/* EstimateModel: top level of iterative estimation process */
void EstimateModel(void)
{
LogFloat totalP,newP,delta;
Boolean converged = FALSE;
int i,iter,numSegs,segLen;
IntVec states; /* array[1..numSegs] of State */
IntVec *mixes; /* array[1..S][1..numSegs] of MixComp */
if (trace&T_TOP) printf("Starting Estimation Process\n");
if (newModel){
UniformSegment();
}
totalP=LZERO;
for (iter=1; !converged && iter<=maxIter; iter++){
ZeroAccs(&hset, uFlags); /* Clear all accumulators */
numSegs = NumSegs(segStore);
/* Align on each training segment and accumulate stats */
for (newP=0.0,i=1;i<=numSegs;i++) {
segLen = SegLength(segStore,i);
states = CreateIntVec(&gstack,segLen);
mixes = (hset.hsKind==DISCRETEHS)?NULL:
CreateMixes(&gstack,segLen);
newP += ViterbiAlign(i,segLen,states,mixes);
if (trace&T_ALN) ShowAlignment(i,segLen,states,mixes);
UpdateCounts(i,segLen,states,mixes);
FreeIntVec(&gstack,states); /* disposes mixes too */
}
/* Update parameters or quit */
newP /= (float)numSegs;
delta = newP - totalP;
converged = (iter>1) && (fabs(delta) < epsilon);
if (!converged)
UpdateParameters();
totalP = newP;
if (trace & T_TOP){
printf("Iteration %d: Average LogP =%12.5f",iter,totalP);
if (iter > 1)
printf(" Change =%12.5f\n",delta);
else
printf("\n");
fflush(stdout);
}
}
if (trace&T_TOP) {
if (converged)
printf("Estimation converged at iteration %d\n",iter);
else
printf("Estimation aborted at iteration %d\n",iter);
fflush(stdout);
}
}
void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
// memory complexity = O(n^3), time complexity = O(n^2)
{
int i, j, shift, cur1, cur2, count;
static TLS int crossscoresize = 0;
static TLS int jumpposi, *jumppos;
static TLS double jumpscorei, *jumpscore;
static TLS int *result1 = NULL;
static TLS int *result2 = NULL;
static TLS int *ocut1 = NULL;
static TLS int *ocut2 = NULL;
double maximum;
static TLS double **crossscore = NULL;
static TLS int **track = NULL;
if( result1 == NULL )
{
result1 = AllocateIntVec( MAXSEG );
result2 = AllocateIntVec( MAXSEG );
ocut1 = AllocateIntVec( MAXSEG );
ocut2 = AllocateIntVec( MAXSEG );
}
if( crossscoresize < *ncut+2 )
{
crossscoresize = *ncut+2;
if( fftkeika ) fprintf( stderr, "allocating crossscore and track, size = %d\n", crossscoresize );
if( track ) FreeIntMtx( track );
if( crossscore ) FreeDoubleMtx( crossscore );
if( jumppos ) FreeIntVec( jumppos );
if( jumpscore ) FreeDoubleVec( jumpscore );
track = AllocateIntMtx( crossscoresize, crossscoresize );
crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
jumppos = AllocateIntVec( crossscoresize );
jumpscore = AllocateDoubleVec( crossscoresize );
}
#if 0
for( i=0; i<*ncut-2; i++ )
fprintf( stderr, "%d.start = %d, score = %f\n", i, seg1[i]->start, seg1[i]->score );
for( i=0; i<*ncut; i++ )
fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
for( i=0; i<*ncut; i++ )
{
for( j=0; j<*ncut; j++ )
fprintf( stderr, "%#4.0f ", ocrossscore[i][j] );
fprintf( stderr, "\n" );
}
#endif
for( i=0; i<*ncut; i++ ) for( j=0; j<*ncut; j++ ) /* mudadanaa */
crossscore[i][j] = ocrossscore[i][j];
for( i=0; i<*ncut; i++ )
{
ocut1[i] = cut1[i];
ocut2[i] = cut2[i];
}
for( j=0; j<*ncut; j++ )
{
jumpscore[j] = -999.999;
jumppos[j] = -1;
}
