int main()
{
int i, j;
char **seq;
static char name[M][B];
static int nlen[M];
double **mtx;
FILE *fp;
int res;
scoremtx = NOTSPECIFIED;
#if 0
PreRead( stdin, &njob, &nlenmax );
#else
getnumlen( stdin );
#endif
rewind( stdin );
seq = AllocateCharMtx( njob, nlenmax+1 );
mtx = AllocateDoubleMtx( njob, njob );
#if 0
FRead( stdin, name, nlen, seq );
#else
readData( stdin, name, nlen, seq );
#endif
for( i=0; i<njob-1; i++ )
{
fprintf( stderr, "%4d/%4d\r", i+1, njob );
for( j=i+1; j<njob; j++ )
mtx[i][j] = (double)substitution_score( seq[i], seq[j] );
}
#if TEST
for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
#endif
fp = fopen( "hat2", "w" );
WriteHat2( fp, njob, name, mtx );
fclose( fp );
exit( 0 );
/*
res = system( ALNDIR "/spgsdl < hat2" );
if( res ) exit( 1 );
else exit( 0 );
*/
}
int main( int argc, char *argv[] )
{
static int nlen[M];
static char **name, **seq;
int i, j, alloclen, c;
double **mtx;
double *self;
double tmpdouble;
FILE *fp;
arguments( argc, argv );
getnumlen( stdin );
rewind( stdin );
if( njob < 2 )
{
fprintf( stderr, "At least 2 sequences should be input!\n"
"Only %d sequence found.\n", njob );
exit( 1 );
}
name = AllocateCharMtx( njob, B+1 );
seq = AllocateCharMtx( njob, nlenmax*9+1 );
mtx = AllocateDoubleMtx( njob, njob );
self = AllocateDoubleVec( njob );
alloclen = nlenmax*9;
readData_pointer( stdin, name, nlen, seq );
constants( njob, seq );
c = seqcheck( seq );
if( c )
{
fprintf( stderr, "Illeagal character %c\n", c );
exit( 1 );
}
for( i=0; i<njob; i++ )
{
self[i] = (double)substitution_nid( seq[i], seq[i] );
// fprintf( stdout, "self[%d] = %f\n", i, self[i] );
}
for( i=0; i<njob-1; i++ )
for( j=i+1; j<njob; j++ )
{
tmpdouble = (double)substitution_score( seq[i], seq[j] );
// fprintf( stdout, "tmpdouble = %f\n", tmpdouble );
mtx[i][j] = ( 1.0 - tmpdouble / MIN( self[i], self[j] ) );
if( mtx[i][j] < 0.95 )
mtx[i][j] = - log( 1.0 - mtx[i][j] );
else
mtx[i][j] = 3.0;
}
#if TEST
for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
#endif
fp = fopen( "hat2", "w" );
WriteHat2_pointer( fp, njob, name, mtx );
fclose( fp );
exit( 0 );
return( 0 );
}
int main( int argc, char **argv )
{
int i, j;
FILE *fp, *infp;
char **seq;
int *grpseq;
char *tmpseq;
int **pointt;
static char name[M][B];
static int nlen[M];
double **mtx;
double **mtx2;
double score, score0;
static short *table1;
char b[B];
arguments( argc, argv );
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
#if 0
PreRead( stdin, &njob, &nlenmax );
#else
getnumlen( infp );
#endif
rewind( infp );
if( njob < 2 )
{
fprintf( stderr, "At least 2 sequences should be input!\n"
"Only %d sequence found.\n", njob );
exit( 1 );
}
tmpseq = AllocateCharVec( nlenmax+1 );
seq = AllocateCharMtx( njob, nlenmax+1 );
grpseq = AllocateIntVec( nlenmax+1 );
pointt = AllocateIntMtx( njob, nlenmax+1 );
mtx = AllocateDoubleMtx( njob, njob );
mtx2 = AllocateDoubleMtx( njob, njob );
pamN = NOTSPECIFIED;
#if 0
FRead( infp, name, nlen, seq );
#else
readData( infp, name, nlen, seq );
#endif
fclose( infp );
constants( njob, seq );
if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
else tsize = (int)pow( 6, 6 );
maxl = 0;
for( i=0; i<njob; i++ )
{
gappick0( tmpseq, seq[i] );
nlen[i] = strlen( tmpseq );
if( nlen[i] < 6 )
{
fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
exit( 1 );
}
if( nlen[i] > maxl ) maxl = nlen[i];
if( dorp == 'd' ) /* nuc */
{
seq_grp_nuc( grpseq, tmpseq );
makepointtable_nuc( pointt[i], grpseq );
}
else /* amino */
{
seq_grp( grpseq, tmpseq );
makepointtable( pointt[i], grpseq );
}
}
for( i=0; i<njob; i++ )
{
table1 = (short *)calloc( tsize, sizeof( short ) );
if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
if( i % 10 == 0 )
{
fprintf( stderr, "%4d / %4d\r", i+1, njob );
}
makecompositiontable_p( table1, pointt[i] );
for( j=i; j<njob; j++ )
{
score = (double)commonsextet_p( table1, pointt[j] );
mtx[i][j] = score;
}
free( table1 );
}
for( i=0; i<njob; i++ )
{
score0 = mtx[i][i];
for( j=0; j<njob; j++ )
mtx2[i][j] = ( score0 - mtx[MIN(i,j)][MAX(i,j)] ) / score0 * 3.0;
}
for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
{
#if TEST
double jscore;
jscore = mtx[i][j] / ( MIN( strlen( seq[i] ), strlen( seq[j] ) ) - 2 );
fprintf( stdout, "jscore = %f\n", jscore );
fprintf( stdout, "mtx2[%d][%d] = %f, mtx2[%d][%d] = %f\n", i, j, mtx2[i][j], j, i, mtx2[j][i] );
#endif
mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
#if TEST
fprintf( stdout, "sonokekka mtx2[%d][%d] %f\n", i, j, mtx2[i][j] );
#endif
}
if( disopt )
{
for( i=0; i<njob; i++ )
{
sprintf( b, "=lgth = %04d", nlen[i] );
strins( b, name[i] );
}
}
fp = fopen( "hat2", "w" );
if( !fp ) ErrorExit( "Cannot open hat2." );
WriteHat2( fp, njob, name, mtx2 );
fclose( fp );
fprintf( stderr, "\n" );
SHOWVERSION;
exit( 0 );
}
void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut )
{
int i, j, k, shift, cur1, cur2, count, klim;
static TLS int crossscoresize = 0;
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;
static TLS double maxj, maxi;
static TLS int pointj, pointi;
if( cut1 == NULL)
{
if( result1 )
{
if( result1 ) free( result1 ); result1 = NULL;
if( result2 ) free( result2 ); result2 = NULL;
if( ocut1 ) free( ocut1 ); ocut1 = NULL;
if( ocut2 ) free( ocut2 ); ocut2 = NULL;
if( track ) FreeIntMtx( track ); track = NULL;
if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = NULL;
}
crossscoresize = 0;
return;
}
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 );
track = AllocateIntMtx( crossscoresize, crossscoresize );
crossscore = AllocateDoubleMtx( crossscoresize, 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( i=1; i<*ncut; i++ )
{
#if 0
fprintf( stderr, "### i=%d/%d\n", i,*ncut );
#endif
for( j=1; j<*ncut; j++ )
{
pointi = 0; maxi = 0.0;
klim = j-2;
for( k=0; k<klim; 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;
klim = i-2;
for( k=0; k<klim; 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;
maximum = crossscore[i-1][j-1];
track[i][j] = 0;
if( maximum < maxi )
{
maximum = maxi ;
track[i][j] = j - pointi;
}
if( maximum < maxj )
{
maximum = maxj ;
track[i][j] = pointj - i;
}
crossscore[i][j] += maximum;
}
}
#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
}
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
}
static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, int alloclen )
{
int i, j, ilim;
int clus1, clus2;
int off1, off2;
float pscore = 0.0; // by D.Mathog
static char *indication1, *indication2;
FILE *hat2p, *hat3p;
static double **distancemtx;
static double *effarr1 = NULL;
static double *effarr2 = NULL;
char *pt;
char *hat2file = "hat2";
LocalHom **localhomtable, *tmpptr;
static char **pair;
int intdum;
double bunbo;
localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
for( i=0; i<njob; i++)
{
localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
for( j=0; j<njob; j++)
{
localhomtable[i][j].start1 = -1;
localhomtable[i][j].end1 = -1;
localhomtable[i][j].start2 = -1;
localhomtable[i][j].end2 = -1;
localhomtable[i][j].opt = -1.0;
localhomtable[i][j].next = NULL;
localhomtable[i][j].nokori = 0;
}
}
if( effarr1 == NULL )
{
distancemtx = AllocateDoubleMtx( njob, njob );
effarr1 = AllocateDoubleVec( njob );
effarr2 = AllocateDoubleVec( njob );
indication1 = AllocateCharVec( 150 );
indication2 = AllocateCharVec( 150 );
#if 0
#else
pair = AllocateCharMtx( njob, njob );
#endif
}
#if 0
fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
#endif
#if 0
for( i=0; i<njob; i++ )
fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
#endif
// writePre( njob, name, nlen, aseq, 0 );
for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
for( i=0; i<njob; i++ ) pair[i][i] = 1;
if( alg == 'H' )
{
fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
callfoldalign( njob, seq );
fprintf( stderr, "done.\n" );
}
if( alg == 'B' )
{
fprintf( stderr, "Calling LARA\n" );
calllara( njob, seq, "" );
fprintf( stderr, "done.\n" );
}
if( alg == 'T' )
{
fprintf( stderr, "Calling SLARA\n" );
calllara( njob, seq, "-s" );
fprintf( stderr, "done.\n" );
}
ilim = njob - 1;
for( i=0; i<ilim; i++ )
{
fprintf( stderr, "% 5d / %d\r", i, njob );
for( j=i+1; j<njob; j++ )
{
if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
{
distancemtx[i][j] = pscore;
continue;
}
strcpy( aseq[i], seq[i] );
strcpy( aseq[j], seq[j] );
clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
// fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
// fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
#if 0
fprintf( stderr, "group1 = %.66s", indication1 );
fprintf( stderr, "\n" );
fprintf( stderr, "group2 = %.66s", indication2 );
fprintf( stderr, "\n" );
#endif
// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
#if 1
if( use_fft )
{
pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
off1 = off2 = 0;
}
else
#endif
{
switch( alg )
{
case( 'a' ):
pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
off1 = off2 = 0;
break;
case( 'A' ):
pscore = G__align11( mseq1, mseq2, alloclen, NULL, 0, NULL );
off1 = off2 = 0;
break;
#if 0
case( 'V' ):
pscore = VAalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
break;
case( 'S' ):
fprintf( stderr, "aligning %d-%d\n", i, j );
pscore = suboptalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
break;
#endif
case( 'N' ):
pscore = genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
// fprintf( stderr, "pscore = %f\n", pscore );
break;
case( 'L' ):
pscore = L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
// fprintf( stderr, "pscore (1) = %f\n", pscore );
// pscore = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
// fprintf( stderr, "pscore (2) = %f\n\n", pscore );
break;
case( 'H' ):
pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
break;
case( 'B' ):
case( 'T' ):
pscore = recalllara( mseq1, mseq2, alloclen );
off1 = off2 = 0;
// fprintf( stderr, "lara, pscore = %f\n", pscore );
break;
case( 's' ):
pscore = callmxscarna( mseq1, mseq2, alloclen );
off1 = off2 = 0;
// fprintf( stderr, "scarna, pscore = %f\n", pscore );
break;
case( 'M' ):
// pscore = MSalign11( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
pscore = MSalign11( mseq1, mseq2, alloclen );
// fprintf( stderr, "pscore = %f\n", pscore );
break;
ErrorExit( "ERROR IN SOURCE FILE" );
}
}
distancemtx[i][j] = pscore;
#if SCOREOUT
fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
#endif
// fprintf( stderr, "pslocal = %d\n", pslocal );
// offset = makelocal( *mseq1, *mseq2, pslocal );
#if 0
fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
fprintf( stderr, ">%d\n%s\n>%d\n%s\n>\n", i, mseq1[0], j, mseq2[0] );
#endif
// putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, countamino( *mseq1, off1 ), countamino( *mseq2, off2 ), pscore, strlen( mseq1[0] ) );
// fprintf( stderr, "pscore = %f\n", pscore );
if( alg == 'H' )
// if( alg == 'H' || alg == 's' || alg == 'B' ) // next version
putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
else if( alg != 'S' && alg != 'V' )
putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
}
}
for( i=0; i<njob; i++ )
{
pscore = 0.0;
for( pt=seq[i]; *pt; pt++ )
pscore += amino_dis[(int)*pt][(int)*pt];
distancemtx[i][i] = pscore;
}
ilim = njob-1;
for( i=0; i<ilim; i++ )
{
for( j=i+1; j<njob; j++ )
{
bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
if( bunbo == 0.0 )
distancemtx[i][j] = 2.0;
else
distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
}
}
hat2p = fopen( hat2file, "w" );
if( !hat2p ) ErrorExit( "Cannot open hat2." );
WriteHat2( hat2p, njob, name, distancemtx );
fclose( hat2p );
fprintf( stderr, "##### writing hat3\n" );
hat3p = fopen( "hat3", "w" );
if( !hat3p ) ErrorExit( "Cannot open hat3." );
ilim = njob-1;
for( i=0; i<ilim; i++ )
{
for( j=i+1; j<njob; j++ )
{
for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
{
if( tmpptr->opt == -1.0 ) continue;
fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
}
}
}
fclose( hat3p );
#if DEBUG
fprintf( stderr, "calling FreeLocalHomTable\n" );
#endif
FreeLocalHomTable( localhomtable, njob );
#if DEBUG
fprintf( stderr, "done. FreeLocalHomTable\n" );
#endif
}
int main( int argc, char **argv )
{
int i, j;
char **seq;
static char **name;
static int nlen[M];
float *selfscore;
double **mtx;
FILE *fp;
FILE *infp;
float ssi, ssj, bunbo;
arguments( argc, argv );
#ifndef enablemultithread
nthread = 0;
#endif
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
#if 0
PreRead( stdin, &njob, &nlenmax );
#else
getnumlen( infp );
#endif
rewind( infp );
seq = AllocateCharMtx( njob, nlenmax+1 );
name = AllocateCharMtx( njob, B+1 );
mtx = AllocateDoubleMtx( njob, njob );
selfscore = AllocateFloatVec( njob );
#if 0
FRead( stdin, name, nlen, seq );
#else
readData_pointer( infp, name, nlen, seq );
#endif
fclose( infp );
constants( njob, seq );
#if 0
for( i=0; i<njob-1; i++ )
{
fprintf( stderr, "%4d/%4d\r", i+1, njob );
for( j=i+1; j<njob; j++ )
mtx[i][j] = (double)substitution_hosei( seq[i], seq[j] );
// fprintf( stderr, "i=%d,j=%d, l=%d &&& %f\n", i, j, nlen[0], mtx[i][j] );
}
#else // 061003
for( i=0; i<njob; i++ )
{
selfscore[i] = (float)naivepairscore11( seq[i], seq[i], penalty );
}
#ifdef enablemultithread
if( nthread > 0 )
{
thread_arg_t *targ;
Jobtable jobpos;
pthread_t *handle;
pthread_mutex_t mutex;
jobpos.i = 0;
jobpos.j = 0;
targ = calloc( nthread, sizeof( thread_arg_t ) );
handle = calloc( nthread, sizeof( pthread_t ) );
pthread_mutex_init( &mutex, NULL );
for( i=0; i<nthread; i++ )
{
targ[i].thread_no = i;
targ[i].njob = njob;
targ[i].selfscore = selfscore;
targ[i].mtx = mtx;
targ[i].seq = seq;
targ[i].jobpospt = &jobpos;
targ[i].mutex = &mutex;
pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
}
for( i=0; i<nthread; i++ )
{
pthread_join( handle[i], NULL );
}
pthread_mutex_destroy( &mutex );
}
else
#endif
{
for( i=0; i<njob-1; i++ )
{
ssi = selfscore[i];
fprintf( stderr, "%4d/%4d\r", i+1, njob );
for( j=i+1; j<njob; j++ )
{
ssj = selfscore[j];
bunbo = MIN( ssi, ssj );
if( bunbo == 0.0 )
mtx[i][j] = 1.0;
else
mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / bunbo;
// mtx[i][j] = 1.0 - (double)naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
// fprintf( stderr, "i=%d,j=%d, l=%d### %f, score = %d\n", i, j, nlen[0], mtx[i][j], naivepairscore11( seq[i], seq[j], penalty ) );
}
}
}
#endif
#if TEST
for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
fprintf( stdout, "i=%d, j=%d, mtx[][] = %f\n", i, j, mtx[i][j] );
#endif
fp = fopen( "hat2", "w" );
WriteHat2_pointer( fp, njob, name, mtx );
fclose( fp );
#if 0
if( treeout )
{
int ***topol;
double **len;
topol = AllocateIntCub( njob, 2, njob );
len = AllocateDoubleMtx( njob, njob );
veryfastsupg_double_outtree( njob, mtx, topol, len );
}
#endif
SHOWVERSION;
exit( 0 );
/*
res = system( ALNDIR "/spgsdl < hat2" );
if( res ) exit( 1 );
else exit( 0 );
*/
}
int main( int argc, char *argv[] )
{
char **argv2;
static int *nlen;
static char **name, **seq;
static char **seq1, **seq2;
static char **mseq1, **mseq2;
static char **aseq;
static char **bseq;
static double **pscore;
static double *eff;
int i, j, len1, len2;
static int ***topol;
static double **len;
FILE *gp1, *gp2;
char c;
int nlenmax1, nlenmax2, nseq1, nseq2;
int alloclen;
argv2 = arguments( argc, argv );
fprintf( stderr, "####### in galn\n" );
initFiles();
fprintf( stderr, "file1 = %s\n", argv2[0] );
fprintf( stderr, "file2 = %s\n", argv2[1] );
gp1 = fopen( argv2[0], "r" ); if( !gp1 ) ErrorExit( "cannot open file1" );
gp2 = fopen( argv2[1], "r" ); if( !gp2 ) ErrorExit( "cannot open file2" );
#if 0
PreRead( gp1, &nseq1, &nlenmax1 );
PreRead( gp2, &nseq2, &nlenmax2 );
#else
getnumlen( gp1 );
nseq1 = njob; nlenmax1 = nlenmax;
getnumlen( gp2 );
nseq2 = njob; nlenmax2 = nlenmax;
#endif
njob = nseq1 + nseq2;
nlenmax = MAX( nlenmax1, nlenmax2 );
rewind( gp1 );
rewind( gp2 );
name = AllocateCharMtx( njob, B );
nlen = AllocateIntVec( njob );
seq1 = AllocateCharMtx( nseq1, nlenmax*3 );
seq2 = AllocateCharMtx( nseq2, nlenmax*3 );
seq = AllocateCharMtx( njob, 1 );
aseq = AllocateCharMtx( njob, nlenmax*3 );
bseq = AllocateCharMtx( njob, nlenmax*3 );
mseq1 = AllocateCharMtx( njob, 1 );
mseq2 = AllocateCharMtx( njob, 1 );
alloclen = nlenmax * 3;
topol = AllocateIntCub( njob, 2, njob );
len = AllocateDoubleMtx( njob, 2 );
pscore = AllocateDoubleMtx( njob, njob );
eff = AllocateDoubleVec( njob );
#if 0
njob=nseq2; FRead( gp2, name+nseq1, nlen+nseq1, seq2 );
njob=nseq1; FRead( gp1, name, nlen, seq1 );
#else
njob=nseq2; readDataforgaln( gp2, name+nseq1, nlen+nseq1, seq2 );
njob=nseq1; readDataforgaln( gp1, name, nlen, seq1 );
#endif
njob = nseq1 + nseq2;
#if 0 // CHUUI
commongappick( nseq1, seq1 );
commongappick( nseq2, seq2 );
#endif
for( i=0; i<nseq1; i++ ) seq[i] = seq1[i];
for( i=nseq1; i<njob; i++ ) seq[i] = seq2[i-nseq1];
/*
Write( stdout, njob, name, nlen, seq );
*/
constants( njob, seq );
WriteOptions( trap_g );
c = seqcheck( seq );
if( c )
{
fprintf( stderr, "Illeagal character %c\n", c );
exit( 1 );
}
for( i=1; i<nseq1; i++ )
{
if( nlen[i] != nlen[0] )
ErrorExit( "group1 is not aligned." );
}
for( i=nseq1+1; i<njob; i++ )
{
if( nlen[i] != nlen[nseq1] )
ErrorExit( "group2 is not aligned." );
}
if( tbutree == 0 )
{
for( i=0; i<nseq1; i++ )
{
for( j=i+1; j<nseq1; j++ )
{
pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
}
for( j=nseq1; j<njob; j++ )
{
pscore[i][j] = 3.0;
// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
}
}
for( i=nseq1; i<njob-1; i++ )
{
for( j=i+1; j<njob; j++ )
{
pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
// fprintf( stderr, "%d-%d, %5.1f \n", i, j, pscore[i][j] );
}
}
// fprintf( stderr, "\n" );
}
else
{
fprintf( stderr, "Not supported\n" );
exit( 1 );
#if 0
prep = fopen( "hat2", "r" );
if( prep == NULL ) ErrorExit( "Make hat2." );
