X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2Ftbfast.c;fp=binaries%2Fsrc%2Fmafft%2Fcore%2Ftbfast.c;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=dd7e7b5902b32f9baffbd9a270f6beb49cea22ce;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git

diff --git a/binaries/src/mafft/core/tbfast.c b/binaries/src/mafft/core/tbfast.c
deleted file mode 100644
index dd7e7b5..0000000
--- a/binaries/src/mafft/core/tbfast.c
+++ /dev/null
@@ -1,1070 +0,0 @@
-#include "mltaln.h"
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-static int treein;
-static int topin;
-static int treeout;
-static int distout;
-static int noalign;
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-	treein = 0;
-	topin = 0;
-	rnaprediction = 'm';
-	rnakozo = 0;
-	nevermemsave = 0;
-	inputfile = NULL;
-	fftkeika = 0;
-	constraint = 0;
-	nblosum = 62;
-	fmodel = 0;
-	calledByXced = 0;
-	devide = 0;
-	use_fft = 0; // chuui
-	force_fft = 0;
-	fftscore = 1;
-	fftRepeatStop = 0;
-	fftNoAnchStop = 0;
-    weight = 3;
-    utree = 1;
-	tbutree = 1;
-    refine = 0;
-    check = 1;
-    cut = 0.0;
-    disp = 0;
-    outgap = 1;
-    alg = 'A';
-    mix = 0;
-	tbitr = 0;
-	scmtd = 5;
-	tbweight = 0;
-	tbrweight = 3;
-	checkC = 0;
-	treemethod = 'X';
-	contin = 0;
-	scoremtx = 1;
-	kobetsubunkatsu = 0;
-	dorp = NOTSPECIFIED;
-	ppenalty = NOTSPECIFIED;
-	ppenalty_ex = NOTSPECIFIED;
-	poffset = NOTSPECIFIED;
-	kimuraR = NOTSPECIFIED;
-	pamN = NOTSPECIFIED;
-	geta2 = GETA2;
-	fftWinSize = NOTSPECIFIED;
-	fftThreshold = NOTSPECIFIED;
-	RNAppenalty = NOTSPECIFIED;
-	RNAppenalty_ex = NOTSPECIFIED;
-	RNApthr = NOTSPECIFIED;
-	TMorJTT = JTT;
-	consweight_multi = 1.0;
-	consweight_rna = 0.0;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-	{
-        while ( ( c = *++argv[0] ) )
-		{
-            switch( c )
-            {
-				case 'i':
-					inputfile = *++argv;
-					fprintf( stderr, "inputfile = %s\n", inputfile );
-					--argc;
-                    goto nextoption;
-				case 'e':
-					RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
-					--argc;
-					goto nextoption;
-				case 'o':
-					RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
-					--argc;
-					goto nextoption;
-				case 'f':
-					ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
-//					fprintf( stderr, "ppenalty = %d\n", ppenalty );
-					--argc;
-					goto nextoption;
-				case 'g':
-					ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
-					fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
-					--argc;
-					goto nextoption;
-				case 'h':
-					poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
-//					fprintf( stderr, "poffset = %d\n", poffset );
-					--argc;
-					goto nextoption;
-				case 'k':
-					kimuraR = atoi( *++argv );
-					fprintf( stderr, "kappa = %d\n", kimuraR );
-					--argc;
-					goto nextoption;
-				case 'b':
-					nblosum = atoi( *++argv );
-					scoremtx = 1;
-					fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
-					--argc;
-					goto nextoption;
-				case 'j':
-					pamN = atoi( *++argv );
-					scoremtx = 0;
-					TMorJTT = JTT;
-					fprintf( stderr, "jtt/kimura %d\n", pamN );
-					--argc;
