X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2Fsplittbfast.c;fp=binaries%2Fsrc%2Fmafft%2Fcore%2Fsplittbfast.c;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=356a74934958db7ff10e4691b9b73c2b499d036c;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git

diff --git a/binaries/src/mafft/core/splittbfast.c b/binaries/src/mafft/core/splittbfast.c
deleted file mode 100644
index 356a749..0000000
--- a/binaries/src/mafft/core/splittbfast.c
+++ /dev/null
@@ -1,3274 +0,0 @@
-#include "mltaln.h"
-
-
-#define TREE 1
-#define PICKSIZE 50 // must be >= 3
-#define WEIGHT 0
-#define TOKYORIPARA 0.70 // 0.70
-#define TOKYORIPARA_A 0.70  // changed
-#define LENFAC 1
-#define HUKINTOTREE 1
-#define DIANA 0
-#define MAX6DIST 10.0
-
-// kouzoutai ni sasareru pointer ha static
-
-#define DEBUG 0
-#define IODEBUG 0
-#define SCOREOUT 0
-
-#define END_OF_VEC -1
-
-static char *fastapath;
-static int doalign;
-static int fromaln;
-static int uselongest;
-static int treeout;
-static int classsize;
-static int picksize;
-static int maxl;
-static int tsize;
-static int reorder;
-static int pid;
-static int maxdepth = 0;
-static double tokyoripara;
-
-static double lenfaca, lenfacb, lenfacc, lenfacd;
-#define PLENFACA 0.01
-#define PLENFACB 10000
-#define PLENFACC 10000
-#define PLENFACD 0.1
-#define DLENFACA 0.01
-#define DLENFACB 2500
-#define DLENFACC 2500
-#define DLENFACD 0.1
-
-static char datafile[1000];
-static char queryfile[1000];
-static char resultfile[1000];
-
-typedef struct _scores
-{
-	double score;
-	int selfscore;
-	int orilen;
-	int *pointt;
-	int numinseq;
-	char *name;
-//	char *seq; // reallo
-//	char **seqpt;
-	int shimon;
-} Scores;
-
-int intcompare( const int *a, const int *b )
-{
-	return( *a - *b );
-}
-
-int lcompare( const Scores *a, const Scores *b )
-{
-	if( a->orilen < b->orilen ) return 1;
-	else if( a->orilen > b->orilen ) return -1;
-	else return 0;
-}
-
-int dcompare( const Scores *a, const Scores *b )
-{
-	if( a->score > b->score ) return 1;
-	else if( a->score < b->score ) return -1;
-	else
-	{
-		if( a->selfscore < b->selfscore ) return 1;
-		else if( a->selfscore > b->selfscore ) return -1;
-		else 
-		{
-			if( a->orilen < b->orilen ) return 1;
-			else if( a->orilen > b->orilen ) return -1;
-			else return 0;
-		}
-	}
-}
-
-#if 0
-static void	gappickandx0( char *out, char *in )
-{
-	char c;
-	if( scoremtx == -1 )
-	{
-		while( *in )
-		{
-			if( (c=*in++) == '-' )
-				;	
-			else if( c == 'u' )
-				*out++ = 't';
-			else if( amino_n[c] < 4 && amino_n[c] > -1 )
-				*out++ = c;
-			else
-				*out++ = 'n';
-		}
-	}
-	else
-	{
-		while( *in )
-		{
-			if( (c=*in++) == '-' )
-				;	
-			else if( amino_n[c] < 20 && amino_n[c] > -1 )
-				*out++ = c;
-			else
-				*out++ = 'X';
-		}
-	}
-	*out = 0;
-}	
-
-static int getkouho( int *pickkouho, double prob, int nin, Scores *scores, char **seq ) // 0 < prob < 1
-{
-	int nkouho = 0;
-	int i, j;
-	int *iptr = pickkouho;
-	for( i=1; i<nin; i++ )
-	{
-		if( ( nkouho==0 || rnd() < prob ) && ( scores[i].shimon != scores->shimon || strcmp( seq[scores->numinseq], seq[scores[i].numinseq] ) ) )
-		{
-#if 0
-			for( j=0; j<nkouho; j++ )
-			{
-				if( scores[i].shimon == scores[pickkouho[j]].shimon || !strcmp( seq[scores[pickkouho[j]].numinseq], seq[scores[i].numinseq] ) ) 
-					break;
-			}
-			if( j == nkouho )
-#endif
-			{
-				*iptr++ = i;
-				nkouho++;
-//				fprintf( stderr, "ok! nkouho=%d\n", nkouho );
-			}
-		}
-		else
-		{
-			;
-//			fprintf( stderr, "no! %d-%d\n", 0, scores[i].numinseq );
-		}
-	}
-	fprintf( stderr, "\ndone\n\n"  );
-	return nkouho;
-}
-
-#endif
-
-static void getfastascoremtx( int **tmpaminodis )
-{
-	FILE *qfp;
-	FILE *dfp;
-	FILE *rfp;
-	int i, j;
-	char aa;
-	int slen;
-	int res;
-	char com[10000];
-	static char *tmpseq;
-	static char *tmpname;
-	double *resvec;
-
-	if( scoremtx == -1 )
-	{
-		tmpaminodis['a']['a'] = 5;
-		tmpaminodis['g']['g'] = 5;
-		tmpaminodis['c']['c'] = 5;
-		tmpaminodis['t']['t'] = 5;
-		tmpaminodis['n']['n'] = -1;
-
-		return;
-	}
-
-
-	tmpseq = calloc( 2000, sizeof( char ) );
-	tmpname = calloc( B, sizeof( char ) );
-	resvec = calloc( 1, sizeof( double ) );
-
-//	fprintf( stderr, "xformatting .. " );
-	dfp = fopen( datafile, "w" );
-	if( !dfp ) ErrorExit( "Cannot open datafile." );
-	sprintf( tmpname, ">+===========+%d                      ", 0 );
-	strcpy( tmpseq, "AAAAAAXXXXXX" );
-	strcat( tmpseq, "CCCCCCXXXXXX" );
-	strcat( tmpseq, "DDDDDDXXXXXX" );
-	strcat( tmpseq, "EEEEEEXXXXXX" );
-	strcat( tmpseq, "FFFFFFXXXXXX" );
-	strcat( tmpseq, "GGGGGGXXXXXX" );
-	strcat( tmpseq, "HHHHHHXXXXXX" );
-	strcat( tmpseq, "IIIIIIXXXXXX" );
-	strcat( tmpseq, "KKKKKKXXXXXX" );
-	strcat( tmpseq, "LLLLLLXXXXXX" );
-	strcat( tmpseq, "MMMMMMXXXXXX" );
-	strcat( tmpseq, "NNNNNNXXXXXX" );
-	strcat( tmpseq, "PPPPPPXXXXXX" );
-	strcat( tmpseq, "QQQQQQXXXXXX" );
-	strcat( tmpseq, "RRRRRRXXXXXX" );
-	strcat( tmpseq, "SSSSSSXXXXXX" );
-	strcat( tmpseq, "TTTTTTXXXXXX" );
-	strcat( tmpseq, "VVVVVVXXXXXX" );
-	strcat( tmpseq, "WWWWWWXXXXXX" );
-	strcat( tmpseq, "YYYYYYXXXXXX" );
-	slen = strlen( tmpseq );
-	writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
-	fclose( dfp );
-	fprintf( stderr, "done.\n" );
-
-	for( i=0; i<20; i++ )
-	{
-		aa = amino[i];
-//		fprintf( stderr, "checking %c\n", aa );
-		*tmpseq = 0;
-		sprintf( tmpname, ">+===========+%d                      ", 0 );
-		for( j=0; j<6; j++ )
-			sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
-		qfp = fopen( queryfile, "w" );
-		if( !qfp ) ErrorExit( "Cannot open queryfile." );
-		writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
-		fclose( qfp );
-
-		if( scoremtx == -1 ) 
-			sprintf( com, "%s -z3 -m10  -n -Q -H -b%d -E%d -d%d %s %s %d > %s", fastapath,  M, M, 0, queryfile, datafile, 6, resultfile );
-		else
-			sprintf( com, "%s -z3 -m10  -p -Q -H -b%d -E%d -d%d %s %s %d > %s", fastapath,  M, M, 0, queryfile, datafile, 2, resultfile );
-		res = system( com );
-		if( res )
-		{
-			fprintf( stderr, "error in %s", fastapath );
-			exit( 1 );
-		}
-
-		rfp = fopen( resultfile, "r" );
-		if( rfp == NULL )  
-			ErrorExit( "file 'fasta.$$' does not exist\n" );
-		res = ReadFasta34m10_scoreonly( rfp, resvec, 1 );
-		fprintf( stderr, "%c: %f\n", 'A'+i, *resvec/6 );
-		fclose( rfp );
-		if( ( (int)*resvec % 6 ) > 0.0 )
-		{
-			fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
-			fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
-			exit( 1 );
-		}
-		tmpaminodis[(int)aa][(int)aa] = (int)( *resvec / 6 );
-//		fprintf( stderr, "*resvec=%f, tmpaminodis[aa][aa] = %d\n", *resvec, tmpaminodis[aa][aa] );
-	}
-	tmpaminodis['X']['X'] = -1;
-	free( tmpname );
-	free( tmpseq );
-	free( resvec );
-}
-
-#if 0
-static void getblastscoremtx( int **tmpaminodis )
-{
-	FILE *qfp;
-	FILE *dfp;
-	FILE *rfp;
-	int i, j;
-	char aa;
-	int slen;
-	int res;
-	char com[10000];
-	static char *tmpseq;
-	static char *tmpname;
-	double *resvec;
-
-	if( scoremtx == -1 )
-	{
-		tmpaminodis['a']['a'] = 1;
-		tmpaminodis['g']['g'] = 1;
-		tmpaminodis['c']['c'] = 1;
-		tmpaminodis['t']['t'] = 1;
-
-		return;
-	}
-
-
-	tmpseq = calloc( 2000, sizeof( char ) );
-	tmpname = calloc( B, sizeof( char ) );
-	resvec = calloc( 1, sizeof( double ) );
-
-//	fprintf( stderr, "xformatting .. " );
-	dfp = fopen( datafile, "w" );
-	if( !dfp ) ErrorExit( "Cannot open datafile." );
-	sprintf( tmpname, "\0", i ); // BUG!!
