diff mafft/core/io.c @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/io.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,5370 @@
+#include "mltaln.h"
+
+static int upperCase = 0;
+
+#define DEBUG   0
+#define IODEBUG 0
+
+char creverse( char f )
+{
+	static char *table = NULL;
+	if( table == NULL )
+	{
+		int i;
+		table = AllocateCharVec(0x80);
+		for( i=0; i<0x80; i++ ) table[i] = i;
+		table['A'] = 'T';
+		table['C'] = 'G';
+		table['G'] = 'C';
+		table['T'] = 'A';
+		table['U'] = 'A';
+		table['M'] = 'K';
+		table['R'] = 'Y';
+		table['W'] = 'W';
+		table['S'] = 'S';
+		table['Y'] = 'R';
+		table['K'] = 'M';
+		table['V'] = 'B';
+		table['H'] = 'D';
+		table['D'] = 'H';
+		table['B'] = 'V';
+		table['N'] = 'N';
+		table['a'] = 't';
+		table['c'] = 'g';
+		table['g'] = 'c';
+		table['t'] = 'a';
+		table['u'] = 'a';
+		table['m'] = 'k';
+		table['r'] = 'y';
+		table['w'] = 'w';
+		table['s'] = 's';
+		table['y'] = 'r';
+		table['k'] = 'm';
+		table['v'] = 'b';
+		table['h'] = 'd';
+		table['d'] = 'h';
+		table['b'] = 'v';
+		table['n'] = 'n';
+//		table['-'] = '-';
+//		table['.'] = '.';
+//		table['*'] = '*';
+	}
+	return( table[(int)f] );
+}
+
+void sreverse( char *r, char *s )
+{
+	r += strlen( s );
+	*r-- = 0;
+	while( *s )
+		*r-- = creverse( *s++ );
+//		*r-- = ( *s++ );
+}
+
+void gappick_samestring( char *seq )
+{
+	char *aseq = seq;
+
+	for( ; *seq != 0; seq++ )
+	{
+		if( *seq != '-' )
+			*aseq++ = *seq;
+	}
+	*aseq = 0;
+}
+
+#if 0
+
+static int addlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
+{
+	int pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	int iscore;
+	int isumscore;
+	int sumoverlap;
+	LocalHom *tmppt;
+	int st;
+	int nlocalhom = 0;
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+	isumscore = 0;
+	sumoverlap = 0;
+
+#if 0
+	fprintf( stderr, "nlocalhom = %d in addlocalhom\n", nlocalhom );
+	fprintf( stderr, "al1 = %s, al2 = %s\n", al1, al2 );
+	fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
+	fprintf( stderr, "localhopt = %p, skip = %d\n", localhompt, skip );
+	fprintf( stderr, "pt1 = \n%s\n, pt2 = \n%s\n", pt1, pt2 );
+#endif
+
+	if( skip )
+	{
+		while( --skip > 0 ) localhompt = localhompt->next;
+		localhompt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+		localhompt = localhompt->next;
+//		fprintf( stderr, "tmppt = %p, localhompt = %p\n", tmppt, localhompt );
+	}
+	tmppt = localhompt;
+
+	st = 0;
+	iscore = 0;
+	while( *pt1 != 0 )
+	{
+//		fprintf( stderr, "In in while loop\n" );
+//		fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+		if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+		{
+			end1 = pos1 - 1;
+			end2 = pos2 - 1;
+
+			if( nlocalhom++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ...\n" );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+#if 1
+			isumscore += iscore;
+			sumoverlap += end2-start2+1;
+#else
+			tmppt->overlapaa   = end2-start2+1;
+			tmppt->opt = iscore * 5.8 / 600;
+			tmppt->overlapaa   = overlapaa;
+			tmppt->opt = (double)opt;
+#endif
+
+#if 0
+			fprintf( stderr, "iscore (1)= %d\n", iscore );
+			fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+			fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+			iscore = 0;
+			st = 0;
+		}
+		else if( *pt1 != '-' && *pt2 != '-' )
+		{
+			if( st == 0 )
+			{
+				start1 = pos1; start2 = pos2;
+				st = 1;
+			}
+			iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
+//			fprintf( stderr, "%c-%c, score(0) = %d\n", *pt1, *pt2, iscore );
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+	}
+
+	if( st )
+	{
+		if( nlocalhom++ > 0 )
+		{
+//			fprintf( stderr, "reallocating ...\n" );
+			tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//			fprintf( stderr, "done\n" );
+			tmppt = tmppt->next;
+			tmppt->next = NULL;
+		}
+		end1 = pos1 - 1;
+		end2 = pos2 - 1;
+		tmppt->start1 = start1;
+		tmppt->start2 = start2;
+		tmppt->end1   = end1  ;
+		tmppt->end2   = end2  ;
+
+#if 1
+		isumscore += iscore;
+		sumoverlap += end2-start2+1;
+#else
+		tmppt->overlapaa   = end2-start2+1;
+		tmppt->opt = (double)iscore * 5.8 / 600;
+		tmppt->overlapaa   = overlapaa;
+		tmppt->opt = (double)opt;
+#endif
+#if 0
+		fprintf( stderr, "score (2)= %d\n", iscore );
+		fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+		fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+	}
+
+	for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+	{
+		tmppt->overlapaa = sumoverlap;
+		tmppt->opt = (double)sumscore * 5.8 / 600 / sumoverlap;
+	}
+	return( nlocalhom );
+}
+
+#endif
+
+
+
+static int addlocalhom_r( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa, int skip )
+{
+	int pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	double score;
+	double sumscore;
+	int sumoverlap;
+	LocalHom *tmppt = NULL; // by D.Mathog, a guess
+	int st;
+	int nlocalhom = 0;
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+	sumscore = 0.0;
+	sumoverlap = 0;
+	start1 = 0; // by D.Mathog, a guess
+	start2 = 0; // by D.Mathog, a guess
+
+#if 0
+	fprintf( stderr, "nlocalhom = %d in addlocalhom\n", nlocalhom );
+	fprintf( stderr, "al1 = %s, al2 = %s\n", al1, al2 );
+	fprintf( stderr, "off1 = %d, off2 = %d\n", off1, off2 );
+	fprintf( stderr, "localhopt = %p, skip = %d\n", localhompt, skip );
+#endif
+	fprintf( stderr, "pt1 = \n%s\n, pt2 = \n%s\n", pt1, pt2 );
+
+	if( skip )
+	{
+		while( --skip > 0 ) localhompt = localhompt->next;
+		localhompt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+		localhompt = localhompt->next;