-					goto nextoption;
-				case 'm':
-					pamN = atoi( *++argv );
-					scoremtx = 0;
-					TMorJTT = TM;
-					fprintf( stderr, "tm %d\n", pamN );
-					--argc;
-					goto nextoption;
-				case 'l':
-					fastathreshold = atof( *++argv );
-					constraint = 2;
-					--argc;
-					goto nextoption;
-				case 'r':
-					consweight_rna = atof( *++argv );
-					rnakozo = 1;
-					--argc;
-					goto nextoption;
-				case 'c':
-					consweight_multi = atof( *++argv );
-					--argc;
-					goto nextoption;
-				case 'R':
-					rnaprediction = 'r';
-					break;
-				case 's':
-					RNAscoremtx = 'r';
-					break;
-#if 1
-				case 'a':
-					fmodel = 1;
-					break;
-#endif
-				case 'y':
-					distout = 1;
-					break;
-				case 't':
-					treeout = 1;
-					break;
-				case 'T':
-					noalign = 1;
-					break;
-				case 'D':
-					dorp = 'd';
-					break;
-				case 'P':
-					dorp = 'p';
-					break;
-				case 'O':
-					fftNoAnchStop = 1;
-					break;
-#if 0
-				case 'e':
-					fftscore = 0;
-					break;
-				case 'r':
-					fmodel = -1;
-					break;
-				case 'R':
-					fftRepeatStop = 1;
-					break;
-				case 's':
-					treemethod = 's';
-					break;
-#endif
-				case 'X':
-					treemethod = 'X';
-					break;
-				case 'E':
-					treemethod = 'E';
-					break;
-				case 'q':
-					treemethod = 'q';
-					break;
-#if 0
-				case 'a':
-					alg = 'a';
-					break;
-#endif
-				case 'Q':
-					alg = 'Q';
-					break;
-				case 'H':
-					alg = 'H';
-					break;
-				case 'A':
-					alg = 'A';
-					break;
-				case 'S':
-					alg = 'S';
-					break;
-				case 'M':
-					alg = 'M';
-					break;
-				case 'N':
-					nevermemsave = 1;
-					break;
-				case 'B':
-					break;
-				case 'C':
-					alg = 'C';
-					break;
-				case 'F':
-					use_fft = 1;
-					break;
-				case 'G':
-					force_fft = 1;
-					use_fft = 1;
-					break;
-				case 'U':
-					treein = 1;
-					break;
-				case 'V':
-					topin = 1;
-					break;
-				case 'u':
-					tbrweight = 0;
-					weight = 0;
-					break;
-				case 'v':
-					tbrweight = 3;
-					break;
-				case 'd':
-					disp = 1;
-					break;
-#if 0
-				case 'o':
-					outgap = 0;
-					break;
-#endif
-/* Modified 01/08/27, default: user tree */
-				case 'J':
-					tbutree = 0;
-					break;
-/* modification end. */
-				case 'z':
-					fftThreshold = atoi( *++argv );
-					--argc; 
-					goto nextoption;
-				case 'w':
-					fftWinSize = atoi( *++argv );
-					--argc;
-					goto nextoption;
-				case 'Z':
-					checkC = 1;
-					break;
-                default:
-                    fprintf( stderr, "illegal option %c\n", c );
-                    argc = 0;
-                    break;
-            }
-		}
-		nextoption:
-			;
-	}
-    if( argc == 1 )
-    {
-        cut = atof( (*argv) );
-        argc--;
-    }
-    if( argc != 0 ) 
-    {
-        fprintf( stderr, "options: Check source file !\n" );
-        exit( 1 );
-    }
-	if( tbitr == 1 && outgap == 0 )
-	{
-		fprintf( stderr, "conflicting options : o, m or u\n" );
-		exit( 1 );
-	}
-	if( alg == 'C' && outgap == 0 )
-	{
-		fprintf( stderr, "conflicting options : C, o\n" );
-		exit( 1 );
-	}
-}
-
-
