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 )
{
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 )
{
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 );
}
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 );
}