+		fprintf( stderr, "tmppt = %p, localhompt = %p\n", (void *)tmppt, (void *)localhompt );
+	}
+	tmppt = localhompt;
+
+	st = 0;
+	score = 0.0;
+	while( *pt1 != 0 )
+	{
+		fprintf( stderr, "In in while loop\n" );
+		fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+		if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+		{
+			end1 = pos1 - 1;
+			end2 = pos2 - 1;
+
+			if( nlocalhom++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ...\n" );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+#if 1
+			sumscore += score;
+			sumoverlap += end2-start2+1;
+#else
+			tmppt->overlapaa   = end2-start2+1;
+			tmppt->opt = score * 5.8 / 600;
+			tmppt->overlapaa   = overlapaa;
+			tmppt->opt = (double)opt;
+#endif
+
+			fprintf( stderr, "score (1)= %f\n", score );
+			fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+			fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+			score = 0.0;
+			st = 0;
+		}
+		else if( *pt1 != '-' && *pt2 != '-' )
+		{
+			if( st == 0 )
+			{
+				start1 = pos1; start2 = pos2;
+				st = 1;
+			}
+			score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]];
+//			fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+	}
+	if( nlocalhom++ > 0 )
+	{
+//		fprintf( stderr, "reallocating ...\n" );
+		tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//		fprintf( stderr, "done\n" );
+		tmppt = tmppt->next;
+		tmppt->next = NULL;
+	}
+	end1 = pos1 - 1;
+	end2 = pos2 - 1;
+	tmppt->start1 = start1;
+	tmppt->start2 = start2;
+	tmppt->end1   = end1  ;
+	tmppt->end2   = end2  ;
+
+#if 1
+	sumscore += score;
+	sumoverlap += end2-start2+1;
+#else
+	tmppt->overlapaa   = end2-start2+1;
+	tmppt->opt = score * 5.8 / 600;
+	tmppt->overlapaa   = overlapaa;
+	tmppt->opt = (double)opt;
+#endif
+
+	fprintf( stderr, "score (2)= %f\n", score );
+	fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+	fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+
+	for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+	{
+		tmppt->overlapaa = sumoverlap;
+		tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+	}
+	return( nlocalhom );
+}
+void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+	int pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	double score;
+	double sumscore;
+	int sumoverlap;
+	LocalHom *tmppt;
+	LocalHom *subnosento;
+	int st;
+	int saisho;
+
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+	sumscore = 0.0;
+	sumoverlap = 0;
+	start1 = 0; // by Mathog, a guess
+	start2 = 0; // by Mathog, a guess
+
+	subnosento = localhompt;
+	while( subnosento->next ) subnosento = subnosento->next;
+	tmppt = subnosento;
+
+	saisho = ( localhompt->nokori == 0 );
+
+	fprintf( stderr, "localhompt = %p\n", (void *)localhompt );
+	fprintf( stderr, "tmppt = %p\n", (void *)tmppt );
+	fprintf( stderr, "subnosento = %p\n", (void *)subnosento );
+
+	st = 0;
+	score = 0.0;
+	while( *pt1 != 0 )
+	{
+//		fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+		if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+		{
+			end1 = pos1 - 1;
+			end2 = pos2 - 1;
+
+			if( localhompt->nokori++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ...\n" );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+#if 1
+			if( divpairscore )
+			{
+				tmppt->overlapaa   = end2-start2+1;
+				tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+			}
+			else
+			{
+				sumscore += score;
+				sumoverlap += end2-start2+1;
+			}
+#else
+			tmppt->overlapaa   = overlapaa;
+			tmppt->opt = (double)opt;
+#endif
+
+#if 0
+			fprintf( stderr, "score (1)= %f\n", score );
+			fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+			fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+			score = 0.0;
+			st = 0;
+		}
+		else if( *pt1 != '-' && *pt2 != '-' )
+		{
+			if( st == 0 )
+			{
+				start1 = pos1; start2 = pos2;
+				st = 1;
+			}
+			score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset はいらないかも
+//			fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+	}
+	if( *(pt1-1) != '-' && *(pt2-1) != '-'  )
+	{
+		if( localhompt->nokori++ > 0 )
+		{
+//			fprintf( stderr, "reallocating ...\n" );
+			tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//			fprintf( stderr, "done\n" );
+			tmppt = tmppt->next;
+			tmppt->next = NULL;
+		}
+
+		end1 = pos1 - 1;
+		end2 = pos2 - 1;
+		tmppt->start1 = start1;
+		tmppt->start2 = start2;
+		tmppt->end1   = end1  ;
+		tmppt->end2   = end2  ;
+
+
+#if 1
+		if( divpairscore )
+		{
+			tmppt->overlapaa   = end2-start2+1;
+			tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+		}
+		else
+		{
+			sumscore += score;
+			sumoverlap += end2-start2+1;
+		}
+#else
+		tmppt->overlapaa   = overlapaa;
+		tmppt->opt = (double)opt;
+#endif
+
+#if 0
+		fprintf( stderr, "score (2)= %f\n", score );
+		fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+		fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+	}
+
+	fprintf( stderr, "sumscore = %f\n", sumscore );
+	if( !divpairscore )
+	{
+
+		if( !saisho ) subnosento = subnosento->next;
+		for( tmppt=subnosento; tmppt; tmppt=tmppt->next )
+		{
+			tmppt->overlapaa = sumoverlap;
+			tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+			fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+		}
+	}
+}
+void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+	int pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	int iscore;
+	int isumscore;
+	int sumoverlap;
+	LocalHom *tmppt = localhompt;
+	int nlocalhom = 0;
+	int st;
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+
+	isumscore = 0;