-void treebase( int nlen[M], char **aseq, char **mseq1, char **mseq2, int ***topol, double *effarr, int *alloclen, LocalHom **localhomtable, RNApair ***singlerna, double *effarr_kozo )
-{
-	int i, l;
-	int len1, len2;
-	int clus1, clus2;
-	float pscore, tscore;
-	static char *indication1, *indication2;
-	static double *effarr1 = NULL;
-	static double *effarr2 = NULL;
-	static double *effarr1_kozo = NULL;
-	static double *effarr2_kozo = NULL;
-	static LocalHom ***localhomshrink = NULL;
-	static int *fftlog;
-	int m1, m2;
-	float dumfl = 0.0;
-	int ffttry;
-	RNApair ***grouprna1, ***grouprna2;
-
-	if( rnakozo && rnaprediction == 'm' )
-	{
-		grouprna1 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
-		grouprna2 = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
-	}
-	else
-	{
-		grouprna1 = grouprna2 = NULL;
-	}
-
-	if( effarr1 == NULL ) 
-	{
-		fftlog = AllocateIntVec( njob );
-		effarr1 = AllocateDoubleVec( njob );
-		effarr2 = AllocateDoubleVec( njob );
-		indication1 = AllocateCharVec( 150 );
-		indication2 = AllocateCharVec( 150 );
-#if 0
-#else
-		if( constraint )
-		{
-			localhomshrink = (LocalHom ***)calloc( njob, sizeof( LocalHom ** ) );
-			for( i=0; i<njob; i++)
-				localhomshrink[i] = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
-		}
-#endif
-		effarr1_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
-		effarr2_kozo = AllocateDoubleVec( njob ); //tsuneni allocate sareru.
-		for( i=0; i<njob; i++ ) effarr1_kozo[i] = 0.0;
-		for( i=0; i<njob; i++ ) effarr2_kozo[i] = 0.0;
-	}
-
-	for( l=0; l<njob; l++ ) fftlog[l] = 1;
-
-#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
-
-
-	if( constraint )
-		calcimportance( njob, effarr, aseq, localhomtable );
-
-
-//	writePre( njob, name, nlen, aseq, 0 );
-
-	tscore = 0.0;
-	for( l=0; l<njob-1; l++ )
-	{
-		m1 = topol[l][0][0];
-		m2 = topol[l][1][0];
-        len1 = strlen( aseq[m1] );
-        len2 = strlen( aseq[m2] );
-        if( *alloclen < len1 + len2 )
-        {
-			fprintf( stderr, "\nReallocating.." );
-			*alloclen = ( len1 + len2 ) + 1000;
-			ReallocateCharMtx( aseq, njob, *alloclen + 10  );
-			fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
-		}
-
-		if( effarr_kozo )
-		{
-			clus1 = fastconjuction_noname_kozo( topol[l][0], aseq, mseq1, effarr1, effarr, effarr1_kozo, effarr_kozo, indication1 );
-			clus2 = fastconjuction_noname_kozo( topol[l][1], aseq, mseq2, effarr2, effarr, effarr2_kozo, effarr_kozo, indication2 );
-		}
-		else
-		{
-			clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1 );
-			clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2 );
-		}
-
-
-		fprintf( trap_g, "\nSTEP-%d\n", l );
-		fprintf( trap_g, "group1 = %s\n", indication1 );
-		fprintf( trap_g, "group2 = %s\n", indication2 );
-
-#if 1
-		fprintf( stderr, "\rSTEP % 5d /%d ", l+1, njob-1 );
-#else
-		fprintf( stdout, "STEP %d /%d\n", l+1, njob-1 );
-		fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
-		fprintf( stderr, "group1 = %.66s", indication1 );
-		if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "group2 = %.66s", indication2 );
-		if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
-		fprintf( stderr, "\n" );
-#endif
-
-
-
