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 );
}
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 **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 );
}