for( i=1; i<*ncut; i++ )
{
jumpscorei = -999.999;
jumpposi = -1;
for( j=1; j<*ncut; j++ )
{
#if 1
fprintf( stderr, "in blockalign3, ### i=%d, j=%d\n", i, j );
#endif
#if 0
for( k=0; k<j-2; k++ )
{
/*
fprintf( stderr, "k=%d, i=%d\n", k, i );
*/
if( k && k<*ncut-1 && j<*ncut-1 && !permit( seg1[k-1], seg1[j-1] ) ) continue;
if( crossscore[i-1][k] > maxj )
{
pointi = k;
maxi = crossscore[i-1][k];
}
}
pointj = 0; maxj = 0.0;
for( k=0; k<i-2; k++ )
{
if( k && k<*ncut-1 && i<*ncut-1 && !permit( seg2[k-1], seg2[i-1] ) ) continue;
if( crossscore[k][j-1] > maxj )
{
pointj = k;
maxj = crossscore[k][j-1];
}
}
maxi += penalty;
maxj += penalty;
#endif
maximum = crossscore[i-1][j-1];
track[i][j] = 0;
if( maximum < jumpscorei && permit( seg1[jumpposi], seg1[i] ) )
{
maximum = jumpscorei;
track[i][j] = j - jumpposi;
}
if( maximum < jumpscore[j] && permit( seg2[jumppos[j]], seg2[j] ) )
{
maximum = jumpscore[j];
track[i][j] = jumpscore[j] - i;
}
crossscore[i][j] += maximum;
if( jumpscorei < crossscore[i-1][j] )
{
jumpscorei = crossscore[i-1][j];
jumpposi = j;
}
if( jumpscore[j] < crossscore[i][j-1] )
{
jumpscore[j] = crossscore[i][j-1];
jumppos[j] = i;
}
}
}
#if 0
for( i=0; i<*ncut; i++ )
{
for( j=0; j<*ncut; j++ )
fprintf( stderr, "%3d ", track[i][j] );
fprintf( stderr, "\n" );
}
#endif
result1[MAXSEG-1] = *ncut-1;
result2[MAXSEG-1] = *ncut-1;
for( i=MAXSEG-1; i>=1; i-- )
{
cur1 = result1[i];
cur2 = result2[i];
if( cur1 == 0 || cur2 == 0 ) break;
shift = track[cur1][cur2];
if( shift == 0 )
{
result1[i-1] = cur1 - 1;
result2[i-1] = cur2 - 1;
continue;
}
else if( shift > 0 )
{
result1[i-1] = cur1 - 1;
result2[i-1] = cur2 - shift;
}
else if( shift < 0 )
{
result1[i-1] = cur1 + shift;
result2[i-1] = cur2 - 1;
}
}
count = 0;
for( j=i; j<MAXSEG; j++ )
{
if( ocrossscore[result1[j]][result2[j]] == 0.0 ) continue;
if( result1[j] == result1[j-1] || result2[j] == result2[j-1] )
if( ocrossscore[result1[j]][result2[j]] > ocrossscore[result1[j-1]][result2[j-1]] )
count--;
cut1[count] = ocut1[result1[j]];
cut2[count] = ocut2[result2[j]];
count++;
}
*ncut = count;
#if 0
for( i=0; i<*ncut; i++ )
fprintf( stderr, "i=%d, cut1 = %d, cut2 = %d\n", i, cut1[i], cut2[i] );
#endif
}
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 );
}
int alignableReagion( int clus1, int clus2,
char **seq1, char **seq2,
double *eff1, double *eff2,
Segment *seg )
{
int i, j, k;
int status, starttmp = 0; // by D.Mathog, a gess
double score;
int value = 0;
int len, maxlen;
int length = 0; // by D.Mathog, a gess
static TLS double *stra = NULL;
static TLS int alloclen = 0;
double totaleff;
double cumscore;
static TLS double threshold;
static TLS double *prf1 = NULL;
static TLS double *prf2 = NULL;
static TLS int *hat1 = NULL;
static TLS int *hat2 = NULL;
int pre1, pre2;
#if 0
char **seq1pt;
char **seq2pt;
double *eff1pt;
double *eff2pt;
#endif
#if 0
fprintf( stderr, "### In alignableRegion, clus1=%d, clus2=%d \n", clus1, clus2 );
fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
fprintf( stderr, "seq2[0] = %s\n", seq2[0] );
fprintf( stderr, "eff1[0] = %f\n", eff1[0] );
fprintf( stderr, "eff2[0] = %f\n", eff2[0] );
#endif
if( clus1 == 0 )
{
if( stra ) FreeDoubleVec( stra ); stra = NULL;
if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