+	sumoverlap = 0;
+	start1 = 0; // by D.Mathog, a guess
+	start2 = 0; // by D.Mathog, a guess
+
+	st = 0;
+	iscore = 0;
+	while( *pt1 != 0 )
+	{
+//		fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+		if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+		{
+			end1 = pos1 - 1;
+			end2 = pos2 - 1;
+
+			if( nlocalhom++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ...\n" );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+#if 1
+			if( divpairscore )
+			{
+				tmppt->overlapaa   = end2-start2+1;
+				tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+			}
+			else
+			{
+				isumscore += iscore;
+				sumoverlap += end2-start2+1;
+			}
+#else
+			tmppt->overlapaa   = overlapaa;
+			tmppt->opt = (double)opt;
+#endif
+
+#if 0
+			fprintf( stderr, "iscore (1)= %d\n", iscore );
+			fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+			fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+			iscore = 0;
+			st = 0;
+		}
+		else if( *pt1 != '-' && *pt2 != '-' )
+		{
+			if( st == 0 )
+			{
+				start1 = pos1; start2 = pos2;
+				st = 1;
+			}
+			iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset はいらないかも
+//			fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+	}
+	if( *(pt1-1) != '-' && *(pt2-1) != '-'  )
+	{
+		if( nlocalhom++ > 0 )
+		{
+//			fprintf( stderr, "reallocating ...\n" );
+			tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//			fprintf( stderr, "done\n" );
+			tmppt = tmppt->next;
+			tmppt->next = NULL;
+		}
+		end1 = pos1 - 1;
+		end2 = pos2 - 1;
+		tmppt->start1 = start1;
+		tmppt->start2 = start2;
+		tmppt->end1   = end1  ;
+		tmppt->end2   = end2  ;
+	
+#if 1
+		if( divpairscore )
+		{
+			tmppt->overlapaa   = end2-start2+1;
+			tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+		}
+		else
+		{
+			isumscore += iscore;
+			sumoverlap += end2-start2+1;
+		}
+#else
+		tmppt->overlapaa   = overlapaa;
+		tmppt->opt = (double)opt;
+#endif
+
+#if 0
+		fprintf( stderr, "iscore (2)= %d\n", iscore );
+		fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+		fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+	}
+
+	if( !divpairscore )
+	{
+		for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+		{
+			tmppt->overlapaa = sumoverlap;
+//			tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
+			tmppt->opt = (double)600 * 5.8 / 600;
+//			fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+		}
+	}
+}
+
+void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+	int posinaln, pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	int isumscore;
+	int sumoverlap;
+	LocalHom *tmppt = localhompt;
+	int nlocalhom = 0;
+//	int st;
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+	isumscore = 0;
+	sumoverlap = 0;
+	start1 = 0; // by D.Mathog, a guess
+	start2 = 0; // by D.Mathog, a guess
+
+	posinaln = 0;
+	while( *pt1 != 0 )
+	{
+		if( *pt1 != '-' && *pt2 != '-' && equiv[posinaln] > 0.0 )
+		{
+			start1 = end1 = pos1; start2 = end2 = pos2;
+			if( nlocalhom++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ... (posinaln=%d)\n", posinaln );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+			tmppt->overlapaa   = 1;
+//			tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+			tmppt->opt = equiv[posinaln] * scale;
+//			fprintf( stdout, "*pt1=%c, *pt2=%c, equiv=%f\n", *pt1, *pt2, equiv[posinaln] );
+
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+		posinaln++;
+	}
+}
+
+
+void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+	int pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	int iscore;
+	int isumscore;
+	int sumoverlap;
+	LocalHom *tmppt = localhompt;
+	int nlocalhom = 0;
+	int st;
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+
+	isumscore = 0;
+	sumoverlap = 0;
+	start1 = 0; // by D.Mathog, a guess
+	start2 = 0; // by D.Mathog, a guess
+
+	st = 0;
+	iscore = 0;
+	while( *pt1 != 0 )
+	{
+//		fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+		if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+		{
+			end1 = pos1 - 1;
+			end2 = pos2 - 1;
+
+			if( nlocalhom++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ...\n" );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+#if 1
+			if( divpairscore )
+			{
+				tmppt->overlapaa   = end2-start2+1;
+				tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+			}
+			else
+			{
+				isumscore += iscore;
+				sumoverlap += end2-start2+1;
+			}
+#else
+			tmppt->overlapaa   = overlapaa;
+			tmppt->opt = (double)opt;
+#endif
+
+#if 0
+			fprintf( stderr, "iscore (1)= %d\n", iscore );
+			fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+			fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+			iscore = 0;
+			st = 0;
+		}
+		else if( *pt1 != '-' && *pt2 != '-' )
+		{
+			if( st == 0 )
+			{
+				start1 = pos1; start2 = pos2;
+				st = 1;
+			}
+			iscore += n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset はいらないかも
+//			fprintf( stderr, "%c-%c, iscore(0) = %d\n", *pt1, *pt2, iscore );
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+	}
+	if( *(pt1-1) != '-' && *(pt2-1) != '-'  )
+	{
+		if( nlocalhom++ > 0 )
+		{
+//			fprintf( stderr, "reallocating ...\n" );
+			tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//			fprintf( stderr, "done\n" );
+			tmppt = tmppt->next;
+			tmppt->next = NULL;
+		}
+		end1 = pos1 - 1;
+		end2 = pos2 - 1;
+		tmppt->start1 = start1;
+		tmppt->start2 = start2;
+		tmppt->end1   = end1  ;
+		tmppt->end2   = end2  ;
+	
+#if 1
+		if( divpairscore )
+		{
+			tmppt->overlapaa   = end2-start2+1;
