float MSalign11( char **seq1, char **seq2, int alloclen )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
register int i, j;
int lasti, lastj;
int iin = 0, jin = 0; // by Mathog, a guess
int lgth1, lgth2;
int resultlen;
float wm = 0.0; /* int ?????? */
float g;
float *currentw, *previousw;
float fpenalty = (float)penalty;
#if USE_PENALTY_EX
float fpenalty_ex = (float)penalty_ex;
#endif
float *maxinw = NULL, *maxinwpt = NULL; // by D.Mathog, guess
float *maxinh = NULL; // by D.Mathog, guess
#if 1
float wmmax;
float *wtmp;
int *ijppt;
float *mjpt, *prept, *curpt;
int *mpjpt;
#endif
static float mi, *m;
static int **ijp;
static int mpi, *mp;
static float *w1, *w2;
static float *match;
static float *initverticalw; /* kufuu sureba iranai */
static float *lastverticalw; /* kufuu sureba iranai */
static char **mseq1;
static char **mseq2;
static char **mseq;
static float **cpmx1;
static float **cpmx2;
static int **intwork;
static float **WMMTX;
static float **floatwork;
static int orlgth1 = 0, orlgth2 = 0;
if( orlgth1 == 0 )
{
mseq1 = AllocateCharMtx( njob, 0 );
mseq2 = AllocateCharMtx( njob, 0 );
}
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[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( maxinw );
FreeFloatVec( maxinh );
FreeFloatVec( m );
FreeIntVec( mp );
FreeCharMtx( mseq );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
FreeFloatMtx( floatwork );
FreeIntMtx( intwork );
}
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
#if DEBUG
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
#endif
w1 = AllocateFloatVec( ll2+2 );
w2 = AllocateFloatVec( ll2+2 );
match = AllocateFloatVec( ll2+2 );
initverticalw = AllocateFloatVec( ll1+2 );
lastverticalw = AllocateFloatVec( ll1+2 );
maxinw = AllocateFloatVec( ll1+2 );
m = AllocateFloatVec( ll2+2 );
mp = AllocateIntVec( ll2+2 );
maxinh = AllocateFloatVec( ll2+2 );
mseq = AllocateCharMtx( njob, ll1+ll2 );
cpmx1 = AllocateFloatMtx( 26, ll1+2 );
cpmx2 = AllocateFloatMtx( 26, ll2+2 );
floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
#if DEBUG
fprintf( stderr, "succeeded\n" );
#endif
orlgth1 = ll1 - 100;
orlgth2 = ll2 - 100;
}
mseq1[0] = mseq[0];
mseq2[0] = mseq[1];
if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
{
int ll1, ll2;
if( commonAlloc1 && commonAlloc2 )
{
FreeIntMtx( commonIP );
FreeFloatMtx( WMMTX );
}
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 );
WMMTX = AllocateFloatMtx( ll1+10, ll2+10 );
#if DEBUG
fprintf( stderr, "succeeded\n\n" );
#endif
commonAlloc1 = ll1;
commonAlloc2 = ll2;
}
ijp = commonIP;
#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, seq2, seq1, 0, lgth1 );
match_calc( currentw, seq1, seq2, 0, lgth2 );
WMMTX[0][0] = initverticalw[0];
maxinh[0] = initverticalw[0];
for( i=1; i<lgth1+1; i++ )
{
initverticalw[i] += fpenalty;
WMMTX[i][0] = initverticalw[i];
if( maxinh[0] < initverticalw[i] ) maxinh[0] = initverticalw[i];
}
maxinw[0] = currentw[0];
for( j=1; j<lgth2+1; j++ )
{
currentw[j] += fpenalty;
WMMTX[0][j] = currentw[j];
if( maxinw[0] < currentw[j] ) maxinw[0] = currentw[j];
}
for( j=1; j<lgth2+1; ++j )
{
m[j] = currentw[j-1]; mp[j] = 0;
}
lastverticalw[0] = currentw[lgth2-1];
lasti = lgth1+1;
for( i=1; i<lasti; i++ )
{
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
previousw[0] = initverticalw[i-1];
match_calc( currentw, seq1, seq2, i, lgth2 );
currentw[0] = initverticalw[i];
mi = previousw[0]; mpi = 0;
maxinwpt = maxinw + i;
*maxinwpt = currentw[0];
fprintf( stderr, "currentw[0] = %f, *maxinwpt = %f\n", currentw[0], maxinw[i] );
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;
*ijppt = 0;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
g = mi + fpenalty;
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( g > wm )
{
wm = g;
*ijppt = -( j - mpi );
}
g = *prept;
if( g >= mi )
{
mi = g;
mpi = j-1;
}
#if USE_PENALTY_EX
mi += fpenalty_ex;
#endif
g = *mjpt + fpenalty;
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( g > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
}
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;
WMMTX[i][j] = *curpt;
