void align()
{
pairalign(0, nseqs,0, nseqs);
}
int main( int argc, char *argv[] )
{
static int nlen[M];
static char name[M][B], **seq;
static char **mseq1, **mseq2;
static char **aseq;
static char **bseq;
static double *eff;
int i;
FILE *infp;
char c;
int alloclen;
arguments( argc, argv );
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
getnumlen( infp );
rewind( infp );
if( njob < 2 )
{
fprintf( stderr, "At least 2 sequences should be input!\n"
"Only %d sequence found.\n", njob );
exit( 1 );
}
if( njob > M )
{
fprintf( stderr, "The number of sequences must be < %d\n", M );
fprintf( stderr, "Please try the splittbfast program for such large data.\n" );
exit( 1 );
}
seq = AllocateCharMtx( njob, nlenmax*9+1 );
aseq = AllocateCharMtx( njob, nlenmax*9+1 );
bseq = AllocateCharMtx( njob, nlenmax*9+1 );
mseq1 = AllocateCharMtx( njob, 0 );
mseq2 = AllocateCharMtx( njob, 0 );
alloclen = nlenmax*9;
eff = AllocateDoubleVec( njob );
#if 0
Read( name, nlen, seq );
#else
readData( infp, name, nlen, seq );
#endif
fclose( infp );
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, "Illegal character %c\n", c );
exit( 1 );
}
// writePre( njob, name, nlen, seq, 0 );
for( i=0; i<njob; i++ ) eff[i] = 1.0;
for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
pairalign( name, nlen, bseq, aseq, mseq1, mseq2, eff, alloclen );
fprintf( trap_g, "done.\n" );
#if DEBUG
fprintf( stderr, "closing trap_g\n" );
#endif
fclose( trap_g );
// writePre( njob, name, nlen, aseq, !contin );
#if 0
writeData( stdout, njob, name, nlen, aseq );
#endif
#if IODEBUG
fprintf( stderr, "OSHIMAI\n" );
#endif
SHOWVERSION;
return( 0 );
}
int main( int argc, char *argv[] )
{
static int nlen[M];
static char **name, **seq;
static char **bseq;
static double *eff;
int i;
char c;
int alloclen;
FILE *infp;
arguments( argc, argv );
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
if( !pairfile )
{
fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
exit( 1 );
}
getnumlen( infp );
rewind( infp );
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 );
bseq = AllocateCharMtx( njob, nlenmax*9+1 );
alloclen = nlenmax*9;
eff = AllocateDoubleVec( njob );
#if 0
Read( name, nlen, seq );
#else
readData_pointer( infp, name, nlen, seq );
#endif
fclose( infp );
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 );
for( i=0; i<njob; i++ ) eff[i] = 1.0;
for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
pairalign( name, nlen, bseq, eff, alloclen );
fprintf( trap_g, "done.\n" );
#if DEBUG
fprintf( stderr, "closing trap_g\n" );
#endif
fclose( trap_g );
#if IODEBUG
fprintf( stderr, "OSHIMAI\n" );
#endif
SHOWVERSION;
return( 0 );
}
int main( int argc, char *argv[] )
{
static int nlen[M];
static char name[M][B], **seq;
static char **mseq1, **mseq2;
static char **aseq;
static char **bseq;
static double *eff;
static double *equiv;
char **strfiles;
char **chainids;
int i;
FILE *infp;
char c;
int alloclen;
arguments( argc, argv );
if( equivthreshold < 1 || 9 < equivthreshold )
{
fprintf( stderr, "-t n, n must be 1..9\n" );
exit( 1 );
}
if( ( equivwinsize + 1 ) % 2 != 0 )
{
fprintf( stderr, "equivwinsize = %d\n", equivwinsize );
fprintf( stderr, "It must be an odd number.\n" );
exit( 1 );
}
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
nlenmax = 10000; // tekitou
if( alg == 'R' )
prepareash( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
else if( alg == 'T' )
preparetmalign( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
fclose( infp );
aseq = AllocateCharMtx( njob, nlenmax*2+1 );
bseq = AllocateCharMtx( njob, nlenmax*2+1 );
eff = AllocateDoubleVec( njob );
for( i=0; i<njob; i++ )
{
fprintf( stderr, "str%d = %s-%s\n", i, strfiles[i], chainids[i] );
}
if( njob < 1 )
{
fprintf( stderr, "No structure found.\n" );
exit( 1 );
}
if( njob < 2 )
{
fprintf( stderr, "Only %d structure found.\n", njob );
exit( 0 );
}
if( njob > M )
{
fprintf( stderr, "The number of structures must be < %d\n", M );
fprintf( stderr, "Please try sequence-based methods for such large data.\n" );
exit( 1 );
}
#if 0
readData( infp, 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, "Illegal character %c\n", c );
exit( 1 );
}
// writePre( njob, name, nlen, seq, 0 );
for( i=0; i<njob; i++ ) eff[i] = 1.0;
for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
pairalign( name, nlen, bseq, aseq, mseq1, mseq2, equiv, eff, strfiles, chainids, alloclen );
fprintf( trap_g, "done.\n" );
#if DEBUG
fprintf( stderr, "closing trap_g\n" );
#endif
fclose( trap_g );
// writePre( njob, name, nlen, aseq, !contin );
#if 0
writeData( stdout, njob, name, nlen, aseq );
#endif
#if IODEBUG
fprintf( stderr, "OSHIMAI\n" );
#endif
SHOWVERSION;
return( 0 );
}
