 100
+ if( imid < firstmp-1 ) // naze 100
+ {
+ jumpi = firstmp;
+ imid = firstmp+1;
+ }
+#if 0
+ else
+ {
+ jumpi = 0;
+ imid = 1;
+ }
+#endif
+#endif
+ }
+
+#if 0
+ else if( jmid == lgth2 )
+ {
+ fprintf( stderr, "CHUI1!\n" );
+ jumpi=0; jumpj=0;
+ imid=jumpforwi[0]; jmid=lgth2-1;
+ }
+#else // 060414
+ else if( jmid >= lgth2 )
+ {
+// fprintf( stderr, "CHUI1!\n" );
+ jumpi=imid-1; jmid=lgth2;
+ jumpj = lgth2-1;
+ }
+#endif
+ else
+ {
+// fprintf( stderr, "#### CHUI3!\n" );
+ imid = jumpforwi[jumpj];
+ jmid = jumpforwj[jumpj];
+ if( imid == jumpi ) jumpi = imid-1;
+ }
+#if 0
+ fprintf( stderr, "jumpi -> %d\n", jumpi );
+ fprintf( stderr, "jumpj -> %d\n", jumpj );
+ fprintf( stderr, "imid -> %d\n", imid );
+ fprintf( stderr, "jmid -> %d\n", jmid );
+#endif
+// fprintf( stderr, "#### FINAL i=%d, jumpi<imid=%d<%d, ist=%d, ien=%d, firstmp=%d\n", i, jumpi, imid, ist, ien, firstmp );
+
+#if STOREWM
+ break;
+#else
+ break;
+#endif
+ }
+ }
+
+// fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+// fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+// for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+// for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+// for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+ fprintf( stderr, "WMMTX = \n" );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+// fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+ for( i=0; i<lgth1; i++ )
+ {
+ fprintf( stderr, "%d ", i );
+ for( j=0; j<lgth2+1; j++ )
+ {
+ fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+ }
+ fprintf( stderr, "\n" );
+ }
+
+ fprintf( stderr, "jumpbacki = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbacki[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpbackj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpbackj[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwi = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwi[j] );
+ }
+ fprintf( stderr, "\n" );
+ fprintf( stderr, "jumpforwj = \n" );
+ for( j=0; j<lgth2; j++ )
+ {
+ fprintf( stderr, "% 7d ", jumpforwj[j] );
+ }
+ fprintf( stderr, "\n" );
+
+
+#endif
+
+
+// Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+ 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" );
+ }
+#endif
+
+
+
+#if 0
+ fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+ fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+ fprintf( stderr, "imid = %d\n", imid );
+ fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+ freearrays_rec1_variousdist
+ (
+ w1, w2, initverticalw, lastverticalw, midw, midm, midn,
+ jumpbacki, jumpbackj, jumpforwi, jumpforwj, jumpdummi, jumpdummj,
+ m, mp,
+ doublework, intwork
+#if STOREWM
+ , WMMTX, WMMTX2
+#endif
+ );
+
+
+// fprintf( stderr, "==== calling myself (first)\n" );
+
+ value = MSalignmm_rec_variousdist( matrices, icyc, jcyc, seq1, seq2, cpmx1s, cpmx2s, ist, ist+jumpi, jst, jst+jumpj, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp, headgapfreq1_g, headgapfreq2_g ); // chudan mada
+#if 0
+ fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
+ fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
+#endif
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+// fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+ len = strlen( mseq1[0] );
+// fprintf( stderr, "len = %d\n", len );
+ l = jmid - jumpj - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+// for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strcat( mseq1[i], gaps );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+ mseq2[j][len+l] = 0;
+ }
+// fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+ value += ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+// value += fpenalty;
+ }
+ len = strlen( mseq1[0] );
+ l = imid - jumpi - 1;
+// fprintf( stderr, "l=%d\n", l );
+ if( l > 0 )
+ {
+// for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+ for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
+ for( i=0; i<icyc; i++ )
+ {
+ strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+ mseq1[i][len+l] = 0;
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ strcat( mseq2[j], gaps );
+ mseq2[j][len+l] = 0;
+ }
+