if( j<lgth2 && *maxinwpt < *curpt ) *maxinwpt = *curpt;
if( j<lgth2 && maxinh[j] < *curpt ) maxinh[j] = *curpt;
// fprintf( stderr, "maxintwpt = %f\n", *maxinwpt );
ijppt++;
mjpt++;
prept++;
mpjpt++;
curpt++;
}
lastverticalw[i] = currentw[lgth2-1];
}
wmmax = -999.9;
for( i=0; i<lgth1; i++ )
{
g = lastverticalw[i];
if( g > wmmax )
{
wmmax = g;
iin = i;
jin = lgth2-1;
}
}
for( j=0; j<lgth2; j++ )
{
g = currentw[j];
if( g > wmmax )
{
wmmax = g;
iin = lgth1-1;
jin = j;
}
}
for( i=0; i<lgth1; i++ )
fprintf( stderr, "maxinw[%d] = %f\n", i, maxinw[i] );
for( j=0; j<lgth2; j++ )
fprintf( stderr, "maxinh[%d] = %f\n", j, maxinh[j] );
fprintf( stderr, "wmmax = %f (%d,%d)\n", wmmax, iin, jin );
if( iin == lgth1 - 1 && jin == lgth2 - 1 )
;
else
wmmax += fpenalty;
fprintf( stderr, "wmmax = %f\n", wmmax );
#if 0
for( i=0; i<lgth1; i++ )
{
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
}
fprintf( stderr, "\n" );
}
#endif
mseq1[0] += lgth1+lgth2;
*mseq1[0] = 0;
mseq2[0] += lgth1+lgth2;
*mseq2[0] = 0;
backdp( WMMTX, wmmax, maxinw, maxinh, lgth1, lgth2, alloclen, w1, w2, initverticalw, m, mp, iin, jin, seq1, seq2, mseq1, mseq2 );
fprintf( stderr, "\n" );
#if 1
fprintf( stderr, "\n" );
fprintf( stderr, ">MSres\n%s\n", mseq1[0] );
fprintf( stderr, ">MSres\n%s\n", mseq2[0] );
#endif
#if 0
for( i=0; i<lgth1; i++ )
{
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
}
fprintf( stderr, "\n" );
}
#endif
mseq1[0] = mseq[0];
mseq2[0] = mseq[1];
mseq1[0] += lgth1+lgth2;
*mseq1[0] = 0;
mseq2[0] += lgth1+lgth2;
*mseq2[0] = 0;
Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp );
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" );
}
strcpy( seq1[0], mseq1[0] );
strcpy( seq2[0], mseq2[0] );
#if 1
fprintf( stderr, "\n" );
fprintf( stderr, ">\n%s\n", mseq1[0] );
fprintf( stderr, ">\n%s\n", mseq2[0] );
#endif
return( wm );
}
float G__align11( char **seq1, char **seq2, int alloclen )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
register int i, j;
int lasti; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
int lgth1, lgth2;
int resultlen;
float wm; /* int ?????? */
float g;
float *currentw, *previousw;
float fpenalty = (float)penalty;
#if USE_PENALTY_EX
float fpenalty_ex = (float)penalty_ex;
#endif
#if 1
float *wtmp;
int *ijppt;
float *mjpt, *prept, *curpt;
int *mpjpt;
#endif
static float mi, *m;
static int **ijp;
static int mpi, *mp;
static float *w1, *w2;
static float *match;
static float *initverticalw; /* kufuu sureba iranai */
static float *lastverticalw; /* kufuu sureba iranai */
static char **mseq1;
static char **mseq2;
static char **mseq;
static int **intwork;
static float **floatwork;
static int orlgth1 = 0, orlgth2 = 0;
wm = 0.0;
if( orlgth1 == 0 )
{
mseq1 = AllocateCharMtx( njob, 0 );
mseq2 = AllocateCharMtx( njob, 0 );
}
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
if( lgth1 <= 0 || lgth2 <= 0 )
{
fprintf( stderr, "WARNING (g11): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
}
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 );
FreeFloatMtx( floatwork );
FreeIntMtx( intwork );
}
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
#if DEBUG
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
#endif
w1 = AllocateFloatVec( ll2+2 );
w2 = AllocateFloatVec( ll2+2 );
match = AllocateFloatVec( ll2+2 );
initverticalw = AllocateFloatVec( ll1+2 );
lastverticalw = AllocateFloatVec( ll1+2 );
m = AllocateFloatVec( ll2+2 );
mp = AllocateIntVec( ll2+2 );
mseq = AllocateCharMtx( njob, ll1+ll2 );
floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
#if DEBUG
fprintf( stderr, "succeeded\n" );
#endif
orlgth1 = ll1 - 100;
orlgth2 = ll2 - 100;
}
mseq1[0] = mseq[0];
mseq2[0] = mseq[1];
if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
{
int ll1, ll2;
if( commonAlloc1 && commonAlloc2 )
{
FreeIntMtx( commonIP );
}
ll1 = MAX( orlgth1, commonAlloc1 );
ll2 = MAX( orlgth2, commonAlloc2 );
#if DEBUG
fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
#endif
commonIP = AllocateIntMtx( ll1+10, ll2+10 );
#if DEBUG
fprintf( stderr, "succeeded\n\n" );
#endif
commonAlloc1 = ll1;
commonAlloc2 = ll2;
}
ijp = commonIP;