readhat2( prep, njob, name, pscore );
fclose( prep );
#endif
}
fprintf( stderr, "Constructing dendrogram ... " );
if( treemethod == 'x' )
veryfastsupg( njob, pscore, topol, len );
else
ErrorExit( "Incorrect tree\n" );
fprintf( stderr, "done.\n" );
if( tbrweight )
{
weight = 3;
counteff_simple( njob, topol, len, eff );
// for( i=0; i<njob; i++ ) fprintf( stderr, "eff[%d] = %f\n", i, eff[i] );
}
else
{
for( i=0; i<njob; i++ ) eff[i] = 1.0;
}
len1 = strlen( seq[0] );
len2 = strlen( seq[nseq1] );
if( len1 > 30000 || len2 > 30000 )
{
fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
alg = 'M';
}
GroupAlign( nseq1, nseq2, name, nlen, seq, aseq, mseq1, mseq2, topol, len, eff, alloclen );
#if 0
writePre( njob, name, nlen, aseq, 1 );
#else
writeDataforgaln( stdout, njob, name, nlen, aseq );
#endif
SHOWVERSION;
return( 0 );
}
void constants( int nseq, char **seq )
{
int i, j, x;
// double tmp;
if( dorp == 'd' ) /* DNA */
{
int k, m;
double average;
double **pamx = AllocateDoubleMtx( 11,11 );
double **pam1 = AllocateDoubleMtx( 4, 4 );
double *freq = AllocateDoubleVec( 4 );
scoremtx = -1;
if( RNAppenalty == NOTSPECIFIED ) RNAppenalty = DEFAULTRNAGOP_N;
if( RNAppenalty_ex == NOTSPECIFIED ) RNAppenalty_ex = DEFAULTRNAGEP_N;
if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_N;
if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_N;
if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_N;
if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_N;
if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_N;
if( RNApthr == NOTSPECIFIED ) RNApthr = DEFAULTRNATHR_N;
if( pamN == NOTSPECIFIED ) pamN = DEFAULTPAMN;
if( kimuraR == NOTSPECIFIED ) kimuraR = 2;
RNApenalty = (int)( 3 * 600.0 / 1000.0 * RNAppenalty + 0.5 );
RNApenalty_ex = (int)( 3 * 600.0 / 1000.0 * RNAppenalty_ex + 0.5 );
// fprintf( stderr, "DEFAULTRNAGOP_N = %d\n", DEFAULTRNAGOP_N );
// fprintf( stderr, "RNAppenalty = %d\n", RNAppenalty );
// fprintf( stderr, "RNApenalty = %d\n", RNApenalty );
RNAthr = (int)( 3 * 600.0 / 1000.0 * RNApthr + 0.5 );
penalty = (int)( 3 * 600.0 / 1000.0 * ppenalty + 0.5);
penalty_OP = (int)( 3 * 600.0 / 1000.0 * ppenalty_OP + 0.5);
penalty_ex = (int)( 3 * 600.0 / 1000.0 * ppenalty_ex + 0.5);
penalty_EX = (int)( 3 * 600.0 / 1000.0 * ppenalty_EX + 0.5);
offset = (int)( 3 * 600.0 / 1000.0 * poffset + 0.5);
offsetFFT = (int)( 3 * 600.0 / 1000.0 * (-0) + 0.5);
offsetLN = (int)( 3 * 600.0 / 1000.0 * 100 + 0.5);
penaltyLN = (int)( 3 * 600.0 / 1000.0 * -2000 + 0.5);
penalty_exLN = (int)( 3 * 600.0 / 1000.0 * -100 + 0.5);
sprintf( modelname, "%s%d (%d), %6.3f (%6.3f), %6.3f (%6.3f)", rnakozo?"RNA":"DNA", pamN, kimuraR,
-(double)ppenalty*0.001, -(double)ppenalty*0.003, -(double)poffset*0.001, -(double)poffset*0.003 );
if( kimuraR == 9999 )
{
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] = (double)locn_disn[i][j];
#if NORMALIZE1
average = 0.0;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
average += pamx[i][j];
average /= 16.0;
if( disp )
fprintf( stderr, "average = %f\n", average );
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] -= average;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] *= 600.0 / average;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] -= offset;
#endif
}
else
{
double f = 0.99;
double s = (double)kimuraR / ( 2 + kimuraR ) * 0.01;
double v = (double)1 / ( 2 + kimuraR ) * 0.01;
pam1[0][0] = f; pam1[0][1] = s; pam1[0][2] = v; pam1[0][3] = v;
pam1[1][0] = s; pam1[1][1] = f; pam1[1][2] = v; pam1[1][3] = v;
pam1[2][0] = v; pam1[2][1] = v; pam1[2][2] = f; pam1[2][3] = s;
pam1[3][0] = v; pam1[3][1] = v; pam1[3][2] = s; pam1[3][3] = f;
fprintf( stderr, "generating %dPAM scoring matrix for nucleotides ... ", pamN );
if( disp )
{
fprintf( stderr, " TPM \n" );
for( i=0; i<4; i++ )
{
for( j=0; j<4; j++ )
fprintf( stderr, "%+#6.10f", pam1[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
MtxuntDouble( pamx, 4 );
for( x=0; x < pamN; x++ ) MtxmltDouble( pamx, pam1, 4 );
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] /= 1.0 / 4.0;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
{
if( pamx[i][j] == 0.0 )
{
fprintf( stderr, "WARNING: pamx[i][j] = 0.0 ?\n" );
pamx[i][j] = 0.00001; /* by J. Thompson */
}
pamx[i][j] = log10( pamx[i][j] ) * 1000.0;
}
if( disp )
{
fprintf( stderr, " after log\n" );
for( i=0; i<4; i++ )
{
for( j=0; j<4; j++ )
fprintf( stderr, "%+#6.10f", pamx[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
// ?????
for( i=0; i<26; i++ ) amino[i] = locaminon[i];
for( i=0; i<0x80; i++ ) amino_n[i] = -1;
for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
if( fmodel == 1 )
calcfreq_nuc( nseq, seq, freq );
else
{
freq[0] = 0.25;
freq[1] = 0.25;
freq[2] = 0.25;
freq[3] = 0.25;
}
// fprintf( stderr, "a, freq[0] = %f\n", freq[0] );
// fprintf( stderr, "g, freq[1] = %f\n", freq[1] );
// fprintf( stderr, "c, freq[2] = %f\n", freq[2] );
// fprintf( stderr, "t, freq[3] = %f\n", freq[3] );
average = 0.0;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
average += pamx[i][j] * freq[i] * freq[j];
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] -= average;
average = 0.0;
for( i=0; i<4; i++ )
average += pamx[i][i] * 1.0 / 4.0;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] *= 600.0 / average;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] -= offset; /* extending gap cost */
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
pamx[i][j] = shishagonyuu( pamx[i][j] );
if( disp )
{
fprintf( stderr, " after shishagonyuu\n" );
for( i=0; i<4; i++ )
{
for( j=0; j<4; j++ )
fprintf( stderr, "%+#6.10f", pamx[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
fprintf( stderr, "done\n" );
}
for( i=0; i<5; i++ )
{
pamx[4][i] = pamx[3][i];
pamx[i][4] = pamx[i][3];
}
for( i=5; i<10; i++ ) for( j=5; j<10; j++ )
{
pamx[i][j] = pamx[i-5][j-5];
}
if( disp )
{
fprintf( stderr, " before dis\n" );
for( i=0; i<4; i++ )
{
for( j=0; j<4; j++ )
fprintf( stderr, "%+#6.10f", pamx[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
if( disp )
{
fprintf( stderr, " score matrix \n" );
for( i=0; i<4; i++ )
{
for( j=0; j<4; j++ )
fprintf( stderr, "%+#6.10f", pamx[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
for( i=0; i<26; i++ ) amino[i] = locaminon[i];
for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpn[i];
for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
for( i=0; i<10; i++ ) for( j=0; j<10; j++ ) n_dis[i][j] = shishagonyuu( pamx[i][j] );
if( disp )
{
fprintf( stderr, " score matrix \n" );
for( i=0; i<26; i++ )
{
for( j=0; j<26; j++ )
fprintf( stderr, "%+6d", n_dis[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
// RIBOSUM
#if 1
average = 0.0;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
average += ribosum4[i][j] * freq[i] * freq[j];
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
ribosum4[i][j] -= average;
average = 0.0;
for( i=0; i<4; i++ ) for( j=0; j<4; j++ ) for( k=0; k<4; k++ ) for( m=0; m<4; m++ )
{
// if( i%4==0&&j%4==3 || i%4==3&&j%4==0 || i%4==1&&j%4==2 || i%4==2&&j%4==1 || i%4==1&&j%4==3 || i%4==3&&j%4==1 )
// if( k%4==0&&m%4==3 || k%4==3&&m%4==0 || k%4==1&&m%4==2 || k%4==2&&m%4==1 || k%4==1&&m%4==3 || k%4==3&&m%4==1 )
average += ribosum16[i*4+j][k*4+m] * freq[i] * freq[j] * freq[k] * freq[m];
}
for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
ribosum16[i][j] -= average;
average = 0.0;
for( i=0; i<4; i++ )
average += ribosum4[i][i] * freq[i];
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
ribosum4[i][j] *= 600.0 / average;
average = 0.0;
average += ribosum16[0*4+3][0*4+3] * freq[0] * freq[3]; // AU
average += ribosum16[3*4+0][3*4+0] * freq[3] * freq[0]; // UA
average += ribosum16[1*4+2][1*4+2] * freq[1] * freq[2]; // CG
average += ribosum16[2*4+1][2*4+1] * freq[2] * freq[1]; // GC
average += ribosum16[1*4+3][1*4+3] * freq[1] * freq[3]; // GU
average += ribosum16[3*4+1][3*4+1] * freq[3] * freq[1]; // UG
for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
ribosum16[i][j] *= 600.0 / average;
#if 1
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
ribosum4[i][j] -= offset; /* extending gap cost ?????*/
for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
ribosum16[i][j] -= offset; /* extending gap cost ?????*/
#endif
for( i=0; i<4; i++ ) for( j=0; j<4; j++ )
ribosum4[i][j] = shishagonyuu( ribosum4[i][j] );
for( i=0; i<16; i++ ) for( j=0; j<16; j++ )
ribosum16[i][j] = shishagonyuu( ribosum16[i][j] );
if( disp )
{
fprintf( stderr, "ribosum after shishagonyuu\n" );
for( i=0; i<4; i++ )
{
for( j=0; j<4; j++ )
fprintf( stderr, "%+#6.10f", ribosum4[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
fprintf( stderr, "ribosum16 after shishagonyuu\n" );
for( i=0; i<16; i++ )
{
for( j=0; j<16; j++ )
fprintf( stderr, "%+#7.0f", ribosum16[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
fprintf( stderr, "done\n" );
#if 1