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+// for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+// fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+ value += ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+// value += fpenalty;
+ }
+#if 0
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+ for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+// fprintf( stderr, "==== calling myself (second)\n" );
+
+#if MEMSAVE
+ alnlen = strlen( aseq1[0] );
+ for( i=0; i<icyc; i++ ) aseq1[i] += alnlen;
+ for( i=0; i<jcyc; i++ ) aseq2[i] += alnlen;
+#endif
+
+ value += MSalignmm_rec_variousdist( matrices, icyc, jcyc, seq1, seq2, cpmx1s, cpmx2s, ist+imid, ien, jst+jmid, jen, alloclen, fulllen1, fulllen2, aseq1, aseq2, depth, gapinfo, NULL, 0, NULL, headgp, tailgp, headgapfreq1_g, headgapfreq2_g ); // chudan mada
+#if 0
+ fprintf( stderr, "aseq1[0] = %s\n", aseq1[0] );
+ fprintf( stderr, "aseq2[0] = %s\n", aseq2[0] );
+#endif
+
+
+
+#if DEBUG
+ if( value - maxwm > 1 || maxwm - value > 1 )
+ {
+ fprintf( stderr, "WARNING value = %f, but maxwm = %f\n", value, maxwm );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+ fprintf( stderr, "%s\n", aseq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+ fprintf( stderr, "%s\n", aseq2[i] );
+ }
+
+// exit( 1 );
+ }
+ else
+ {
+ fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+ }
+#endif
+
+#if MEMSAVE
+#else
+ for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+#endif
+
+// fprintf( stderr, "====(s) aseq1[0] (%d) = \n%s\n (a%d-a%d)\n", depth, mseq1[0], ist, ien );
+// fprintf( stderr, "====(s) aseq2[0] (%d) = \n%s\n (b%d-b%d)\n", depth, mseq2[0], jst, jen );
+
+ freearrays_rec2( gaps, aseq1, aseq2 );
+
+#if 0
+ if( seqlen( seq1[0] ) != nglen1 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ exit( 1 );
+ }
+ else
+ fprintf( stderr, "nglen1 is ok in _rec\n" );
+ if( seqlen( seq2[0] ) != nglen2 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+ exit( 1 );
+ }
+ else
+ fprintf( stderr, "nglen2 is ok in _rec\n" );
+#endif
+
+ return( value );
+}
+
+static void freearrays_variousdist(
+ double *ogcp1,
+ double *ogcp2,
+ double *fgcp1,
+ double *fgcp2,
+ double ***cpmx1s,
+ double ***cpmx2s,
+ double *gapfreq1f,
+ double *gapfreq2f,
+ double **gapinfo,
+ char **mseq1,
+ char **mseq2
+)
+{
+ FreeFloatVec( ogcp1 );
+ FreeFloatVec( ogcp2 );
+ FreeFloatVec( fgcp1 );
+ FreeFloatVec( fgcp2 );
+ FreeFloatCub( cpmx1s );
+ FreeFloatCub( cpmx2s );
+ FreeFloatVec( gapfreq1f );
+ FreeFloatVec( gapfreq2f );
+ free( (void *)gapinfo );
+
+ FreeCharMtx( mseq1 );
+ FreeCharMtx( mseq2 );
+}
+
+
+double MSalignmm_variousdist( double **pairoffset, double ***matrices, double **dummy_mtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, 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 */
+{
+// fprintf( stderr, "IN MSalignmm_variousdist\n" );
+// int k;
+ int i, j, c;
+ int ll1, ll2;
+ int lgth1, lgth2;
+ double wm = 0.0; /* int ?????? */
+ char **mseq1;
+ char **mseq2;
+ double *ogcp1;
+ double *ogcp2;
+ double *fgcp1;
+ double *fgcp2;
+ double ***cpmx1s;
+ double ***cpmx2s;
+ double **gapinfo;
+ double fpenalty = (double)penalty;
+ double *gapfreq1f;
+ double *gapfreq2f;
+ int nglen1, nglen2;
+ double headgapfreq1;
+ double headgapfreq2;
+
+#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
+
+ nglen1 = seqlen( seq1[0] );
+ nglen2 = seqlen( seq2[0] );
+
+#if 0
+ fprintf( stderr, "\n" );
+ for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[%d] at root = %s\n", i, seq1[i] );
+ for( j=0; j<jcyc; j++ ) fprintf( stderr, "seq2[%d] at root = %s\n", j, seq2[j] );
+ fprintf( stderr, "\n" );
+#endif
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+
+ ll1 = ( (int)(lgth1) ) + 100;
+ ll2 = ( (int)(lgth2) ) + 100;
+
+ mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+ mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+ gapinfo = AllocateFloatMtx( 6, 0 );
+ ogcp1 = AllocateFloatVec( ll1+2 );
+ ogcp2 = AllocateFloatVec( ll2+2 );
+ fgcp1 = AllocateFloatVec( ll1+2 );
+ fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+ cpmx1s = AllocateFloatCub( maxdistclass, ll1+2, nalphabets+1 );
+ cpmx2s = AllocateFloatCub( maxdistclass, ll2+2, nalphabets+1 );
+
+ gapfreq1f = AllocateFloatVec( ll1+2 ); // must be filled with 0.0
+ gapfreq2f = AllocateFloatVec( ll2+2 ); // must be filled with 0.0
