void FreeFloatCub( float ***cub )
{
int i;
for( i=0; cub[i]; i++ )
{
FreeFloatMtx( cub[i] );
}
free( cub );
}
void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *additionalpair )
{
int i, j;
// int ui, uj;
// int uiup, ujup;
int uido, ujdo;
static TLS char **useq1, **useq2;
static TLS char **oseq1, **oseq2, **oseq1r, **oseq2r, *odir1, *odir2;
static TLS RNApair **pairprob1, **pairprob2;
static TLS RNApair *pairpt1, *pairpt2;
int lgth1 = strlen( seq1[0] );
int lgth2 = strlen( seq2[0] );
static TLS float **impmtx2;
static TLS float **map;
// double lenfac;
float prob;
int **sgapmap1, **sgapmap2;
char *nogapdum;
float **tbppmtx;
// fprintf( stderr, "nseq1=%d, lgth1=%d\n", nseq1, lgth1 );
useq1 = AllocateCharMtx( nseq1, lgth1+10 );
useq2 = AllocateCharMtx( nseq2, lgth2+10 );
oseq1 = AllocateCharMtx( nseq1, lgth1+10 );
oseq2 = AllocateCharMtx( nseq2, lgth2+10 );
oseq1r = AllocateCharMtx( nseq1, lgth1+10 );
oseq2r = AllocateCharMtx( nseq2, lgth2+10 );
odir1 = AllocateCharVec( lgth1+10 );
odir2 = AllocateCharVec( lgth2+10 );
sgapmap1 = AllocateIntMtx( nseq1, lgth1+1 );
sgapmap2 = AllocateIntMtx( nseq2, lgth2+1 );
nogapdum = AllocateCharVec( MAX( lgth1, lgth2 ) );
pairprob1 = (RNApair **)calloc( lgth1, sizeof( RNApair *) );
pairprob2 = (RNApair **)calloc( lgth2, sizeof( RNApair *) );
map = AllocateFloatMtx( lgth1, lgth2 );
impmtx2 = AllocateFloatMtx( lgth1, lgth2 );
tbppmtx = AllocateFloatMtx( lgth1, lgth2 );
for( i=0; i<nseq1; i++ ) strcpy( useq1[i], seq1[i] );
for( i=0; i<nseq2; i++ ) strcpy( useq2[i], seq2[i] );
for( i=0; i<nseq1; i++ ) strcpy( oseq1[i], seq1[i] );
for( i=0; i<nseq2; i++ ) strcpy( oseq2[i], seq2[i] );
for( i=0; i<nseq1; i++ ) commongappick_record( 1, useq1+i, sgapmap1[i] );
for( i=0; i<nseq2; i++ ) commongappick_record( 1, useq2+i, sgapmap2[i] );
for( i=0; i<lgth1; i++ )
{
pairprob1[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
pairprob1[i][0].bestpos = -1;
pairprob1[i][0].bestscore = -1;
}
for( i=0; i<lgth2; i++ )
{
pairprob2[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
pairprob2[i][0].bestpos = -1;
pairprob2[i][0].bestscore = -1;
}
utot( nseq1, lgth1, oseq1 );
utot( nseq2, lgth2, oseq2 );
// fprintf( stderr, "folding group1\n" );
// rnalocal( oseq1, useq1, eff1, eff1, nseq1, nseq1, lgth1+10, pair1 );
/* base-pairing probability of group 1 */
if( rnaprediction == 'r' )
rnaalifoldcall( oseq1, nseq1, pairprob1 );
else
mccaskillextract( oseq1, useq1, nseq1, pairprob1, grouprna1, sgapmap1, eff1 );
// fprintf( stderr, "folding group2\n" );
// rnalocal( oseq2, useq2, eff2, eff2, nseq2, nseq2, lgth2+10, pair2 );
/* base-pairing probability of group 2 */
if( rnaprediction == 'r' )
rnaalifoldcall( oseq2, nseq2, pairprob2 );
else
mccaskillextract( oseq2, useq2, nseq2, pairprob2, grouprna2, sgapmap2, eff2 );
#if 0
makerseq( oseq1, oseq1r, odir1, pairprob1, nseq1, lgth1 );
makerseq( oseq2, oseq2r, odir2, pairprob2, nseq2, lgth2 );
fprintf( stderr, "%s\n", odir2 );
for( i=0; i<nseq1; i++ )
{
fprintf( stdout, ">ori\n%s\n", oseq1[0] );
fprintf( stdout, ">rev\n%s\n", oseq1r[0] );
}
#endif
/* similarity score */
Lalignmm_hmout( oseq1, oseq2, eff1, eff2, nseq1, nseq2, 10000, NULL, NULL, NULL, NULL, map );
if( 1 )
{
if( RNAscoremtx == 'n' )
{
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
{
// impmtx2[i][j] = osoiaveragescore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
impmtx2[i][j] = 0.0;
}
}
else if( RNAscoremtx == 'r' )
{
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