for( i=0; i<37; i++ ) for( j=0; j<37; j++ ) ribosumdis[i][j] = 0.0; //iru
for( m=0; m<9; m++ ) for( i=0; i<4; i++ ) // loop
for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = ribosum4[i][j]; // loop-loop
// for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = n_dis[i][j]; // loop-loop
for( i=0; i<16; i++ ) for( j=0; j<16; j++ ) ribosumdis[i+4][j+4] = ribosum16[i][j]; // stem5-stem5
for( i=0; i<16; i++ ) for( j=0; j<16; j++ ) ribosumdis[i+20][j+20] = ribosum16[i][j]; // stem5-stem5
#else // do not use ribosum
for( i=0; i<37; i++ ) for( j=0; j<37; j++ ) ribosumdis[i][j] = 0.0; //iru
for( m=0; m<9; m++ ) for( i=0; i<4; i++ ) // loop
for( k=0; k<9; k++ ) for( j=0; j<4; j++ ) ribosumdis[m*4+i][k*4+j] = n_dis[i][j]; // loop-loop
#endif
if( disp )
{
fprintf( stderr, "ribosumdis\n" );
for( i=0; i<37; i++ )
{
for( j=0; j<37; j++ )
fprintf( stderr, "%+5d", ribosumdis[i][j] );
fprintf( stderr, "\n" );
}
fprintf( stderr, "\n" );
}
fprintf( stderr, "done\n" );
#endif
FreeDoubleMtx( pam1 );
FreeDoubleMtx( pamx );
free( freq );
}
else if( dorp == 'p' && scoremtx == 1 ) /* Blosum */
{
double *freq;
double *freq1;
double *datafreq;
double average;
// double tmp;
double **n_distmp;
n_distmp = AllocateDoubleMtx( 20, 20 );
datafreq = AllocateDoubleVec( 20 );
freq = AllocateDoubleVec( 20 );
if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_B;
if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_B;
if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_B;
if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_B;
if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_B;
if( pamN == NOTSPECIFIED ) pamN = 0;
if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
penalty = (int)( 600.0 / 1000.0 * ppenalty + 0.5 );
penalty_OP = (int)( 600.0 / 1000.0 * ppenalty_OP + 0.5 );
penalty_ex = (int)( 600.0 / 1000.0 * ppenalty_ex + 0.5 );
penalty_EX = (int)( 600.0 / 1000.0 * ppenalty_EX + 0.5 );
offset = (int)( 600.0 / 1000.0 * poffset + 0.5 );
offsetFFT = (int)( 600.0 / 1000.0 * (-0) + 0.5);
offsetLN = (int)( 600.0 / 1000.0 * 100 + 0.5);
penaltyLN = (int)( 600.0 / 1000.0 * -2000 + 0.5);
penalty_exLN = (int)( 600.0 / 1000.0 * -100 + 0.5);
BLOSUMmtx( nblosum, n_distmp, freq, amino, amino_grp );
if( nblosum == -1 )
sprintf( modelname, "User-defined, %6.3f, %+6.3f, %+6.3f", -(double)ppenalty/1000, -(double)poffset/1000, -(double)ppenalty_ex/1000 );
else
sprintf( modelname, "BLOSUM%d, %6.3f, %+6.3f, %+6.3f", nblosum, -(double)ppenalty/1000, -(double)poffset/1000, -(double)ppenalty_ex/1000 );
#if 0
for( i=0; i<26; i++ ) amino[i] = locaminod[i];
for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpd[i];
for( i=0; i<0x80; i++ ) amino_n[i] = 0;
for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
#endif
for( i=0; i<0x80; i++ )amino_n[i] = -1;
for( i=0; i<26; i++) amino_n[(int)amino[i]] = i;
if( fmodel == 1 )
{
calcfreq( nseq, seq, datafreq );
freq1 = datafreq;
}
else
freq1 = freq;
#if TEST
fprintf( stderr, "raw scoreing matrix : \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stdout, "%6.2f", n_distmp[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
if( fmodel == -1 )
average = 0.0;
else
{
for( i=0; i<20; i++ )
#if TEST
fprintf( stdout, "freq[%c] = %f, datafreq[%c] = %f, freq1[] = %f\n", amino[i], freq[i], amino[i], datafreq[i], freq1[i] );
#endif
average = 0.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
average += n_distmp[i][j] * freq1[i] * freq1[j];
}
#if TEST
fprintf( stdout, "####### average2 = %f\n", average );
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
n_distmp[i][j] -= average;
#if TEST
fprintf( stdout, "average2 = %f\n", average );
fprintf( stdout, "after average substruction : \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stdout, "%6.2f", n_distmp[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
average = 0.0;
for( i=0; i<20; i++ )
average += n_distmp[i][i] * freq1[i];
#if TEST
fprintf( stdout, "####### average1 = %f\n", average );
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
n_distmp[i][j] *= 600.0 / average;
#if TEST
fprintf( stdout, "after average division : \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<=i; j++ )
{
fprintf( stdout, "%7.1f", n_distmp[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
n_distmp[i][j] -= offset;
#if TEST
fprintf( stdout, "after offset substruction (offset = %d): \n", offset );
for( i=0; i<20; i++ )
{
for( j=0; j<=i; j++ )
{
fprintf( stdout, "%7.1f", n_distmp[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
#if 0
/* 注意 ！！！！！！！！！！ */
penalty -= offset;
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
n_distmp[i][j] = shishagonyuu( n_distmp[i][j] );
if( disp )
{
fprintf( stdout, " scoring matrix \n" );
for( i=0; i<20; i++ )
{
fprintf( stdout, "%c ", amino[i] );
for( j=0; j<20; j++ )
fprintf( stdout, "%5.0f", n_distmp[i][j] );
fprintf( stdout, "\n" );
}
fprintf( stdout, " " );
for( i=0; i<20; i++ )
fprintf( stdout, " %c", amino[i] );
average = 0.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
average += n_distmp[i][j] * freq1[i] * freq1[j];
fprintf( stdout, "average = %f\n", average );
average = 0.0;
for( i=0; i<20; i++ )
average += n_distmp[i][i] * freq1[i];
fprintf( stdout, "itch average = %f\n", average );
fprintf( stderr, "parameters: %d, %d, %d\n", penalty, penalty_ex, offset );
exit( 1 );
}
for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) n_dis[i][j] = (int)n_distmp[i][j];
FreeDoubleMtx( n_distmp );
FreeDoubleVec( datafreq );
FreeDoubleVec( freq );
fprintf( stderr, "done.\n" );
}
else if( dorp == 'p' && scoremtx == 2 ) /* Miyata-Yasunaga */
{
fprintf( stderr, "Not supported\n" );
exit( 1 );
for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = locn_dism[i][j];
for( i=0; i<26; i++ ) if( i != 24 ) n_dis[i][24] = n_dis[24][i] = exgpm;
n_dis[24][24] = 0;
if( ppenalty == NOTSPECIFIED ) ppenalty = locpenaltym;
if( poffset == NOTSPECIFIED ) poffset = -20;
if( pamN == NOTSPECIFIED ) pamN = 0;
if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
penalty = ppenalty;
offset = poffset;
sprintf( modelname, "Miyata-Yasunaga, %6.3f, %6.3f", -(double)ppenalty/1000, -(double)poffset/1000 );
for( i=0; i<26; i++ ) amino[i] = locaminom[i];
for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpm[i];
#if DEBUG
fprintf( stdout, "scoreing matrix : \n" );
for( i=0; i<26; i++ )
{
for( j=0; j<26; j++ )
{
fprintf( stdout, "%#5d", n_dis[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
}
else /* JTT */
{
double **rsr;
double **pam1;
double **pamx;
double *freq;
double *freq1;
double *mutab;
double *datafreq;
double average;
double tmp;
double delta;
rsr = AllocateDoubleMtx( 20, 20 );
pam1 = AllocateDoubleMtx( 20, 20 );
pamx = AllocateDoubleMtx( 20, 20 );
freq = AllocateDoubleVec( 20 );
mutab = AllocateDoubleVec( 20 );
datafreq = AllocateDoubleVec( 20 );
if( ppenalty == NOTSPECIFIED ) ppenalty = DEFAULTGOP_J;
if( ppenalty_OP == NOTSPECIFIED ) ppenalty_OP = DEFAULTGOP_J;
if( ppenalty_ex == NOTSPECIFIED ) ppenalty_ex = DEFAULTGEP_J;
if( ppenalty_EX == NOTSPECIFIED ) ppenalty_EX = DEFAULTGEP_J;
if( poffset == NOTSPECIFIED ) poffset = DEFAULTOFS_J;
if( pamN == NOTSPECIFIED ) pamN = DEFAULTPAMN;
if( kimuraR == NOTSPECIFIED ) kimuraR = 1;
penalty = (int)( 600.0 / 1000.0 * ppenalty + 0.5 );
penalty_OP = (int)( 600.0 / 1000.0 * ppenalty_OP + 0.5 );
penalty_ex = (int)( 600.0 / 1000.0 * ppenalty_ex + 0.5 );
penalty_EX = (int)( 600.0 / 1000.0 * ppenalty_EX + 0.5 );
offset = (int)( 600.0 / 1000.0 * poffset + 0.5 );
offsetFFT = (int)( 600.0 / 1000.0 * (-0) + 0.5 );
offsetLN = (int)( 600.0 / 1000.0 * 100 + 0.5);
penaltyLN = (int)( 600.0 / 1000.0 * -2000 + 0.5);
penalty_exLN = (int)( 600.0 / 1000.0 * -100 + 0.5);
sprintf( modelname, "%s %dPAM, %6.3f, %6.3f", (TMorJTT==TM)?"Transmembrane":"JTT", pamN, -(double)ppenalty/1000, -(double)poffset/1000 );
JTTmtx( rsr, freq, amino, amino_grp, (int)(TMorJTT==TM) );
#if TEST
fprintf( stdout, "rsr = \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stdout, "%9.2f ", rsr[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
for( i=0; i<0x80; i++ ) amino_n[i] = -1;
for( i=0; i<26; i++ ) amino_n[(int)amino[i]] = i;
if( fmodel == 1 )
{
calcfreq( nseq, seq, datafreq );
freq1 = datafreq;
}
else
freq1 = freq;
fprintf( stderr, "generating %dPAM %s scoring matrix for amino acids ... ", pamN, (TMorJTT==TM)?"Transmembrane":"JTT" );
tmp = 0.0;
for( i=0; i<20; i++ )
{
mutab[i] = 0.0;
for( j=0; j<20; j++ )
mutab[i] += rsr[i][j] * freq[j];
tmp += mutab[i] * freq[i];
}
#if TEST
fprintf( stdout, "mutability = \n" );
for( i=0; i<20; i++ )
fprintf( stdout, "%5.3f\n", mutab[i] );
fprintf( stdout, "tmp = %f\n", tmp );
#endif
delta = 0.01 / tmp;
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
if( i != j )
pam1[i][j] = delta * rsr[i][j] * freq[i];
else
pam1[i][j] = 1.0 - delta * mutab[i];
}
}
if( disp )
{