alloclen = 0;
return( 0 );
}
if( prf1 == NULL )
{
prf1 = AllocateDoubleVec( nalphabets );
prf2 = AllocateDoubleVec( nalphabets );
hat1 = AllocateIntVec( nalphabets+1 );
hat2 = AllocateIntVec( nalphabets+1 );
}
len = MIN( strlen( seq1[0] ), strlen( seq2[0] ) );
maxlen = MAX( strlen( seq1[0] ), strlen( seq2[0] ) ) + fftWinSize;
if( alloclen < maxlen )
{
if( alloclen )
{
FreeDoubleVec( stra );
}
else
{
threshold = (int)fftThreshold / 100.0 * 600.0 * fftWinSize;
}
stra = AllocateDoubleVec( maxlen );
alloclen = maxlen;
}
totaleff = 0.0;
for( i=0; i<clus1; i++ ) for( j=0; j<clus2; j++ ) totaleff += eff1[i] * eff2[j];
for( i=0; i<len; i++ )
{
/* make prfs */
for( j=0; j<nalphabets; j++ )
{
prf1[j] = 0.0;
prf2[j] = 0.0;
}
#if 0
seq1pt = seq1;
eff1pt = eff1;
j = clus1;
while( j-- ) prf1[amino_n[(*seq1pt++)[i]]] += *eff1pt++;
#else
for( j=0; j<clus1; j++ ) prf1[amino_n[(int)seq1[j][i]]] += eff1[j];
#endif
for( j=0; j<clus2; j++ ) prf2[amino_n[(int)seq2[j][i]]] += eff2[j];
/* make hats */
pre1 = pre2 = nalphabets;
for( j=25; j>=0; j-- )
{
if( prf1[j] )
{
hat1[pre1] = j;
pre1 = j;
}
if( prf2[j] )
{
hat2[pre2] = j;
pre2 = j;
}
}
hat1[pre1] = -1;
hat2[pre2] = -1;
/* make site score */
stra[i] = 0.0;
for( k=hat1[nalphabets]; k!=-1; k=hat1[k] )
for( j=hat2[nalphabets]; j!=-1; j=hat2[j] )
// stra[i] += n_dis[k][j] * prf1[k] * prf2[j];
stra[i] += n_disFFT[k][j] * prf1[k] * prf2[j];
stra[i] /= totaleff;
}
(seg+0)->skipForeward = 0;
(seg+1)->skipBackward = 0;
status = 0;
cumscore = 0.0;
score = 0.0;
for( j=0; j<fftWinSize; j++ ) score += stra[j];
for( i=1; i<len-fftWinSize; i++ )
{
score = score - stra[i-1] + stra[i+fftWinSize-1];
#if TMPTMPTMP
fprintf( stderr, "%d %10.0f ? %10.0f\n", i, score, threshold );
#endif
if( score > threshold )
{
#if 0
seg->start = i;
seg->end = i;
seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
seg->score = score;
status = 0;
value++;
#else
if( !status )
{
status = 1;
starttmp = i;
length = 0;
cumscore = 0.0;
}
length++;
cumscore += score;
#endif
}
if( score <= threshold || length > SEGMENTSIZE )
{
if( status )
{
if( length > fftWinSize )
{
seg->start = starttmp;
seg->end = i;
seg->center = ( seg->start + seg->end + fftWinSize ) / 2 ;
seg->score = cumscore;
#if 0
fprintf( stderr, "%d-%d length = %d, score = %f, value = %d\n", seg->start, seg->end, length, cumscore, value );
#endif
if( length > SEGMENTSIZE )
{
(seg+0)->skipForeward = 1;
(seg+1)->skipBackward = 1;
}
else
{
(seg+0)->skipForeward = 0;
(seg+1)->skipBackward = 0;
}
value++;
seg++;
}
length = 0;
cumscore = 0.0;
status = 0;
starttmp = i;
if( value > MAXSEG - 3 ) ErrorExit( "TOO MANY SEGMENTS!");
}
}
}
if( status && length > fftWinSize )
{
seg->end = i;
seg->start = starttmp;
seg->center = ( starttmp + i + fftWinSize ) / 2 ;
seg->score = cumscore;
#if 0
fprintf( stderr, "%d-%d length = %d\n", seg->start, seg->end, length );
#endif
value++;
}
#if TMPTMPTMP
exit( 0 );
#endif
// fprintf( stderr, "returning %d\n", value );
return( value );
}
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 );
}
float L__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; /* 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 TLS float mi, *m;
static TLS int **ijp;