+			tmppt->opt = (double)iscore / tmppt->overlapaa * 5.8 / 600;
+		}
+		else
+		{
+			isumscore += iscore;
+			sumoverlap += end2-start2+1;
+		}
+#else
+		tmppt->overlapaa   = overlapaa;
+		tmppt->opt = (double)opt;
+#endif
+
+#if 0
+		fprintf( stderr, "iscore (2)= %d\n", iscore );
+		fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+		fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+	}
+
+	if( !divpairscore )
+	{
+		for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+		{
+			tmppt->overlapaa = sumoverlap;
+			tmppt->opt = (double)isumscore * 5.8 / ( 600 * sumoverlap );
+//			fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+		}
+	}
+}
+void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa )
+{
+	int pos1, pos2, start1, start2, end1, end2;
+	char *pt1, *pt2;
+	double score;
+	double sumscore;
+	int sumoverlap;
+	LocalHom *tmppt = localhompt;
+	int nlocalhom = 0;
+	int st;
+	pt1 = al1; pt2 = al2;
+	pos1 = off1; pos2 = off2;
+
+
+	sumscore = 0.0;
+	sumoverlap = 0;
+	start1 = 0; // by D.Mathog, a guess
+	start2 = 0; // by D.Mathog, a guess
+
+	st = 0;
+	score = 0.0;
+	while( *pt1 != 0 )
+	{
+//		fprintf( stderr, "pt = %c, %c, st=%d\n", *pt1, *pt2, st );
+		if( st == 1 && ( *pt1 == '-' || *pt2 == '-' ) )
+		{
+			end1 = pos1 - 1;
+			end2 = pos2 - 1;
+
+			if( nlocalhom++ > 0 )
+			{
+//				fprintf( stderr, "reallocating ...\n" );
+				tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//				fprintf( stderr, "done\n" );
+				tmppt = tmppt->next;
+				tmppt->next = NULL;
+			}
+			tmppt->start1 = start1;
+			tmppt->start2 = start2;
+			tmppt->end1   = end1  ;
+			tmppt->end2   = end2  ;
+
+#if 1
+			if( divpairscore )
+			{
+				tmppt->overlapaa   = end2-start2+1;
+				tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+			}
+			else
+			{
+				sumscore += score;
+				sumoverlap += end2-start2+1;
+			}
+#else
+			tmppt->overlapaa   = overlapaa;
+			tmppt->opt = (double)opt;
+#endif
+
+#if 0
+			fprintf( stderr, "score (1)= %f\n", score );
+			fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+			fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+			score = 0.0;
+			st = 0;
+		}
+		else if( *pt1 != '-' && *pt2 != '-' )
+		{
+			if( st == 0 )
+			{
+				start1 = pos1; start2 = pos2;
+				st = 1;
+			}
+			score += (double)n_dis[(int)amino_n[(int)*pt1]][(int)amino_n[(int)*pt2]]; // - offset はいらないかも
+//			fprintf( stderr, "%c-%c, score(0) = %f\n", *pt1, *pt2, score );
+		}
+		if( *pt1++ != '-' ) pos1++;
+		if( *pt2++ != '-' ) pos2++;
+	}
+	if( nlocalhom++ > 0 )
+	{
+//		fprintf( stderr, "reallocating ...\n" );
+		tmppt->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+//		fprintf( stderr, "done\n" );
+		tmppt = tmppt->next;
+		tmppt->next = NULL;
+	}
+	end1 = pos1 - 1;
+	end2 = pos2 - 1;
+	tmppt->start1 = start1;
+	tmppt->start2 = start2;
+	tmppt->end1   = end1  ;
+	tmppt->end2   = end2  ;
+
+#if 1
+	if( divpairscore )
+	{
+		tmppt->overlapaa   = end2-start2+1;
+		tmppt->opt = score / tmppt->overlapaa * 5.8 / 600;
+	}
+	else
+	{
+		sumscore += score;
+		sumoverlap += end2-start2+1;
+	}
+#else
+	tmppt->overlapaa   = overlapaa;
+	tmppt->opt = (double)opt;
+#endif
+
+#if 0
+	fprintf( stderr, "score (2)= %f\n", score );
+	fprintf( stderr, "al1: %d - %d\n", start1, end1 );
+	fprintf( stderr, "al2: %d - %d\n", start2, end2 );
+#endif
+
+	if( !divpairscore )
+	{
+		for( tmppt=localhompt; tmppt; tmppt=tmppt->next )
+		{
+			tmppt->overlapaa = sumoverlap;
+			tmppt->opt = sumscore * 5.8 / 600 / sumoverlap;
+//			fprintf( stderr, "tmpptr->opt = %f\n", tmppt->opt );
+		}
+	}
+}
+
+char *cutal( char *al, int al_display_start, int start, int end )
+{
+	int pos;
+	char *pt = al;
+	char *val = NULL;
+
+	pos = al_display_start;
+	do
+	{
+		if( start == pos ) val = pt;
+		if( end == pos ) break;
+//		fprintf( stderr, "pos=%d, *pt=%c, val=%p\n", pos, *pt, val );
+		if( *pt != '-' ) pos++;
+	} while( *pt++ != 0 );
+	*(pt+1) = 0;
+	return( val );
+}
+
+void ErrorExit( char *message )
+{
+	fprintf( stderr, "%s\n", message );
+	exit( 1 );
+}
+
+void strncpy_caseC( char *str1, char *str2, int len )
+{
+	if( dorp == 'd' && upperCase > 0 ) 
+	{
+		while( len-- )
+			*str1++ = toupper( *str2++ );
+	}
+	else strncpy( str1, str2, len );
+}
+	
+void seqUpper( int nseq, char **seq )
+{
+	int i, j, len;
+	for( i=0; i<nseq; i++ ) 
+	{
+		len = strlen( seq[i] );
+		for( j=0; j<len; j++ ) 
+			seq[i][j] = toupper( seq[i][j] );
+	}
+}
+
+void seqLower( int nseq, char **seq )
+{
+	int i, j, len;
+	for( i=0; i<nseq; i++ ) 
+	{
+		len = strlen( seq[i] );
+		for( j=0; j<len; j++ ) 
+			seq[i][j] = tolower( seq[i][j] );
+	}
+}
+
+int getaline_fp_eof( char *s, int l, FILE *fp )  /* end of file -> return 1 */
+{
+    int c, i = 0 ;
+    int noteofflag = 0;
+    for( i=0; i<l && ( noteofflag = ( (c=getc(fp)) != EOF ) ) && c != '\n'; i++ ) 
+    	*s++ = c;
+    *s = '\0' ;
+     return( !noteofflag );
+}
+
+int getaline_fp_eof_new(s, l, fp)  /* end of file -> return 1 */
+char    s[] ; int l ; FILE *fp ;
+{
+        int c = 0, i = 0 ;
+		int noteofflag = 0;
+
+		if( feof( fp ) ) return( 1 );
+
+		for( i=0; i<l && ( noteofflag = ( (c=getc(fp)) != EOF ) ) && c != '\n'; i++ ) 
+        { *s++ = c ; }
+        *s = '\0' ;
+		if( c != '\n' && c != EOF ) while( getc(fp) != '\n' )
+			;
+		return( !noteofflag );
+}
+
+int myfgets(s, l, fp)  /* l以上は、行末まで読み飛ばす */
+char    s[] ; int l ; FILE *fp ;
+{
+        int     c = 0, i = 0 ;
+
+		if( feof( fp ) ) return( 1 );
+
+		for( i=0; i<l && ( c=getc( fp ) ) != '\n'; i++ ) 