{
tbppmtx[i][j] = 1.0;
impmtx2[i][j] = 0.0;
}
for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
{
for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
{
uido = pairpt1->bestpos;
ujdo = pairpt2->bestpos;
prob = pairpt1->bestscore * pairpt2->bestscore;
if( uido > -1 && ujdo > -1 )
{
if( uido > i && j > ujdo )
{
impmtx2[i][j] += prob * pairedribosumscore53( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
tbppmtx[i][j] -= prob;
}
else if( i < uido && j < ujdo )
{
impmtx2[i][j] += prob * pairedribosumscore35( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j, uido, ujdo ) * consweight_multi;
tbppmtx[i][j] -= prob;
}
}
}
}
for( i=0; i<lgth1; i++ )
{
for( j=0; j<lgth2; j++ )
{
impmtx2[i][j] += tbppmtx[i][j] * singleribosumscore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
}
}
}
/* four-way consistency */
for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
{
// if( pairprob1[i] == NULL ) continue;
for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
{
// fprintf( stderr, "i=%d, j=%d, pn1=%d, pn2=%d\n", i, j, pairpt1-pairprob1[i], pairpt2-pairprob2[j] );
// if( pairprob2[j] == NULL ) continue;
uido = pairpt1->bestpos;
ujdo = pairpt2->bestpos;
prob = pairpt1->bestscore * pairpt2->bestscore;
// prob = 1.0;
// fprintf( stderr, "i=%d->uido=%d, j=%d->ujdo=%d\n", i, uido, j, ujdo );
// fprintf( stderr, "impmtx2[%d][%d] = %f\n", i, j, impmtx2[i][j] );
// if( i < uido && j > ujdo ) continue;
// if( i > uido && j < ujdo ) continue;
// posdistj = abs( ujdo-j );
// if( uido > -1 && ujdo > -1 )
if( uido > -1 && ujdo > -1 && ( ( i > uido && j > ujdo ) || ( i < uido && j < ujdo ) ) )
{
{
impmtx2[i][j] += MAX( 0, map[uido][ujdo] ) * consweight_rna * 600 * prob; // osoi
}
}
}
}
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
{
impmtx[i][j] += impmtx2[i][j];
// fprintf( stderr, "fastathreshold=%f, consweight_multi=%f, consweight_rna=%f\n", fastathreshold, consweight_multi, consweight_rna );
// impmtx[i][j] *= 0.5;
}
// impmtx[0][0] += 10000.0;
// impmtx[lgth1-1][lgth2-1] += 10000.0;
#if 0
fprintf( stdout, "#impmtx2 = \n" );
for( i=0; i<lgth1; i++ )
{
for( j=0; j<lgth2; j++ )
{
fprintf( stdout, "%d %d %f\n", i, j, impmtx2[i][j] );
}
fprintf( stdout, "\n" );
}
exit( 1 );
#endif
}
FreeCharMtx( useq1 );
FreeCharMtx( useq2 );
FreeCharMtx( oseq1 );
FreeCharMtx( oseq2 );
FreeCharMtx( oseq1r );
FreeCharMtx( oseq2r );
free( odir1 );
free( odir2 );
FreeFloatMtx( impmtx2 );
FreeFloatMtx( map );
FreeIntMtx( sgapmap1 );
FreeIntMtx( sgapmap2 );
FreeFloatMtx( tbppmtx );
for( i=0; i<lgth1; i++ ) free( pairprob1[i] );
for( i=0; i<lgth2; i++ ) free( pairprob2[i] );
free( pairprob1 );
free( pairprob2 );
}
float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
// int k;
register int i, j;
int lasti, lastj;
int lgth1, lgth2;
int resultlen;
float wm = 0.0; /* int ?????? */
float g;
float *currentw, *previousw;
#if 1
float *wtmp;
int *ijpipt;
int *ijpjpt;
float *mjpt, *Mjpt, *prept, *curpt;
int *mpjpt, *Mpjpt;
#endif
static TLS float mi, *m;
static TLS float Mi, *largeM;
static TLS int **ijpi;
static TLS int **ijpj;
static TLS int mpi, *mp;
static TLS int Mpi, *Mp;
static TLS float *w1, *w2;
static TLS float *match;
static TLS float *initverticalw; /* kufuu sureba iranai */
static TLS float *lastverticalw; /* kufuu sureba iranai */
static TLS char **mseq1;
static TLS char **mseq2;
static TLS char **mseq;
static TLS float **cpmx1;
static TLS float **cpmx2;
static TLS int **intwork;