fprintf( stdout, "pam1 = \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stdout, "%9.6f ", pam1[i][j] );
}
fprintf( stdout, "\n" );
}
}
MtxuntDouble( pamx, 20 );
for( x=0; x < pamN; x++ ) MtxmltDouble( pamx, pam1, 20 );
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
pamx[i][j] /= freq[j];
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
{
if( pamx[i][j] == 0.0 )
{
fprintf( stderr, "WARNING: pamx[%d][%d] = 0.0?\n", i, j );
pamx[i][j] = 0.00001; /* by J. Thompson */
}
pamx[i][j] = log10( pamx[i][j] ) * 1000.0;
}
#if TEST
fprintf( stdout, "raw scoring matrix : \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stdout, "%5.0f", pamx[i][j] );
}
fprintf( stdout, "\n" );
}
average = tmp = 0.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
{
average += pamx[i][j] * freq1[i] * freq1[j];
tmp += freq1[i] * freq1[j];
}
average /= tmp;
fprintf( stdout, "Zenbu average = %f, tmp = %f \n", average, tmp );
average = tmp = 0.0;
for( i=0; i<20; i++ ) for( j=i; j<20; j++ )
{
average += pamx[i][j] * freq1[i] * freq1[j];
tmp += freq1[i] * freq1[j];
}
average /= tmp;
fprintf( stdout, "Zenbu average2 = %f, tmp = %f \n", average, tmp );
average = tmp = 0.0;
for( i=0; i<20; i++ )
{
average += pamx[i][i] * freq1[i];
tmp += freq1[i];
}
average /= tmp;
fprintf( stdout, "Itch average = %f, tmp = %f \n", average, tmp );
#endif
#if NORMALIZE1
if( fmodel == -1 )
average = 0.0;
else
{
#if TEST
for( i=0; i<20; i++ )
fprintf( stdout, "freq[%c] = %f, datafreq[%c] = %f, freq1[] = %f\n", amino[i], freq[i], amino[i], datafreq[i], freq1[i] );
#endif
average = 0.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
average += pamx[i][j] * freq1[i] * freq1[j];
}
#if TEST
fprintf( stdout, "####### average2 = %f\n", average );
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
pamx[i][j] -= average;
#if TEST
fprintf( stdout, "average2 = %f\n", average );
fprintf( stdout, "after average substruction : \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stdout, "%5.0f", pamx[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
average = 0.0;
for( i=0; i<20; i++ )
average += pamx[i][i] * freq1[i];
#if TEST
fprintf( stdout, "####### average1 = %f\n", average );
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
pamx[i][j] *= 600.0 / average;
#if TEST
fprintf( stdout, "after average division : \n" );
for( i=0; i<20; i++ )
{
for( j=0; j<=i; j++ )
{
fprintf( stdout, "%5.0f", pamx[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
pamx[i][j] -= offset;
#if TEST
fprintf( stdout, "after offset substruction (offset = %d): \n", offset );
for( i=0; i<20; i++ )
{
for( j=0; j<=i; j++ )
{
fprintf( stdout, "%5.0f", pamx[i][j] );
}
fprintf( stdout, "\n" );
}
#endif
#if 0
/* 注意 ！！！！！！！！！！ */
penalty -= offset;
#endif
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
pamx[i][j] = shishagonyuu( pamx[i][j] );
#else
average = 0.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
average += pamx[i][j];
average /= 400.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
{
pamx[i][j] -= average;
pamx[i][j] = shishagonyuu( pamx[i][j] );
}
#endif
if( disp )
{
fprintf( stdout, " scoring matrix \n" );
for( i=0; i<20; i++ )
{
fprintf( stdout, "%c ", amino[i] );
for( j=0; j<20; j++ )
fprintf( stdout, "%5.0f", pamx[i][j] );
fprintf( stdout, "\n" );
}
fprintf( stdout, " " );
for( i=0; i<20; i++ )
fprintf( stdout, " %c", amino[i] );
average = 0.0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ )
average += pamx[i][j] * freq1[i] * freq1[j];
fprintf( stdout, "average = %f\n", average );
average = 0.0;
for( i=0; i<20; i++ )
average += pamx[i][i] * freq1[i];
fprintf( stdout, "itch average = %f\n", average );
fprintf( stderr, "parameters: %d, %d, %d\n", penalty, penalty_ex, offset );
exit( 1 );
}
for( i=0; i<26; i++ ) for( j=0; j<26; j++ ) n_dis[i][j] = 0;
for( i=0; i<20; i++ ) for( j=0; j<20; j++ ) n_dis[i][j] = (int)pamx[i][j];
fprintf( stderr, "done.\n" );
FreeDoubleMtx( rsr );
FreeDoubleMtx( pam1 );
FreeDoubleMtx( pamx );
FreeDoubleVec( freq );
FreeDoubleVec( mutab );
FreeDoubleVec( datafreq );
}
fprintf( stderr, "scoremtx = %d\n", scoremtx );
#if DEBUG
fprintf( stderr, "scoremtx = %d\n", scoremtx );
fprintf( stderr, "amino[] = %s\n", amino );
#endif
for( i=0; i<0x80; i++ )amino_n[i] = -1;
for( i=0; i<26; i++) amino_n[(int)amino[i]] = i;
for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_dis[i][j] = 0;
for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_disLN[i][j] = 0;
for( i=0; i<0x80; i++ ) for( j=0; j<0x80; j++ ) amino_dis_consweight_multi[i][j] = 0.0;
for( i=0; i<26; i++) for( j=0; j<26; j++ )
{
amino_dis[(int)amino[i]][(int)amino[j]] = n_dis[i][j];
n_dis_consweight_multi[i][j] = (float)n_dis[i][j] * consweight_multi;
amino_dis_consweight_multi[(int)amino[i]][(int)amino[j]] = (double)n_dis[i][j] * consweight_multi;
}
if( dorp == 'd' ) /* DNA */
{
for( i=0; i<5; i++) for( j=0; j<5; j++ )
amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
for( i=5; i<10; i++) for( j=5; j<10; j++ )
amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
for( i=0; i<5; i++) for( j=0; j<5; j++ )
n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
for( i=5; i<10; i++) for( j=5; j<10; j++ )
n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
}
else // protein
{
for( i=0; i<20; i++) for( j=0; j<20; j++ )
amino_disLN[(int)amino[i]][(int)amino[j]] = n_dis[i][j] + offset - offsetLN;
for( i=0; i<20; i++) for( j=0; j<20; j++ )
n_disFFT[i][j] = n_dis[i][j] + offset - offsetFFT;
}
#if 0
fprintf( stderr, "amino_dis (offset = %d): \n", offset );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stderr, "%5d", amino_dis[(int)amino[i]][(int)amino[j]] );
}
fprintf( stderr, "\n" );
}
fprintf( stderr, "amino_disLN (offsetLN = %d): \n", offsetLN );
for( i=0; i<20; i++ )
{
for( j=0; j<20; j++ )
{
fprintf( stderr, "%5d", amino_disLN[(int)amino[i]][(int)amino[j]] );
}
fprintf( stderr, "\n" );
}
fprintf( stderr, "n_dis (offset = %d): \n", offset );
for( i=0; i<26; i++ )
{
for( j=0; j<26; j++ )
{
fprintf( stderr, "%5d", n_dis[i][j] );
}
fprintf( stderr, "\n" );
}
fprintf( stderr, "n_disFFT (offsetFFT = %d): \n", offsetFFT );
for( i=0; i<26; i++ )
{
for( j=0; j<26; j++ )
{
fprintf( stderr, "%5d", n_disFFT[i][j] );
}
fprintf( stderr, "\n" );
}
exit( 1 );
#endif
ppid = 0;
if( fftThreshold == NOTSPECIFIED )
{
fftThreshold = FFT_THRESHOLD;
}
if( fftWinSize == NOTSPECIFIED )
{
if( dorp == 'd' )
fftWinSize = FFT_WINSIZE_D;
else
fftWinSize = FFT_WINSIZE_P;
}
if( fftscore )
{
double av, sd;
for( i=0; i<20; i++ ) polarity[i] = polarity_[i];
for( av=0.0, i=0; i<20; i++ ) av += polarity[i];
av /= 20.0;
for( sd=0.0, i=0; i<20; i++ ) sd += ( polarity[i]-av ) * ( polarity[i]-av );
sd /= 20.0; sd = sqrt( sd );
for( i=0; i<20; i++ ) polarity[i] -= av;
for( i=0; i<20; i++ ) polarity[i] /= sd;
for( i=0; i<20; i++ ) volume[i] = volume_[i];
for( av=0.0, i=0; i<20; i++ ) av += volume[i];
av /= 20.0;
for( sd=0.0, i=0; i<20; i++ ) sd += ( volume[i]-av ) * ( volume[i]-av );
sd /= 20.0; sd = sqrt( sd );
for( i=0; i<20; i++ ) volume[i] -= av;
for( i=0; i<20; i++ ) volume[i] /= sd;
#if 0
for( i=0; i<20; i++ ) fprintf( stdout, "amino=%c, pol = %f<-%f, vol = %f<-%f\n", amino[i], polarity[i], polarity_[i], volume[i], volume_[i] );
for( i=0; i<20; i++ ) fprintf( stdout, "%c %+5.3f %+5.3f\n", amino[i], volume[i], polarity[i] );
#endif
}
}
static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *equiv, double *effarr, char **strfiles, char **chainids, int alloclen )
{
int i, j, ilim;
int clus1, clus2;
int off1, off2;
float pscore = 0.0; // by D.Mathog
static char *indication1, *indication2;
FILE *hat2p, *hat3p;
static double **distancemtx;
static double *effarr1 = NULL;
static double *effarr2 = NULL;
char *pt;
char *hat2file = "hat2";
LocalHom **localhomtable, *tmpptr;
static char **pair;
// int intdum;
double bunbo;
char **checkseq;
localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
for( i=0; i<njob; i++)
{
localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
for( j=0; j<njob; j++)
{
localhomtable[i][j].start1 = -1;
localhomtable[i][j].end1 = -1;
localhomtable[i][j].start2 = -1;
localhomtable[i][j].end2 = -1;
localhomtable[i][j].opt = -1.0;
localhomtable[i][j].next = NULL;
localhomtable[i][j].nokori = 0;
}
}
if( effarr1 == NULL )
{
distancemtx = AllocateDoubleMtx( njob, njob );
effarr1 = AllocateDoubleVec( njob );
effarr2 = AllocateDoubleVec( njob );
indication1 = AllocateCharVec( 150 );
indication2 = AllocateCharVec( 150 );
checkseq = AllocateCharMtx( njob, alloclen );
#if 0
#else
pair = AllocateCharMtx( njob, njob );
#endif
}
#if 0
fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
#endif
#if 0
for( i=0; i<njob; i++ )
fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
#endif
// writePre( njob, name, nlen, aseq, 0 );
for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
for( i=0; i<njob; i++ ) pair[i][i] = 1;
for( i=0; i<njob; i++ )
{