#if 0
for( i=0; i<lgth1; i++ )
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif
currentw = w1;
previousw = w2;
match_calc( initverticalw, seq2, seq1, 0, lgth1 );
match_calc( currentw, seq1, seq2, 0, lgth2 );
if( outgap == 1 )
{
for( i=1; i<lgth1+1; i++ )
{
initverticalw[i] += fpenalty;
}
for( j=1; j<lgth2+1; j++ )
{
currentw[j] += fpenalty;
}
}
for( j=1; j<lgth2+1; ++j )
{
m[j] = currentw[j-1]; mp[j] = 0;
}
if( lgth2 == 0 )
lastverticalw[0] = 0.0; // lgth2==0 no toki error
else
lastverticalw[0] = currentw[lgth2-1]; // lgth2==0 no toki error
if( outgap ) lasti = lgth1+1; else lasti = lgth1;
#if XXXXXXX
fprintf( stderr, "currentw = \n" );
for( i=0; i<lgth1+1; i++ )
{
fprintf( stderr, "%5.2f ", currentw[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "initverticalw = \n" );
for( i=0; i<lgth2+1; i++ )
{
fprintf( stderr, "%5.2f ", initverticalw[i] );
}
fprintf( stderr, "\n" );
#endif
for( i=1; i<lasti; i++ )
{
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
previousw[0] = initverticalw[i-1];
match_calc( currentw, seq1, seq2, i, lgth2 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
currentw[0] = initverticalw[i];
mi = previousw[0]; mpi = 0;
ijppt = ijp[i] + 1;
mjpt = m + 1;
prept = previousw;
curpt = currentw + 1;
mpjpt = mp + 1;
for( j=1; j<lgth2+1; j++ )
{
wm = *prept;
*ijppt = 0;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=mi+fpenalty) > wm )
{
wm = g;
*ijppt = -( j - mpi );
}
if( (g=*prept) >= mi )
{
mi = g;
mpi = j-1;
}
#if USE_PENALTY_EX
mi += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=*mjpt + fpenalty) > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
}
if( (g=*prept) >= *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++;
}
lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
}
Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp );
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" );
}
strcpy( seq1[0], mseq1[0] );
strcpy( seq2[0], mseq2[0] );
#if 0
fprintf( stderr, "\n" );
fprintf( stderr, ">\n%s\n", mseq1[0] );
fprintf( stderr, ">\n%s\n", mseq2[0] );
fprintf( stderr, "wm = %f\n", wm );
#endif
return( wm );
}
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 )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
register int i, j;
int lasti, lastj; /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
int lgth1, lgth2;
int resultlen;
float wm = 0.0; /* int ?????? */
float g;
float *currentw, *previousw;
#if 1
float *wtmp;
int *ijppt;
float *mjpt, *prept, *curpt;
int *mpjpt;
#endif
static float mi, *m;
static int **ijp;
static int mpi, *mp;
static float *w1, *w2;
static float *match;
static float *initverticalw; /* kufuu sureba iranai */
static float *lastverticalw; /* kufuu sureba iranai */
static char **mseq1;
static char **mseq2;
static char **mseq;
static float *ogcp1;
static float *ogcp2;
static float *fgcp1;
static float *fgcp2;
static float **cpmx1;
static float **cpmx2;
static int **intwork;
static float **floatwork;
static int orlgth1 = 0, orlgth2 = 0;
float fpenalty = (float)penalty;
#if USE_PENALTY_EX
float fpenalty_ex = (float)penalty_ex;
#endif
float *fgcp2pt;
float *ogcp2pt;
float fgcp1va;
float ogcp1va;
#if 0
fprintf( stderr, "eff in SA+++align\n" );
for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
#endif
if( orlgth1 == 0 )
{
mseq1 = AllocateCharMtx( njob, 0 );
mseq2 = AllocateCharMtx( njob, 0 );
}
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
if( lgth1 > orlgth1 || lgth2 > orlgth2 )
{
int ll1, ll2;
if( orlgth1 > 0 && orlgth2 > 0 )
{
FreeFloatVec( w1 );
FreeFloatVec( w2 );
FreeFloatVec( match );
FreeFloatVec( initverticalw );
FreeFloatVec( lastverticalw );
FreeFloatVec( m );
FreeIntVec( mp );
FreeCharMtx( mseq );
FreeFloatVec( ogcp1 );
FreeFloatVec( ogcp2 );
FreeFloatVec( fgcp1 );
FreeFloatVec( fgcp2 );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
FreeFloatMtx( floatwork );
FreeIntMtx( intwork );
}
ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
#if DEBUG
fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
#endif
w1 = AllocateFloatVec( ll2+2 );
w2 = AllocateFloatVec( ll2+2 );
match = AllocateFloatVec( ll2+2 );