-//		for( i=0; i<clus1; i++ ) fprintf( stderr, "## STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
-
-		if( constraint )
-		{
-			fastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-//			msfastshrinklocalhom( topol[l][0], topol[l][1], localhomtable, localhomshrink );
-//			fprintf( stderr, "localhomshrink =\n" );
-//			outlocalhompt( localhomshrink, clus1, clus2 );
-//			weightimportance4( clus1, clus2, effarr1, effarr2, localhomshrink );
-//			fprintf( stderr, "after weight =\n" );
-//			outlocalhompt( localhomshrink, clus1, clus2 );
-		}
-		if( rnakozo && rnaprediction == 'm' )
-		{
-			makegrouprna( grouprna1, singlerna, topol[l][0] );
-			makegrouprna( grouprna2, singlerna, topol[l][1] );
-		}
-
-		free( topol[l][0] );
-		free( topol[l][1] );
-
-/*
-		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" );
-*/
-
-		if( !nevermemsave && ( constraint != 2  && alg != 'M'  && ( len1 > 10000 || len2 > 10000 ) ) )
-		{
-			fprintf( stderr, "\nlen1=%d, len2=%d, Switching to the memsave mode.\n", len1, len2 );
-			alg = 'M';
-			if( commonIP ) FreeIntMtx( commonIP );
-			commonAlloc1 = 0;
-			commonAlloc2 = 0;
-		}
-		
-
-//		if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 );
-		if( fftlog[m1] && fftlog[m2] ) ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 1000 && clus2 < 1000 );
-		else						   ffttry = 0;
-//		ffttry = ( nlen[m1] > clus1 && nlen[m2] > clus2 && clus1 < 5000 && clus2 < 5000 ); // v6.708
-//		fprintf( stderr, "f=%d, len1/fftlog[m1]=%f, clus1=%d, len2/fftlog[m2]=%f, clus2=%d\n", ffttry, (float)len1/fftlog[m1], clus1, (float)len2/fftlog[m2], clus2 );
-//		fprintf( stderr, "f=%d, clus1=%d, fftlog[m1]=%d, clus2=%d, fftlog[m2]=%d\n", ffttry, clus1, fftlog[m1], clus2, fftlog[m2] );
-		if( constraint == 2 )
-		{
-			if( alg == 'M' )
-			{
-				fprintf( stderr, "\n\nMemory saving mode is not supported.\n\n" );
-				exit( 1 );
-			}
-			fprintf( stderr, "c" );
-			if( alg == 'A' )
-			{
-				imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, 1 );
-				if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
-				pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
-			}
-			else if( alg == 'H' )
-			{
-				imp_match_init_strictH( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
-				pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
-			}
-			else if( alg == 'Q' )
-			{
-				imp_match_init_strictQ( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
-				if( rnakozo ) imp_rnaQ( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
-				pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
-			}
-			else if( alg == 'R' )
-			{
-				imp_match_init_strictR( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, localhomshrink, 1 );
-				pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumfl, NULL, NULL, NULL, NULL );
-			}
-		}
-		else if( force_fft || ( use_fft && ffttry ) )
-		{
-			fprintf( stderr, "f" );
-			if( alg == 'M' )
-			{
-				fprintf( stderr, "m" );
-				pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
-			}
-			else
-				pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
-		}
-		else
-		{
-			fprintf( stderr, "d" );
-			fftlog[m1] = 0;
-			switch( alg )
-			{