strcpy( checkseq[i], seq[i] );
// fprintf( stderr, "checkseq[%d] = %s\n", i, checkseq[i] );
}
ilim = njob - 1;
for( i=0; i<ilim; i++ )
{
fprintf( stderr, "% 5d / %d\r", i, njob );
for( j=i+1; j<njob; j++ )
{
#if 0
if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
{
distancemtx[i][j] = pscore;
continue;
}
#endif
strcpy( aseq[i], seq[i] );
strcpy( aseq[j], seq[j] );
clus1 = conjuctionfortbfast( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
clus2 = conjuctionfortbfast( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
// fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
// fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
#if 0
fprintf( stderr, "group1 = %.66s", indication1 );
fprintf( stderr, "\n" );
fprintf( stderr, "group2 = %.66s", indication2 );
fprintf( stderr, "\n" );
#endif
// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
#if 1
{
switch( alg )
{
case( 'T' ):
fprintf( stderr, " Calling tmalign %d-%d/%d \r", i+1, j+1, njob );
pscore = calltmalign( mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
off1 = off2 = 0;
break;
case( 'R' ):
fprintf( stderr, " Calling PDP_ASH.pl %d-%d/%d \r", i+1, j+1, njob );
pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
off1 = off2 = 0;
break;
ErrorExit( "ERROR IN SOURCE FILE" );
}
}
#endif
distancemtx[i][j] = pscore;
#if SCOREOUT
fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
#endif
putlocalhom_str( mseq1[0], mseq2[0], equiv, scale, localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
#if 1
if( alreadyoutput[i] == 0 )
{
alreadyoutput[i] = 1;
gappick0( seq[i], mseq1[0] );
fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, strfiles[i], chainids[i], seq[i] );
strcpy( checkseq[i], seq[i] );
}
else
{
gappick0( seq[i], mseq1[0] );
fprintf( stderr, "checking seq%d\n", i );
// fprintf( stderr, " seq=%s\n", seq[i] );
// fprintf( stderr, "checkseq=%s\n", checkseq[i] );
if( strcmp( checkseq[i], seq[i] ) )
{
fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
fprintf( stderr, "i=%d\n", i );
fprintf( stderr, " seq=%s\n", seq[i] );
fprintf( stderr, "checkseq=%s\n", checkseq[i] );
exit( 1 );
}
}
if( alreadyoutput[j] == 0 )
{
alreadyoutput[j] = 1;
gappick0( seq[j], mseq2[0] );
fprintf( stdout, ">%d_%s-%s\n%s\n", j+1, strfiles[j], chainids[j], seq[j] );
strcpy( checkseq[j], seq[j] );
}
else
{
gappick0( seq[j], mseq2[0] );
fprintf( stderr, "checking seq%d\n", j );
if( strcmp( checkseq[j], seq[j] ) )
{
fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
fprintf( stderr, "j=%d\n", j );
fprintf( stderr, " seq=%s\n", seq[j] );
fprintf( stderr, "checkseq=%s\n", checkseq[j] );
exit( 1 );
}
}
#endif
}
}
for( i=0; i<njob; i++ )
{
pscore = 0.0;
for( pt=seq[i]; *pt; pt++ )
pscore += amino_dis[(int)*pt][(int)*pt];
distancemtx[i][i] = pscore;
}
ilim = njob-1;
for( i=0; i<ilim; i++ )
{
for( j=i+1; j<njob; j++ )
{
bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
if( bunbo == 0.0 )
distancemtx[i][j] = 2.0;
else
distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
}
}
hat2p = fopen( hat2file, "w" );
if( !hat2p ) ErrorExit( "Cannot open hat2." );
WriteHat2( hat2p, njob, name, distancemtx );
fclose( hat2p );
fprintf( stderr, "##### writing hat3\n" );
hat3p = fopen( "hat3", "w" );
if( !hat3p ) ErrorExit( "Cannot open hat3." );
ilim = njob-1;
for( i=0; i<ilim; i++ )
{
for( j=i+1; j<njob; j++ )
{
for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
{
if( tmpptr->opt == -1.0 ) continue;
fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d k\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
}
}
}
fclose( hat3p );
#if DEBUG
fprintf( stderr, "calling FreeLocalHomTable\n" );
#endif
FreeLocalHomTable( localhomtable, njob );
#if DEBUG
fprintf( stderr, "done. FreeLocalHomTable\n" );
#endif
}
float L__align11_noalign( double **n_dynamicmtx, char **seq1, char **seq2 )
// warp mitaiou
{
// 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;
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 );
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] );
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 );
if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
}
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;
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 0 // IRUKAMO!!!!
if( ijp[endali][endalj] == localstop )
{
strcpy( seq1[0], "" );
strcpy( seq2[0], "" );
*off1pt = *off2pt = 0;
fprintf( stderr, "maxwm <- 0.0 \n" );
return( 0.0 );
}
#else
if( maxwm < localthr )
{
fprintf( stderr, "maxwm <- 0.0 \n" );
return( 0.0 );
}
#endif
// 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 );
}
int main( int argc, char *argv[] )
{
static int nlen[M];
static char **name, **seq;
static char **oseq;
static double **pscore;
static double *eff;
static double **node0, **node1;
static double *gapc;
static double *avgap;
double tmpavgap;
int i, j, m, goffset;
static int ***topol;
static double **len;
FILE *prep;
char c;
int corestart, coreend;
int alloclen;
int winsize;
char *pt, *ot;
double gapmin;
arguments( argc, argv );
getnumlen( stdin );
rewind( stdin );
if( njob < 2 )
{
fprintf( stderr, "At least 2 sequences should be input!\n"
"Only %d sequence found.\n", njob );
exit( 1 );
}
seq = AllocateCharMtx( njob, nlenmax*9+1 );
name = AllocateCharMtx( njob, B+1 );
oseq = AllocateCharMtx( njob, nlenmax*9+1 );
alloclen = nlenmax*9;
topol = AllocateIntCub( njob, 2, njob );
len = AllocateDoubleMtx( njob, 2 );
pscore = AllocateDoubleMtx( njob, njob );
eff = AllocateDoubleVec( njob );
node0 = AllocateDoubleMtx( njob, njob );
node1 = AllocateDoubleMtx( njob, njob );
gapc = AllocateDoubleVec( alloclen );
avgap = AllocateDoubleVec( alloclen );
#if 0
Read( name, nlen, seq );
#else
readData_pointer( stdin, name, nlen, seq );
#endif
constants( njob, seq );
#if 0
fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
#endif
initSignalSM();
initFiles();
WriteOptions( trap_g );
c = seqcheck( seq );
if( c )
{
fprintf( stderr, "Illeagal character %c\n", c );
exit( 1 );
}
writePre( njob, name, nlen, seq, 0 );
if( tbutree == 0 )
{
for( i=1; i<njob; i++ )
{
if( nlen[i] != nlen[0] )
{
fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
exit( 1 );
}
}
for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
{
/*
pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
*/
pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
}
}
else
{
fprintf( stderr, "Loading 'hat2' ... " );
prep = fopen( "hat2", "r" );
if( prep == NULL ) ErrorExit( "Make hat2." );
readhat2_pointer( prep, njob, name, pscore );
fclose( prep );
fprintf( stderr, "done.\n" );
#if 0
prep = fopen( "hat2_check", "w" );
WriteHat2( prep, njob, name, pscore );
fclose( prep );
#endif
}
fprintf( stderr, "Constructing dendrogram ... " );
if( treemethod == 'x' )
supg( njob, pscore, topol, len );
else if( treemethod == 's' )
spg( njob, pscore, topol, len );
else if( treemethod == 'p' )
upg2( njob, pscore, topol, len );
else
ErrorExit( "Incorrect tree\n" );
fprintf( stderr, "done.\n" );
countnode( njob, topol, node0 );
if( tbrweight )
{
weight = 3;
#if 0
utree = 0; counteff( njob, topol, len, eff ); utree = 1;
#else
counteff_simple( njob, topol, len, eff );
#endif
}
else
{
for( i=0; i<njob; i++ ) eff[i] = 1.0;
}
for( i=0; i<nlenmax; i++ )
{
gapc[i] = 0.0;
for( j=0; j<njob; j++ )
{
if( seq[j][i] == '-' ) gapc[i] += eff[j];
}
}
gapmin = 1.0;
winsize = fftWinSize;
goffset = winsize/2;
tmpavgap = 0.0;
corestart = coreend = -1;
for( i=0; i<winsize; i++ )
{
tmpavgap += gapc[i];
}
for( i=winsize; i<nlenmax; i++ )
{
m = i - goffset;
avgap[m] = tmpavgap / winsize;
// fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
if( avgap[m] < corethr )
{
if( corestart == -1 )
corestart = i - winsize;
// fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
if( avgap[m] < gapmin )
{
gapmin = avgap[m];
}
coreend = i;
}
tmpavgap -= gapc[i-winsize];
tmpavgap += gapc[i];
}
if( corestart == -1 || coreend == -1 )
{
corestart = 0;
coreend = nlenmax-1;
}
for( i=0; i<njob; i++ )
{
pt = oseq[i];
m = winsize;
while( m-- ) *pt++ = '-';
for( j=corestart; j<=coreend; j++ )
*pt++ = seq[i][j];
m = winsize;
while( m-- ) *pt++ = '-';
*pt = 0;
ot = oseq[i]+winsize-1;
pt = seq[i]+corestart-1;
if( coreext ) m = winsize;
else m = 0;
while( m && --pt > seq[i] )
if( *pt != '-' )
{
*ot-- = *pt;
m--;
}
ot = oseq[i]+winsize+coreend-corestart+1;
pt = seq[i]+coreend;
if( coreext ) m = winsize;
else m = 0;
while( m && *(++pt) )
{
if( *pt != '-' )
{
*ot++ = *pt;
m--;
}
}
fprintf( stdout, ">%s\n", name[i] );
fprintf( stdout, "%s\n", oseq[i] );
}
exit( 1 );
SHOWVERSION;
return( 0 );
}
float Falign_localhom( char **seq1, char **seq2,
double *eff1, double *eff2,
int clus1, int clus2,
int alloclen,
LocalHom ***localhom, float *totalimpmatch,
int *gapmap1, int *gapmap2,
int *chudanpt, int chudanref, int *chudanres )
{
// tditeration.c deha alloclen ha huhen nanode
// prevalloclen ha iranai.
