Пример #1
0
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
}
Пример #2
0
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 );
*/
}