-				case( 'a' ):
-					pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
-					break;
-				case( 'M' ):
-					fprintf( stderr, "m" );
-					pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL );
-					break;
-				case( 'A' ):
-					pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-					break;
-				case( 'Q' ):
-					pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-					break;
-				case( 'R' ):
-					pscore = R__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-					break;
-				case( 'H' ):
-					pscore = H__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-					break;
-				case ( 'C' ):
-					if( outgap && ( ( clus1 == 1 && clus2 != 1 ) || ( clus1 != 1 && clus2 == 1 ) ) )
-					{
-						pscore = translate_and_Calign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
-					}
-					else
-					{
-						pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-					}
-					break;
-				default:
-					ErrorExit( "ERROR IN SOURCE FILE" );
-			}
-		}
-
-		nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
-
-#if SCOREOUT
-		fprintf( stderr, "score = %10.2f\n", pscore );
-#endif
-		tscore += pscore;
-/*
-		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" );
-*/
-
-//		writePre( njob, name, nlen, aseq, 0 );
-
-		if( disp ) display( aseq, njob );
-	}
-#if SCOREOUT
-	fprintf( stderr, "totalscore = %10.2f\n\n", tscore );
-#endif
-}
-
-static void WriteOptions( FILE *fp )
-{
-
-	if( dorp == 'd' ) fprintf( fp, "DNA\n" );
-	else
-	{
-		if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
-		else if( scoremtx ==  1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
-		else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
-	}
-    fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-    if( use_fft ) fprintf( fp, "FFT on\n" );
-
-	fprintf( fp, "tree-base method\n" );
-	if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
-	else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
-	if( tbitr || tbweight ) 
-	{
-		fprintf( fp, "iterate at each step\n" );
-		if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" ); 
-		if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" ); 
-		if( tbweight ) fprintf( fp, "  weighted\n" ); 
-		fprintf( fp, "\n" );
-	}
-
-   	 fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
-
-	if( alg == 'a' )
-		fprintf( fp, "Algorithm A\n" );
-	else if( alg == 'A' ) 
-		fprintf( fp, "Algorithm A+\n" );
-	else if( alg == 'S' ) 
-		fprintf( fp, "Apgorithm S\n" );
-	else if( alg == 'C' ) 
-		fprintf( fp, "Apgorithm A+/C\n" );
-	else
-		fprintf( fp, "Unknown algorithm\n" );
-
-	if( treemethod == 'X' )
-		fprintf( fp, "Tree = UPGMA (mix).\n" );
-	else if( treemethod == 'E' )
-		fprintf( fp, "Tree = UPGMA (average).\n" );
-	else if( treemethod == 'q' )
-		fprintf( fp, "Tree = Minimum linkage.\n" );
-	else
-		fprintf( fp, "Unknown tree.\n" );
-
-    if( use_fft )
-    {
-        fprintf( fp, "FFT on\n" );
-        if( dorp == 'd' )
-            fprintf( fp, "Basis : 4 nucleotides\n" );
-        else
-        {
-            if( fftscore )
-                fprintf( fp, "Basis : Polarity and Volume\n" );
-            else
-                fprintf( fp, "Basis : 20 amino acids\n" );
