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;
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 );
*/
}
