static float recalllara( char **mseq1, char **mseq2, int alloclen )
{
static FILE *fp = NULL;
static char *ungap1;
static char *ungap2;
static char *ori1;
static char *ori2;
int res;
static char com[10000];
float value;
if( fp == NULL )
{
fp = fopen( "_laraout", "r" );
if( fp == NULL )
{
fprintf( stderr, "Cannot open _laraout\n" );
exit( 1 );
}
ungap1 = AllocateCharVec( alloclen );
ungap2 = AllocateCharVec( alloclen );
ori1 = AllocateCharVec( alloclen );
ori2 = AllocateCharVec( alloclen );
}
strcpy( ori1, *mseq1 );
strcpy( ori2, *mseq2 );
fgets( com, 999, fp );
myfgets( com, 9999, fp );
strcpy( *mseq1, com );
myfgets( com, 9999, fp );
strcpy( *mseq2, com );
gappick0( ungap1, *mseq1 );
gappick0( ungap2, *mseq2 );
t2u( ungap1 );
t2u( ungap2 );
if( strcmp( ungap1, ori1 ) || strcmp( ungap2, ori2 ) )
{
fprintf( stderr, "SEQUENCE CHANGED!!\n" );
fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
fprintf( stderr, "ungap1 = %s\n", ungap1 );
fprintf( stderr, "ori1 = %s\n", ori1 );
fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
fprintf( stderr, "ungap2 = %s\n", ungap2 );
fprintf( stderr, "ori2 = %s\n", ori2 );
exit( 1 );
}
value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
// fclose( fp ); // saigo dake yatta houga yoi.
return( value );
}
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[] )
{
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 );
}
static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen )
{
FILE *tmpfp;
static char dumm1[B], dumm0[B];
int i, j;
char *res;
FILE *hat3p;
static double *effarr1 = NULL;
static double *effarr2 = NULL;
static char **pseq;
LocalHom **localhomtable, *tmpptr;
float pscore = 0.0; // by D.Mathog, aguess
char *aseq = NULL; // by D.Mathog
char **usedseqs = NULL; // by D.Mathog
char **usednames = NULL; // by D.Mathog
int nused;
double tsuyosa;
tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
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;
}
}
if( effarr1 == NULL )
{
effarr1 = AllocateDoubleVec( njob );
effarr2 = AllocateDoubleVec( njob );
pseq = AllocateCharMtx( 2, nlenmax*9+1 );
aseq = AllocateCharVec( nlenmax*9+1 );
usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
usednames = AllocateCharMtx( njob, B );
#if 0
#else
#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 );
fprintf( stderr, "opening %s\n", pairfile );
tmpfp = fopen( pairfile, "r" );
if( !tmpfp )
{
fprintf( stderr, "Cannot open %s\n", pairfile );
exit( 1 );
}
searchKUorWA( tmpfp );
hat3p = fopen( "hat3", "w" );
if( !hat3p ) ErrorExit( "Cannot open hat3." );
nused = 0;
while( 1 )
{
res = fgets( dumm0, B-1, tmpfp );
strip( dumm0 );
if( res == NULL )
{
break;
}
load1SeqWithoutName_new( tmpfp, pseq[0] );
gappick0( aseq, pseq[0] );
i = searchused( aseq, usedseqs, nused );
if( i == -1 )
{
strcpy( usednames[nused], dumm0+1 );
strcpy( usedseqs[nused], aseq );
i = nused;
nused++;
}
fprintf( stderr, "i = %d\n", i );
res = fgets( dumm1, B-1, tmpfp );
strip( dumm1 );
if( res == NULL )
{
fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
exit( 1 );
}
load1SeqWithoutName_new( tmpfp, pseq[1] );
gappick0( aseq, pseq[1] );
j = searchused( aseq, usedseqs, nused );
if( j == -1 )
{
strcpy( usednames[nused], dumm1+1 );
strcpy( usedseqs[nused], aseq );
j = nused;
nused++;
}
fprintf( stderr, "j = %d\n", j );
if( strlen( pseq[0] ) != strlen( pseq[1] ) )
{
fprintf( stderr, "Not aligned, %s - %s\n", dumm0, dumm1 );
exit( 1 );
}
fprintf( stderr, "adding %d-%d\n", i, j );
putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
{
if( tmpptr->opt == -1.0 ) continue;
fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
}
}
fclose( tmpfp );
fclose( hat3p );
for( i=0; i<nused; i++ )
fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );
#if 0
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 %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next );
}
}
}
fclose( hat3p );
#endif
#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[] )
{
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 );
}
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
}
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 );
}