-        }
-        fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
-        fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
-    }
-	else
-        fprintf( fp, "FFT off\n" );
-	fflush( fp );
-}
-	 
-
-int main( int argc, char *argv[] )
-{
-	static int  *nlen;	
-	static float *selfscore;
-	int nogaplen;
-	static char **name, **seq;
-	static char **mseq1, **mseq2;
-	static char **bseq;
-	static float **iscore, **iscore_kozo;
-	static double *eff, *eff_kozo, *eff_kozo_mapped = NULL;
-	int i, j, ien, ik, jk;
-	static int ***topol, ***topol_kozo;
-	static float **len, **len_kozo;
-	FILE *prep;
-	FILE *infp;
-	FILE *orderfp;
-	FILE *hat2p;
-	
-	char c;
-	int alloclen;
-	LocalHom **localhomtable;
-	RNApair ***singlerna;
-	float ssi, ssj, bunbo;
-	static char *kozoarivec;
-	int nkozo;
-
-	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 );
-
-	nkozo = 0;
-
-	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+1 );
-	mseq1 = AllocateCharMtx( njob, 0 );
-	mseq2 = AllocateCharMtx( njob, 0 );
-
-	name = AllocateCharMtx( njob, B+1 );
-	nlen = AllocateIntVec( njob );
-	selfscore = AllocateFloatVec( njob );
-
-	topol = AllocateIntCub( njob, 2, 0 );
-	len = AllocateFloatMtx( njob, 2 );
-	iscore = AllocateFloatHalfMtx( njob );
-	eff = AllocateDoubleVec( njob );
-	kozoarivec = AllocateCharVec( njob );
-	if( constraint )
-	{
-		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].overlapaa = -1.0;
-				localhomtable[i][j].opt = -1.0;
-				localhomtable[i][j].importance = -1.0;
-				localhomtable[i][j].next = NULL;
-				localhomtable[i][j].korh = 'h';
-			}
-		}
-
-		fprintf( stderr, "Loading 'hat3' ... " );
-		prep = fopen( "hat3", "r" );
-		if( prep == NULL ) ErrorExit( "Make hat3." );
-		readlocalhomtable( prep, njob, localhomtable, kozoarivec );
-		fclose( prep );
-		fprintf( stderr, "\ndone.\n" );
-
-
-		nkozo = 0;
-		for( i=0; i<njob; i++ ) 
-		{
-//			fprintf( stderr, "kozoarivec[%d] = %d\n", i, kozoarivec[i] );
-			if( kozoarivec[i] ) nkozo++;
-		}
-		if( nkozo )
-		{
-			topol_kozo = AllocateIntCub( nkozo, 2, 0 );
-			len_kozo = AllocateFloatMtx( nkozo, 2 );
-			iscore_kozo = AllocateFloatHalfMtx( nkozo );
-			eff_kozo = AllocateDoubleVec( nkozo );
-			eff_kozo_mapped = AllocateDoubleVec( njob );
-		}
-
-
-//		outlocalhom( localhomtable, njob );
-
-#if 0
-		fprintf( stderr, "Extending localhom ... " );
-		extendlocalhom2( njob, localhomtable );
-		fprintf( stderr, "done.\n" );
-#endif
-	}
-
-#if 0
-	readData( infp, 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, "Illegal character %c\n", c );
-		exit( 1 );
-	}
-
-//	writePre( njob, name, nlen, seq, 0 );
-
-	if( treein )
-	{
-#if 0
-		if( nkozo )
-		{
-			fprintf( stderr, "Both structure and user tree have been given. Not yet supported!\n" );
-			exit( 1 );
-		}
-#endif
-		fprintf( stderr, "Loading a tree ... " );
-		loadtree( njob, topol, len, name, nlen );
-		fprintf( stderr, "\ndone.\n\n" );
-	}
-	else
-	{
-		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 );
-				}
-			}
-	
-			fprintf( stderr, "Making a distance matrix .. \n" );
-			ien = njob-1;
-#if 0 //060424
-			for( i=0; i<njob; i++ ) 
-			{