+        	*s++ = c;
+        *s = '\0' ;
+		if( c != '\n' ) 
+			while( getc(fp) != '\n' )
+				;
+		return( 0 );
+}
+
+float input_new( FILE *fp, int d )
+{
+	char mojiretsu[10];
+	int i, c;
+
+	c = getc( fp );
+	if( c != '\n' )
+		ungetc( c, fp );
+
+	for( i=0; i<d; i++ )
+		mojiretsu[i] = getc( fp );
+	mojiretsu[i] = 0;
+
+	return( atof( mojiretsu ) );
+}
+
+
+void PreRead( FILE *fp, int *locnjob, int *locnlenmax )
+{
+	int i, nleni;
+	char b[B];
+
+	fgets( b, B-1, fp ); *locnjob = atoi( b );
+	*locnlenmax = 0;
+	i=0; 
+	while( i<*locnjob )
+	{
+		fgets( b, B-1, fp );
+		if( !strncmp( b, "=", 1 ) )
+		{
+			i++;
+			fgets( b, B-1, fp ); nleni = atoi( b );
+			if( nleni > *locnlenmax ) *locnlenmax = nleni;
+		}
+	}
+	if( *locnlenmax > N )
+	{
+		fprintf( stderr, "TOO LONG SEQUENCE!\n" );
+		exit( 1 );
+	}
+	if( njob > M  ) 
+	{
+		fprintf( stderr, "TOO MANY SEQUENCE!\n" );
+		fprintf( stderr, "%d > %d\n", njob, M );
+		exit( 1 );
+	}
+}	
+
+int allSpace( char *str )
+{
+	int value = 1;
+	while( *str ) value *= ( !isdigit( *str++ ) );
+	return( value );
+}
+	
+void Read( char name[M][B], int nlen[M], char **seq )
+{
+	extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
+	FRead( stdin, name, nlen, seq );
+}
+
+
+void FRead( FILE *fp, char name[][B], int nlen[], char **seq )
+{
+	int i, j; 
+	char b[B];
+
+	fgets( b, B-1, fp );
+#if DEBUG
+	fprintf( stderr, "b = %s\n", b );
+#endif
+
+    if( strstr( b, "onnet" ) ) scoremtx = 1;
+    else if( strstr( b, "DnA" ) ) 
+	{
+		scoremtx = -1; 
+		upperCase = -1;
+	}
+    else if( strstr( b, "dna" ) ) 
+	{
+		scoremtx = -1; 
+		upperCase = 0;
+	}
+	else if( strstr( b, "DNA" ) )
+	{
+		scoremtx = -1; 
+		upperCase = 1;
+	}
+    else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2; 
+    else scoremtx = 0;
+#if DEBUG
+	fprintf( stderr, " %s->scoremtx = %d\n", b, scoremtx );
+#endif
+
+	geta2 = GETA2;
+
+#if 0
+	if( strlen( b ) >=25 )
+	{
+		b[25] = 0;
+	#if DEBUG
+		fprintf( stderr, "kimuraR = %s\n", b+20 );
+	#endif
+		kimuraR = atoi( b+20 );
+
+		if( kimuraR < 0 || 20 < kimuraR ) ErrorExit( "Illeagal kimuraR value.\n" );
+		if( allSpace( b+20 ) ) kimuraR = NOTSPECIFIED;
+	}
+	else kimuraR = NOTSPECIFIED;
+	#if DEBUG
+	fprintf( stderr, "kimuraR = %d\n", kimuraR );
+	#endif
+
+	if( strlen( b ) >=20 )
+	{
+		b[20] = 0;
+	#if DEBUG
+		fprintf( stderr, "pamN = %s\n", b+15 );
+	#endif
+		pamN = atoi( b+15 );
+		if( pamN < 0 || 400 < pamN ) ErrorExit( "Illeagal pam value.\n" );
+		if( allSpace( b+15 ) ) pamN = NOTSPECIFIED;
+	}
+	else pamN = NOTSPECIFIED;
+
+	if( strlen( b ) >= 15 )
+	{
+		b[15] = 0;
+	#if DEBUG
+		fprintf( stderr, "poffset = %s\n", b+10 );
+	#endif
+		poffset = atoi( b+10 );
+		if( poffset > 500 ) ErrorExit( "Illegal extending gap ppenalty\n" );
+		if( allSpace( b+10 ) ) poffset = NOTSPECIFIED;
+	}
+	else poffset = NOTSPECIFIED;
+
+	if( strlen( b ) >= 10 )
+	{
+		b[10] = 0;
+	#if DEBUG
+		fprintf( stderr, "ppenalty = %s\n", b+5 );
+	#endif
+		ppenalty = atoi( b+5 );
+		if( ppenalty > 0 ) ErrorExit( "Illegal opening gap ppenalty\n" );
+		if( allSpace( b+5 ) ) ppenalty = NOTSPECIFIED;
+	}
+	else ppenalty = NOTSPECIFIED;
+#endif
+
+	for( i=0; i<njob; i++ )
+	{
+		getaline_fp_eof_new( b, B-1, fp );
+		strcpy( name[i], b );
+#if DEBUG
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		fgets( b, B-1, fp ); nlen[i] = atoi( b );      /* seq i no nagasa */
+		seq[i][0] = 0;
+		if( nlen[i] ) for( j=0; j <= (nlen[i]-1)/C; j++ )
+		{
+			getaline_fp_eof_new( b, B-1, fp );
+			/*	b[C] = 0;  */
+			strcat( seq[i], b );
+		} 
+		seq[i][nlen[i]] = 0;
+	}
+	if( scoremtx == -1 && upperCase != -1 ) seqLower( njob, seq );
+}
+
+
+static int countKUorWA( FILE *fp )
+{
+	int value;
+	int c, b;
+
+	value= 0;
+	b = '\n';
+	while( ( c = getc( fp ) ) != EOF )
+	{
+		if( b == '\n' && ( c == '>' ) )
+			value++;
+		b = c;
+	}
+	rewind( fp );
+	return( value );
+}
+
+void searchKUorWA( FILE *fp )
+{
+	int c, b;
+	b = '\n';
+	while( !( ( ( c = getc( fp ) ) == '>' || c == EOF ) && b == '\n' ) )
+		b = c;
+	ungetc( c, fp );
+}
+
+static int onlyGraph( char *str )
+{
+	char tmp;
+	char *res = str;
+	char *bk = str;
+
+//	while( (tmp=*str++) ) if( isgraph( tmp ) ) *res++ = tmp;
+	while( (tmp=*str++) ) 
+	{
+		if( 0x20 < tmp && tmp < 0x7f ) *res++ = tmp;
+		if( tmp == '>' || tmp == '(' )
+		{
+			fprintf( stderr, "========================================================\n" );
+			fprintf( stderr, "========================================================\n" );
+			fprintf( stderr, "=== \n" );
+			fprintf( stderr, "=== ERROR!! \n" );
+			fprintf( stderr, "=== In the '--anysymbol' and '--preservecase' modes, \n" );
+			fprintf( stderr, "=== '>' and '(' are unacceptable.\n" );
+			fprintf( stderr, "=== \n" );
+			fprintf( stderr, "========================================================\n" );
+			fprintf( stderr, "========================================================\n" );
+			exit( 1 );
+		}
+	}
+	*res = 0;
+	return( res - bk );
+}
+
+static int charfilter( char *str )
+{
+	char tmp;
+	char *res = str;
+	char *bk = str;
+
+	while( (tmp=*str++) )
+	{
+		if( tmp == '=' || tmp == '*' || tmp == '<' || tmp == '>' || tmp == '(' || tmp == ')' )
+		{
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "Characters '= * < > ( )' are not accepted in the --text mode, \nalthough most printable characters are ok.\n" );
+			fprintf( stderr, "\n" );
+			exit( 1 );
+		}
+		if( 0x20 < tmp && tmp < 0x7f )
+//		if( tmp != '\n' && tmp != ' ' && tmp != '\t' ) // unprintable characters mo ok.