-	strcpy( tmpseq, "AAAAAAXXXXXX" );
-	strcat( tmpseq, "CCCCCCXXXXXX" );
-	strcat( tmpseq, "DDDDDDXXXXXX" );
-	strcat( tmpseq, "EEEEEEXXXXXX" );
-	strcat( tmpseq, "FFFFFFXXXXXX" );
-	strcat( tmpseq, "GGGGGGXXXXXX" );
-	strcat( tmpseq, "HHHHHHXXXXXX" );
-	strcat( tmpseq, "IIIIIIXXXXXX" );
-	strcat( tmpseq, "KKKKKKXXXXXX" );
-	strcat( tmpseq, "LLLLLLXXXXXX" );
-	strcat( tmpseq, "MMMMMMXXXXXX" );
-	strcat( tmpseq, "NNNNNNXXXXXX" );
-	strcat( tmpseq, "PPPPPPXXXXXX" );
-	strcat( tmpseq, "QQQQQQXXXXXX" );
-	strcat( tmpseq, "RRRRRRXXXXXX" );
-	strcat( tmpseq, "SSSSSSXXXXXX" );
-	strcat( tmpseq, "TTTTTTXXXXXX" );
-	strcat( tmpseq, "VVVVVVXXXXXX" );
-	strcat( tmpseq, "WWWWWWXXXXXX" );
-	strcat( tmpseq, "YYYYYYXXXXXX" );
-	slen = strlen( tmpseq );
-	writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
-	fclose( dfp );
-	if( scoremtx == -1 )
-		sprintf( com, "formatdb  -p f -i %s -o F", datafile );
-	else
-		sprintf( com, "formatdb  -i %s -o F", datafile );
-	system( com );
-	fprintf( stderr, "done.\n" );
-
-	for( i=0; i<20; i++ )
-	{
-		aa = amino[i];
-		fprintf( stderr, "checking %c\n", aa );
-		*tmpseq = 0;
-		for( j=0; j<6; j++ )
-			sprintf( tmpseq+strlen( tmpseq ), "%c", aa );
-		qfp = fopen( queryfile, "w" );
-		if( !qfp ) ErrorExit( "Cannot open queryfile." );
-		writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
-		fclose( qfp );
-
-		sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7  -i %s -d %s >  %s\0", 1, queryfile, datafile, resultfile );
-		res = system( com );
-		if( res )
-		{
-			fprintf( stderr, "error in %s", "blastall" );
-			exit( 1 );
-		}
-
-		rfp = fopen( resultfile, "r" );
-		if( rfp == NULL )  
-			ErrorExit( "file 'fasta.$$' does not exist\n" );
-		res = ReadBlastm7_scoreonly( rfp, resvec, 1 );
-		fprintf( stdout, "%c: %f\n", 'A'+i, *resvec/6 );
-		fclose( rfp );
-		if( ( (int)*resvec % 6 ) > 0.0 )
-		{
-			fprintf( stderr, "Error in blast, *resvec=%f\n", *resvec );
-			fprintf( stderr, "Error in blast, *resvec/6=%f\n", *resvec/6 );
-			exit( 1 );
-		}
-		tmpaminodis[aa][aa] = (int)( *resvec / 6 );
-	}
-	tmpaminodis['X']['X'] = 0;
-	free( tmpname );
-	free( tmpseq );
-	free( resvec );
-	
-}
-#endif
-
-static double *callfasta( char **seq, Scores *scores, int nin, int *picks, int query, int rewritedata )
-{
-	double *val;
-	FILE *qfp;
-	FILE *dfp;
-	FILE *rfp;
-	int i;
-	char com[10000];
-	static char datafile[1000];
-	static char queryfile[1000];
-	static char resultfile[1000];
-	static int pid;
-	static char *tmpseq;
-	static char *tmpname;
-	int slen;
-	int res;
-	static Scores *scoresbk = NULL;
-	static int ninbk = 0;
-
-	if( pid == 0 )
-	{
-		pid = (int)getpid();
-		sprintf( datafile, "/tmp/data-%d", pid );
-		sprintf( queryfile, "/tmp/query-%d", pid );
-		sprintf( resultfile, "/tmp/fasta-%d", pid );
-
-		tmpseq = calloc( nlenmax+1, sizeof( char ) );
-		tmpname = calloc( B+1, sizeof( char ) );
-	}
-
-	val = calloc( nin, sizeof( double ) );
-//	fprintf( stderr, "nin=%d, q=%d\n", nin, query );
-
-	if( rewritedata )
-	{
-		scoresbk = scores;
-		ninbk = nin;
-//		fprintf( stderr, "\nformatting .. " );
-		dfp = fopen( datafile, "w" );
-		if( !dfp ) ErrorExit( "Cannot open datafile." );
-		if( picks == NULL ) for( i=0; i<nin; i++ )
-		{
-//			fprintf( stderr, "i=%d / %d / %d\n", i,  nin, njob );
-//			fprintf( stderr, "nlenmax = %d\n", nlenmax );
-//			fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
-//			fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
-			gappick0( tmpseq, seq[scores[i].numinseq] );
-			sprintf( tmpname, ">+===========+%d                      ", i );
-			slen = scores[i].orilen;
-			writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
-		}
-		else for( i=0; i<nin; i++ )
-		{
-			gappick0( tmpseq, seq[scores[picks[i]].numinseq] );
-			sprintf( tmpname, ">+===========+%d                      ", i );
-			slen = scores[picks[i]].orilen;
-			writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
-		}
-		fclose( dfp );
-	}
-
-
-	gappick0( tmpseq, seq[scores[query].numinseq] );
-	sprintf( tmpname, ">+==========+%d                      ", 0 );
-	slen = scores[query].orilen;
-	qfp = fopen( queryfile, "w" );
-	if( !qfp ) ErrorExit( "Cannot open queryfile." );
-	writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
-	fclose( qfp );
-
-//	fprintf( stderr, "calling fasta, nin=%d\n", nin );
-
-	if( scoremtx == -1 ) 
-		sprintf( com, "%s  -z3 -m10  -n -Q -H -b%d -E%d -d%d %s %s %d > %s",  fastapath, nin, nin, 0, queryfile, datafile, 6, resultfile );
-	else
-		sprintf( com, "%s  -z3 -m10  -p -Q -H -b%d -E%d -d%d %s %s %d > %s",  fastapath, nin, nin, 0, queryfile, datafile, 2, resultfile );
-	res = system( com );
-	if( res )
-	{
-		fprintf( stderr, "error in %s", fastapath );
-		exit( 1 );
-	}
-//	fprintf( stderr, "fasta done\n" );
-
-//exit( 1 );
-
-	rfp = fopen( resultfile, "r" );
-	if( rfp == NULL )  
-		ErrorExit( "file 'fasta.$$' does not exist\n" );
-
-//	fprintf( stderr, "reading fasta\n" );
-	if( scoremtx == -1 ) 
-		res = ReadFasta34m10_scoreonly_nuc( rfp, val, nin );
-	else
-		res = ReadFasta34m10_scoreonly( rfp, val, nin );
-//	fprintf( stderr, "done. val[0] = %f\n", val[0] );
-
-
-	fclose( rfp );
-
-#if 0
-	for( i=0; i<nin; i++ )
-		fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
-	exit( 1 );
-#endif
-
-	return( val );
-}
-#if 0
-static double *callblast( char **seq, Scores *scores, int nin, int query, int rewritedata )
-{
-	double *val;
-	FILE *qfp;
-	FILE *dfp;
-	FILE *rfp;
-	int i, j;
-	char com[10000];
-	static char datafile[1000];
-	static char queryfile[1000];
-	static char resultfile[1000];
-	static int pid;
-	static char *tmpseq;
-	static char *tmpname;
-	char *seqptr;
-	int slen;
-	int res;
-	static Scores *scoresbk = NULL;
-	static int ninbk = 0;
-
-	if( pid == 0 )
-	{
-		pid = (int)getpid();
-		sprintf( datafile, "/tmp/data-%d\0", pid );
-		sprintf( queryfile, "/tmp/query-%d\0", pid );
-		sprintf( resultfile, "/tmp/fasta-%d\0", pid );
-
-		tmpseq = calloc( nlenmax+1, sizeof( char ) );
-		tmpname = calloc( B+1, sizeof( char ) );
-	}
-
-	val = calloc( nin, sizeof( double ) );
-//	fprintf( stderr, "nin=%d, q=%d\n", nin, query );
-
-	if( rewritedata )
-	{
-		scoresbk = scores;
-		ninbk = nin;
-		fprintf( stderr, "\nformatting .. " );
-		dfp = fopen( datafile, "w" );
-		if( !dfp ) ErrorExit( "Cannot open datafile." );
-		for( i=0; i<nin; i++ )
-		{
-//			fprintf( stderr, "i=%d / %d / %d\n", i,  nin, njob );
-//			fprintf( stderr, "nlenmax = %d\n", nlenmax );
-//			fprintf( stderr, "scores[i].orilen = %d\n", scores[i].orilen );
-//			fprintf( stderr, "strlen( seq[scores[i].numinseq] = %d\n", strlen( seq[scores[i].numinseq] ) );
-			gappick0( tmpseq, seq[scores[i].numinseq] );
-			sprintf( tmpname, "+===========+%d                      \0", i );
-			slen = scores[i].orilen;
-			writeData_pointer( dfp, 1, &tmpname, &slen, &tmpseq );
-		}
-		fclose( dfp );
-			
-		if( scoremtx == -1 )
-			sprintf( com, "formatdb  -p f -i %s -o F", datafile );
-		else
-			sprintf( com, "formatdb  -i %s -o F", datafile );
-		system( com );
-//		fprintf( stderr, "done.\n" );
-	}
-
-
-	gappick0( tmpseq, seq[scores[query].numinseq] );
-	sprintf( tmpname, "+==========+%d                      \0", 0 );
-	slen = scores[query].orilen;
-	qfp = fopen( queryfile, "w" );
-	if( !qfp ) ErrorExit( "Cannot open queryfile." );
-	writeData_pointer( qfp, 1, &tmpname, &slen, &tmpseq );
-	fclose( qfp );
-//	fprintf( stderr, "q=%s\n", tmpseq );
-
-	fprintf( stderr, "\ncalling blast .. \n" );
-	if( scoremtx == -1 ) 
-		sprintf( com, "blastall -b %d -e 1e10 -p blastn -m 7  -i %s -d %s >  %s\0", nin, queryfile, datafile, resultfile );
-	else
-		sprintf( com, "blastall -b %d -G 10 -E 1 -e 1e10 -p blastp -m 7  -i %s -d %s >  %s\0", nin, queryfile, datafile, resultfile );
-	res = system( com );
-	if( res ) ErrorExit( "error in blast" );
-
-	rfp = fopen( resultfile, "r" );
-	if( rfp == NULL )  
-		ErrorExit( "file 'fasta.$$' does not exist\n" );
-	res = ReadBlastm7_scoreonly( rfp, val, nin );
-	fclose( rfp );
-
-#if 0
-	for( i=0; i<nin; i++ )
-		fprintf( stderr, "r[%d-%d] = %f\n", 0, i, val[i] );
-#endif
-
-	return( val );
-}
-#endif
-
-#if 0
-static void selhead( int *ar, int n )
-{
-	int min = *ar;
-	int *minptr = ar;
-	int *ptr = ar;
-	int tmp;
-	n--;
-	ar++;
-	while( n-- )
-	{
-		if( ( tmp = *ptr++ ) < min )
-		{
-			min = tmp;
-			minptr = ptr;
-		}
-	}
-	if( minptr != ar )
-	{
-		tmp = *ar;
-		*ar = min;
-		*minptr = tmp;
-	}
-	return;
-}
-#endif
-
-void arguments( int argc, char *argv[] )
-{
-    int c;
-
-	doalign = 0;
-	fromaln = 0;
-	treeout = 0;
-	uselongest = 1;
-	reorder = 1;
-	nevermemsave = 0;
-	inputfile = NULL;
-	fftkeika = 0;
-	constraint = 0;
-	nblosum = 62;
-	fmodel = 0;
-	calledByXced = 0;
-	devide = 0;
-	use_fft = 0;
-	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 = -1530;
-	ppenalty_ex = NOTSPECIFIED;
-	poffset = -123;
-	kimuraR = NOTSPECIFIED;
-	pamN = NOTSPECIFIED;
-	geta2 = GETA2;
-	fftWinSize = NOTSPECIFIED;
-	fftThreshold = NOTSPECIFIED;
-	TMorJTT = JTT;
-	classsize = NOTSPECIFIED;
-	picksize = NOTSPECIFIED;
-	tokyoripara = NOTSPECIFIED;
-
-    while( --argc > 0 && (*++argv)[0] == '-' )
-	{
-        while ( ( c = *++argv[0] ) )
-		{
-            switch( c )
-            {
-				case 'p':
-					picksize = atoi( *++argv );
-					fprintf( stderr, "picksize = %d\n", picksize );
-					--argc;
-					goto nextoption;
-				case 's':
-					classsize = atoi( *++argv );
-					fprintf( stderr, "groupsize = %d\n", classsize );
-					--argc;
-					goto nextoption;
-				case 'i':
-					inputfile = *++argv;
-					fprintf( stderr, "inputfile = %s\n", inputfile );
-					--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, "kimuraR = %d\n", kimuraR );
-					--argc;
-					goto nextoption;
-				case 'b':
-					nblosum = atoi( *++argv );
-					scoremtx = 1;
-//					fprintf( stderr, "blosum %d\n", nblosum );
-					--argc;
-					goto nextoption;
-				case 'j':
-					pamN = atoi( *++argv );
-					scoremtx = 0;
-					TMorJTT = JTT;
-					fprintf( stderr, "jtt %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 'T':
-					tokyoripara = (double)atof( *++argv );
-					--argc;
-					goto nextoption;
-				case 'l':
-					uselongest = 0;
-					break;
-#if 1
-				case 'a':
-					fmodel = 1;
-					break;
-#endif
-				case 'S':
-					doalign = 'f';
-					break;
-				case 'Z':
-					fromaln = 1;
-					break;
-				case 'L':
-					doalign = 1;
-					break;
-				case 'x':
-					reorder = 0;
-					break;
-				case 't':
-					treeout = 1;
-					break;
-				case 'r':
-					fmodel = -1;
-					break;
-				case 'D':
-					dorp = 'd';
-					break;
-				case 'P':
-					dorp = 'p';
-					break;
-				case 'e':
-					fftscore = 0;
-					break;
-				case 'O':
-					fftNoAnchStop = 1;
-					break;
-#if 0
-				case 'R':
-					fftRepeatStop = 1;
-					break;
-				case 'Q':
-					calledByXced = 1;
-					break;
-				case 'a':
-					alg = 'a';
-					break;
-#endif
-				case 'R':
-					alg = 'R';
-					break;
-				case 'Q':
-					alg = 'Q';
-					break;
-				case 'A':
-					alg = 'A';
-					break;
-				case 'N':
-					nevermemsave = 1;
-					break;
-				case 'M':
-					alg = 'M';
-					break;
-				case 'C':
-					alg = 'C';
-					break;
-				case 'F':
-					use_fft = 1;
-					break;
-				case 'G':
-					use_fft = 1;
-					force_fft = 1;
-					break;
-				case 'v':
-					tbrweight = 3;
-					break;
-				case 'd':
-					disp = 1;
-					break;
-				case 'o':
-					outgap = 0;
-					break;
-				case 'J':
-					tbutree = 0;
-					break;
-				case 'X':
-					treemethod = 'X'; // mix
-					break;
-				case 'E':
-					treemethod = 'E'; // upg (average)
-					break;
-				case 'q':
-					treemethod = 'q'; // minimum
-					break;
-				case 'z':
-					fftThreshold = atoi( *++argv );
-					--argc; 
-					goto nextoption;
-				case 'w':
-					fftWinSize = atoi( *++argv );