-				fprintf( stderr, "\r% 5d / %d", i, ien );
-				for( j=i; j<njob; j++ ) 
-				{
-					iscore[i][j-i] = score_calcp( seq[i], seq[j], nlen[0] );
-					fprintf( stderr, "i=%d,j=%d### %f\n", i, j, iscore[i][j-i] );
-				}
-			}
-			fprintf( stderr, "\ndone.\n\n" );
-   	    	for( i=0; i<ien; i++ )
-	   	    {
-   		        for( j=i+1; j<njob; j++ ) 
-   		        {
-   		            iscore[i][j-i] = ( 1.0 - iscore[i][j-i] / MIN( iscore[i][0], iscore[j][0] ) ) * 3;
-					fprintf( stderr, "i=%d,j=%d### %f\n", i, j, iscore[i][j-i] );
-   		        }
-   		    }
-#else
-			for( i=0; i<njob; i++ ) 
-			{
-				selfscore[i] = naivepairscore11( seq[i], seq[i], penalty );
-			}
-			for( i=0; i<ien; i++ ) 
-			{
-				if( i % 10 == 0 ) fprintf( stderr, "\r% 5d / %d", i, ien );
-				ssi = selfscore[i];
-				for( j=i+1; j<njob; j++ ) 
-				{
-					ssj = selfscore[j];
-					bunbo = MIN( ssi, ssj );
-					if( bunbo == 0.0 )
-						iscore[i][j-i] = 1.0;
-					else
-						iscore[i][j-i] = 1.0 - naivepairscore11( seq[i], seq[j], penalty ) / MIN( selfscore[i], selfscore[j] );
-
-#if 0
-					fprintf( stderr, "### ssj = %f\n", ssj );
-					fprintf( stderr, "### selfscore[i] = %f\n", selfscore[i] );
-					fprintf( stderr, "### selfscore[j] = %f\n", selfscore[j] );
-					fprintf( stderr, "### rawscore = %f\n", naivepairscore11( seq[i], seq[j], penalty ) );
-#endif
-				}
-			}
-			fprintf( stderr, "\ndone.\n\n" );
-#endif
-	
-		}
-		else
-		{
-			fprintf( stderr, "Loading 'hat2' ... " );
-			prep = fopen( "hat2", "r" );
-			if( prep == NULL ) ErrorExit( "Make hat2." );
-			readhat2_floathalf_pointer( prep, njob, name, iscore );
-			fclose( prep );
-			fprintf( stderr, "done.\n" );
-		}
-#if 1
-		if( distout )
-		{
-			hat2p = fopen( "hat2", "w" );
-			WriteFloatHat2_pointer_halfmtx( hat2p, njob, name, iscore );
-			fclose( hat2p );
-		}
-#endif
-		if( nkozo )
-		{
-			ien = njob-1;
-			ik = 0;
-			for( i=0; i<ien; i++ )
-			{
-				jk = ik+1;
-				for( j=i+1; j<njob; j++ ) 
-				{
-					if( kozoarivec[i] && kozoarivec[j] )
-					{
-						iscore_kozo[ik][jk-ik] = iscore[i][j-i];
-					}
-					if( kozoarivec[j] ) jk++;
-				}
-				if( kozoarivec[i] ) ik++;
-			}
-		}
-
-		fprintf( stderr, "Constructing a UPGMA tree ... " );
-		if( topin )
-		{
-			fprintf( stderr, "Loading a topology ... " );
-			loadtop( njob, iscore, topol, len );
-			fprintf( stderr, "\ndone.\n\n" );
-		}
-		else if( treeout )
-		{
-			fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( njob, iscore, topol, len, name, nlen );
-		}
-		else
-		{
-			fixed_musclesupg_float_realloc_nobk_halfmtx( njob, iscore, topol, len );
-		}
-//		else 
-//			ErrorExit( "Incorrect tree\n" );
-
-		if( nkozo )
-		{
-//			for( i=0; i<nkozo-1; i++ )
-//				for( j=i+1; j<nkozo; j++ )
-//					fprintf( stderr, "iscore_kozo[%d][%d] =~ %f\n", i, j, iscore_kozo[i][j-i] );
-			fixed_musclesupg_float_realloc_nobk_halfmtx( nkozo, iscore_kozo, topol_kozo, len_kozo );
-		}
-		fprintf( stderr, "\ndone.\n\n" );
-	}
-
-
-	orderfp = fopen( "order", "w" );
-	if( !orderfp )
-	{
-		fprintf( stderr, "Cannot open 'order'\n" );
-		exit( 1 );
-	}
-	for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
-	{
-		fprintf( orderfp, "%d\n", j );