static TLS float **floatwork;
static TLS int orlgth1 = 0, orlgth2 = 0;
float maxwm;
float tbk;
int tbki, tbkj;
int endali, endalj;
// float localthr = 0.0;
// float localthr2 = 0.0;
float fpenalty = (float)penalty;
float fpenalty_OP = (float)penalty_OP;
float fpenalty_ex = (float)penalty_ex;
// float fpenalty_EX = (float)penalty_EX;
float foffset = (float)offset;
float localthr = -foffset;
float localthr2 = -foffset;
if( seq1 == NULL )
{
if( orlgth1 > 0 && orlgth2 > 0 )
{
orlgth1 = 0;
orlgth2 = 0;
free( mseq1 );
free( mseq2 );
FreeFloatVec( w1 );
FreeFloatVec( w2 );
FreeFloatVec( match );
FreeFloatVec( initverticalw );
FreeFloatVec( lastverticalw );
FreeFloatVec( m );
FreeIntVec( mp );
free( largeM );
free( Mp );
FreeCharMtx( mseq );
FreeFloatMtx( cpmx1 );
FreeFloatMtx( cpmx2 );
FreeFloatMtx( floatwork );
FreeIntMtx( intwork );
}
return( 0.0 );
}
// fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
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 );
FreeFloatVec( largeM );
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 );
m = AllocateFloatVec( ll2+2 );
mp = AllocateIntVec( ll2+2 );
largeM = AllocateFloatVec( ll2+2 );
Mp = AllocateIntVec( ll2+2 );
mseq = AllocateCharMtx( njob, ll1+ll2 );
cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 );
intwork = AllocateIntMtx( nalphabets, 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 );
FreeIntMtx( commonJP );
}
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 );
commonJP = AllocateIntMtx( ll1+10, ll2+10 );
#if DEBUG
fprintf( stderr, "succeeded\n\n" );
#endif
commonAlloc1 = ll1;
commonAlloc2 = ll2;
}
ijpi = commonIP;
ijpj = commonJP;
#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 );
lasti = lgth2+1;
for( j=1; j<lasti; ++j )
{
m[j] = currentw[j-1]; mp[j] = 0;
largeM[j] = currentw[j-1]; Mp[j] = 0;
}
lastverticalw[0] = currentw[lgth2-1];
#if 0
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
#if DEBUG2
fprintf( stderr, "\n" );
fprintf( stderr, " " );
for( j=0; j<lgth2+1; j++ )
fprintf( stderr, "%c ", seq2[0][j] );
fprintf( stderr, "\n" );
#endif
localstop = lgth1+lgth2+1;
maxwm = -999999999.9;
endali = endalj = 0;
#if DEBUG2
fprintf( stderr, "\n" );
fprintf( stderr, "%c ", seq1[0][0] );
for( j=0; j<lgth2+1; j++ )
fprintf( stderr, "%5.0f ", currentw[j] );
fprintf( stderr, "\n" );
#endif
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 );
#if DEBUG2
fprintf( stderr, "%c ", seq1[0][i] );
fprintf( stderr, "%5.0f ", currentw[0] );
#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
#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;
Mi = previousw[0]; Mpi = 0;
#if 0
if( mi < localthr ) mi = localthr2;
#endif
ijpipt = ijpi[i] + 1;
ijpjpt = ijpj[i] + 1;
mjpt = m + 1;
Mjpt = largeM + 1;
prept = previousw;
curpt = currentw + 1;
mpjpt = mp + 1;
Mpjpt = Mp + 1;
tbk = -999999.9;
tbki = 0;
tbkj = 0;
lastj = lgth2+1;
for( j=1; j<lastj; j++ )
{
wm = *prept;
*ijpipt = i-1;
*ijpjpt = j-1;
// fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
// fprintf( stderr, "wm=%f\n", wm );
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
g = mi + fpenalty;
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( g > wm )
{
wm = g;
// *ijpipt = i - 1;
*ijpjpt = mpi;
}
g = *prept;
if( g > mi )
{
mi = g;
mpi = j-1;
}
#if USE_PENALTY_EX
mi += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
g = *mjpt + fpenalty;
#if 0
fprintf( stderr, "m%5.0f?", g );
#endif
if( g > wm )
{
wm = g;
*ijpipt = *mpjpt;
*ijpjpt = j - 1; //IRU!