static TLS int mpi, *mp;
static TLS float *w1, *w2;
static TLS float *match;
static TLS float *initverticalw; /* kufuu sureba iranai */
static TLS float *lastverticalw; /* kufuu sureba iranai */
static TLS char **mseq1;
static TLS char **mseq2;
static TLS char **mseq;
// static TLS int **intwork;
// static TLS float **floatwork;
static TLS int orlgth1 = 0, orlgth2 = 0;
float maxwm;
int endali = 0, endalj = 0; // by D.Mathog, a guess
// int endali, endalj;
float localthr = -offset;
float localthr2 = -offset;
// float localthr = 100;
// float localthr2 = 100;
float fpenalty = (float)penalty;
float fpenalty_ex = (float)penalty_ex;
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 );
FreeCharMtx( mseq );
}
return( 0.0 );
}
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( 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 );
lasti = lgth2+1;
for( j=1; j<lasti; ++j )
{
m[j] = currentw[j-1]; mp[j] = 0;
#if 0
if( m[j] < localthr ) m[j] = localthr2;
#endif
}
lastverticalw[0] = currentw[lgth2-1];
lasti = lgth1+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; j++ )
fprintf( stderr, "%c ", seq2[0][j] );
fprintf( stderr, "\n" );
#endif
localstop = lgth1+lgth2+1;
maxwm = -999999999.9;
#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
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;
#if 0
if( mi < localthr ) mi = localthr2;
#endif
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
#if 0
fprintf( stderr, "%5.0f?", g );
#endif
if( (g=mi+fpenalty) > wm )
{
wm = g;
*ijppt = -( j - mpi );
}
if( *prept > mi )
{
mi = *prept;
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( *prept > *mjpt )
{
*mjpt = *prept;
*mpjpt = i-1;
}
#if USE_PENALTY_EX
*mjpt += fpenalty_ex;
#endif
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 );
*ijppt = 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;
ijppt++;
mjpt++;
prept++;
mpjpt++;
}
#if DEBUG2
fprintf( stderr, "\n" );
#endif
lastverticalw[i] = currentw[lgth2-1];
}
#if 0
fprintf( stderr, "maxwm = %f\n", maxwm );
fprintf( stderr, "endali = %d\n", endali );
fprintf( stderr, "endalj = %d\n", endalj );
#endif
if( ijp[endali][endalj] == localstop )
{
strcpy( seq1[0], "" );
strcpy( seq2[0], "" );
*off1pt = *off2pt = 0;
fprintf( stderr, "maxwm <- 0.0 \n" );
return( 0.0 );
}
Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj );
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, "wm=%f\n", wm );
fprintf( stderr, ">\n%s\n", mseq1[0] );
fprintf( stderr, ">\n%s\n", mseq2[0] );
fprintf( stderr, "maxwm = %f\n", maxwm );
fprintf( stderr, " wm = %f\n", wm );
#endif
return( maxwm );
}
float L__align11( double **n_dynamicmtx, float scoreoffset, 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;
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 TLS float mi, *m;
static TLS int **ijp;
static TLS int mpi, *mp;
static TLS float *w1, *w2;
static TLS float *match;
static TLS float *initverticalw; /* kufuu sureba iranai */
static TLS float *lastverticalw; /* kufuu sureba iranai */
static TLS char **mseq1;
static TLS char **mseq2;
static TLS char **mseq;
// static TLS int **intwork;
// static TLS float **floatwork;
static TLS int orlgth1 = 0, orlgth2 = 0;
static TLS double **amino_dynamicmtx = NULL; // ??