-					--argc;
-					goto nextoption;
-                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 );
-	}
-}
-
-static int maxl;
-static int tsize;
-
-int seq_grp_nuc( int *grp, char *seq )
-{
-	int tmp;
-	int *grpbk = grp;
-	while( *seq )
-	{
-		tmp = amino_grp[(int)*seq++];
-		if( tmp < 4 )
-			*grp++ = tmp;
-		else
-			fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
-	}
-	*grp = END_OF_VEC;
-	return( grp-grpbk );
-}
-
-int seq_grp( int *grp, char *seq )
-{
-	int tmp;
-	int *grpbk = grp;
-	while( *seq )
-	{
-		tmp = amino_grp[(int)*seq++];
-		if( tmp < 6 )
-			*grp++ = tmp;
-		else
-			fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
-	}
-	*grp = END_OF_VEC;
-	return( grp-grpbk );
-}
-
-void makecompositiontable_p( short *table, int *pointt )
-{
-	int point;
-
-	while( ( point = *pointt++ ) != END_OF_VEC )
-		table[point]++;
-}
-
-int commonsextet_p( short *table, int *pointt )
-{
-	int value = 0;
-	short tmp;
-	int point;
-	static short *memo = NULL;
-	static int *ct = NULL;
-	static int *cp;
-
-	if( !memo )
-	{
-		memo = (short *)calloc( tsize, sizeof( short ) );
-		if( !memo ) ErrorExit( "Cannot allocate memo\n" );
-		ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) );
-		if( !ct ) ErrorExit( "Cannot allocate memo\n" );
-	}
-
-	cp = ct;
-	while( ( point = *pointt++ ) != END_OF_VEC )
-	{
-		tmp = memo[point]++;
-		if( tmp < table[point] )
-			value++;
-		if( tmp == 0 ) *cp++ = point;
-	}
-	*cp = END_OF_VEC;
-	
-	cp =  ct;
-	while( *cp != END_OF_VEC )
-		memo[*cp++] = 0;
-
-	return( value );
-}
-
-void makepointtable_nuc( int *pointt, int *n )
-{
-	int point;
-	register int *p;
-
-	p = n;
-	point  = *n++ *  1024;
-	point += *n++ *   256;
-	point += *n++ *    64;
-	point += *n++ *    16;
-	point += *n++ *     4;
-	point += *n++;
-	*pointt++ = point;
-
-	while( *n != END_OF_VEC )
-	{
-		point -= *p++ * 1024;
-		point *= 4;
-		point += *n++;
-		*pointt++ = point;
-	}
-	*pointt = END_OF_VEC;
-}
-
-void makepointtable( int *pointt, int *n )
-{
-	int point;
-	register int *p;
-
-	p = n;
-	point  = *n++ *  7776;
-	point += *n++ *  1296;
-	point += *n++ *   216;
-	point += *n++ *    36;
-	point += *n++ *     6;
-	point += *n++;
-	*pointt++ = point;
-
-	while( *n != END_OF_VEC )
-	{
-		point -= *p++ * 7776;
-		point *= 6;
-		point += *n++;
-		*pointt++ = point;
-	}
-	*pointt = END_OF_VEC;
-}
-
-#if 1
-static void pairalign( int nseq, int *nlen, char **seq, int *mem1, int *mem2, double *weight, int *alloclen )
-{
-	int l, len1, len2;
-	int clus1, clus2;
-	float pscore, tscore;
-	static int *fftlog;
-	static char *indication1, *indication2;
-	static double *effarr1 = NULL;
-	static double *effarr2 = NULL;
-	static char **mseq1, **mseq2;
-	float dumfl = 0.0;
-	int ffttry;
-	int m1, m2;
-#if 0
-	int i, j;
-#endif
-
-
-	if( effarr1 == NULL ) 
-	{
-		fftlog = AllocateIntVec( nseq );
-		effarr1 = AllocateDoubleVec( nseq );
-		effarr2 = AllocateDoubleVec( nseq );
-		indication1 = AllocateCharVec( 150 );
-		indication2 = AllocateCharVec( 150 );
-		mseq1 = AllocateCharMtx( nseq, 0 );
-		mseq2 = AllocateCharMtx( nseq, 0 );
-		for( l=0; l<nseq; l++ ) fftlog[l] = 1;
-	}
-
-	tscore = 0.0;
-	m1 = mem1[0];
-	m2 = mem2[0];
-	len1 = strlen( seq[m1] );
-	len2 = strlen( seq[m2] );
-	if( *alloclen < len1 + len2 )
-	{
-		fprintf( stderr, "\nReallocating.." );
-		*alloclen = ( len1 + len2 ) + 1000;
-		ReallocateCharMtx( seq, nseq, *alloclen + 10 ); 
-		fprintf( stderr, "done. *alloclen = %d\n", *alloclen );
-	}
-
-#if WEIGHT
-	clus1 = fastconjuction_noname( mem1, seq, mseq1, effarr1, weight, indication1 );
-	clus2 = fastconjuction_noname( mem2, seq, mseq2, effarr2, weight, indication2 );
-#else
-	clus1 = fastconjuction_noweight( mem1, seq, mseq1, effarr1, indication1 );
-	clus2 = fastconjuction_noweight( mem2, seq, mseq2, effarr2, indication2 );
-#endif
-
-#if 0
-	for( i=0; i<clus1; i++ )
-		fprintf( stderr, "in p seq[%d] = %s\n", mem1[i], seq[mem1[i]] );
-	for( i=0; i<clus2; i++ )
-		fprintf( stderr, "in p seq[%d] = %s\n", mem2[i], seq[mem2[i]] );
-#endif
-
-#if 0
-	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
-
-//	fprintf( stdout, "mseq1 = %s\n", mseq1[0] );
-//	fprintf( stdout, "mseq2 = %s\n", mseq2[0] );
-
-	if( !nevermemsave && ( 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 );
-	else	    				   ffttry = 0;
-
-	if( force_fft || ( use_fft && ffttry ) )
-	{
-		fprintf( stderr, "\bf" );
-		if( alg == 'M' )
-		{
-			fprintf( stderr, "\bm" );
-//			fprintf( stderr, "%d-%d", clus1, clus2 );
-			pscore = Falign_udpari_long( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
-		}
-		else
-		{
-//			fprintf( stderr, "%d-%d", clus1, clus2 );
-			pscore = Falign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, fftlog+m1 );
-		}
-	}
-	else
-	{
-		fprintf( stderr, "\bd" );
-		fftlog[m1] = 0;
-		switch( alg )
-		{
-			case( 'a' ):
-				pscore = Aalign( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen );
-				break;
-			case( 'M' ):
-				fprintf( stderr, "\bm" );
-//				fprintf( stderr, "%d-%d", clus1, clus2 );
-				pscore = MSalignmm( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL );
-				break;
-			case( 'Q' ):
-				if( clus1 == 1 && clus2 == 1 )
-				{
-//					fprintf( stderr, "%d-%d", clus1, clus2 );
-					pscore = G__align11( mseq1, mseq2, *alloclen );
-				}
-				else
-				{
-//					fprintf( stderr, "%d-%d", clus1, clus2 );
-					pscore = Q__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-				}
-				break;
-			case( 'A' ):
-				if( clus1 == 1 && clus2 == 1 )
-				{
-//					fprintf( stderr, "%d-%d", clus1, clus2 );
-					pscore = G__align11( mseq1, mseq2, *alloclen );
-				}
-				else
-				{
-//					fprintf( stderr, "%d-%d", clus1, clus2 );
-					pscore = A__align( mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumfl, NULL, NULL, NULL, NULL );
-				}
-				break;
-			default:
-				ErrorExit( "ERROR IN SOURCE FILE" );
-		}
-	}
-#if SCOREOUT
-	fprintf( stderr, "score = %10.2f\n", pscore );
-#endif
-	nlen[m1] = 0.5 * ( nlen[m1] + nlen[m2] );
-	return;
-}
-#endif
-
-#if 0
-static void treebase( int nseq, int *nlen, char **aseq, double *eff, int nalign, int ***topol, int *alloclen ) // topol
-{
-	int i, l;
-	int nlim;
-	int clus1, clus2;
-
-	nlim = nalign-1;
-	for( l=0; l<nlim; l++ )
-	{
-		fprintf( stderr, "in treebase, l = %d\n", l );
-		fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
-		fprintf( stderr, "aseq[topol[l][0][0]] = %s\n", aseq[topol[l][0][0]] );
-		pairalign( nseq, nlen, aseq, topol[l][0], topol[l][1], eff, alloclen );
-		free( topol[l][0] );
-		free( topol[l][1] );
-	}
-}
-#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 );
-}
-	 
-#if 1
-static int splitseq_mq( Scores *scores, int nin, int *nlen, char **seq, char **orialn, char **name, char *inputfile, int uniform, char **tree, int *alloclen, int *order, int *whichgroup, double *weight, int *depthpt, int qinoya )
-{
-	int val;
-	int ii, jj;
-	int *mptr;
-	int treelen = 0; // by Mathog, a guess
-	static int groupid = 0;
-	static int branchid = 0;
-	int i, j;
-	int selfscore0;
-	double **dfromc;
-	double **dfromcp;
-	float **pickmtx;
-	float **yukomtx;
-	static short *table1;
-	Scores **outs, *ptr;
-	int *numin;
-	int *tsukau;
-	int belongto;
-	char **children = NULL; // by Mathog, a guess
-	char *tmptree;
-	static int *orderpos = NULL;
-	int rn;
-	int npick;
-	int nyuko;
-	int *picks;
-	int *yukos;
-	int *s_p_map;
-	int *p_o_map;
-	int *s_y_map;
-	int *y_o_map;
-	int *closeh;
-	int nkouho;
-	int *pickkouho;
-	int *iptr;
-	int *jptr;
-	int aligned;
-	int ***topol;
-	int *treeorder;
-	int picktmp;
-	float **len;
-	double minscore;
-//	double *minscoreinpick;
-	float *hanni;
-	double lenfac;
-	double longer;
-	double shorter;
-	static char **mseq1 = NULL;
-	static char **mseq2 = NULL;
-	double *blastresults = NULL; // by Mathog, a guess
-	static int palloclen = 0;
-	float maxdist;
-
-	if( orderpos == NULL )
-		orderpos = order;
-	if( palloclen == 0 )
-		palloclen = *alloclen * 2;
-	if( mseq1 == NULL && doalign == 1 )
-	{
-		mseq1 = AllocateCharMtx( 1, palloclen );
-		mseq2 = AllocateCharMtx( 1, palloclen );
-	}
-
-	if( nin == 0 ) 
-	{
-#if TREE
-		if( treeout )
-		{
-			*tree = (char *)calloc( 1, sizeof( char ) );
-			**tree = 0;
-		}
-#endif
-		return 1;
-	}
-
-	if( nin < 2 || uniform == -1 ) // kokodato muda deha nai ga
-	{
-		fprintf( stderr, "\nLeaf  %d / %d                ", ++branchid, njob );
-#if 0
-		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
-		sprintf( outputfile, "%s-%d", inputfile, branchid );
-		if( uniform > 0 )
-//			sprintf( outputfile, "%su%d", outputfile, uniform );
-			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
-		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
-		outfp = fopen( outputfile, "w" );
-		free( outputfile );
-		if( outfp == NULL )
-		{
-			fprintf( stderr, "Cannot open %s\n", outputfile );
-			exit( 1 );
-		}
-		for( j=0; j<nin; j++ )
-			fprintf( outfp, ">G%d %s\n%s\n", branchid, scores[j].name+1, seq[scores[j].numinseq] );
-		fclose( outfp );
-#endif
-
-
-#if TREE
-		if( treeout )
-		{
-			treelen = 0;
-			tmptree = calloc( 100, sizeof( char ) );
-			for( j=0; j<nin; j++ )
-			{
-				treelen += sprintf( tmptree, "%d", scores[j].numinseq+1 );
-			}
-			free( tmptree );
-	
-			*tree = (char *)calloc( treelen + nin + 5, sizeof( char ) );
-			if( nin > 1 ) **tree = '(';
-			else		  **tree = '\0';
-//			**tree = '\0';
-			for( j=0; j<nin-1; j++ )
-			{
-				sprintf( *tree+strlen( *tree ), "%d,", scores[j].numinseq+1 );
-			}
-			sprintf( *tree+strlen( *tree ), "%d", scores[j].numinseq+1 );
-			if( nin > 1 ) strcat( *tree, ")" );
-//			fprintf( stdout, "*tree = %s\n", *tree );
-		}
-
-#endif
-		for( j=0; j<nin; j++ )
-		{
-			*orderpos++ = scores[j].numinseq;
-//			fprintf( stderr, "*order = %d\n", scores[j].numinseq );
-		}
-
-		return 1;
-	}
-
-
-
-	if( uselongest )
-	{
-		i = nin;
-		ptr = scores;
-		selfscore0 = scores->selfscore;
-		belongto = 0;
-		while( i-- )
-		{
-//			fprintf( stderr, "ptr-scores=%d, numinseq = %d, score = %f\n", ptr-scores, ptr->numinseq+1, ptr->score );
-			if( ptr->selfscore > selfscore0 )
-			{
-				selfscore0 = ptr->selfscore;
-				belongto = ptr-scores;
-			}
-			ptr++;
-		} 
-#if 1 
-		if( belongto != 0 )
-		{
-//			fprintf( stderr, "swap %d %s\n<->\n%d %s\n", 0, scores->name, belongto, (scores+belongto)->name );
-			ptr = calloc( 1, sizeof( Scores ) );
-			*ptr = scores[belongto];
-			scores[belongto] = *scores;
-			*scores = *ptr;
-			free( ptr );
-		}
-#endif
-	}
-	else
-	{
-		qsort( scores, nin, sizeof( Scores ), (int (*)())lcompare );
-		belongto = (int)( 0.5 * nin );
-//		fprintf( stderr, "lengths = %d, %d, %d\n", scores->orilen, scores[belongto].orilen, scores[nin-1].orilen );
-		if( belongto != 0 )
-		{
-//			fprintf( stderr, "swap %d %s\n<->\n%d %s\n", 0, scores->name, belongto, (scores+belongto)->name );
-			ptr = calloc( 1, sizeof( Scores ) );
-			*ptr = scores[belongto];
-			scores[belongto] = *scores;
-			*scores = *ptr;
-			free( ptr );
-		}
-	}
-
-	if( qinoya != scores->numinseq )
-//	if( 1 || qinoya != scores->numinseq )
-	{
-//		fprintf( stdout, "### scores->numinseq = %d, qinoya=%d, depth=%d\n", scores->numinseq, qinoya, *depthpt );
-
-
-		if( doalign )
-		{
-			if( doalign == 'f' )
-			{
-				blastresults = callfasta( seq, scores, nin, NULL, 0, 1 );
-				if( scores->selfscore != (int)blastresults[0] )
-				{
-					fprintf( stderr, "\n\nWARNING1: selfscore\n" );
-					fprintf( stderr, "scores->numinseq = %d\n", scores->numinseq+1 );
-					fprintf( stderr, "scores->orilen = %d\n", scores->orilen );
-					fprintf( stderr, "scores->selfscore = %d, but blastresults[0] = %f\n", scores->selfscore, blastresults[0] );
-//					if( abs( scores->selfscore - (int)blastresults[0] ) > 2 )
-//						exit( 1 );
-//					scores->selfscore = (int)blastresults[0]; //iinoka?