+
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
+ exit( 1 );
+ }
+ }
+
+ for( c=0; c<maxdistclass; c++ )
+ {
+ MScpmx_calc_new( seq1, cpmx1s[c], eff1s[c], lgth1, icyc );
+ MScpmx_calc_new( seq2, cpmx2s[c], eff2s[c], lgth2, jcyc );
+ }
+
+
+#if 1
+
+ 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, egap2 );
+ new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+ outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
+ outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
+ outgapcount( gapfreq1f+lgth1, icyc, egap1, eff1 );
+ outgapcount( gapfreq2f+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;
+ gapfreq1f[lgth1] = 0.0;
+ gapfreq2f[lgth2] = 0.0;
+ }
+
+ if( legacygapcost == 0 )
+ {
+ gapcountf( gapfreq1f, seq1, icyc, eff1, lgth1 );
+ gapcountf( gapfreq2f, seq2, jcyc, eff2, lgth2 );
+ for( i=0; i<lgth1+1; i++ ) gapfreq1f[i] = 1.0 - gapfreq1f[i];
+ for( i=0; i<lgth2+1; i++ ) gapfreq2f[i] = 1.0 - gapfreq2f[i];
+ headgapfreq1 = 1.0 - headgapfreq1;
+ headgapfreq2 = 1.0 - headgapfreq2;
+ }
+ else
+ {
+ for( i=0; i<lgth1+1; i++ ) gapfreq1f[i] = 1.0;
+ for( i=0; i<lgth2+1; i++ ) gapfreq2f[i] = 1.0;
+ headgapfreq1 = 1.0;
+ headgapfreq2 = 1.0;
+ }
+
+#if 1
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1f[i] );
+ fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1f[i] );
+// fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2f[i] );
+ fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2f[i] );
+// fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+ }
+#else
+ for( i=0; i<lgth1; i++ )
+ {
+ ogcp1[i] = 0.5 * fpenalty;
+ fgcp1[i] = 0.5 * fpenalty;
+ }
+ for( i=0; i<lgth2; i++ )
+ {
+ ogcp2[i] = 0.5 * fpenalty;
+ fgcp2[i] = 0.5 * fpenalty;
+ }
+#endif
+
+ gapinfo[0] = ogcp1;
+ gapinfo[1] = fgcp1;
+ gapinfo[2] = ogcp2;
+ gapinfo[3] = fgcp2;
+ gapinfo[4] = gapfreq1f;
+ gapinfo[5] = gapfreq2f;
+#endif
+
+#if 0
+ fprintf( stdout, "in MSalignmm.c\n" );
+ for( i=0; i<icyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP1\n", i );
+ fprintf( stdout, "%s\n", seq1[i] );
+ }
+ for( i=0; i<jcyc; i++ )
+ {
+ fprintf( stdout, ">%d of GROUP2\n", i );
+ fprintf( stdout, "%s\n", seq2[i] );
+ }
+ fflush( stdout );
+#endif
+
+ wm = MSalignmm_rec_variousdist( matrices, icyc, jcyc, seq1, seq2, cpmx1s, cpmx2s, 0, lgth1-1, 0, lgth2-1, alloclen, lgth1, lgth2, mseq1, mseq2, 0, gapinfo, chudanpt, chudanref, chudanres, headgp, tailgp, headgapfreq1, headgapfreq2 );
+#ifdef enablemultithread
+ if( chudanres && *chudanres )
+ {
+// fprintf( stderr, "\n\n## CHUUDAN!!! relay\n" );
+ *chudanres = 1;
+ freearrays_variousdist( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1s, cpmx2s, gapfreq1f, gapfreq2f, gapinfo, mseq1, mseq2 );
+ return( -1.0 );
+ }
+#endif
+
+#if 0
+ fprintf( stderr, "\n" );
+ fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
+ fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
+ fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
+ fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
+ fprintf( stderr, "\n" );
+#endif
+
+// fprintf( stderr, "wm = %f\n", wm );
+
+
+ for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+ for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+ if( seqlen( seq1[0] ) != nglen1 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
+ fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
+ exit( 1 );
+ }
+ if( seqlen( seq2[0] ) != nglen2 )
+ {
+ fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
+ exit( 1 );
+ }
+
+
+ freearrays_variousdist( ogcp1, ogcp2, fgcp1, fgcp2, cpmx1s, cpmx2s, gapfreq1f, gapfreq2f, gapinfo, mseq1, mseq2 );
+
+ lgth1 = strlen( seq1[0] );
+ lgth2 = strlen( seq2[0] );
+ for( i=0; i<icyc; i++ )
+ {
+ if( strlen( seq1[i] ) != lgth1 )
+ {
+ fprintf( stderr, "i = %d / %d\n", i, icyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+ for( j=0; j<jcyc; j++ )
+ {
+ if( strlen( seq2[j] ) != lgth2 )
+ {
+ fprintf( stderr, "j = %d / %d\n", j, jcyc );
+ fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
+ exit( 1 );
+ }
+ }
+
+#if 0
+ fprintf( stderr, "\n" );
+ 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] );
+ fprintf( stderr, "\n" );
+#endif
+
return( wm );
}
git://source.jalview.org / jabaws.git / blobdiff