+			*res++ = tmp;
+	}
+	*res = 0;
+	return( res - bk );
+}
+static int onlyAlpha_lower( char *str )
+{
+	char tmp;
+	char *res = str;
+	char *bk = str;
+
+	while( (tmp=*str++) )
+		if( isalpha( tmp ) || tmp == '-' || tmp == '*' || tmp == '.' )
+			*res++ = tolower( tmp );
+	*res = 0;
+	return( res - bk );
+}
+static int onlyAlpha_upper( char *str )
+{
+	char tmp;
+	char *res = str;
+	char *bk = str;
+
+	while( (tmp=*str++) )
+		if( isalpha( tmp ) || tmp == '-' || tmp == '*' || tmp == '.' )
+			*res++ = toupper( tmp );
+	*res = 0;
+	return( res - bk );
+}
+
+void kake2hiku( char *str )
+{
+	do
+		if( *str == '*' ) *str = '-';
+	while( *str++ );
+}
+
+char *load1SeqWithoutName_realloc_casepreserve( FILE *fpp )
+{
+	int c, b;
+	char *cbuf;
+	int size = N;
+	char *val;
+
+	val = malloc( (size+1) * sizeof( char ) );
+	cbuf = val;
+
+	b = '\n';
+	while( ( c = getc( fpp ) ) != EOF &&           
+          !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+	{
+		*cbuf++ = (char)c;  /* 長すぎてもしらない */
+		if( cbuf - val == size )
+		{
+			size += N;
+			fprintf( stderr, "reallocating...\n" );
+			val = (char *)realloc( val, (size+1) * sizeof( char ) );
+			if( !val )
+			{
+				fprintf( stderr, "Allocation error in load1SeqWithoutName_realloc \n" );
+				exit( 1 );
+			}
+			fprintf( stderr, "done.\n" );
+			cbuf = val + size-N;
+		}
+		b = c;
+	}
+	ungetc( c, fpp );
+	*cbuf = 0;
+	onlyGraph( val );
+//	kake2hiku( val );
+	return( val );
+}
+
+char *load1SeqWithoutName_realloc( FILE *fpp )
+{
+	int c, b;
+	char *cbuf;
+	int size = N;
+	char *val;
+
+	val = malloc( (size+1) * sizeof( char ) );
+	cbuf = val;
+
+	b = '\n';
+	while( ( c = getc( fpp ) ) != EOF &&           
+          !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+	{
+		*cbuf++ = (char)c;  /* 長すぎてもしらない */
+		if( cbuf - val == size )
+		{
+			size += N;
+			fprintf( stderr, "reallocating...\n" );
+			val = (char *)realloc( val, (size+1) * sizeof( char ) );
+			if( !val )
+			{
+				fprintf( stderr, "Allocation error in load1SeqWithoutName_realloc \n" );
+				exit( 1 );
+			}
+			fprintf( stderr, "done.\n" );
+			cbuf = val + size-N;
+		}
+		b = c;
+	}
+	ungetc( c, fpp );
+	*cbuf = 0;
+
+	if( nblosum == -2 )
+	{
+		charfilter( val );
+	}
+	else
+	{
+		if( dorp == 'd' )
+			onlyAlpha_lower( val );
+		else
+			onlyAlpha_upper( val );
+		kake2hiku( val );
+	}
+	return( val );
+}
+
+int load1SeqWithoutName_new( FILE *fpp, char *cbuf )
+{
+	int c, b;
+	char *bk = cbuf;
+
+	b = '\n';
+	while( ( c = getc( fpp ) ) != EOF &&                    /* by T. Nishiyama */
+          !( ( c == '>' || c == '(' || c == EOF ) && b == '\n' ) )
+	{
+		*cbuf++ = (char)c;  /* 長すぎてもしらない */
+		b = c;
+	}
+	ungetc( c, fpp );
+	*cbuf = 0;
+	if( dorp == 'd' )
+		onlyAlpha_lower( bk );
+	else
+		onlyAlpha_upper( bk );
+	kake2hiku( bk );
+	return( 0 );
+}
+
+
+void readDataforgaln( FILE *fp, char **name, int *nlen, char **seq )
+{
+	int i; 
+	static char *tmpseq = NULL;
+
+#if 0
+	if( !tmpseq )
+	{
+		tmpseq = AllocateCharVec( N );
+	}
+#endif
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		name[i][0] = '='; getc( fp ); 
+#if 0
+		fgets( name[i]+1, B-2, fp ); 
+		j = strlen( name[i] );
+		if( name[i][j-1] != '\n' )
+			ErrorExit( "Too long name\n" );
+		name[i][j-1] = 0;
+#else
+		myfgets( name[i]+1, B-2, fp ); 
+#endif
+#if 0
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		strcpy( seq[i], tmpseq );
+		nlen[i] = strlen( seq[i] );
+		free( tmpseq );
+	}
+	if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+	free( tmpseq );
+#endif
+}
+
+void readData_varlen( FILE *fp, char **name, int *nlen, char **seq )
+{
+	int i; 
+	static char *tmpseq = NULL;
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		name[i][0] = '='; getc( fp ); 
+#if 0
+		fgets( name[i]+1, B-2, fp ); 
+		j = strlen( name[i] );
+		if( name[i][j-1] != '\n' )
+			ErrorExit( "Too long name\n" );
+		name[i][j-1] = 0;
+#else
+		myfgets( name[i]+1, B-2, fp ); 
+#endif
+#if 0
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		nlen[i] = strlen( tmpseq );
+//		fprintf( stderr, "nlen[%d] = %d\n", i+1, nlen[i] );
+		seq[i] = calloc( nlen[i]+1, sizeof( char ) );
+		strcpy( seq[i], tmpseq );
+		free( tmpseq );
+	}
+	if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+	free( tmpseq );
+#endif
+}
+
+void readData_pointer2( FILE *fp, int nseq, char **name, int *nlen, char **seq )
+{
+	int i; 
+	static char *tmpseq = NULL;
+
+#if 0
+	if( !tmpseq )
+	{
+		tmpseq = AllocateCharVec( N );
+	}
+#endif
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<nseq; i++ )
+	{
+		name[i][0] = '='; getc( fp ); 
+#if 0
+		fgets( name[i]+1, B-2, fp ); 
+		j = strlen( name[i] );
+		if( name[i][j-1] != '\n' )
+			ErrorExit( "Too long name\n" );
+		name[i][j-1] = 0;
+#else
+		myfgets( name[i]+1, B-2, fp ); 
+#endif
+#if 0
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		strcpy( seq[i], tmpseq );
+		free( tmpseq );
+		nlen[i] = strlen( seq[i] );
+	}
+	if( dorp == 'd' && upperCase != -1 ) seqLower( nseq, seq );
+#if 0
+	free( tmpseq );
+#endif
+	if( outnumber )
+	{
+		char *namebuf;
+		char *cptr;
+		namebuf = calloc( B+100, sizeof( char ) );
+		for( i=0; i<nseq; i++ )
+		{
+			namebuf[0] = '=';
+			cptr = strstr( name[i], "_numo_e_" );
+			if( cptr )
+				sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
+			else
+				sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