-	
-//					exit( 1 );
-				}
-			}
-			else
-				gappick0( mseq1[0], seq[scores->numinseq] );
-		}
-		else
-		{
-			table1 = (short *)calloc( tsize, sizeof( short ) );
-			if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
-			makecompositiontable_p( table1, scores[0].pointt );
-		}
-	
-		selfscore0 = scores[0].selfscore;
-		for( i=0; i<nin; i++ ) 
-		{
-			if( scores->orilen > scores[i].orilen )
-			{
-				longer = (double)scores->orilen;
-				shorter = (double)scores[i].orilen;
-			}
-			else
-			{
-				longer = (double)scores[i].orilen; // nai
-				shorter = (double)scores->orilen; //nai
-			}
-
-#if LENFAC
-			lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
-//			lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
-//			fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
-#else
-			lenfac = 1.0;
-#endif
-
-			if( doalign )
-			{
-				if( doalign == 'f' )
-				{
-					scores[i].score = ( 1.0 - blastresults[i] / MIN( scores->selfscore, scores[i].selfscore ) ) * 1;
-					if( scores[i].score < 0.0 ) scores[i].score = 0.0;
-				}
-				else
-				{
-					if( fromaln )
-					{
-//						scores[i].score = ( 1.0 - (double)G__align11_noalign( amino_disLN, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
-						scores[i].score = ( 1.0 - (double)naivepairscore11( orialn[scores[i].numinseq], orialn[scores->numinseq], penalty ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
-					}
-					else
-					{
-						if( *depthpt == 0 ) fprintf( stderr, "\r%d / %d   ", i, nin );
-						gappick0( mseq2[0], seq[scores[i].numinseq] );
-//						fprintf( stdout, "### before calc scores[%d] = %f (%c)\n", i, scores[i].score, qinoya == scores->numinseq?'o':'x' );
-						scores[i].score = ( 1.0 - (double)G__align11_noalign( amino_disLN, -1200, -60, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[i].selfscore ) ) * 1;
-//						fprintf( stderr, "scores[i] = %f\n", scores[i].score );
-//						fprintf( stderr, "m1=%s\n", seq[scores[0].numinseq] );
-//						fprintf( stderr, "m2=%s\n", seq[scores[i].numinseq] );
-//						fprintf( stdout, "### before calc scores[%d] = %f (%c)\n", i, scores[i].score, qinoya == scores->numinseq?'o':'x' );
-					}
-				}
-			}
-			else
-			{
-				scores[i].score = ( 1.0 - (double)commonsextet_p( table1, scores[i].pointt ) / MIN( selfscore0, scores[i].selfscore ) ) * lenfac;
-				if( scores[i].score > MAX6DIST ) scores[i].score = MAX6DIST;
-			}
-//			if( i ) fprintf( stderr, "%d-%d d %4.2f len %d %d\n", 1, i+1, scores[i].score, scores->orilen, scores[i].orilen );
-		}
-		if( doalign == 'f' ) free( blastresults );
-		if( doalign == 0 ) free( table1 );
-//exit( 1 );
-	}
-
-//	fprintf( stderr, "sorting .. " );
-	qsort( scores, nin, sizeof( Scores ), (int (*)())dcompare );
-//	fprintf( stderr, "done.\n" );
-
-
-	maxdist = scores[nin-1].score;
-	if( fromaln ) // kanzen itch ga misalign sareteiru kamoshirenai.
-	{
-		if( scores[0].shimon == scores[nin-1].shimon && !strcmp( seq[scores[0].numinseq], seq[scores[nin-1].numinseq] ) ) 
-		{
-			maxdist = 0.0;
-		}
-//		fprintf( stderr, "maxdist?? = %f, nin=%d, %d inori\n", scores[nin-1].score, nin, scores[nin-1].numinseq+1 );
-	}
-
-//	fprintf( stderr, "maxdist? = %f, nin=%d\n", scores[nin-1].score, nin );
-
-	if( nin == 1 ) fprintf( stderr, "nin=1, scores[0].score = %f\n", scores[0].score );
-
-// kokoni if( nin < 2 || ... )
-
-	picks = AllocateIntVec( nin+1 );
-	s_p_map = AllocateIntVec( nin+1 );
-	s_y_map = AllocateIntVec( nin+1 );
-	pickkouho = AllocateIntVec( nin+1 );
-	closeh = AllocateIntVec( nin+1 );
-
-//	nkouho = getkouho( pickkouho, (picksize+100)/nin, nin, scores, seq );
-//	nkouho = getkouho( pickkouho, 1.0, nin, scores, seq ); // zenbu
-//	fprintf( stderr, "selecting kouhos phase 2\n"  );
-//	if( nkouho == 0 )
-//	{
-//		fprintf( stderr, "selecting kouhos, phase 2\n"  );
-//		nkouho = getkouho( pickkouho, 1.0, nin, scores, seq );
-//	}
-//	fprintf( stderr, "\ndone\n\n"  );
-	for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
-
-
-
-	iptr = picks;
-	*iptr++ = 0;
-	npick = 1;
-	if( nkouho > 0 )
-	{
-//		fprintf( stderr, "pickkouho[0] = %d\n", pickkouho[0] );
-//		fprintf( stderr, "pickkouho[nin-1] = %d\n", pickkouho[nin-1] );
-		picktmp = pickkouho[nkouho-1];
-//		fprintf( stderr, "\nMOST DISTANT kouho=%d, nin=%d, nkouho=%d\n", picktmp, nin, nkouho );
-		nkouho--;
-		if( ( scores[picktmp].shimon == scores[0].shimon ) && ( !strcmp( seq[scores[0].numinseq], seq[scores[picktmp].numinseq] ) ) )
-		{
-//			fprintf( stderr, "known, j=%d (%d inori)\n", 0, scores[picks[0]].numinseq );
-//			fprintf( stderr, "%s\n%s\n", seq[scores[picktmp].numinseq], seq[scores[picks[0]].numinseq] );
-			;
-		}
-		else
-		{
-			*iptr++ = picktmp;
-			npick++;
-//			fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
-		}
-	}
-	i = 1;
-	while( npick<picksize && nkouho>0 )
-	{
-		if( i )
-		{
-			i = 0;
-			rn = nkouho * 0.5;
-//			fprintf( stderr, "rn = %d\n", rn );
-		}
-		else
-		{
-			rn = rnd() * (nkouho);
-		}
-		picktmp = pickkouho[rn];
-//		fprintf( stderr, "rn=%d/%d (%d inori), kouho=%d, nin=%d, nkouho=%d\n", rn, nkouho, scores[pickkouho[rn]].numinseq, pickkouho[rn], nin, nkouho );
-
-//		fprintf( stderr, "#kouho before swap\n" );
-//		for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ",  pickkouho[i] ); fprintf( stderr, "\n" );
-
-		nkouho--;
-		pickkouho[rn] = pickkouho[nkouho];
-#if 1
-//		fprintf( stderr, "#kouho after swap\n" ); 
-//		for( i=0; i<nkouho; i++ ) fprintf( stderr, "%d ",  pickkouho[i] ); fprintf( stderr, "\n" );
-		for( j=0; j<npick; j++ )
-		{
-			if( scores[picktmp].shimon == scores[picks[j]].shimon && !strcmp( seq[scores[picks[j]].numinseq], seq[scores[picktmp].numinseq] ) ) 
-				break;
-		}
-		if( j == npick )
-#endif
-		{
-//			fprintf( stderr, "ok, %dth pick = %d (%d inori)\n", npick, picktmp, scores[picktmp].numinseq );
-			npick++;
-			*iptr++ = picktmp;
-		}
-		else
-		{
-//			fprintf( stderr, "known, j=%d (%d inori)\n", j, scores[picks[j]].numinseq );
-		}
-	}
-#if 0
-	for( i=0; i<nin; i++ )
-	{
-		fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, nin, i, scores[i].score, scores[i].numinseq );
-	}
-	fprintf( stderr, "range:nin=%d scores[%d].score <= %f\n", nin, npick, scores[nin-1].score);
-	for( i=0; i<npick; i++ )
-	{
-		fprintf( stderr, "i=%d/%d, scores[%d].score = %f, inori=%d\n", i, npick, picks[i], scores[picks[i]].score, scores[picks[i]].numinseq );
-	}
-exit( 1 );
-#endif
-
-//	fprintf( stderr, "\nnkouho=%d, defaultq2 = %d (%d inori)\n", nkouho, picks[npick-1], scores[picks[npick-1]].numinseq );
-
-	qsort( picks, npick, sizeof( int ), (int (*)())intcompare );
-
-//	fprintf( stderr, "allocating..\n" );
-
-//	fprintf( stderr, "allocating outs, npick = %d\n", npick );
-	numin = calloc( npick, sizeof( int ) );
-	tsukau = calloc( npick, sizeof( int ) );
-	outs = calloc( npick, sizeof( Scores * ) );
-	for( i=0; i<npick; i++ ) outs[i] = NULL;
-	topol = AllocateIntCub( npick, 2, 0 );
-	treeorder = AllocateIntVec( npick + 1 );
-	len = AllocateFloatMtx( npick, 2 );
-	pickmtx = AllocateFloatHalfMtx( npick );
-//	yukomtx = AllocateFloatHalfMtx( npick );
-//	minscoreinpick = AllocateDoubleVec( npick );
-	yukos = AllocateIntVec( npick );
-	p_o_map = AllocateIntVec( npick+1 );
-	y_o_map = AllocateIntVec( npick+1 );
-	hanni = AllocateFloatVec( npick );
-
-	for( i=0; i<nin; i++ ) s_p_map[i] = -1;
-//	fprintf( stderr, "npick = %d\n", npick );
-//	fprintf( stderr, "picks =" );
-	for( i=0; i<npick; i++ )
-	{
-		s_p_map[picks[i]] = i;
-		p_o_map[i] = scores[picks[i]].numinseq;
-//		fprintf( stderr, " %d (%dinori)\n", picks[i], scores[picks[i]].numinseq+1 );
-	}
-//	fprintf( stderr, "\n" );
-
-#if 0
-	fprintf( stderr, "p_o_map =" );
-	for( i=0; i<npick; i++ )
-	{
-		fprintf( stderr, " %d", p_o_map[i]+1 );
-	}
-	fprintf( stderr, "\n" );
-	fprintf( stderr, "picks =" );
-	for( i=0; i<npick; i++ )
-	{
-		fprintf( stderr, " %d", picks[i] );
-	}
-	fprintf( stderr, "\n" );
-#endif
-
-	for( j=0; j<nin; j++ )
-	{
-		if( s_p_map[j] != -1 )
-		{
-			pickmtx[0][s_p_map[j]] = (float)scores[j].score;
-//			fprintf( stderr, "pickmtx[0][%d] = %f\n", s_p_map[j], pickmtx[0][s_p_map[j]] );
-		}
-	}
-
-	for( j=1; j<npick; j++ )
-	{
-		if( doalign )
-		{
-			if( doalign == 'f' )
-			{
-//				blastresults = callfasta( seq, scores, npick-j+1, picks+j-1, picks[j], 1 );
-				blastresults = callfasta( seq, scores, npick, picks, picks[j], (j==1) );
-				if( scores[picks[j]].selfscore != (int)blastresults[j] )
-				{
-					fprintf( stderr, "\n\nWARNING2: selfscore j=%d/%d\n", j, npick );
-					fprintf( stderr, "scores[picks[j]].numinseq = %d\n", scores[picks[j]].numinseq+1 );
-					fprintf( stderr, "scores[picks[j]].orilen = %d\n", scores[picks[j]].orilen );
-					fprintf( stderr, "scores[picks[j]].selfscore = %d, but blastresults[j] = %f\n", scores[picks[j]].selfscore, blastresults[j] );
-//					if( abs( scores[picks[j]].selfscore - (int)blastresults[j] ) > 2 )
-//						exit( 1 );
-//					scores->selfscore = (int)blastresults[0]; //iinoka?