int i, j, k, l, m, maxk;
int nlen, nlen2, nlen4;
static TLS int crossscoresize = 0;
static TLS char **tmpseq1 = NULL;
static TLS char **tmpseq2 = NULL;
static TLS char **tmpptr1 = NULL;
static TLS char **tmpptr2 = NULL;
static TLS char **tmpres1 = NULL;
static TLS char **tmpres2 = NULL;
static TLS char **result1 = NULL;
static TLS char **result2 = NULL;
#if RND
static TLS char **rndseq1 = NULL;
static TLS char **rndseq2 = NULL;
#endif
static TLS Fukusosuu **seqVector1 = NULL;
static TLS Fukusosuu **seqVector2 = NULL;
static TLS Fukusosuu **naiseki = NULL;
static TLS Fukusosuu *naisekiNoWa = NULL;
static TLS double *soukan = NULL;
static TLS double **crossscore = NULL;
int nlentmp;
static TLS int *kouho = NULL;
static TLS Segment *segment = NULL;
static TLS Segment *segment1 = NULL;
static TLS Segment *segment2 = NULL;
static TLS Segment **sortedseg1 = NULL;
static TLS Segment **sortedseg2 = NULL;
static TLS int *cut1 = NULL;
static TLS int *cut2 = NULL;
static TLS char *sgap1, *egap1, *sgap2, *egap2;
static TLS int localalloclen = 0;
int lag;
int tmpint;
int count, count0;
int len1, len2;
int totallen;
float totalscore;
float impmatch;
extern Fukusosuu *AllocateFukusosuuVec();
extern Fukusosuu **AllocateFukusosuuMtx();
if( seq1 == NULL )
{
if( result1 )
{
// fprintf( stderr, "Freeing localarrays in Falign\n" );
localalloclen = 0;
mymergesort( 0, 0, NULL );
alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
fft( 0, NULL, 1 );
A__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
G__align11( NULL, NULL, 0, 0, 0 );
partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
if( crossscore ) FreeDoubleMtx( crossscore );
FreeCharMtx( result1 );
FreeCharMtx( result2 );
FreeCharMtx( tmpres1 );
FreeCharMtx( tmpres2 );
FreeCharMtx( tmpseq1 );
FreeCharMtx( tmpseq2 );
free( sgap1 );
free( egap1 );
free( sgap2 );
free( egap2 );
free( kouho );
free( cut1 );
free( cut2 );
free( tmpptr1 );
free( tmpptr2 );
free( segment );
free( segment1 );
free( segment2 );
free( sortedseg1 );
free( sortedseg2 );
if( !kobetsubunkatsu )
{
FreeFukusosuuMtx ( seqVector1 );
FreeFukusosuuMtx ( seqVector2 );
FreeFukusosuuVec( naisekiNoWa );
FreeFukusosuuMtx( naiseki );
FreeDoubleVec( soukan );
}
}
else
{
// fprintf( stderr, "Did not allocate localarrays in Falign\n" );
}
return( 0.0 );
}
len1 = strlen( seq1[0] );
len2 = strlen( seq2[0] );
nlentmp = MAX( len1, len2 );
nlen = 1;
while( nlentmp >= nlen ) nlen <<= 1;
#if 0
fprintf( stderr, "### nlen = %d\n", nlen );
#endif
nlen2 = nlen/2; nlen4 = nlen2 / 2;
#if DEBUG
fprintf( stderr, "len1 = %d, len2 = %d\n", len1, len2 );
fprintf( stderr, "nlentmp = %d, nlen = %d\n", nlentmp, nlen );
#endif
if( !localalloclen )
{
sgap1 = AllocateCharVec( njob );
egap1 = AllocateCharVec( njob );
sgap2 = AllocateCharVec( njob );
egap2 = AllocateCharVec( njob );
kouho = AllocateIntVec( NKOUHO );
cut1 = AllocateIntVec( MAXSEG );
cut2 = AllocateIntVec( MAXSEG );
tmpptr1 = AllocateCharMtx( njob, 0 );
tmpptr2 = AllocateCharMtx( njob, 0 );
result1 = AllocateCharMtx( njob, alloclen );
result2 = AllocateCharMtx( njob, alloclen );
tmpres1 = AllocateCharMtx( njob, alloclen );
tmpres2 = AllocateCharMtx( njob, alloclen );
// crossscore = AllocateDoubleMtx( MAXSEG, MAXSEG );
segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
segment1 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
segment2 = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
sortedseg1 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
sortedseg2 = (Segment **)calloc( MAXSEG, sizeof( Segment * ) );
if( !( segment && segment1 && segment2 && sortedseg1 && sortedseg2 ) )
ErrorExit( "Allocation error\n" );
if ( scoremtx == -1 ) n20or4or2 = 4;
else if( fftscore == 1 ) n20or4or2 = 2;
else n20or4or2 = 20;
}
if( localalloclen < nlen )
{
if( localalloclen )
{
#if 1
if( !kobetsubunkatsu )
{
FreeFukusosuuMtx ( seqVector1 );
FreeFukusosuuMtx ( seqVector2 );
FreeFukusosuuVec( naisekiNoWa );
FreeFukusosuuMtx( naiseki );
FreeDoubleVec( soukan );
}
FreeCharMtx( tmpseq1 );
FreeCharMtx( tmpseq2 );
#endif
#if RND
FreeCharMtx( rndseq1 );
FreeCharMtx( rndseq2 );
#endif
}
tmpseq1 = AllocateCharMtx( njob, nlen );
tmpseq2 = AllocateCharMtx( njob, nlen );
if( !kobetsubunkatsu )
{
naisekiNoWa = AllocateFukusosuuVec( nlen );
naiseki = AllocateFukusosuuMtx( n20or4or2, nlen );
seqVector1 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
seqVector2 = AllocateFukusosuuMtx( n20or4or2+1, nlen+1 );
soukan = AllocateDoubleVec( nlen+1 );
}
#if RND
rndseq1 = AllocateCharMtx( njob, nlen );
rndseq2 = AllocateCharMtx( njob, nlen );
for( i=0; i<njob; i++ )
{
generateRndSeq( rndseq1[i], nlen );
generateRndSeq( rndseq2[i], nlen );
}
#endif
localalloclen = nlen;
}
for( j=0; j<clus1; j++ ) strcpy( tmpseq1[j], seq1[j] );
for( j=0; j<clus2; j++ ) strcpy( tmpseq2[j], seq2[j] );
#if 0
fftfp = fopen( "input_of_Falign", "w" );
fprintf( fftfp, "nlen = %d\n", nlen );
fprintf( fftfp, "seq1: ( %d sequences ) \n", clus1 );
for( i=0; i<clus1; i++ )
fprintf( fftfp, "%s\n", seq1[i] );
fprintf( fftfp, "seq2: ( %d sequences ) \n", clus2 );
for( i=0; i<clus2; i++ )
fprintf( fftfp, "%s\n", seq2[i] );
fclose( fftfp );
system( "less input_of_Falign < /dev/tty > /dev/tty" );
#endif
if( !kobetsubunkatsu )
{
fprintf( stderr, "FFT ... " );
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus1; i++ )
{
seq_vec_2( seqVector1[0], polarity, eff1[i], tmpseq1[i] );
seq_vec_2( seqVector1[1], volume, eff1[i], tmpseq1[i] );
}
}
else
{
#if 0
for( i=0; i<clus1; i++ ) for( j=0; j<n20or4or2; j++ )
seq_vec( seqVector1[j], amino[j], eff1[i], tmpseq1[i] );
#else
for( i=0; i<clus1; i++ )
seq_vec_3( seqVector1, eff1[i], tmpseq1[i] );
#endif
}
#if RND
for( i=0; i<clus1; i++ )
{
vec_init2( seqVector1, rndseq1[i], eff1[i], len1, nlen );
}
#endif
#if 0
fftfp = fopen( "seqVec", "w" );
fprintf( fftfp, "before transform\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "nlen=%d\n", nlen );
fprintf( fftfp, "%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector1[k][l].R, seqVector1[k][l].I );
}
fclose( fftfp );
system( "less seqVec < /dev/tty > /dev/tty" );
#endif
for( j=0; j<n20or4or2; j++ ) vec_init( seqVector2[j], nlen );
if( fftscore && scoremtx != -1 )
{
for( i=0; i<clus2; i++ )
{
seq_vec_2( seqVector2[0], polarity, eff2[i], tmpseq2[i] );
seq_vec_2( seqVector2[1], volume, eff2[i], tmpseq2[i] );
}
}
else
{
#if 0
for( i=0; i<clus2; i++ ) for( j=0; j<n20or4or2; j++ )
seq_vec( seqVector2[j], amino[j], eff2[i], tmpseq2[i] );
#else
for( i=0; i<clus2; i++ )
seq_vec_3( seqVector2, eff2[i], tmpseq2[i] );
#endif
}
#if RND
for( i=0; i<clus2; i++ )
{
vec_init2( seqVector2, rndseq2[i], eff2[i], len2, nlen );
}
#endif
#if 0
fftfp = fopen( "seqVec2", "w" );
fprintf( fftfp, "before fft\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
}
fclose( fftfp );
system( "less seqVec2 < /dev/tty > /dev/tty" );
#endif
for( j=0; j<n20or4or2; j++ )
{
fft( nlen, seqVector2[j], (j==0) );
fft( nlen, seqVector1[j], 0 );
}
#if 0
fftfp = fopen( "seqVec2", "w" );
fprintf( fftfp, "#after fft\n" );
for( k=0; k<n20or4or2; k++ )
{
fprintf( fftfp, "#%c\n", amino[k] );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%f %f\n", seqVector2[k][l].R, seqVector2[k][l].I );
}
fclose( fftfp );
system( "less seqVec2 < /dev/tty > /dev/tty" );
#endif
for( k=0; k<n20or4or2; k++ )
{
for( l=0; l<nlen; l++ )
calcNaiseki( naiseki[k]+l, seqVector1[k]+l, seqVector2[k]+l );
}
for( l=0; l<nlen; l++ )
{
naisekiNoWa[l].R = 0.0;
naisekiNoWa[l].I = 0.0;
for( k=0; k<n20or4or2; k++ )
{
naisekiNoWa[l].R += naiseki[k][l].R;
naisekiNoWa[l].I += naiseki[k][l].I;
}
}
#if 0
fftfp = fopen( "naisekiNoWa", "w" );
fprintf( fftfp, "#Before fft\n" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f %f\n", l, naisekiNoWa[l].R, naisekiNoWa[l].I );
fclose( fftfp );
system( "less naisekiNoWa < /dev/tty > /dev/tty " );
#endif
fft( -nlen, naisekiNoWa, 0 );
for( m=0; m<=nlen2; m++ )
soukan[m] = naisekiNoWa[nlen2-m].R;
for( m=nlen2+1; m<nlen; m++ )
soukan[m] = naisekiNoWa[nlen+nlen2-m].R;
#if 0
fftfp = fopen( "naisekiNoWa", "w" );
fprintf( fftfp, "#After fft\n" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f\n", l, naisekiNoWa[l].R );
fclose( fftfp );