}
g = *prept;
if( g > *mjpt )
{
*mjpt = g;
*mpjpt = i-1;
}
#if USE_PENALTY_EX
*mjpt += fpenalty_ex;
#endif
g = tbk + fpenalty_OP;
// g = tbk;
if( g > wm )
{
wm = g;
*ijpipt = tbki;
*ijpjpt = tbkj;
// fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
}
// g = Mi;
if( Mi > tbk )
{
tbk = Mi; //error desu.
tbki = i-1;
tbkj = Mpi;
}
// g = *Mjpt;
if( *Mjpt > tbk )
{
tbk = *Mjpt;
tbki = *Mpjpt;
tbkj = j-1;
}
// tbk += fpenalty_EX;// + foffset;
// g = *prept;
if( *prept > *Mjpt )
{
*Mjpt = *prept;
*Mpjpt = i-1;
}
// *Mjpt += fpenalty_EX;// + foffset;
// g = *prept;
if( *prept > Mi )
{
Mi = *prept;
Mpi = j-1;
}
// Mi += fpenalty_EX;// + foffset;
// fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
// fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
if( maxwm < wm )
{
maxwm = wm;
endali = i;
endalj = j;
}
#if 1
if( wm < localthr )
{
// fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
*ijpipt = localstop;
// *ijpjpt = localstop;
wm = localthr2;
}
#endif
#if 0
fprintf( stderr, "%5.0f ", *curpt );
#endif
#if DEBUG2
fprintf( stderr, "%5.0f ", wm );
// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
#endif
*curpt += wm;
ijpipt++;
ijpjpt++;
mjpt++;
Mjpt++;
prept++;
mpjpt++;
Mpjpt++;
curpt++;
}
#if DEBUG2
fprintf( stderr, "\n" );
#endif
lastverticalw[i] = currentw[lgth2-1];
}
#if DEBUG2
fprintf( stderr, "maxwm = %f\n", maxwm );
fprintf( stderr, "endali = %d\n", endali );
fprintf( stderr, "endalj = %d\n", endalj );
#endif
if( ijpi[endali][endalj] == localstop ) // && ijpj[endali][endalj] == localstop )
{
strcpy( seq1[0], "" );
strcpy( seq2[0], "" );
*off1pt = *off2pt = 0;
return( 0.0 );
}
gentracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, endali, endalj );
// 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" );
}
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] );
#endif
return( maxwm );
}
float G__align11_noalign( int scoremtx[0x80][0x80], int penal, int penal_ex, 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)penal;
#if USE_PENALTY_EX
float fpenalty_ex = (float)penal_ex;
#endif
#if 1
float *wtmp;
float *mjpt, *prept, *curpt;
// int *mpjpt;
#endif
static float mi, *m;
static float *w1, *w2;
static float *match;
static float *initverticalw; /* kufuu sureba iranai */
static float *lastverticalw; /* kufuu sureba iranai */
static int **intwork;
static float **floatwork;
static int orlgth1 = 0, orlgth2 = 0;
wm = 0.0;
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 );
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 );
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;
}
#if 0
for( i=0; i<lgth1; i++ )
fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
#endif
currentw = w1;
previousw = w2;
match_calc_mtx( scoremtx, initverticalw, seq2, seq1, 0, lgth1 );
match_calc_mtx( scoremtx, 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];
}
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_mtx( scoremtx, 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];
mjpt = m + 1;
prept = previousw;
curpt = currentw + 1;
for( j=1; j<lgth2+1; j++ )
{
wm = *prept;
#if 0
fprintf( stderr, "%5.0f->", wm );
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=mi+fpenalty) > wm )
{
wm = g;
}
if( (g=*prept) >= mi )
{
mi = g;
}
#if USE_PENALTY_EX
mi += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=*mjpt + fpenalty) > wm )
{
wm = g;
}
if( (g=*prept) >= *mjpt )
{
*mjpt = g;
}
#if USE_PENALTY_EX
m[j] += fpenalty_ex;
#endif