+			strncpy( name[i], namebuf, B );
+			name[i][B-1] = 0;
+		}
+		free( namebuf );
+//		exit( 1 );
+	}
+}
+
+
+void readData_pointer_casepreserve( FILE *fp, char **name, int *nlen, char **seq )
+{
+	int i; 
+	static char *tmpseq = NULL;
+
+#if 0
+	if( !tmpseq )
+	{
+		tmpseq = AllocateCharVec( N );
+	}
+#endif
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		name[i][0] = '='; getc( fp ); 
+#if 0
+		fgets( name[i]+1, B-2, fp ); 
+		j = strlen( name[i] );
+		if( name[i][j-1] != '\n' )
+			ErrorExit( "Too long name\n" );
+		name[i][j-1] = 0;
+#else
+		myfgets( name[i]+1, B-2, fp ); 
+#endif
+#if 0
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+		strcpy( seq[i], tmpseq );
+		free( tmpseq );
+		nlen[i] = strlen( seq[i] );
+	}
+}
+
+
+int copydatafromgui( char **namegui, char **seqgui, char **name, int *nlen, char **seq )
+{
+	int i; 
+
+
+	for( i=0; i<njob; i++ )
+	{
+		name[i][0] = '='; 
+		strncpy( name[i]+1, namegui[i], B-2 );
+		name[i][B-1] = 0;
+
+		strcpy( seq[i], seqgui[i] );
+		nlen[i] = strlen( seq[i] );
+	}
+	if( dorp == 'd' ) 
+		seqLower( njob, seq );
+	else if( dorp == 'p' ) 
+		seqUpper( njob, seq );
+	else
+	{
+		reporterr( "DNA or Protein?\n" );
+		return( 1 );
+	}
+#if 0
+	free( tmpseq );
+#endif
+	if( outnumber )
+	{
+		char *namebuf;
+		char *cptr;
+		namebuf = calloc( B+100, sizeof( char ) );
+		for( i=0; i<njob; i++ )
+		{
+			namebuf[0] = '=';
+			cptr = strstr( name[i], "_numo_e_" );
+			if( cptr )
+				sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
+			else
+				sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
+			strncpy( name[i], namebuf, B );
+			name[i][B-1] = 0;
+		}
+		free( namebuf );
+	}
+	return( 0 );
+}
+
+void readData_pointer( FILE *fp, char **name, int *nlen, char **seq )
+{
+	int i; 
+	static char *tmpseq = NULL;
+
+#if 0
+	if( !tmpseq )
+	{
+		tmpseq = AllocateCharVec( N );
+	}
+#endif
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		name[i][0] = '='; getc( fp ); 
+#if 0
+		fgets( name[i]+1, B-2, fp ); 
+		j = strlen( name[i] );
+		if( name[i][j-1] != '\n' )
+			ErrorExit( "Too long name\n" );
+		name[i][j-1] = 0;
+#else
+		myfgets( name[i]+1, B-2, fp ); 
+#endif
+#if 0
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		strcpy( seq[i], tmpseq );
+		free( tmpseq );
+		nlen[i] = strlen( seq[i] );
+	}
+	if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+	free( tmpseq );
+#endif
+	if( outnumber )
+	{
+		char *namebuf;
+		char *cptr;
+		namebuf = calloc( B+100, sizeof( char ) );
+		for( i=0; i<njob; i++ )
+		{
+			namebuf[0] = '=';
+			cptr = strstr( name[i], "_numo_e_" );
+			if( cptr )
+				sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, cptr+8 );
+			else
+				sprintf( namebuf+1, "_numo_s_%08d_numo_e_%s", i+1, name[i]+1 );
+			strncpy( name[i], namebuf, B );
+			name[i][B-1] = 0;
+		}
+		free( namebuf );
+//		exit( 1 );
+	}
+}
+
+void readData( FILE *fp, char name[][B], int nlen[], char **seq )
+{
+	int i; 
+	static char *tmpseq = NULL;
+
+#if 0
+	if( !tmpseq )
+	{
+		tmpseq = AllocateCharVec( N );
+	}
+#endif
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		name[i][0] = '='; getc( fp ); 
+#if 0
+		fgets( name[i]+1, B-2, fp ); 
+		j = strlen( name[i] );
+		if( name[i][j-1] != '\n' )
+			ErrorExit( "Too long name\n" );
+		name[i][j-1] = 0;
+#else
+		myfgets( name[i]+1, B-2, fp ); 
+#endif
+#if 0
+		fprintf( stderr, "name[%d] = %s\n", i, name[i] );
+#endif
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		strcpy( seq[i], tmpseq );
+		nlen[i] = strlen( seq[i] );
+		free( tmpseq );
+	}
+	if( dorp == 'd' && upperCase != -1 ) seqLower( njob, seq );
+#if 0
+	free( tmpseq );
+#endif
+}
+
+void cutAlignment( FILE *fp, int **regtable, char **revtable, int *outtable, char **name, char **outseq )
+{
+	int i, j; 
+	int outlen;
+	static char *tmpseq = NULL;
+	static char *dumname = NULL;
+	char *fs, *rs;
+	int npos, lpos;
+	int startpos, endpos, seqlen;
+
+	if( dumname == NULL )
+	{
+		dumname = AllocateCharVec( N );
+	}
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+
+	npos = 0;
+	for( i=0; i<njob; i++ )
+	{
+		dumname[0] = '>'; getc( fp ); 
+		myfgets( dumname+1, B-1, fp ); 
+		tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+
+		if( outtable[i] )
+		{
+//			putc( '>', stdout );
+//			puts( dumname+1 );
+
+	
+			strncat( name[npos], dumname, B-1 );
+			name[npos][B-1] = 0;
+	
+			if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
+			seqlen = strlen( tmpseq );
+			lpos = 0;
+			for( j=0; j<5; j++ )
+			{
+				if( regtable[0][j*2] == -1 && regtable[0][j*2+1] == -1 ) continue;
+
+				startpos = regtable[0][j*2];
+				endpos   = regtable[0][j*2+1];
+				if( startpos > endpos )
+				{
+					endpos   = regtable[0][j*2];
+					startpos = regtable[0][j*2+1];
+				}
+
+				if( startpos < 0 ) startpos = 0;
+				if( endpos   < 0 ) endpos   = 0;
+				if( endpos   >= seqlen ) endpos   = seqlen-1;
+				if( startpos >= seqlen ) startpos = seqlen-1;
+
+//				fprintf( stderr, "startpos = %d, endpos = %d\n", startpos, endpos );
+
+				outlen = endpos - startpos+1;
+				if( revtable[0][j] == 'f' )
+				{
+//					fprintf( stderr, "regtable[%d][st] = %d\n", i, regtable[0][j*2+0] );
+//					fprintf( stderr, "regtable[%d][en] = %d\n", i, regtable[0][j*2+1] );
+//					fprintf( stderr, "outlen = %d\n", outlen );
+//					fprintf( stdout, "%.*s\n", outlen, tmpseq+regtable[0][j*2] );
