static float callmxscarna( char **mseq1, char **mseq2, int alloclen )
{
FILE *fp;
int res;
static char com[10000];
float value;
t2u( *mseq1 );
t2u( *mseq2 );
fp = fopen( "_mxscarnain", "w" );
if( !fp )
{
fprintf( stderr, "Cannot open _mxscarnain\n" );
exit( 1 );
}
fprintf( fp, ">1\n" );
fprintf( fp, "%s\n", *mseq1 );
fprintf( fp, ">2\n" );
fprintf( fp, "%s\n", *mseq2 );
fclose( fp );
sprintf( com, "env PATH=%s mxscarna _mxscarnain > _mxscarnaout 2>/dev/null", whereispairalign );
res = system( com );
if( res )
{
fprintf( stderr, "Error in mxscarna\n" );
exit( 1 );
}
fp = fopen( "_mxscarnaout", "r" );
if( !fp )
{
fprintf( stderr, "Cannot open _mxscarnaout\n" );
exit( 1 );
}
fgets( com, 999, fp );
load1SeqWithoutName_new( fp, *mseq1 );
fgets( com, 999, fp );
load1SeqWithoutName_new( fp, *mseq2 );
fclose( fp );
// fprintf( stderr, "*mseq1 = %s\n", *mseq1 );
// fprintf( stderr, "*mseq2 = %s\n", *mseq2 );
value = (float)naivepairscore11( *mseq1, *mseq2, penalty );
return( value );
}
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
}