#if 0
fprintf( stderr, "%5.0f ", wm );
#endif
*curpt++ += wm;
mjpt++;
prept++;
}
lastverticalw[i] = currentw[lgth2-1]; // lgth2==0 no toki error
}
#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 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 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 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 );
}
void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
{
int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
static int impalloclen = 0;
char *pt;
static char *nocount1 = NULL;
static char *nocount2 = NULL;
if( impalloclen < lgth1 || impalloclen < lgth2 )
{
if( impmtx ) FreeFloatMtx( impmtx );
if( nocount1 ) free( nocount1 );
if( nocount2 ) free( nocount2 );
impalloclen = MAX( lgth1, lgth2 ) + 2;
impmtx = AllocateFloatMtx( impalloclen, impalloclen );
nocount1 = AllocateCharVec( impalloclen );
nocount2 = AllocateCharVec( impalloclen );
impalloclen -= 2;
}
for( i=0; i<lgth1; i++ )
{
for( j=0; j<clus1; j++ )
if( seq1[j][i] == '-' ) break;
if( j != clus1 ) nocount1[i] = 1;
else nocount1[i] = 0;
}
for( i=0; i<lgth2; i++ )
{
for( j=0; j<clus2; j++ )
if( seq2[j][i] == '-' ) break;
if( j != clus2 ) nocount2[i] = 1;
else nocount2[i] = 0;
}
#if 0
fprintf( stderr, "nocount2 =\n" );
for( i = 0; i<impalloclen; i++ )
{
fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
}
#endif
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
impmtx[i][j] = 0.0;
for( i=0; i<clus1; i++ )
{
fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
fprintf( stderr, "end1 = %d\n", localhom[i][j]->end1 );
fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
pt = seq1[i];
tmpint = -1;
while( *pt != 0 )
{
if( *pt++ != '-' ) tmpint++;
if( tmpint == localhom[i][j]->start1 ) break;
}
start1 = pt - seq1[i] - 1;
while( *pt != 0 )
{
// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
if( *pt++ != '-' ) tmpint++;
if( tmpint == localhom[i][j]->end1 ) break;
}
end1 = pt - seq1[i] - 1;
pt = seq2[j];
tmpint = -1;
while( *pt != 0 )
{
if( *pt++ != '-' ) tmpint++;
if( tmpint == localhom[i][j]->start2 ) break;
}
start2 = pt - seq2[j] - 1;
while( *pt != 0 )
{
if( *pt++ != '-' ) tmpint++;
if( tmpint == localhom[i][j]->end2 ) break;
}
end2 = pt - seq2[j] - 1;
// fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
k1 = start1;
k2 = start2;
fprintf( stderr, "step 0\n" );
while( k1 <= end1 && k2 <= end2 )
{
#if 0
if( !nocount1[k1] && !nocount2[k2] )
impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
k1++; k2++;
#else
if( !nocount1[k1] && !nocount2[k2] )
impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
k1++; k2++;
#endif
}
dif = ( end1 - start1 ) - ( end2 - start2 );
fprintf( stderr, "dif = %d\n", dif );
if( dif > 0 )
{
do
{
fprintf( stderr, "dif = %d\n", dif );
k1 = start1;
k2 = start2 - dif;
while( k1 <= end1 && k2 <= end2 )
{
if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
k1++; k2++;
}
}
while( dif-- );
}
else
{
do
{
k1 = start1 + dif;
k2 = start2;
while( k1 <= end1 )
{
if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
k1++; k2++;
}
}
while( dif++ );
}
}
}
#if 0
fprintf( stderr, "impmtx = \n" );
for( k2=0; k2<lgth2; k2++ )
fprintf( stderr, "%6.3f ", (double)k2 );
fprintf( stderr, "\n" );
for( k1=0; k1<lgth1; k1++ )
{
fprintf( stderr, "%d", k1 );
for( k2=0; k2<lgth2; k2++ )
fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
fprintf( stderr, "\n" );
}
exit( 1 );
#endif
}
void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore )
{
int i, j, k1, k2, tmpint, start1, start2, end1, end2;
double effij, effijx;
char *pt, *pt1, *pt2;
LocalHom *tmpptr;
if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
{
if( impmtx ) FreeFloatMtx( impmtx );
impalloclen = MAX( lgth1, lgth2 ) + 2;
impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
}
#if 0
fprintf( stderr, "eff1 in _init_strict = \n" );
for( i=0; i<clus1; i++ )
fprintf( stderr, "eff1[] = %f\n", eff1[i] );
for( i=0; i<clus2; i++ )
fprintf( stderr, "eff2[] = %f\n", eff2[i] );
#endif
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
impmtx[i][j] = 0.0;
effijx = 1.0 * fastathreshold;
for( i=0; i<clus1; i++ )
{
for( j=0; j<clus2; j++ )
{
effij = eff1[i] * eff2[j] * effijx;
tmpptr = localhom[i][j];
while( tmpptr )
{
// fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
// fprintf( stderr, "end1 = %d\n", tmpptr->end1 );
// fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
// fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
pt = seq1[i];
tmpint = -1;
while( *pt != 0 )
{
if( *pt++ != '-' ) tmpint++;
if( tmpint == tmpptr->start1 ) break;
}
start1 = (int)( pt - seq1[i] ) - 1;
if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
else
{
#if MACHIGAI
while( *pt != 0 )
{
if( tmpint == tmpptr->end1 ) break;
if( *pt++ != '-' ) tmpint++;
}
end1 = (int)( pt - seq1[i] ) - 1;
#else
while( *pt != 0 )
{
// fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
if( *pt++ != '-' ) tmpint++;
if( tmpint == tmpptr->end1 ) break;
}
end1 = (int)( pt - seq1[i] ) - 1;
#endif
}
pt = seq2[j];
tmpint = -1;
while( *pt != 0 )
{
if( *pt++ != '-' ) tmpint++;
if( tmpint == tmpptr->start2 ) break;
}
start2 = (int)( pt - seq2[j] ) - 1;
if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
else
{
#if MACHIGAI
while( *pt != 0 )
{
if( tmpint == tmpptr->end2 ) break;
if( *pt++ != '-' ) tmpint++;
}
end2 = (int)( pt - seq2[j] ) - 1;
#else
while( *pt != 0 )
{
if( *pt++ != '-' ) tmpint++;
if( tmpint == tmpptr->end2 ) break;
}
end2 = (int)( pt - seq2[j] ) - 1;
#endif
}
// fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
// fprintf( stderr, "step 0\n" );
if( end1 - start1 != end2 - start2 )
{
// fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
}
k1 = start1; k2 = start2;
pt1 = seq1[i] + k1;
pt2 = seq2[j] + k2;
while( *pt1 && *pt2 )
{
if( *pt1 != '-' && *pt2 != '-' )
{
// 重みを二重にかけないように注意して下さい。
// impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
// impmtx[k1][k2] += tmpptr->importance * effij;
impmtx[k1][k2] += tmpptr->fimportance * effij;
// fprintf( stderr, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
// fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
k1++; k2++;
pt1++; pt2++;
}
else if( *pt1 != '-' && *pt2 == '-' )
{
// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
k2++; pt2++;
}
else if( *pt1 == '-' && *pt2 != '-' )
{
// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
k1++; pt1++;
}
else if( *pt1 == '-' && *pt2 == '-' )
{
// fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
k1++; pt1++;
k2++; pt2++;
}
if( k1 > end1 || k2 > end2 ) break;
}
tmpptr = tmpptr->next;
}
}
}
#if 0
fprintf( stderr, "impmtx = \n" );
for( k2=0; k2<lgth2; k2++ )
fprintf( stderr, "%6.3f ", (double)k2 );
fprintf( stderr, "\n" );
for( k1=0; k1<lgth1; k1++ )
{
fprintf( stderr, "%d", k1 );
for( k2=0; k2<lgth2; k2++ )
fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
fprintf( stderr, "\n" );
}
exit( 1 );
#endif
}