-				}
-			}
-			else
-				gappick0( mseq1[0], seq[scores[picks[j]].numinseq] );
-		}
-		else
-		{
-			table1 = (short *)calloc( tsize, sizeof( short ) );
-			if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
-			makecompositiontable_p( table1, scores[picks[j]].pointt );
-		}
-	
-		selfscore0 = scores[picks[j]].selfscore;
-		pickmtx[j][0] = 0.0;
-	    for( i=j+1; i<npick; i++ ) 
-		{
-			if( scores[picks[j]].orilen > scores[picks[i]].orilen )
-			{
-				longer = (double)scores[picks[j]].orilen;
-				shorter = (double)scores[picks[i]].orilen;
-			}
-			else
-			{
-				longer = (double)scores[picks[i]].orilen;
-				shorter = (double)scores[picks[j]].orilen;
-			}
-	
-	#if LENFAC
-			lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
-	//		lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
-	//		fprintf( stderr, "lenfac = %f l=%d,%d\n", lenfac,scores->orilen, scores[i].orilen );
-	#else
-			lenfac = 1.0;
-	#endif
-	
-			if( doalign )
-			{
-				if( doalign == 'f' )
-				{
-					pickmtx[j][i-j] = ( 1.0 - blastresults[i] / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
-					if( pickmtx[j][i-j] < 0.0 ) pickmtx[j][i-j] = 0.0;
-				}
-				else
-				{
-					if( fromaln )
-					{
-						fprintf( stderr, "%d-%d/%d\r", j, i, npick );
-						pickmtx[j][i-j] = ( 1.0 - (double)naivepairscore11(  orialn[scores[picks[i]].numinseq], orialn[scores[picks[j]].numinseq], penalty ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
-					}
-					else
-					{
-//						fprintf( stderr, "\r%d / %d   ", i, nin );
-						gappick0( mseq2[0], seq[scores[picks[i]].numinseq] );
-						pickmtx[j][i-j] = ( 1.0 - (double)G__align11_noalign( amino_disLN, -1200, -60, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * 1;
-	//					fprintf( stderr, "scores[picks[i]] = %f\n", scores[picks[i]].score );
-					}
-				}
-			}
-			else
-			{
-				pickmtx[j][i-j] = ( 1.0 - (double)commonsextet_p( table1, scores[picks[i]].pointt ) / MIN( selfscore0, scores[picks[i]].selfscore ) ) * lenfac;
-				if( pickmtx[j][i-j] > MAX6DIST ) pickmtx[j][i-j] = MAX6DIST;
-			}
-
-		}
-		if( doalign == 'f' ) free( blastresults );
-		if( doalign == 0 ) free( table1 );
-	}
-
-	dfromcp = AllocateDoubleMtx( npick, nin );
-	dfromc = AllocateDoubleMtx( npick, 0 );
-
-	for( i=0; i<npick; i++ ) for( j=0; j<nin; j++ )
-		dfromcp[i][j] = -0.5;
-	for( j=0; j<nin; j++ )
-	{
-		dfromcp[0][j] = ( scores[j].score );
-//		fprintf( stderr, "j=%d, s_p_map[j]=%d\n", j, s_p_map[j] );
-	}
-
-	for( i=0; i<npick; i++ ) for( j=i; j<npick; j++ )
-	{
-		dfromcp[i][picks[j]] = dfromcp[j][picks[i]] = pickmtx[i][j-i];
-	}
-
-#if 0
-	fprintf( stderr, "pickmtx = \n" );
-	for( i=0; i<npick; i++ )
-	{
-		for( j=i; j<npick; j++ )
-		{
-			fprintf( stderr, "pickmtx[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
-		}
-	}
-	exit( 1 );
-#endif
-
-
-
-//	for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
-//		fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
-
-	for( i=0; i<npick; i++ ) tsukau[i] = 1;
-	for( i=0; i<nin; i++ ) closeh[i] = -1;
-	for( i=0; i<npick; i++ ) 
-	{
-		closeh[picks[i]] = picks[i];
-//		fprintf( stderr, "i=%d/%d, picks[i]=%d, %d inori, closeh[%d] = %d \n", i, npick, picks[i], p_o_map[i]+1, picks[i], closeh[picks[i]] );
-	}
-#if 0
-	fprintf( stderr, "closeh = \n" );
-	for( i=0; i<nin; i++ )
-	{
-		fprintf( stderr, "%d ", closeh[i] );
-	}
-	fprintf( stderr, "\n" );
-#endif
-#if DIANA
-	for( i=0; i<npick-1; i++ ) for( j=i; j<npick; j++ )
-		fprintf( stderr, "dist[%d][%d] = %f\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i] );
-	fprintf( stderr, "DIANA!!\n" );
-	if( npick > 2 )
-	{
-		float avdist;
-		float avdist1;
-		float avdist2;
-		float maxavdist;
-		int splinter;
-		int count;
-		int dochokoho;
-		splinter = 0;
-		int *docholist;
-		int *docholistbk;
-		maxavdist = 0.0;
-		for( i=0; i<npick; i++ )
-		{
-			avdist = 0.0;
-			for( j=i+1; j<npick; j++ )
-			{
-				avdist += pickmtx[i][j-i];
-			}
-			for( j=0; j<i; j++ )
-			{
-				avdist += pickmtx[j][i-j];
-			}
-			avdist /= (npick-1);
-			fprintf( stderr, "avdist[%d] = %f\n", p_o_map[i] + 1, avdist );
-			if( maxavdist < avdist ) 
-			{
-				maxavdist = avdist;
-				splinter = i;
-			}
-		}
-		fprintf( stderr, "splinter = %d (%d inori), maxavdist = %f\n", splinter, p_o_map[splinter]+1, maxavdist );
-
-		docholist = AllocateIntVec( npick );
-		docholistbk = AllocateIntVec( npick );
-		for( i=0; i<npick; i++ ) docholist[i] = 0;
-		docholist[splinter] = 1;
-		while( 1 )
-		{
-			for( i=0; i<npick; i++ ) docholistbk[i] = docholist[i]; 
-			for( dochokoho = 0; dochokoho<npick; dochokoho++ )
-			{
-				fprintf( stderr, "dochokoho=%d\n", dochokoho );
-				if( docholist[dochokoho] ) continue;
-				count = 0;
-				avdist1 = 0.0;
-				i=dochokoho;
-				{
-					for( j=i+1; j<npick; j++ )
-					{
-						if( docholist[j] || j == dochokoho ) continue;
-						avdist1 += pickmtx[i][j-i];
-						count++;
-					}
-					for( j=0; j<i; j++ )
-					{
-						if( docholist[j] || j == dochokoho ) continue;
-						avdist1 += pickmtx[j][i-j];
-						count++;
-					}
-				}
-				if( count < 1 ) avdist1 = 0.0;
-				else avdist1 /= (float)count;
-				fprintf( stderr, "docho %d (%dinori), avdist1 = %f\n", dochokoho, p_o_map[dochokoho] + 1, avdist1 );
-
-				count = 0;
-				avdist2 = 0.0;
-				i=dochokoho;
-				{
-					for( j=i+1; j<npick; j++ )
-					{
-						if( !docholist[j] || j == dochokoho ) continue;
-						avdist2 += pickmtx[i][j-i];
-						count++;
-					}
-					for( j=0; j<i; j++ )
-					{
-						if( !docholist[j] || j == dochokoho ) continue;
-						avdist2 += pickmtx[j][i-j];
-						count++;
-					}
-				}
-				if( count < 1 ) avdist2 = 0.0;
-				else avdist2 /= (float)count;
-				fprintf( stderr, "docho %d (%dinori), avdist2 = %f\n", dochokoho, p_o_map[dochokoho] + 1, avdist2 );
-
-				if( avdist2 < avdist1 ) 
-				{
-					docholist[dochokoho] = 1;
-					hanni[dochokoho] = avdist2;
-				}
-				else
-				{
-					docholist[dochokoho] = 0;
-					hanni[dochokoho] = avdist1;
-				}
-				fprintf( stderr, "avdist1=%f, avdist2=%f\n", avdist1, avdist2 );
-
-			}
-			for( i=0; i<npick; i++ ) if( docholist[i] != docholistbk[i] ) break;
-			if( i == npick ) break;
-
-			fprintf( stderr, "docholist = \n" );
-			for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", docholist[i] );
-			fprintf( stderr, "\n" );
-		}
-		fprintf( stderr, "docholist = \n" );
-		for( i=0; i<npick; i++ ) fprintf( stderr, "%d ", docholist[i] );
-		fprintf( stderr, "\n" );
-
-		for( i=0; i<npick; i++ ) if( docholist[i] == 0 ) break;
-		yukos[0] = picks[i];
-		for( i=0; i<npick; i++ ) if( docholist[i] == 1 ) break;
-		yukos[1] = picks[splinter];
-
-		for( i=0; i<npick; i++ ) 
-		{
-			if( docholist[i] == 0 ) closeh[picks[i]] = yukos[0];
-			if( docholist[i] == 1 ) closeh[picks[i]] = yukos[1];
-		}
-//		for( i=0; i<npick; i++ ) closeh[picks[i]] = -1; // CHUUI !! iminai
-		nyuko = 2;
-		free( docholist );
-		free( docholistbk );
-	}
-	else if( npick > 1 )
-	{
-		nyuko = 2;
-		yukos[0] = picks[0]; yukos[1] = picks[1];
-		closeh[picks[0]] = yukos[0];
-		closeh[picks[1]] = yukos[1];
-	}
-	else
-	{
-		nyuko = 1;
-		yukos[0] = picks[0];
-		closeh[picks[0]] = yukos[0];
-	}
-#elif HUKINTOTREE
-	if( npick > 2 )
-	{
-#if 0
-		float avdist;
-		float maxavdist;
-		int count;
-		int splinter;
-		maxavdist = 0.0;
-		splinter=0;
-		for( i=0; i<npick; i++ )
-		{
-			avdist = 0.0;
-			for( j=i+1; j<npick; j++ )
-			{
-				avdist += pickmtx[i][j-i];
-			}
-			for( j=0; j<i; j++ )
-			{
-				avdist += pickmtx[j][i-j];
-			}
-			avdist /= (npick-1);
-			fprintf( stderr, "avdist[%d] = %f\n", p_o_map[i] + 1, avdist );
-			if( maxavdist < avdist ) 
-			{
-				maxavdist = avdist;
-				splinter = i;
-			}
-		}
-		fprintf( stderr, "splinter = %d (%d inori), maxavdist = %f\n", splinter, p_o_map[splinter]+1, maxavdist );
-#endif
-
-
-//		fprintf( stderr, "check kaishi =>, npick=%d members = \n", npick );
-//		for( i=0; i<npick; i++ ) fprintf( stderr, "%d (%d)", p_o_map[i]+1, picks[i] );
-//		fprintf( stderr, "\n" );
-		for( i=0; i<npick-1; i++ ) 
-		{
-			if( tsukau[i] == 0 ) continue;
-			for( j=i+1; j<npick; j++ )
-			{
-//				float kijun = maxdist *  1/(npick-2);
-//				float kijun = maxavdist * tokyoripara;
-				float kijun;
-				kijun = maxdist * tokyoripara;  // atode kakunin
-//				fprintf( stderr, "%d-%d\n", i, j );
-//				fprintf( stderr, "maxdist = %f\n", maxdist );
-//				if( i==0 && j == 1 ) continue; // machigai!! CHUUI!!
