static int reccycle = 0;
-static float localthr;
+static double localthr;
-static void match_ribosum( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+static void match_ribosum( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
int j, k, l;
- float scarr[38];
- float **cpmxpd = floatwork;
+ double scarr[38];
+ double **cpmxpd = doublework;
int **cpmxpdn = intwork;
int count = 0;
- float *matchpt;
- float **cpmxpdpt;
+ double *matchpt;
+ double **cpmxpdpt;
int **cpmxpdnpt;
int cpkd;
scarr[l] += ribosumdis[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;
#endif
}
-static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+static void match_calc( double *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<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]-RNAthr) * 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 );
}
#if 0
-static void match_add( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+static void match_add( 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[nalphabets];
+ double **cpmxpd = doublework;
int **cpmxpdn = intwork;
int count = 0;
- float *matchpt;
- float **cpmxpdpt;
+ double *matchpt;
+ double **cpmxpdpt;
int **cpmxpdnpt;
int cpkd;
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];
}
}
-#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;
#endif
#if 0
-static float Atracking(
+static double Atracking(
char **seq1, char **seq2,
char **mseq1, char **mseq2,
int **ijp, int icyc, int jcyc,
#endif
-static float MSalign2m2m_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, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map )
+static double MSalign2m2m_rec( 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, char **mseq1, char **mseq2, int depth, double **gapinfo, double **map )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
- float value = 0.0;
+ double value = 0.0;
register int i, j;
char **aseq1, **aseq2;
int ll1, ll2;
int lasti, lastj, imid, jmid = 0;
- 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 fpenalty = (float)penalty;
- float *wtmp;
+// double fpenalty = (double)penalty;
+ 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 = 0.0;
+ double maxwm = 0.0;
int *jumpforwi;
int *jumpforwj;
int *jumpbacki;
int jumpi, jumpj = 0;
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 0
static char ttt1[50000];
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_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+ match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );
- match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 );
for( i=1; i<lgth1+1; i++ )
{
previousw[0] = initverticalw[i-1];
- match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[0] = initverticalw[i];
m[0] = ogcp1[i];
// gyakudp
- match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
- match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+ match_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, doublework, intwork, 1 );
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, doublework, intwork, 1 );
for( i=0; i<lgth1-1; i++ )
{
currentw = wtmp;
previousw[lgth2-1] = initverticalw[i+1];
// match_calc( currentw, seq1, seq2, i, lgth2 );
- match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ match_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[lgth2-1] = initverticalw[i];
#if 0
for( i=0; i<lgth1; i++ )
{
- float maxpairscore = -9999.9;
- float tmpscore;
+ double maxpairscore = -9999.9;
+ double tmpscore;
for( j=0; j<lgth2; j++ )
{
}
for( j=0; j<lgth2; j++ )
{
- float maxpairscore = -9999.9;
- float tmpscore;
+ double maxpairscore = -9999.9;
+ double tmpscore;
for( i=0; i<lgth1; i++ )
{
FreeFloatVec( m );
FreeIntVec( mp );
- FreeFloatMtx( floatwork );
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
#if STOREWM
return( value );
}
-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, char **mseq1, char **mseq2, int depth, float **gapinfo, float **map )
+static double MSalignmm_rec( 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, char **mseq1, char **mseq2, int depth, double **gapinfo, double **map )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
- int alnlen;
- float value = 0.0;
+ double value = 0.0;
register int i, j;
char **aseq1, **aseq2;
- int ll1, ll2, l, len;
+ int ll1, ll2;
int lasti, lastj, imid, jmid=0;
- 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)RNApenalty_ex;
+ double fpenalty_ex = (double)RNApenalty_ex;
#endif
-// float fpenalty = (float)penalty;
- float *wtmp;
+// double fpenalty = (double)penalty;
+ 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 = 0.0;
+ double maxwm = 0.0;
int *jumpforwi;
int *jumpforwj;
int *jumpbacki;
int jumpi, jumpj = 0;
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 0
static char ttt1[50000];
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( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );
- match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 1 );
for( i=1; i<lgth1+1; i++ )
{
previousw[0] = initverticalw[i-1];
- match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[0] = initverticalw[i];
m[0] = ogcp1[i];
// 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( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, doublework, intwork, 1 );
+ match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, doublework, intwork, 1 );
for( i=0; i<lgth1-1; i++ )
{
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( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
currentw[lgth2-1] = initverticalw[i];
#if 0
for( i=0; i<lgth1; i++ )
{
- float maxpairscore = -9999.9;
- float tmpscore;
+ double maxpairscore = -9999.9;
+ double tmpscore;
for( j=0; j<lgth2; j++ )
{
}
for( j=0; j<lgth2; j++ )
{
- float maxpairscore = -9999.9;
- float tmpscore;
+ double maxpairscore = -9999.9;
+ double tmpscore;
for( i=0; i<lgth1; i++ )
{
FreeFloatVec( m );
FreeIntVec( mp );
- FreeFloatMtx( floatwork );
+ FreeFloatMtx( doublework );
FreeIntMtx( intwork );
#if STOREWM
FreeFloatMtx( WMMTX2 );
#endif
- return( value );
-
-// fprintf( stderr, "==== calling myself (first)\n" );
-
-#if 0
- fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
- fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
-#endif
- value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo, map );
-#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<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<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
-
-#if 0
- fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
- fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
-#endif
- value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo, map );
-#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) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
-// fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
free( gaps );
#if MEMSAVE
-float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map )
+double Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, double **map )
/* 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;
// char **mseq;
- float *ogcp1;
- float *ogcp2;
- float *fgcp1;
- float *fgcp2;
- float **cpmx1;
- float **cpmx2;
- float **gapinfo;
-// float fpenalty;
- float fpenalty = (float)RNApenalty;
+ double *ogcp1;
+ double *ogcp2;
+ double *fgcp1;
+ double *fgcp2;
+ double **cpmx1;
+ double **cpmx2;
+ double **gapinfo;
+// double fpenalty;
+ double fpenalty = (double)RNApenalty;
int nglen1, nglen2;
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 );
for( i=0; i<icyc; i++ )
{
return( wm );
}
-float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, float **map )
+double Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, double **map )
/* 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;
int nglen1, nglen2;
#if 0
git://source.jalview.org / jabaws.git / blobdiff