float maxwm;
int endali = 0, endalj = 0; // by D.Mathog, a guess
// int endali, endalj;
float localthr = -offset + scoreoffset * 600; // 2013/12/13
float localthr2 = -offset + scoreoffset * 600; // 2013/12/13
// float localthr = -offset;
// float localthr2 = -offset;
float fpenalty = (float)penalty;
float fpenalty_ex = (float)penalty_ex;
float fpenalty_shift = (float)penalty_shift;
float fpenalty_tmp; // atode kesu
int *warpis = NULL;
int *warpjs = NULL;
int *warpi = NULL;
int *warpj = NULL;
int *prevwarpi = NULL;
int *prevwarpj = NULL;
float *wmrecords = NULL;
float *prevwmrecords = NULL;
int warpn = 0;
int warpbase;
float curm = 0.0;
float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
int *warpipt, *warpjpt;
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 );
FreeCharMtx( mseq );
if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
}
return( 0.0 );
}
if( orlgth1 == 0 )
{
mseq1 = AllocateCharMtx( njob, 0 );
mseq2 = AllocateCharMtx( njob, 0 );
}
lgth1 = strlen( seq1[0] );
lgth2 = strlen( seq2[0] );
warpbase = lgth1 + lgth2;
warpis = NULL;
warpjs = NULL;
warpn = 0;
if( trywarp )
{
wmrecords = AllocateFloatVec( lgth2+1 );
warpi = AllocateIntVec( lgth2+1 );
warpj = AllocateIntVec( lgth2+1 );
prevwmrecords = AllocateFloatVec( lgth2+1 );
prevwarpi = AllocateIntVec( lgth2+1 );
prevwarpj = AllocateIntVec( lgth2+1 );
for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
}
if( 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 );
if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
// 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( nalphabets, MAX( ll1, ll2 )+2 );
// intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 );
#if DEBUG
fprintf( stderr, "succeeded\n" );
#endif
amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
orlgth1 = ll1 - 100;
orlgth2 = ll2 - 100;
}
for( i=0; i<nalphabets; i++) for( j=0; j<nalphabets; j++ )
amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
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_mtx( amino_dynamicmtx, initverticalw, seq2, seq1, 0, lgth1 );
match_calc_mtx( amino_dynamicmtx, currentw, seq1, seq2, 0, lgth2 );
lasti = lgth2+1;
for( j=1; j<lasti; ++j )
{
m[j] = currentw[j-1]; mp[j] = 0;
#if 0
if( m[j] < localthr ) m[j] = localthr2;
#endif
}
lastverticalw[0] = currentw[lgth2-1];
lasti = lgth1+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; j++ )
fprintf( stderr, "%c ", seq2[0][j] );
fprintf( stderr, "\n" );
#endif
localstop = lgth1+lgth2+1;
maxwm = -999999999.9;
#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
for( i=1; i<lasti; i++ )
{
wtmp = previousw;
previousw = currentw;
currentw = wtmp;
previousw[0] = initverticalw[i-1];
match_calc_mtx( amino_dynamicmtx, 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;
#if 0
if( mi < localthr ) mi = localthr2;
#endif
ijppt = ijp[i] + 1;
mjpt = m + 1;
prept = previousw;
curpt = currentw + 1;
mpjpt = mp + 1;
lastj = lgth2+1;
if( trywarp )
{
prevwmrecordspt = prevwmrecords;
wmrecordspt = wmrecords+1;
wmrecords1pt = wmrecords;
warpipt = warpi + 1;
warpjpt = warpj + 1;
}
for( j=1; j<lastj; 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( *prept > mi )
{
mi = *prept;
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( *prept > *mjpt )
{
*mjpt = *prept;
*mpjpt = i-1;
}
#if USE_PENALTY_EX
*mjpt += fpenalty_ex;
#endif
if( maxwm < wm )
{
maxwm = wm;
endali = i;
endalj = j;
}
#if 1
if( wm < localthr )
{
// fprintf( stderr, "stop i=%d, j=%d, curpt=%f, localthr = %f\n", i, j, *curpt, localthr );
*ijppt = localstop;
wm = localthr2;
}
#endif
#if 0
fprintf( stderr, "%5.0f ", *curpt );
#endif
#if 0
fprintf( stderr, "wm (%d,%d) = %5.0f\n", i, j, wm );
// fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
#endif
