static void pairalign( char name[M][B], int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double *effarr, 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;
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 );
#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;
if( alg == 'H' )
{
fprintf( stderr, "Calling FOLDALIGN with option '%s'\n", foldalignopt );
callfoldalign( njob, seq );
fprintf( stderr, "done.\n" );
}
if( alg == 'B' )
{
fprintf( stderr, "Calling LARA\n" );
calllara( njob, seq, "" );
fprintf( stderr, "done.\n" );
}
if( alg == 'T' )
{
fprintf( stderr, "Calling SLARA\n" );
calllara( njob, seq, "-s" );
fprintf( stderr, "done.\n" );
}
ilim = njob - 1;
for( i=0; i<ilim; i++ )
{
fprintf( stderr, "% 5d / %d\r", i, njob );
for( j=i+1; j<njob; j++ )
{
if( strlen( seq[i] ) == 0 || strlen( seq[j] ) == 0 )
{
distancemtx[i][j] = pscore;
continue;
}
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
if( use_fft )
{
pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
off1 = off2 = 0;
}
else
#endif
{
switch( alg )
{
case( 'a' ):
pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
off1 = off2 = 0;
break;
case( 'A' ):
pscore = G__align11( mseq1, mseq2, alloclen, NULL, 0, NULL );
off1 = off2 = 0;
break;
#if 0
case( 'V' ):
pscore = VAalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
break;
case( 'S' ):
fprintf( stderr, "aligning %d-%d\n", i, j );
pscore = suboptalign11( mseq1, mseq2, alloclen, &off1, &off2, localhomtable[i]+j );
fprintf( stderr, "i,j = %d,%d, score = %f\n", i,j, pscore );
break;
#endif
case( 'N' ):
pscore = genL__align11( mseq1, mseq2, alloclen, &off1, &off2 );
// fprintf( stderr, "pscore = %f\n", pscore );
break;
case( 'L' ):
pscore = L__align11( mseq1, mseq2, alloclen, &off1, &off2 );
// fprintf( stderr, "pscore (1) = %f\n", pscore );
// pscore = (float)naivepairscore11( *mseq1, *mseq2, penalty ); // nennnotame
// fprintf( stderr, "pscore (2) = %f\n\n", pscore );
break;
case( 'H' ):
pscore = recallpairfoldalign( mseq1, mseq2, i, j, &off1, &off2, alloclen );
break;
case( 'B' ):
case( 'T' ):
pscore = recalllara( mseq1, mseq2, alloclen );
off1 = off2 = 0;
// fprintf( stderr, "lara, pscore = %f\n", pscore );
break;
case( 's' ):
pscore = callmxscarna( mseq1, mseq2, alloclen );
off1 = off2 = 0;
// fprintf( stderr, "scarna, pscore = %f\n", pscore );
break;
case( 'M' ):
// pscore = MSalign11( mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL );
pscore = MSalign11( mseq1, mseq2, alloclen );
// fprintf( stderr, "pscore = %f\n", pscore );
break;
ErrorExit( "ERROR IN SOURCE FILE" );
}
}
distancemtx[i][j] = pscore;
#if SCOREOUT
fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
#endif
// fprintf( stderr, "pslocal = %d\n", pslocal );
// offset = makelocal( *mseq1, *mseq2, pslocal );
#if 0
fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
fprintf( stderr, ">%d\n%s\n>%d\n%s\n>\n", i, mseq1[0], j, mseq2[0] );
#endif
// putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, countamino( *mseq1, off1 ), countamino( *mseq2, off2 ), pscore, strlen( mseq1[0] ) );
// fprintf( stderr, "pscore = %f\n", pscore );
if( alg == 'H' )
// if( alg == 'H' || alg == 's' || alg == 'B' ) // next version
putlocalhom_ext( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
else if( alg != 'S' && alg != 'V' )
putlocalhom2( mseq1[0], mseq2[0], localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
}
}
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 %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
}
}
}
fclose( hat3p );
#if DEBUG
fprintf( stderr, "calling FreeLocalHomTable\n" );
#endif
FreeLocalHomTable( localhomtable, njob );
#if DEBUG
fprintf( stderr, "done. FreeLocalHomTable\n" );
#endif
}
void GroupAlign( int nseq1, int nseq2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, int ***topol, double **len, double *eff, int alloclen )
{
int i;
int clus1, clus2;
int s1, s2;
float pscore;
static char **name1, **name2;
double *effarr = eff;
double *effarr1 = NULL;
double *effarr2 = NULL;
static char *indication1, *indication2;
float dumfl = 0.0;
int intdum;
#if DEBUG
double time1, time2;
#endif
// fprintf( stderr, "in GroupAlign fftWinSize = %d\n", fftWinSize );
// fprintf( stderr, "in GroupAlign fftThreshold = %d\n", fftThreshold );
if( effarr1 == NULL )
{
name1 = AllocateCharMtx( nseq1, B );
name2 = AllocateCharMtx( nseq2, B );
indication1 = AllocateCharVec( 150 );
indication2 = AllocateCharVec( 150 );
effarr1 = AllocateDoubleVec( njob );
effarr2 = AllocateDoubleVec( njob );
#if 0
#else
#endif
}
for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
s1 = 0;
s2 = nseq1;
// fprintf( stdout, "nseq1 = %d\n", nseq1 );
clus1 = conjuctionforgaln( 0, nseq1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
clus2 = conjuctionforgaln( nseq1, njob, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
/*
fprintf( stderr, "before align all\n" );
display( aseq, njob );
fprintf( stderr, "\n" );
fprintf( stderr, "before align 1 %s \n", indication1 );
display( mseq1, clus1 );
fprintf( stderr, "\n" );
fprintf( stderr, "before align 2 %s \n", indication2 );
display( mseq2, clus2 );
fprintf( stderr, "\n" );
*/
commongappick( nseq1, mseq1 );
commongappick( nseq2, mseq2 );
#if DEBUG
time1 = getrusage_sec();
fprintf( stderr, "entering Falign\n" );
#endif
if( use_fft )
{
if( alg == 'M' )
pscore = Falign_udpari_long( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum );
else
pscore = Falign( NULL, NULL, n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, NULL, NULL, clus1, clus2, alloclen, &intdum, NULL, 0, NULL );
}
else
{
if( alg == 'M' )
pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
else
pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
}
#if DEBUG
time2 = getrusage_sec();
fprintf( stdout, "### %d - %d, %f\n", clus1, clus2, time2-time1 );
fflush( stdout );
#endif
/*
fprintf( stderr, "after align 1 %s \n", indication1 );
display( mseq1, clus1 );
fprintf( stderr, "\n" );
fprintf( stderr, "after align 2 %s \n", indication2 );
display( mseq2, clus2 );
fprintf( stderr, "\n" );
*/
fprintf( stderr, "group-to-group %s /%s %f\n", indication1, indication2, pscore );
if( disp ) display( aseq, njob );
fprintf( stderr, "\n" );
/*
trap = fopen( "pre", "r+" );
if( !trap ) ErrorExit( 1 );
WriteGapFill( trap, njob, name, nlen, aseq );
fclose( trap );
fprintf( stdout, "nseq1 = %d\n", nseq1 );
*/
}