-//				if( maxdist == pickmtx[i][j-i] ) continue;
-				if( tsukau[j] == 0 ) continue;
-//				fprintf( stderr, "checking %d-%d (%d-%d) %f, kijun=%f\n", p_o_map[i]+1, p_o_map[j]+1, i, j, pickmtx[i][j-i], kijun );
-				if( pickmtx[i][j-i] < kijun )
-				{
-//					fprintf( stderr, "dame!! %d => %d, because %f < %f\n", p_o_map[j]+1, p_o_map[i]+1, pickmtx[i][j-i], kijun );
-#if 0
-					if( scores[picks[i]].orilen > scores[picks[j]].orilen )
-					{
-						fprintf( stderr, "%d => %d\n", p_o_map[j]+1, p_o_map[i]+1 );
-						tsukau[j] = 0;
-					}
-					else
-					{
-						fprintf( stderr, "%d => %d\n", p_o_map[i]+1, p_o_map[j]+1 );
-						tsukau[i] = 0;
-					}
-					if( 0 && j == npick-1 ) tsukau[i] = 0;
-					else  			   tsukau[j] = 0;
-					fprintf( stderr, "tsukau[%d] = %d (%d inori)\n", j, tsukau[j], p_o_map[j]+1 );
-#else
-					tsukau[j] = 0;
-					closeh[picks[j]] = closeh[picks[i]];
-//					fprintf( stderr, "%d => tsukawanai\n", j );
-#endif
-				}
-			}
-		}
-	}
-	for( ii=0,i=0; i<npick; i++ )
-	{
-		if( tsukau[i] )
-		{
-			dfromc[ii] = dfromcp[i];
-			ii++;
-		}
-		else
-		{
-			free( dfromcp[i] );
-			dfromcp[i] = NULL;
-		}
-	}
-	dfromc[ii] = NULL;
-
-	for( ii=0,i=0; i<npick; i++ )
-	{
-		if( tsukau[i] )
-		{
-			for( jj=ii,j=i; j<npick; j++ )
-			{
-				if( tsukau[j] )
-				{
-					pickmtx[ii][jj-ii] = pickmtx[i][j-i];
-					jj++;
-				}
-			}
-			ii++;
-		}
-	}
-	for( ; ii<npick; ii++ )
-	{
-		free( pickmtx[ii] ); 
-		pickmtx[ii] = NULL;
-	}
-
-	for( ii=0,i=0; i<npick; i++ )
-	{
-		if( tsukau[i] )
-		{
-			yukos[ii++] = picks[i];
-		}
-	}
-
-
-	nyuko = ii;
-	yukomtx = pickmtx;
-	pickmtx = NULL;
-
-#endif
-#if 0
-	for( i=0; i<npick; i++ ) for( j=i; j<npick; j++ )
-	{
-		if( tsukau[i] == 1 && tsukau[j] == 1 )
-			fprintf( stderr, "dist[%d][%d] = %f (ok)\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i]  );
-		else if( tsukau[i] == 0 && tsukau[j] == 0 )
-			fprintf( stderr, "dist[%d][%d] = %f (xx)\n", p_o_map[i]+1, p_o_map[j]+1, pickmtx[i][j-i]  );
-		else	
-			fprintf( stderr, "%d-%d, okashii\n", p_o_map[i]+1, p_o_map[j]+1 );
-	}
-#endif
-//	FreeFloatHalfMtx( pickmtx, npick );
-
-
-	for( i=0; i<nin; i++ ) s_y_map[i] = -1;
-//	fprintf( stderr, "npick = %d\n", npick );
-//	fprintf( stderr, "yukos =" );
-	for( i=0; i<nyuko; i++ )
-	{
-		s_y_map[yukos[i]] = i;
-		y_o_map[i] = scores[yukos[i]].numinseq;
-//		fprintf( stderr, " %d\n", yukos[i] );
-	}
-//	fprintf( stderr, "\n" );
-#if 0
-	for( i=0; i<nyuko; i++ )
-	{
-		fprintf( stderr, "y_o_map[%d] = %d\n", i, y_o_map[i]+1 );
-	}
-	for( i=0; i<nyuko; i++ ) for( j=i; j<nyuko; j++ )
-	{
-		fprintf( stderr, "yukodist[%d][%d] = %f (ok)\n", y_o_map[i]+1, y_o_map[j]+1, yukomtx[i][j-i]  );
-	}
-#endif
-
-	for( i=0; i<nin; i++ )
-	{
-		if( closeh[i] != -1 )
-		{
-//			fprintf( stderr, "closeh[%d,%dinori] = %d,%dinori\n", i, scores[i].numinseq+1, closeh[i], scores[closeh[i]].numinseq+1 );
-		}
-	}
-
-#if 0
-		for( i=0; i<nyuko; i++ )
-		{
-			minscoreinpick[i] = 99.9;
-			for( j=i+1; j<nyuko; j++ )
-			{
-				if( minscoreinpick[i] > yukomtx[i][j-i] )
-					minscoreinpick[i] = yukomtx[i][j-i];
-			}
-			for( j=0; j<i; j++ )
-			{
-				if( minscoreinpick[i] > yukomtx[j][i-j] )
-					minscoreinpick[i] = yukomtx[j][i-j];
-			}
-			fprintf( stderr, "minscoreinpick[%d(%dinori)] = %f\n", i, y_o_map[i]+1, minscoreinpick[i] );
-		}
-#endif
-
-
-#if TREE
-	if( treeout )
-	{
-		children = calloc( nyuko+1, sizeof( char * ) );
-		for( i=0; i<nyuko+1; i++ ) children[i] = NULL;
-	}
-#endif
-//	fprintf( stderr, "done..\n" );
-	
-//	fprintf( stderr, "classifying, nyuko=%d \n", nyuko );
-	if( nyuko == 1 )
-	{
-		if( npick != 1 )
-		{
-			fprintf( stderr, "okashii, nyuko = 1, shikashi npick = %d\n", npick );
-			exit( 1 );
-		}
-//		fprintf( stderr, "### itchi suru hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore );
-//		fprintf( stderr, "seq[%d] = scores->seq = \n%s\n", scores->numinseq, seq[scores->numinseq] );
-
-		uniform = -1;
-		for( j=0; j<nin; j++ ) 
-		{
-			belongto = 0;
-			outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
-			outs[belongto][numin[belongto]] = scores[j];
-			numin[belongto]++;
-		}
-	}
-	else
-	{
-
-#if 0
-		fprintf( stderr, "yukos = \n" );
-		for( i=0; i<nyuko; i++ ) fprintf( stderr, "%d ", y_o_map[i] + 1 );
-		fprintf( stderr, "\n" );
-#endif
-		fprintf( stderr, "\n\n%dx%d distance matrix\n", nyuko, nin );
-
-		for( i=1; i<nyuko; i++ )
-		{
-			fprintf( stderr, "%d / %d \r", i, nyuko );
-
-			if( doalign )
-			{
-				if( doalign == 'f' )
-				{
-					blastresults = callfasta( seq, scores, nin, NULL, yukos[i], (i==1) );
-				}
-				else
-					gappick0( mseq1[0], seq[scores[yukos[i]].numinseq] );
-			}
-			else
-			{
-				table1 = (short *)calloc( tsize, sizeof( short ) );
-				if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
-				makecompositiontable_p( table1, scores[yukos[i]].pointt );
-			}
-		
-			selfscore0 = scores[yukos[i]].selfscore;
-			for( j=0; j<nin; j++ ) 
-			{
-				if( scores[yukos[i]].orilen > scores[j].orilen )
-				{
-					longer = scores[yukos[i]].orilen;
-					shorter = scores[j].orilen;
-				}
-				else
-				{
-					shorter = scores[yukos[i]].orilen;
-					longer = scores[j].orilen;
-				}
-
-#if LENFAC
-//				lenfac = 1.0 / ( (double)LENFACA + (double)LENFACB / ( (double)longer + (double)LENFACC ) + (double)shorter / (double)longer * LENFACD );
-				lenfac = 1.0 / ( shorter / longer * lenfacd + lenfacb / ( longer + lenfacc ) + lenfaca );
-//				lenfac = 1.0 / ( shorter / longer * LENFACD + LENFACB / ( longer + LENFACC ) + LENFACA );
-//				fprintf( stderr, "lenfac = %f, l=%d, %d\n", lenfac, scores[yukos[i]].orilen, scores[j].orilen );
-#else
-				lenfac = 1.0;
-#endif
-#if 0 // iihazu -> dame
-				ii = s_y_map[j]; jj=s_y_map[yukos[i]];
-				if( ii != -1 && jj != -1 )
-				{
-					if( dfromc[ii][yukos[jj]] != -0.5 )
-					{
-						dfromc[i][j] = dfromc[ii][yukos[jj]];
-					}
-					else
-					{
-						if( ii > jj )
-						{
-							kk = jj;
-							jj = ii;
-							ii = kk;
-						}
-						dfromc[ii][yukos[jj]] = 
-						dfromc[i][j] = yukomtx[ii][jj-ii];
-					}
-				}
-				else
-#else
-				if( dfromc[i][j] == -0.5 )
-#endif
-				{
-					if( doalign )
-					{
-						if( doalign == 'f' )
-						{
-							dfromc[i][j] = 
-							( 1.0 - blastresults[j] / MIN( selfscore0, scores[j].selfscore ) ) * 1;
-							if( dfromc[i][j] < 0.0 ) dfromc[i][j] = 0.0;
-						}
-						else
-						{
-							if( fromaln )
-							{
-								dfromc[i][j] = ( 1.0 - (double)naivepairscore11( orialn[scores[j].numinseq], orialn[scores[yukos[i]].numinseq], penalty ) / MIN( selfscore0, scores[j].selfscore ) ) * 1;
-							}
-							else
-							{
-								gappick0( mseq2[0], seq[scores[j].numinseq] );
-								dfromc[i][j] = ( 1.0 - (double)G__align11_noalign( amino_disLN, -1200, -60, mseq1, mseq2, palloclen ) / MIN( selfscore0, scores[j].selfscore ) ) * 1;
-							}
-						}
-					}
-					else
-					{
-						dfromc[i][j] = ( 1.0 - (double)commonsextet_p( table1, scores[j].pointt ) / MIN( selfscore0, scores[j].selfscore ) ) * lenfac;
-						if( dfromc[i][j] > MAX6DIST ) dfromc[i][j] = MAX6DIST;
-					}
-				}
-//				fprintf( stderr, "i,j=%d,%d (%d,%d)/ %d,%d, dfromc[][]=%f \n", i, j, scores[yukos[i]].numinseq+1, scores[j].numinseq+1, nyuko, nin, dfromc[i][j] );
-
-//				if( i == 1 )
-//					fprintf( stdout, "&&& dfromc[%d][%d] (%d,%d) = %f\n", i, j, p_o_map[i], scores[j].numinseq, dfromc[i][j] );
-			}
-//			fprintf( stderr, "i=%d, freeing\n", i );
-			if( !doalign ) free( table1 );
-			if( doalign && doalign == 'f' ) free( blastresults );
-		}
-		fprintf( stderr, "                \r" );
-
-
-
-
-		for( i=0; i<nyuko; i++ ) numin[i] = 0;
-//		fprintf( stderr, "### itchi shinai hazu, nazenara scores[nin-1].score=%f, selfscores=%d,%d, len=%d,%d, nin=%d\n", scores[nin-1].score, scores[nin-1].selfscore, scores->selfscore, scores->orilen, scores[nin-1].orilen, nin );
-		for( j=0; j<nin; j++ ) 
-		{
-#if 0
-			belongto = s_y_map[j];
-			{
-				fprintf( stderr, "belongto = %d (%dinori)\n", belongto, y_o_map[belongto]+1 ); 
-			}
-			if( belongto == -1 && closeh[j] != -1 )
-#endif
-#if 0
-			if( closeh[j] != -1 )
-			{
-				belongto = s_y_map[closeh[j]];
-//				if( belongto != -1 )
-//					fprintf( stderr, "known, %d(%dinori)->%d(%dinori)\n", j, scores[j].numinseq+1, belongto, y_o_map[belongto]+1 );
-			}
-			else
-//			if( belongto == -1 )
-#else
-			belongto = s_y_map[j];
-			if( belongto == -1 )
-#endif
-			{
-				belongto = 0;  // default ha horyu
-				minscore = dfromc[0][j];
-				for( i=0; i<nyuko; i++ )
-				{
-//					fprintf( stderr, "checking %d/%d,%d/%d (%d-%d inori) minscore=%f, dfromc[0][j]=%f, dfromc[i][j]=%f\n", i, nyuko, j, nin, y_o_map[i], scores[j].numinseq, minscore, dfromc[0][j], dfromc[i][j] );
-					if( scores[j].shimon == scores[yukos[i]].shimon && !strcmp( seq[scores[j].numinseq], seq[y_o_map[i]] ) ) 
-					{
-//						fprintf( stderr, "yuko-%d (%d in ori) to score-%d (%d inori) ha kanzen itch\n", i, y_o_map[i], j, scores[j].numinseq );
-						belongto = i;
-						break;
-					}
-					if( dfromc[i][j] < minscore )
-//					if( dfromc[i][j] < minscore && minscore-dfromc[i][j] > ( minscoreinpick[yukos[i]] + minscoreinpick[j] ) * 1.0 )
-//					if( rnd() < 0.5 ) // CHUUI !!!!!