-	}
-	for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
-	{
-		fprintf( orderfp, "%d\n", j );
-	}
-	fclose( orderfp );
-
-	if( treeout && noalign ) 
-	{
-		writeData_pointer( prep_g, njob, name, nlen, seq );
-		fprintf( stderr, "\n" ); 
-		SHOWVERSION;
-		return( 0 );
-	}
-
-//	countnode( njob, topol, node0 );
-	if( tbrweight )
-	{
-		weight = 3; 
-#if 0
-		utree = 0; counteff( njob, topol, len, eff ); utree = 1;
-#else
-		counteff_simple_float( njob, topol, len, eff );
-
-		if( nkozo )
-		{
-//			counteff_simple_float( nkozo, topol_kozo, len_kozo, eff_kozo ); // single weight nanode iranai
-			for( i=0,j=0; i<njob; i++ )
-			{
-				if( kozoarivec[i] )
-				{
-//					eff_kozo_mapped[i] = eff_kozo[j]; //
-					eff_kozo_mapped[i] = eff[i];      // single weight
-					j++;
-				}
-				else
-					eff_kozo_mapped[i] = 0.0;
-//				fprintf( stderr, "eff_kozo_mapped[%d] = %f\n", i, eff_kozo_mapped[i] );
-//				fprintf( stderr, "            eff[%d] = %f\n", i, eff[i] );
-			}
-		}
-
-
-#endif
-	}
-	else
-	{
-		for( i=0; i<njob; i++ ) eff[i] = 1.0;
-		if( nkozo ) 
-		{
-			for( i=0; i<njob; i++ ) 
-			{
-				if( kozoarivec[i] ) 
-					eff_kozo_mapped[i] = 1.0;
-				else
-					eff_kozo_mapped[i] = 0.0;
-			}
-		}
-	}
-
-	FreeFloatHalfMtx( iscore, njob );
-	FreeFloatMtx( len );
-
-	bseq = AllocateCharMtx( njob, nlenmax*2+1 );
-	alloclen = nlenmax*2;
-
-	for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
-
-	if( rnakozo && rnaprediction == 'm' )
-	{
-		singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
-		prep = fopen( "hat4", "r" );
-		if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
-		fprintf( stderr, "Loading 'hat4' ... " );
-		for( i=0; i<njob; i++ )
-		{
-			nogaplen = strlen( bseq[i] );
-			singlerna[i] = (RNApair **)calloc( nogaplen, sizeof( RNApair * ) );
-			for( j=0; j<nogaplen; j++ )
-			{
-				singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
-				singlerna[i][j][0].bestpos = -1;
-				singlerna[i][j][0].bestscore = -1.0;
-			}
-			readmccaskill( prep, singlerna[i], nogaplen );
-		}
-		fclose( prep );
-		fprintf( stderr, "\ndone.\n" );
-	}
-	else
-		singlerna = NULL;
-
-
-	fprintf( stderr, "Progressive alignment ... \n" );
-	treebase( nlen, bseq, mseq1, mseq2, topol, eff, &alloclen, localhomtable, singlerna, eff_kozo_mapped );
-	fprintf( stderr, "\ndone.\n" );
-
-#if 0
-	if( constraint )
-	{
-		LocalHom *tmppt1, *tmppt2;
-		for( i=0; i<njob; i++)
-		{
-			for( j=0; j<njob; j++)
-			{
-				tmppt1 = localhomtable[i]+j;
-				while( tmppt2 = tmppt1->next )
-				{
-					free( (void *)tmppt1 );
-					tmppt1 = tmppt2;
-				}
-				free( (void *)tmppt1 );
-			}
-			free( (void *)(localhomtable[i]+j) );
-		}
-		free( (void *)localhomtable );
-	}
-#endif
-
-	fprintf( trap_g, "done.\n" );
-	fclose( trap_g );
-
-	writeData_pointer( prep_g, njob, name, nlen, bseq );
-#if 0
-	writeData( stdout, njob, name, nlen, bseq );
-	writePre( njob, name, nlen, bseq, !contin );
-	writeData_pointer( prep_g, njob, name, nlen, aseq );
-#endif
-#if IODEBUG
-	fprintf( stderr, "OSHIMAI\n" );
-#endif
-
-	if( constraint ) FreeLocalHomTable( localhomtable, njob );
-
-	SHOWVERSION;
-	return( 0 );
-}