if( trywarp )
{
fpenalty_tmp = fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] );
// fprintf( stderr, "fpenalty_shift = %f\n", fpenalty_tmp );
// fprintf( stderr, "\n\n\nwarp to %c-%c (%d-%d) from %c-%c (%d-%d) ? prevwmrecords[%d] = %f + %f <- wm = %f\n", seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], prevwarpi[j-1], prevwarpj[j-1], seq1[0][i], seq2[0][j], i, j, j, prevwmrecords[j-1], fpenalty_tmp, wm );
// if( (g=prevwmrecords[j-1] + fpenalty_shift )> wm )
if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
{
// fprintf( stderr, "Yes! Warp!! from %d-%d (%c-%c) to %d-%d (%c-%c) fpenalty_tmp = %f! warpn = %d\n", i, j, seq1[0][i], seq2[0][j-1], prevwarpi[j-1], prevwarpj[j-1],seq1[0][prevwarpi[j-1]], seq2[0][prevwarpj[j-1]], fpenalty_tmp, warpn );
if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
{
*ijppt = warpbase + warpn - 1;
}
else
{
*ijppt = warpbase + warpn;
warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
warpis[warpn] = prevwarpi[j-1];
warpjs[warpn] = prevwarpj[j-1];
warpn++;
}
wm = g;
}
else
{
}
curm = *curpt + wm;
// fprintf( stderr, "###### curm = %f at %c-%c, i=%d, j=%d\n", curm, seq1[0][i], seq2[0][j], i, j );
// fprintf( stderr, "copy from i, j-1? %f > %f?\n", wmrecords[j-1], curm );
// if( wmrecords[j-1] > wmrecords[j] )
if( *wmrecords1pt > *wmrecordspt )
{
// fprintf( stderr, "yes\n" );
// wmrecords[j] = wmrecords[j-1];
*wmrecordspt = *wmrecords1pt;
// warpi[j] = warpi[j-1];
// warpj[j] = warpj[j-1];
*warpipt = *(warpipt-1);
*warpjpt = *(warpjpt-1);
// fprintf( stderr, "warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
}
// else
// {
// fprintf( stderr, "no\n" );
// }
// fprintf( stderr, " curm = %f at %c-%c\n", curm, seq1[0][i], seq2[0][j] );
// fprintf( stderr, " wmrecords[%d] = %f\n", j, wmrecords[j] );
// fprintf( stderr, "replace?\n" );
// if( curm > wmrecords[j] )
if( curm > *wmrecordspt )
{
// fprintf( stderr, "yes at %d-%d (%c-%c), replaced warp: warpi[j]=%d, warpj[j]=%d warpn=%d, wmrecords[j] = %f -> %f\n", i, j, seq1[0][i], seq2[0][j], i, j, warpn, wmrecords[j], curm );
// wmrecords[j] = curm;
*wmrecordspt = curm;
// warpi[j] = i;
// warpj[j] = j;
*warpipt = i;
*warpjpt = j;
}
// else
// {
// fprintf( stderr, "No! warpi[j]=%d, warpj[j]=%d wmrecords[j] = %f\n", warpi[j], warpj[j], wmrecords[j] );
// }
// fprintf( stderr, "%d-%d (%c-%c) curm = %5.0f, wmrecords[j]=%f\n", i, j, seq1[0][i], seq2[0][j], curm, wmrecords[j] );
wmrecordspt++;
wmrecords1pt++;
warpipt++;
warpjpt++;
}
*curpt++ += wm;
ijppt++;
mjpt++;
prept++;
mpjpt++;
}
#if DEBUG2
fprintf( stderr, "\n" );
#endif
lastverticalw[i] = currentw[lgth2-1];
if( trywarp )
{
fltncpy( prevwmrecords, wmrecords, lastj );
intncpy( prevwarpi, warpi, lastj );
intncpy( prevwarpj, warpj, lastj );
}
}
// fprintf( stderr, "\nwm = %f\n", wm );
if( trywarp )
{
// if( warpn ) fprintf( stderr, "warpn = %d\n", warpn );
free( wmrecords );
free( prevwmrecords );
free( warpi );
free( warpj );
free( prevwarpi );
free( prevwarpj );
}
#if 0
fprintf( stderr, "maxwm = %f\n", maxwm );
fprintf( stderr, "endali = %d\n", endali );
fprintf( stderr, "endalj = %d\n", endalj );
#endif
if( ijp[endali][endalj] == localstop )
{
strcpy( seq1[0], "" );
strcpy( seq2[0], "" );
*off1pt = *off2pt = 0;
fprintf( stderr, "maxwm <- 0.0 \n" );
return( 0.0 );
}
Ltracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, off1pt, off2pt, endali, endalj, warpis, warpjs, warpbase );
if( warpis ) free( warpis );
if( warpjs ) free( warpjs );
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, "wm=%f\n", wm );
fprintf( stderr, ">\n%s\n", mseq1[0] );
fprintf( stderr, ">\n%s\n", mseq2[0] );
fprintf( stderr, "maxwm = %f\n", maxwm );
fprintf( stderr, " wm = %f\n", wm );
#endif
return( maxwm );
}