-					{
-//						fprintf( stderr, "yuko-%d (%d in ori) to score-%d (%d inori) ha tikai, %f>%f\n", i, y_o_map[i]+1, j, scores[j].numinseq+1, minscore, dfromc[i][j] );
-						minscore = dfromc[i][j];
-						belongto = i;
-					}
-				}
-			}
-#if 0
-			if( dfromc[belongto][j] > minscoreinpick[belongto] )
-			{
-				fprintf( stderr, "dame, %f > %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
-				belongto = npick;
-			}
-			else
-				fprintf( stderr, "ok, %f < %f\n", dfromc[belongto][j], minscoreinpick[belongto] );
-#endif
-//			fprintf( stderr, "j=%d (%d inori) -> %d (%d inori) d=%f\n", j, scores[j].numinseq+1, belongto, y_o_map[belongto]+1, dfromc[belongto][j] );
-//			fprintf( stderr, "numin = %d\n", numin[belongto] );
-			outs[belongto] = realloc( outs[belongto], sizeof( Scores ) * ( numin[belongto] + 1 ) );
-			outs[belongto][numin[belongto]] = scores[j];
-			numin[belongto]++;
-
-		}
-		free( dfromcp );
-		FreeDoubleMtx( dfromc );
-
-//		fprintf( stderr, "##### npick = %d\n", npick );
-//		fprintf( stderr, "##### nyuko = %d\n", nyuko );
-
-
-		if( nyuko > 2 )
-		{
-			fprintf( stderr, "upgma       " );
-//			veryfastsupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
-			fixed_musclesupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
-			fprintf( stderr, "\r                      \r" );
-		}
-		else
-		{
-			topol[0][0] = (int *)realloc( topol[0][0], 2 * sizeof( int ) );
-			topol[0][1] = (int *)realloc( topol[0][1], 2 * sizeof( int ) );
-			topol[0][0][0] = 0;
-			topol[0][0][1] = -1;
-			topol[0][1][0] = 1;
-			topol[0][1][1] = -1;
-		}
-		FreeFloatHalfMtx( yukomtx, npick );
-
-#if 0
-		ii = nyuko-1;
-		fprintf( stderr, "nyuko = %d, topol[][] = \n", nyuko );
-		for( j=0; j<nyuko-1; j++ )
-		{
-			fprintf( stderr, "STEP%d \n", j );
-			for( i=0; ; i++ )
-			{
-				fprintf( stderr, "%d ", ( topol[j][0][i] )+0 );
-				if( topol[j][0][i] == -1 ) break;
-			}
-			fprintf( stderr, "\n" );
-			for( i=0; ; i++ )
-			{
-				fprintf( stderr, "%d ", ( topol[j][1][i] )+0 );
-				if( topol[j][1][i] == -1 ) break;
-			}
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "\n" );
-		}
-		exit( 1 );
-#endif
-		jptr = treeorder; 
-		iptr = topol[nyuko-2][0]; while( *iptr != -1 ) *jptr++ = *iptr++;
-		iptr = topol[nyuko-2][1]; while( *iptr != -1 ) *jptr++ = *iptr++;
-		*jptr++ = -1;
-		for( j=0; j<nyuko; j++ )
-		{
-//			fprintf( stderr, "treeorder[%d] = %d\n", j, treeorder[j] );
-			if( treeorder[j] == -1 ) break;
-		}
-	}
-
-	aligned = 1;
-	for( i=0; i<nyuko; i++ )
-	{
-		ii = treeorder[i];
-#if 0
-		if( numin[ii] > 1 )
-		{
-			fprintf( stderr, "\ncalling a child, pick%d (%d inori): # of mem=%d\n", i, p_o_map[ii]+1, numin[ii] );
-			for( j=0; j<numin[ii]; j++ )
-			{
-				fprintf( stderr, "%d ", outs[ii][j].numinseq+1 );
-			}
-			fprintf( stderr, "\n" );
-		}
-#endif
-		aligned *= splitseq_mq( outs[ii], numin[ii], nlen, seq, orialn, name, inputfile, uniform, children+ii, alloclen, order, whichgroup, weight, depthpt, scores->numinseq );
-	}
-
-
-	for( i=0; i<nyuko; i++ )
-	{
-		if( !numin[i] )
-		{
-			fprintf( stderr, "i=%d/%d, ERROR!\n", i, nyuko );
-			for( j=0; j<nyuko; j++ )
-				fprintf( stderr, "numin[%d] = %d (rep=%d inori)\n", j, numin[j], y_o_map[j] );
-			exit( 1 );
-		}
-	}
-
-#if TREE
-	if( treeout )
-	{
-		treelen = 0;
-		for( i=0; i<nyuko; i++ )
-			treelen += strlen( children[i] );
-		*tree = calloc( treelen + nin * 3, sizeof ( char ) );
-	}
-#endif
-
-
-	if( nin >= classsize || !aligned )
-		val = 0;
-	else
-		val = 1;
-
-	if( nyuko > 1 )
-	{
-		int *mem1p, *mem2p;
-		int mem1size, mem2size;
-		int v1, v2, v3;
-		int nlim;
-		int l;
-		static int *mem1 = NULL;
-		static int *mem2 = NULL;
-		char **parttree = NULL; // by Mathog
-
-#if TREE
-		if( treeout )
-		{
-			parttree = (char **)calloc( nyuko, sizeof( char * ) );
-			for( i=0; i<nyuko; i++ )
-			{
-//				fprintf( stderr, "allocating parttree, size = %d\n", treelen + nin * 5 );
-				parttree[i] = calloc( treelen + nin * 5, sizeof ( char ) );
-				strcpy( parttree[i], children[i] );
-				free( children[i] );
-			}
-			free( children );
-		}
-#endif
-		if( mem1 == NULL )
-		{
-			mem1 = AllocateIntVec( njob+1 );
-			mem2 = AllocateIntVec( njob+1 );
-		}
-
-//		veryfastsupg_float_realloc_nobk_halfmtx( nyuko, yukomtx, topol, len );
-	
-//		counteff_simple_float( nyuko, topol, len, eff );
-
-
-		nlim = nyuko-1;
-		for( l=0; l<nlim; l++ )
-		{
-			mem1p = topol[l][0];
-			mptr = mem1;
-			mem1size = 0;
-			while( *mem1p != -1 )
-			{
-//				fprintf( stderr, "*mem1p = %d (%d inori), numin[]=%d\n", *mem1p, p_o_map[*mem1p], numin[*mem1p] );
-				i = numin[*mem1p]; ptr = outs[*(mem1p++)];
-				mem1size += i;
-				while( i-- )
-				{
-					*mptr++ = (ptr++)->numinseq;
-				}
-			}
-			*mptr = -1;
-
-			mem2p = topol[l][1];
-			mptr = mem2;
-			mem2size = 0;
-			while( *mem2p != -1 )
-			{
-//				fprintf( stderr, "*mem2p = %d (%d inori), numin[]=%d\n", *mem2p, p_o_map[*mem2p], numin[*mem2p] );
-				i = numin[*mem2p]; ptr = outs[*(mem2p++)];
-				mem2size += i;
-				while( i-- )
-				{
-					*mptr++ = (ptr++)->numinseq;
-				}
-			}
-			*mptr = -1;
-
-			qsort( mem1, mem1size, sizeof( int ), (int (*)())intcompare );
-			qsort( mem2, mem2size, sizeof( int ), (int (*)())intcompare );
-//			selhead( mem1, numin[0] );
-//			selhead( mem2, numin[1] );
-
-
-#if 0
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "mem1 (nin=%d) = \n", nin );
-			for( i=0; ; i++ )
-			{
-				fprintf( stderr, "%d ", mem1[i]+1 );
-				if( mem1[i] == -1 ) break;
-			}
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "mem2 (nin=%d) = \n", nin );
-			for( i=0; ; i++ )
-			{
-				fprintf( stderr, "%d ", mem2[i]+1 );
-				if( mem2[i] == -1 ) break;
-			}
-			fprintf( stderr, "\n" );
-#endif
-
-#if 0
-			fprintf( stderr, "before pairalign, l = %d, nyuko=%d, mem1size=%d, mem2size=%d\n", l, nyuko, mem1size, mem2size );
-			fprintf( stderr, "before alignment\n" );
-			for( j=0; j<mem1size; j++ )
-				fprintf( stderr, "%s\n", seq[mem1[j]] );
-			fprintf( stderr, "----\n" );
-			for( j=0; j<mem2size; j++ )
-				fprintf( stderr, "%s\n", seq[mem2[j]] );
-			fprintf( stderr, "----\n\n" );
-#endif
-
-			if( val )
-			{
-				fprintf( stderr, "\r  Alignment %d-%d                                 \r", mem1size, mem2size );
-				if( *mem1 < *mem2 )
-					pairalign( njob, nlen, seq, mem1, mem2, weight, alloclen );
-				else
-					pairalign( njob, nlen, seq, mem2, mem1, weight, alloclen );
-			}
-
-#if TREE
-			if( treeout )
-			{
-				v1 = topol[l][0][0];
-				v2 = topol[l][1][0];
-	
-//				fprintf( stderr, "nyuko=%d, v1=%d, v2=%d\n", nyuko, v1, v2 );
-				if( v1 > v2 )
-				{
-					v3 = v1;
-					v1 = v2;
-					v2 = v3;
-				}
-//				fprintf( stderr, "nyuko=%d, v1=%d, v2=%d after sort\n", nyuko, v1, v2 );
-//				fprintf( stderr, "nyuko=%d, v1=%d, v2=%d\n", nyuko, v1, v2 );
-//				fprintf( stderr, "v1=%d, v2=%d, parttree[v1]=%s, parttree[v2]=%s\n", v1, v2, parttree[v1], parttree[v2] );
-				sprintf( *tree, "(%s,%s)", parttree[v1], parttree[v2] );
-				strcpy( parttree[v1], *tree );
-//				fprintf( stderr, "parttree[%d] = %s\n", v1, parttree[v1] );
-//				fprintf( stderr, "*tree = %s\n", *tree );
-				free( parttree[v2] ); parttree[v2] = NULL;
-			}
-#endif
-
-#if 0
-			fprintf( stderr, "after alignment\n" );
-			for( j=0; j<mem1size; j++ )
-				fprintf( stderr, "%s\n", seq[mem1[j]] );
-			fprintf( stderr, "----\n" );
-			for( j=0; j<mem2size; j++ )
-				fprintf( stderr, "%s\n", seq[mem2[j]] );
-			fprintf( stderr, "----\n\n" );
-#endif
-		}
-#if TREE
-		if( treeout )
-		{
-			free( parttree[v1] ); parttree[v1] = NULL;
-//			fprintf( stderr, "*tree = %s\n", *tree );
-//			FreeCharMtx( parttree );
-			free( parttree ); parttree = NULL;
-		}
-#endif
-
-#if 0
-		fprintf( stderr, "after alignment\n" );
-		for( i=0; i<nyuko; i++ )
-		{
-			for( j=0; j<numin[i]; j++ )
-				fprintf( stderr, "%s\n", seq[outs[i][j].numinseq] );
-		}
-#endif
-
-		if( val )
-		{
-			groupid++;
-			mptr = mem1; while( *mptr != -1 ) 
-			{
-#if 0
-				fprintf( stdout, "==g1-%d \n", *mptr+1 );
-				fprintf( stdout, "%s \n", seq[*mptr] );
-#endif
-				whichgroup[*mptr] = groupid;
-				weight[*mptr++] *= 0.5;
-			}
-	
-			mptr = mem2; while( *mptr != -1 ) 
-			{
-#if 0
-				fprintf( stdout, "=g2-%d ", *mptr+1 );
-				fprintf( stdout, "%s \n", seq[*mptr] );
-#endif
-				whichgroup[*mptr] = groupid;
-				weight[*mptr++] *= 0.5;
-			}
-	
-			if( numin[1] == 0 )
-			{
-				mptr = mem1; while( *mptr != -1 ) 
-				{
-					whichgroup[*mptr] = groupid;
-					weight[*mptr++] *= (double)2.0/numin[0];
-				}
-			}
-		}
-		{
-			if( *depthpt > maxdepth ) maxdepth = *depthpt;
-			(*depthpt)++;
-		}
-	}
-	else
-	{
-#if TREE
-		if( treeout )
-		{
-			sprintf( *tree, "%s", children[0] );
-			free( children[0] );
-			free( children );
-		}
-#endif
-	}
-	for( i=0; i<npick; i++ ) free( (void *)outs[i] );
-//	FreeFloatHalfMtx( pickmtx, npick );
-//	FreeFloatHalfMtx( yukomtx, npick );
-	FreeFloatMtx( len );
-	FreeIntCub( topol );
-	FreeIntVec( treeorder );
-	free( outs );
-	free( numin );
-	free( picks );
-	free( yukos );
-	free( s_p_map );
-	free( s_y_map );
-	free( p_o_map );
-	free( y_o_map );
-	free( hanni );
-	free( closeh );
-	free( pickkouho );
-	free( tsukau );
-//	free( minscoreinpick );
-	return val;
-}
-#endif
-
-static void alignparaphiles( int nseq, int *nlen, double *weight, char **seq, int nmem, int *members, int *alloclen )
-{
-	int i, ilim;
-	int *mem1 = AllocateIntVec( nmem );
-	int *mem2 = AllocateIntVec( 2 );
-
-	mem2[1] = -1;
-	ilim = nmem-1;
-	for( i=0; i<ilim; i++ )
-	{
-		mem1[i] = members[i];
-		mem1[i+1] = -1;
-		mem2[0] = members[i+1];
-		pairalign( nseq, nlen, seq, mem1, mem2, weight, alloclen );
-	}
-	free( mem1 );
-	free( mem2 );
-}
-
-
-
-
-
-
-
-
-
-
-
-int main( int argc, char *argv[] )
-{
-	static char **name, **seq, **orialn;
-	static int *grpseq;
-	static char *tmpseq;
-	static int  **pointt;
-	static int *nlen;
-	int i, st, en;
-	FILE *infp;
-	FILE *treefp;
-	char *treefile = NULL; //by Mathog
-	char c;
-	int alloclen;
-	static int *order;
-	static int *whichgroup;
-	static double *weight;
-	static char tmpname[B+100];
-	int groupnum;
-	int groupid;
-	int pos;
-	int *paramem;
-	int npara;
-	int completed;
-	int orilen;
-	int pscore;
-	char *pt;
-	int **tmpaminodis;
-	static char com[1000];
-	int depth;
-	int aan;
-
-	static Scores *scores;
-	static short *table1;
-	static char **tree;
-
-
-
-	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( picksize == NOTSPECIFIED || picksize < 2 )
-		picksize = PICKSIZE;
-
-	if( classsize == NOTSPECIFIED || classsize < 0 )
-	{
-		classsize = njob + 1;
-	}
-	else
-	{
-//		picksize = MIN( picksize, (int)sqrt( classsize ) + 1);
-	}
-
-	if( tokyoripara == NOTSPECIFIED )
-	{
-		if( doalign ) tokyoripara = TOKYORIPARA_A;
-		else tokyoripara = TOKYORIPARA;
-	}
-	if( picksize > njob )
-		tokyoripara = 0.0;
-
-
-	alloclen = nlenmax * 2;
-	name = AllocateCharMtx( njob, B+1 );
-
-	if( classsize == 1 )
-		seq = AllocateCharMtx( njob, 0 );
-	else
-		seq = AllocateCharMtx( njob, alloclen+1 );
-
-
-	nlen = AllocateIntVec( njob ); 
-	tmpseq = calloc( nlenmax+1, sizeof( char )  );
-	pointt = AllocateIntMtx( njob, 0 );
-	grpseq = AllocateIntVec( nlenmax + 1 );
-	order = (int *)calloc( njob + 1, sizeof( int ) );
-	whichgroup = (int *)calloc( njob, sizeof( int ) );
-	weight = (double *)calloc( njob, sizeof( double ) );
-
-	fprintf( stderr, "alloclen = %d in main\n", alloclen );
-
-	for( i=0; i<njob; i++ ) whichgroup[i] = 0;
-	for( i=0; i<njob; i++ ) weight[i] = 1.0;
-	for( i=0; i<njob; i++ ) order[i] = -1;
-
-	if( classsize == 1 )
-		readData_varlen( infp, name, nlen, seq );
-	else
-		readData_pointer( infp, name, nlen, seq );
-
-	fclose( infp );
-
-	if( fromaln ) doalign = 1;
-
-	if( fromaln )
-	{
-		orialn = AllocateCharMtx( njob, alloclen+1 );
-		for( i=0; i<njob; i++ )
-		{
-			if( strlen( seq[i] ) != nlenmax )
-			{
-				fprintf( stderr, "Input sequences must be aligned\n" );
-				exit( 1 );
-			}
-			strcpy( orialn[i], seq[i] );
-		}
-	}
-
-	constants( njob, seq );
-
-	if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
-	else              tsize = (int)pow( 6, 6 );
-
-	if( dorp == 'd' )
-	{
-		lenfaca = DLENFACA;
-		lenfacb = DLENFACB;
-		lenfacc = DLENFACC;
-		lenfacd = DLENFACD;
-	}
-	else
-	{
-		lenfaca = PLENFACA;
-		lenfacb = PLENFACB;
-		lenfacc = PLENFACC;
-		lenfacd = PLENFACD;
-	}
-
-	maxl = 0;
-	for( i=0; i<njob; i++ ) 
-	{
-		gappick0( tmpseq, seq[i] );
-		nlen[i] = strlen( tmpseq );
-		strcpy( seq[i], tmpseq );
-		pointt[i] = AllocateIntVec( nlen[i]+1 ); // ??