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'naisekiNoWa'\npause -1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot &" );
#endif
#if 0
fprintf( stderr, "frt write start\n" );
fftfp = fopen( "frt", "w" );
for( l=0; l<nlen; l++ )
fprintf( fftfp, "%d %f\n", l-nlen2, soukan[l] );
fclose( fftfp );
system( "less frt < /dev/tty > /dev/tty" );
#if 0
fftfp = fopen( "list.plot", "w" );
fprintf( fftfp, "plot 'frt'\n pause +1" );
fclose( fftfp );
system( "/usr/bin/gnuplot list.plot" );
#endif
#endif
getKouho( kouho, NKOUHO, soukan, nlen );
#if 0
for( i=0; i<NKOUHO; i++ )
{
fprintf( stderr, "kouho[%d] = %d\n", i, kouho[i] );
}
#endif
}
#if KEIKA
fprintf( stderr, "Searching anchors ... " );
#endif
count = 0;
#define CAND 0
#if CAND
fftfp = fopen( "cand", "w" );
fclose( fftfp );
#endif
if( kobetsubunkatsu )
{
maxk = 1;
kouho[0] = 0;
}
else
{
maxk = NKOUHO;
}
for( k=0; k<maxk; k++ )
{
lag = kouho[k];
zurasu2( lag, clus1, clus2, seq1, seq2, tmpptr1, tmpptr2 );
#if CAND
fftfp = fopen( "cand", "a" );
fprintf( fftfp, "Candidate No.%d lag = %d\n", k+1, lag );
fprintf( fftfp, "%s\n", tmpptr1[0] );
fprintf( fftfp, "%s\n", tmpptr2[0] );
fclose( fftfp );
#endif
tmpint = alignableReagion( clus1, clus2, tmpptr1, tmpptr2, eff1, eff2, segment+count );
if( count+tmpint > MAXSEG -3 ) ErrorExit( "TOO MANY SEGMENTS.\n" );
while( tmpint-- > 0 )
{
if( lag > 0 )
{
segment1[count].start = segment[count].start ;
segment1[count].end = segment[count].end ;
segment1[count].center = segment[count].center;
segment1[count].score = segment[count].score;
segment2[count].start = segment[count].start + lag;
segment2[count].end = segment[count].end + lag;
segment2[count].center = segment[count].center + lag;
segment2[count].score = segment[count].score ;
}
else
{
segment1[count].start = segment[count].start - lag;
segment1[count].end = segment[count].end - lag;
segment1[count].center = segment[count].center - lag;
segment1[count].score = segment[count].score ;
segment2[count].start = segment[count].start ;
segment2[count].end = segment[count].end ;
segment2[count].center = segment[count].center;
segment2[count].score = segment[count].score ;
}
#if 0
fftfp = fopen( "cand", "a" );
fprintf( fftfp, "Goukaku=%dko\n", tmpint );
fprintf( fftfp, "in 1 %d\n", segment1[count].center );
fprintf( fftfp, "in 2 %d\n", segment2[count].center );
fclose( fftfp );
#endif
segment1[count].pair = &segment2[count];
segment2[count].pair = &segment1[count];
count++;
#if 0
fprintf( stderr, "count=%d\n", count );
#endif
}
}
#if 1
if( !kobetsubunkatsu )
fprintf( stderr, "%d segments found\n", count );
#endif
if( !count && fftNoAnchStop )
ErrorExit( "Cannot detect anchor!" );
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT before sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( fftfp, "%d score = %f\n", segment2[l].center, segment1[l].score );
}
fclose( fftfp );
#endif
#if KEIKA
fprintf( stderr, "Aligning anchors ... " );
#endif
for( i=0; i<count; i++ )
{
sortedseg1[i] = &segment1[i];
sortedseg2[i] = &segment2[i];
}
#if 0
tmpsort( count, sortedseg1 );
tmpsort( count, sortedseg2 );
qsort( sortedseg1, count, sizeof( Segment * ), segcmp );
qsort( sortedseg2, count, sizeof( Segment * ), segcmp );
#else
mymergesort( 0, count-1, sortedseg1 );
mymergesort( 0, count-1, sortedseg2 );
#endif
for( i=0; i<count; i++ ) sortedseg1[i]->number = i;
for( i=0; i<count; i++ ) sortedseg2[i]->number = i;
if( kobetsubunkatsu )
{
for( i=0; i<count; i++ )
{
cut1[i+1] = sortedseg1[i]->center;
cut2[i+1] = sortedseg2[i]->center;
}
cut1[0] = 0;
cut2[0] = 0;
cut1[count+1] = len1;
cut2[count+1] = len2;
count += 2;
}
else
{
if( crossscoresize < count+2 )
{
crossscoresize = count+2;
#if 1
fprintf( stderr, "######allocating crossscore, size = %d\n", crossscoresize );
#endif
if( crossscore ) FreeDoubleMtx( crossscore );
crossscore = AllocateDoubleMtx( crossscoresize, crossscoresize );
}
for( i=0; i<count+2; i++ ) for( j=0; j<count+2; j++ )
crossscore[i][j] = 0.0;
for( i=0; i<count; i++ )
{
crossscore[segment1[i].number+1][segment1[i].pair->number+1] = segment1[i].score;
cut1[i+1] = sortedseg1[i]->center;
cut2[i+1] = sortedseg2[i]->center;
}
#if DEBUG
fprintf( stderr, "AFTER SORT\n" );
for( i=0; i<count; i++ ) fprintf( stderr, "%d, %d\n", segment1[i].start, segment2[i].start );
#endif
crossscore[0][0] = 10000000.0;
cut1[0] = 0;
cut2[0] = 0;
crossscore[count+1][count+1] = 10000000.0;
cut1[count+1] = len1;
cut2[count+1] = len2;
count += 2;
count0 = count;
blockAlign2( cut1, cut2, sortedseg1, sortedseg2, crossscore, &count );
if( count0 > count )
{
#if 0
fprintf( stderr, "\7 REPEAT!? \n" );
#else
fprintf( stderr, "REPEAT!? \n" );
#endif
if( fftRepeatStop ) exit( 1 );
}
#if KEIKA
else fprintf( stderr, "done\n" );
#endif
}
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT after sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut[%d]=%d, ", l, segment1[l].center );
fprintf( fftfp, "%d\n", segment2[l].center );
}
fclose( fftfp );
#endif
#if 0
fftfp = fopen( "fft", "a" );
fprintf( fftfp, "RESULT after sort:\n" );
for( l=0; l<count; l++ )
{
fprintf( fftfp, "cut : %d %d\n", cut1[l], cut2[l] );
}
fclose( fftfp );
#endif
#if KEIKA
fprintf( trap_g, "Devided to %d segments\n", count-1 );
fprintf( trap_g, "%d %d forg\n", MIN( clus1, clus2 ), count-1 );
#endif
totallen = 0;
for( j=0; j<clus1; j++ ) result1[j][0] = 0;
for( j=0; j<clus2; j++ ) result2[j][0] = 0;
totalscore = 0.0;
*totalimpmatch = 0.0;
for( i=0; i<count-1; i++ )
{
#if DEBUG
fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
#else
#if KEIKA
fprintf( stderr, "DP %03d / %03d\r", i+1, count-1 );
#endif
#endif
if( cut1[i] )
{
getkyokaigap( sgap1, seq1, cut1[i]-1, clus1 );
getkyokaigap( sgap2, seq2, cut2[i]-1, clus2 );
}
else
{
for( j=0; j<clus1; j++ ) sgap1[j] = 'o';
for( j=0; j<clus2; j++ ) sgap2[j] = 'o';
}
if( cut1[i+1] != len1 )
{
getkyokaigap( egap1, seq1, cut1[i+1], clus1 );
getkyokaigap( egap2, seq2, cut2[i+1], clus2 );
}
else
{
for( j=0; j<clus1; j++ ) egap1[j] = 'o';
for( j=0; j<clus2; j++ ) egap2[j] = 'o';
}
for( j=0; j<clus1; j++ )
{
strncpy( tmpres1[j], seq1[j]+cut1[i], cut1[i+1]-cut1[i] );
tmpres1[j][cut1[i+1]-cut1[i]] = 0;
}
if( kobetsubunkatsu ) commongappick_record( clus1, tmpres1, gapmap1 );
for( j=0; j<clus2; j++ )
{
strncpy( tmpres2[j], seq2[j]+cut2[i], cut2[i+1]-cut2[i] );
tmpres2[j][cut2[i+1]-cut2[i]] = 0;
}
if( kobetsubunkatsu ) commongappick_record( clus2, tmpres2, gapmap2 );
#if 0
fprintf( stderr, "count = %d\n", count );
fprintf( stderr, "### reg1 = %d-%d\n", cut1[i], cut1[i+1]-1 );
fprintf( stderr, "### reg2 = %d-%d\n", cut2[i], cut2[i+1]-1 );
#endif
switch( alg )
{
case( 'a' ):
totalscore += Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
break;
case( 'Q' ):
totalscore += partQ__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2 );
*totalimpmatch += impmatch;
// fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
break;
case( 'A' ):
totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
*totalimpmatch += impmatch;
// fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
break;
default:
fprintf( stderr, "alg = %c\n", alg );
ErrorExit( "ERROR IN SOURCE FILE Falign.c" );
break;
}
#ifdef enablemultithread
if( chudanres && *chudanres )
{
// fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" );
return( -1.0 );
}
#endif
nlen = strlen( tmpres1[0] );
if( totallen + nlen > alloclen )
{
fprintf( stderr, "totallen=%d + nlen=%d > alloclen = %d\n", totallen, nlen, alloclen );
ErrorExit( "LENGTH OVER in Falign\n " );
}
for( j=0; j<clus1; j++ ) strcat( result1[j], tmpres1[j] );
for( j=0; j<clus2; j++ ) strcat( result2[j], tmpres2[j] );
totallen += nlen;
#if 0
fprintf( stderr, "%4d\r", totallen );
fprintf( stderr, "\n\n" );
for( j=0; j<clus1; j++ )
{
fprintf( stderr, "%s\n", tmpres1[j] );
}
fprintf( stderr, "-------\n" );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "%s\n", tmpres2[j] );
}
#endif
}
#if KEIKA
fprintf( stderr, "DP ... done \n" );
#endif
for( j=0; j<clus1; j++ ) strcpy( seq1[j], result1[j] );
for( j=0; j<clus2; j++ ) strcpy( seq2[j], result2[j] );
#if 0
for( j=0; j<clus1; j++ )
{
fprintf( stderr, "%s\n", result1[j] );
}
fprintf( stderr, "- - - - - - - - - - -\n" );
for( j=0; j<clus2; j++ )
{
fprintf( stderr, "%s\n", result2[j] );
}
#endif
return( totalscore );
}