initverticalw = AllocateFloatVec( ll1+2 );
lastverticalw = AllocateFloatVec( ll1+2 );
m = AllocateFloatVec( ll2+2 );
mp = AllocateIntVec( ll2+2 );
mseq = AllocateCharMtx( njob, ll1+ll2 );
ogcp1 = AllocateFloatVec( ll1+2 );
ogcp2 = AllocateFloatVec( ll2+2 );
fgcp1 = AllocateFloatVec( ll1+2 );
fgcp2 = AllocateFloatVec( ll2+2 );
cpmx1 = AllocateFloatMtx( 26, ll1+2 );
cpmx2 = AllocateFloatMtx( 26, ll2+2 );
#if FASTMATCHCALC
floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 );
intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 );
#else
floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 );
intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 );
#endif
#if DEBUG
fprintf( stderr, "succeeded\n" );
#endif
orlgth1 = ll1 - 100;
orlgth2 = ll2 - 100;
}
for( i=0; i<icyc; i++ ) mseq1[i] = mseq[i];
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 );
if( sgap1 )
{
new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
}
else
{
st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
}
for( i=0; i<lgth1; i++ )
{
ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
}
for( i=0; i<lgth2; i++ )
{
ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
}
#if 0
for( i=0; i<lgth1; i++ )
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif
currentw = w1;
previousw = w2;
match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
if( localhom )
part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
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] ) ;
}
for( j=1; j<lgth2+1; j++ )
{
currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
}
}
#if OUTGAP0TRY
else
{
for( j=1; j<lgth2+1; j++ )
currentw[j] -= offset * j / 2.0;
for( i=1; i<lgth1+1; i++ )
initverticalw[i] -= offset * i / 2.0;
}
#endif
for( j=1; j<lgth2+1; ++j )
{
m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
}
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++ )
{
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
previousw[0] = initverticalw[i-1];
match_calc( currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
#if XXXXXXX
fprintf( stderr, "\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
if( localhom )
{
// fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
// 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" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, "currentw = \n" );
for( j=0; j<lgth2; j++ )
{
fprintf( stderr, "%5.2f ", currentw[j] );
}
fprintf( stderr, "\n" );
#endif
currentw[0] = initverticalw[i];
mi = previousw[0] + ogcp2[1]; mpi = 0;
ijppt = ijp[i] + 1;
mjpt = m + 1;
prept = previousw;
curpt = currentw + 1;
mpjpt = mp + 1;
fgcp2pt = fgcp2;
ogcp2pt = ogcp2+1;
fgcp1va = fgcp1[i-1];
ogcp1va = ogcp1[i];
for( j=1; j<lastj; j++ )
{
wm = *prept;
*ijppt = 0;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
g = mi + *fgcp2pt;
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( g > wm )
{
wm = g;
*ijppt = -( j - mpi );
}
g = *prept + *ogcp2pt;
if( g >= mi )
{
mi = g;
mpi = j-1;
}
#if USE_PENALTY_EX
mi += fpenalty_ex;
#endif
g = *mjpt + fgcp1va;
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( g > wm )
{
wm = g;
*ijppt = +( i - *mpjpt );
}
g = *prept + ogcp1va;
if( g >= *mjpt )
{
*mjpt = g;
*mpjpt = i-1;
}
#if USE_PENALTY_EX
m[j] += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f ", wm );
#endif
*curpt += wm;
ijppt++;
mjpt++;
prept++;
mpjpt++;
curpt++;
fgcp2pt++;
ogcp2pt++;
}
lastverticalw[i] = currentw[lgth2-1];
}
#if OUTGAP0TRY
if( !outgap )
{
for( j=1; j<lgth2+1; j++ )
currentw[j] -= offset * ( lgth2 - j ) / 2.0;
for( i=1; i<lgth1+1; i++ )
lastverticalw[i] -= offset * ( lgth1 - i / 2.0);
}
#endif
/*
fprintf( stderr, "\n" );
for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
fprintf( stderr, "#####\n" );
for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
fprintf( stderr, "====>" );
for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
*/
if( localhom )
{
Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
}
else
Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
// 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] );
*/
return( wm );
}