-
-		if( nlen[i] < 6 )
-		{
-			fprintf( stderr, "Seq %d, too short, %d characters\n", i+1, nlen[i] );
-			fprintf( stderr, "name = %s\n", name[i] );
-			fprintf( stderr, "seq = %s\n", seq[i] );
-			exit( 1 );
-//			continue;
-		}
-		if( nlen[i] > maxl ) maxl = nlen[i];
-		if( dorp == 'd' ) /* nuc */
-		{
-			if( seq_grp_nuc( grpseq, tmpseq ) < 6 )
-			{
-				fprintf( stderr, "Seq %d, too short.\n", i+1 );
-				fprintf( stderr, "name = %s\n", name[i] );
-				fprintf( stderr, "seq = %s\n", seq[i] );
-				exit( 1 );
-//				continue;
-			}
-			makepointtable_nuc( pointt[i], grpseq );
-		}
-		else                 /* amino */
-		{
-			if( seq_grp( grpseq, tmpseq ) < 6 )
-			{
-				fprintf( stderr, "Seq %d, too short.\n", i+1 );
-				fprintf( stderr, "name = %s\n", name[i] );
-				fprintf( stderr, "seq = %s\n", seq[i] );
-				exit( 1 );
-//				continue;
-			}
-			makepointtable( pointt[i], grpseq );
-		}
-//		fprintf( stdout, ">%s\n", name[i] );
-//		fprintf( stdout, "%s\n", seq[i] );
-	}
-//	exit( 1 );
-
-#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 );
-	}
-
-	pid = (int)getpid();
-	sprintf( datafile, "/tmp/data-%d", pid );
-	sprintf( queryfile, "/tmp/query-%d", pid );
-	sprintf( resultfile, "/tmp/fasta-%d", pid );
-
-	scores = (Scores *)calloc( njob, sizeof( Scores ) );
-
-//	fprintf( stderr, "\nCalculating i-i scores ... \n" );
-	for( i=0; i<njob; i++ ) 
-	{
-		orilen = strlen( seq[i] );
-		scores[i].numinseq = i; // irimasu
-		scores[i].orilen = orilen;
-	}
-
-	if( doalign == 'f' )
-	{
-		fastapath = getenv( "FASTA_4_MAFFT" );
-		if( !fastapath ) fastapath = "fasta34";
-		fprintf( stderr, "fastapath=%s\n", fastapath );
-		tmpaminodis = AllocateIntMtx( 0x80, 0x80 );
-		getfastascoremtx( tmpaminodis );
-	}
-	else
-		tmpaminodis = NULL;
-	
-	for( i=0; i<njob; i++ )
-	{
-		scores[i].pointt = pointt[i];
-		scores[i].shimon = (int)pointt[i][0] + (int)pointt[i][1] + (int)pointt[i][scores[i].orilen-6];
-		scores[i].name = name[i];
-		if( doalign )
-		{
-			fprintf( stderr, "\r %05d/%05d   ", i, njob );
-			free( scores[i].pointt );
-			if( doalign == 'f' )
-			{
-#if 0
-#define KIZAMI 100
-				int ipos = (int)( i / KIZAMI ) * KIZAMI;
-				int iposamari = i % KIZAMI;
-
-				fprintf( stderr, "%d / %d\r", i, njob );
-//				fprintf( stderr, "ipos = %d\n", ipos );
-//				fprintf( stderr, "iposamari = %d\n", iposamari );
-
-//				fprintf( stderr, " calling blast, i=%d\n", i );
-//				blastresults = callfasta( seq, scores+i, 1, 0, 1 );
-				blastresults = callfasta( seq, scores+ipos, MIN(KIZAMI,njob-ipos), NULL, iposamari, (iposamari==0)  );
-//				fprintf( stderr, "done., i=%d\n\n", i );
-				scores[i].selfscore = (int)blastresults[iposamari]; 
-#if 0
-				for( j=0; j<100; j++ )
-				{
-					fprintf( stderr, "res[%d] = %f\n", j, blastresults[j] );
-				}
-#endif
-//				fprintf( stderr, "%d->selfscore = %d\n", i, scores[i].selfscore );
-				free( blastresults );
-#else
-				pscore = 0;
-				if( scoremtx == -1 )
-				{
-					st = 1;
-					en = 0;
-					for( pt=seq[i]; *pt; pt++ )
-					{
-						if( *pt == 'u' ) *pt = 't';
-						aan = amino_n[(int)*pt];
-						if( aan<0 || aan >= 4 ) *pt = 'n';
-
-						if( *pt == 'n' ) 
-						{
-							en++;
-							if( st ) continue;
-							else pscore += tmpaminodis[(int)*pt][(int)*pt];
-						}
-						else
-						{
-							st = 0;
-							en = 0;
-							pscore += tmpaminodis[(int)*pt][(int)*pt];
-						}
-					}
-					scores[i].selfscore = pscore - en * tmpaminodis['n']['n']; 
-				}
-				else
-				{
-					st = 1;
-					en = 0;
-					for( pt=seq[i]; *pt; pt++ )
-					{
-						aan = amino_n[(int)*pt];
-						if( aan<0 || aan >= 20 ) *pt = 'X';
-						if( *pt == 'X' ) 
-						{
-							en++;
-							if( st ) continue;
-							else pscore += tmpaminodis[(int)*pt][(int)*pt];
-						}
-						else
-						{
-							st = 0;
-							en = 0;
-							pscore += tmpaminodis[(int)*pt][(int)*pt];
-						}
-					}
-					scores[i].selfscore = pscore - en * tmpaminodis['X']['X']; 
-				}
-#endif
-			}
-			else
-			{
-				pscore = 0;
-				for( pt=seq[i]; *pt; pt++ )
-				{
-					pscore += amino_dis[(int)*pt][(int)*pt];
-				}
-				scores[i].selfscore = pscore; 
-			}
-//			fprintf( stderr, "selfscore[%d] = %d\n", i+1, scores[i].selfscore );
-		}
-		else
-		{
-			table1 = (short *)calloc( tsize, sizeof( short ) );
-			if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
-			makecompositiontable_p( table1, pointt[i] );
-			scores[i].selfscore = commonsextet_p( table1, pointt[i] );
-			free( table1 );
-		}
-	}
-	if( tmpaminodis ) FreeIntMtx( tmpaminodis );
-
-	depth = 0;
-#if TREE
-	if( treeout )
-	{
-		tree = (char **)calloc( 1, sizeof( char *) );
-		*tree = NULL;
-//		splitseq_bin( scores, njob, nlen, seq, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight );
-		completed = splitseq_mq( scores, njob, nlen, seq, orialn, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth, -1 );
-		treefile = (char *)calloc( strlen( inputfile ) + 10, sizeof( char ) );
-		if( inputfile )
-			sprintf( treefile, "%s.tree", inputfile );
-		else
-			sprintf( treefile, "splittbfast.tree" );
-		treefp = fopen( treefile, "w" );
-		fprintf( treefp, "%s\n", *tree );
-		fclose( treefp );
-	}
-	else
-		completed = splitseq_mq( scores, njob, nlen, seq, orialn, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth, -1 );
-#else
-	completed = splitseq_mq( scores, njob, nlen, seq, orialn, name, inputfile, 0, tree, &alloclen, order, whichgroup, weight, &depth, -1 );
-#endif
-
-	fprintf( stderr, "\nDone.\n\n" );
-
-#if 1
-	groupnum = 0;
-	groupid = -1;
-	paramem = NULL;
-	npara = 0;
-	for( i=0; i<njob; i++ )
-	{
-		pos = order[i];
-		if( whichgroup[pos] != groupid )
-		{
-			groupnum++;
-			groupid = whichgroup[pos];
-		}
-		if( whichgroup[pos] )
-		{
-			if( paramem )
-			{
-				paramem[npara] = -1;
-				if( npara > 1 && classsize > 2 ) 
-				{
-					qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
-//					selhead( paramem, npara );
-					alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
-				}
-				free( paramem ); paramem = NULL; npara = 0;
-			}
-			sprintf( tmpname, "Group-%d %s", groupnum, name[pos]+1 );
-		}
-		else
-		{
-			paramem = realloc( paramem, sizeof( int) * ( npara + 2 ) );
-			paramem[npara++] = pos;
-			sprintf( tmpname, "Group-para %s", name[pos]+1 );
-		}
-		tmpname[B-1] = 0;
-		if( classsize > 1 && classsize <= njob )
-			strcpy( name[pos]+1, tmpname );
-	}
-	if( paramem )
-	{
-		paramem[npara] = -1;
-		if( npara > 1 && classsize > 2 ) 
-		{
-			qsort( paramem, npara, sizeof( int ), (int (*)(const void *, const void*))intcompare );
-//			selhead( paramem, npara );
-			alignparaphiles( njob, nlen, weight, seq, npara, paramem, &alloclen );
-		}
-		free( paramem ); paramem = NULL; npara = 0;
-	}
-#else
-	for( i=0; i<njob; i++ )
-	{
-		sprintf( tmpname, "Group-%d %s", whichgroup[i], name[i]+1 );
-		strcpy( name[i]+1, tmpname );
-	}
-#endif
-
-
-//	maketanni( name, seq,  njob, nlenmax, nlen );
-
-	fclose( trap_g );
-
-#if DEBUG
-	fprintf( stderr, "writing alignment to stdout\n" );
-#endif
-	if( reorder )
-		writeData_reorder_pointer( stdout, njob, name, nlen, seq, order );
-	else
-		writeData_pointer( stdout, njob, name, nlen, seq );
-#if IODEBUG
-	fprintf( stderr, "OSHIMAI\n" );
-#endif
-	if( classsize == 1 )
-	{
-		fprintf( stderr, "\n\n" );
-		fprintf( stderr, "----------------------------------------------------------------------------\n" );
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "nseq = %d\n", njob );
-		fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
-		fprintf( stderr, "The input sequences have been sorted so that similar sequences are close.\n" );
-		if( reorder )
-			fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
-#if TREE
-		if( treeout )
-		{
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
-		}
-//		else
-//		{
-//			fprintf( stderr, "To output guide tree,\n" );
-//			fprintf( stderr, "%% %s -t  -i %s\n", progName( argv[0] ), "inputfile" );
-//		}
-#endif
-		if( !doalign )
-		{
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
-			fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
-		}
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "----------------------------------------------------------------------------\n" );
-	}
-	else if( groupnum > 1 )
-	{
-		fprintf( stderr, "\n\n" );
-		fprintf( stderr, "----------------------------------------------------------------------------\n" );
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "groupsize = %d, picksize=%d\n", classsize, picksize );
-		fprintf( stderr, "The input sequences have been classified into %d groups + some paraphyletic groups\n", groupnum );
-		fprintf( stderr, "Note that the alignment is not completed.\n" );
-		if( reorder )
-			fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
-#if TREE
-		if( treeout )
-		{
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
-		}
-//		else
-//		{
-//			fprintf( stderr, "To output guide tree,\n" );
-//			fprintf( stderr, "%% %s -t  -i %s\n", progName( argv[0] ), "inputfile" );
-//		}
-#endif
-		if( !doalign )
-		{
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
-			fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
-		}
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "----------------------------------------------------------------------------\n" );
-	}			
-	else
-	{
-		fprintf( stderr, "\n\n" );
-		fprintf( stderr, "----------------------------------------------------------------------------\n" );
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "nseq = %d\n", njob );
-		fprintf( stderr, "groupsize = %d, partsize=%d\n", classsize, picksize );
-//		fprintf( stderr, "A single alignment containing all the input sequences has been computed.\n" );
-//		fprintf( stderr, "If the sequences are highly diverged and you feel there are too many gaps,\n" );
-//		fprintf( stderr, "please try \n" );
-//		fprintf( stderr, "%% mafft --parttree --groupsize 100 inputfile\n" );
-//		fprintf( stderr, "which classifies the sequences into several groups with <~ 100 sequences\n" );
-//		fprintf( stderr, "and performs only intra-group alignments.\n" );
-		if( reorder )
-			fprintf( stderr, "The order of sequences has been changed according to estimated similarity.\n" );
-#if TREE
-		if( treeout )
-		{
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "A guide tree is in the '%s' file.\n", treefile );
-		}
-//		else
-//		{
-//			fprintf( stderr, "To output guide tree,\n" );
-//			fprintf( stderr, "%% %s -t  -i %s\n", progName( argv[0] ), "inputfile" );
-//		}
-#endif
-		if( !doalign || fromaln )
-		{
-			fprintf( stderr, "\n" );
-			fprintf( stderr, "mafft --dpparttree might give a better result, although slow.\n" );
-			fprintf( stderr, "mafft --fastaparttree is also available if you have fasta34.\n" );
-		}
-		fprintf( stderr, "\n" );
-		fprintf( stderr, "----------------------------------------------------------------------------\n" );
-	}
-#if TREE
-	if( treeout ) free( treefile );
-#endif
-
-#if 0
-	fprintf( stdout, "weight =\n" );
-	for( i=0; i<njob; i++ )
-		fprintf( stdout, "%d: %f\n", i+1, weight[i] );
-#endif
-
-	if( doalign == 'f' )
-	{
-		strcpy( com, "rm -f" );
-		strcat( com, " " );
-		strcat( com, datafile );
-		strcat( com, "*  " );
-		strcat( com, queryfile );
-		strcat( com, " " );
-		strcat( com, resultfile );
-		fprintf( stderr, "%s\n", com );
-		system( com );
-	}
-
-	SHOWVERSION;
-
-	return( 0 );
-}