+					strncpy( outseq[npos] + lpos, tmpseq+startpos, outlen );
+					lpos += outlen;
+				}
+				else
+				{
+					fs = AllocateCharVec( outlen+1 );
+					rs = AllocateCharVec( outlen+1 );
+
+					fs[outlen] = 0;
+					strncpy( fs, tmpseq+startpos, outlen );
+					sreverse( rs, fs );
+//					fprintf( stdout, "%s\n", rs );
+					strncpy( outseq[npos] + lpos, rs, outlen );
+					lpos += outlen;
+					free( fs );
+					free( rs );
+				}
+				outseq[npos][lpos] = 0;
+			}
+			npos++;
+		}
+		free( tmpseq );
+	}
+}
+
+void cutData( FILE *fp, int **regtable, char **revtable, int *outtable )
+{
+	int i, j; 
+	int outlen, seqlen, startpos, endpos;
+	static char *tmpseq = NULL;
+	static char *dumname = NULL;
+	char *fs, *rs;
+
+	if( dumname == NULL )
+	{
+		dumname = AllocateCharVec( N );
+	}
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		dumname[0] = '='; getc( fp ); 
+		myfgets( dumname+1, B-2, fp ); 
+		tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+
+		if( outtable[i] )
+		{
+			gappick_samestring( tmpseq );
+			putc( '>', stdout );
+			puts( dumname+1 );
+
+			seqlen = strlen( tmpseq );
+
+			if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
+			if( outtable[i] == 2 )
+			{
+				startpos = 0;
+				endpos   = seqlen-1;
+				outlen = endpos - startpos + 1;
+				fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
+			}
+			else
+			{
+				for( j=0; j<5; j++ )
+				{
+					if( regtable[i][j*2] == -1 && regtable[i][j*2+1] == -1 ) continue;
+	
+					startpos = regtable[i][j*2];
+					endpos   = regtable[i][j*2+1];
+	
+					if( startpos > endpos )
+					{
+						endpos   = regtable[i][j*2];
+						startpos = regtable[i][j*2+1];
+					}
+	
+					if( startpos < 0 ) startpos = 0;
+					if( endpos   < 0 ) endpos   = 0;
+					if( endpos   >= seqlen ) endpos   = seqlen-1;
+					if( startpos >= seqlen ) startpos = seqlen-1;
+	
+					outlen = endpos - startpos + 1;
+					if( revtable[i][j] == 'f' )
+					{
+						fprintf( stderr, "startpos = %d\n", startpos );
+						fprintf( stderr, "endpos   = %d\n", endpos );
+						fprintf( stderr, "outlen = %d\n", outlen );
+						fprintf( stdout, "%.*s\n", outlen, tmpseq+startpos );
+					}
+					else
+					{
+						fs = AllocateCharVec( outlen+1 );
+						rs = AllocateCharVec( outlen+1 );
+	
+						fs[outlen] = 0;
+						strncpy( fs, tmpseq+startpos, outlen );
+						sreverse( rs, fs );
+						fprintf( stdout, "%s\n", rs );
+						free( fs );
+						free( rs );
+					}
+				}
+			}
+		}
+		free( tmpseq );
+	}
+}
+
+void catData( FILE *fp )
+{
+	int i; 
+	static char *tmpseq = NULL;
+	static char *dumname = NULL;
+//	char *cptr;
+
+	if( dumname == NULL )
+	{
+		dumname = AllocateCharVec( N );
+	}
+
+	rewind( fp );
+	searchKUorWA( fp );
+
+	for( i=0; i<njob; i++ )
+	{
+		dumname[0] = '='; getc( fp ); 
+		myfgets( dumname+1, B-2, fp ); 
+		if( outnumber )
+		{
+			fprintf( stdout, ">_numo_s_%08d_numo_e_", i+1 );
+		}
+		else
+		{
+			putc( '>', stdout );
+		}
+		puts( dumname+1 );
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		if( dorp == 'd' && upperCase != -1 ) seqLower( 1, &tmpseq );
+		puts( tmpseq );
+		free( tmpseq );
+	}
+}
+
+int countATGC( char *s, int *total )
+{
+	int nATGC;
+	int nChar;
+	char c;
+	nATGC = nChar = 0;
+
+	if( *s == 0 ) 
+	{
+		*total = 0;
+		return( 0 );
+	}
+
+	do
+	{
+		c = tolower( *s );
+		if( isalpha( c ) )
+		{
+			nChar++;
+			if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
+				nATGC++;
+		}
+	}
+	while( *++s );
+
+	*total = nChar;
+	return( nATGC );
+}
+
+double countATGCbk( char *s )
+{
+	int nATGC;
+	int nChar;
+	char c;
+	nATGC = nChar = 0;
+
+	do
+	{
+		c = tolower( *s );
+		if( isalpha( c ) )
+		{
+			nChar++;
+			if( c == 'a' || c == 't' || c == 'g' || c == 'c' || c == 'u' || c == 'n' )
+				nATGC++;
+		}
+	}
+	while( *++s );
+	return( (double)nATGC / nChar );
+}
+
+
+int countnogaplen( char *seq )
+{
+	int val = 0;
+	while( *seq )
+		if( *seq++ != '-' ) val++;
+	return( val );
+}
+
+int countnormalletters( char *seq, char *ref )
+{
+	int val = 0;
+	while( *seq )
+		if( strchr( ref, *seq++ ) ) val++;
+	return( val );
+}
+
+void getnumlen_casepreserve( FILE *fp, int *nlenminpt )
+{
+	int total;
+	int nsite = 0;
+	int atgcnum;
+	int i, tmp;
+	char *tmpseq, *tmpname;
+	double atgcfreq;
+	tmpname = AllocateCharVec( N );
+	njob = countKUorWA( fp );
+	searchKUorWA( fp );
+	nlenmax = 0;
+	*nlenminpt = 99999999;
+	atgcnum = 0;
+	total = 0;
+	for( i=0; i<njob; i++ )
+	{
+		myfgets( tmpname, N-1, fp );
+		tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+		tmp = strlen( tmpseq );
+		if( tmp > nlenmax ) nlenmax  = tmp;
+		if( tmp < *nlenminpt ) *nlenminpt  = tmp;
+		atgcnum += countATGC( tmpseq, &nsite );
+		total += nsite;
+		free( tmpseq );
+	}
+	free( tmpname );
+	atgcfreq = (double)atgcnum / total;
+//	fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+	if( dorp == NOTSPECIFIED )
+	{
+		if( atgcfreq > 0.75 ) 	
+		{
+			dorp = 'd';
+			upperCase = -1;
+		}
+		else                  
+		{
+			dorp = 'p';
+			upperCase = 0;
+		}
+	}
+}
+
+void getnumlen_nogap( FILE *fp, int *nlenminpt )
+{
+	int total;
+	int nsite = 0;
+	int atgcnum;
+	int i, tmp;
+	char *tmpseq, *tmpname;
+	double atgcfreq;
+	tmpname = AllocateCharVec( N );
+	njob = countKUorWA( fp );
+	searchKUorWA( fp );
+	nlenmax = 0;
+	*nlenminpt = 99999999;
+	atgcnum = 0;
+	total = 0;
+	for( i=0; i<njob; i++ )
+	{
+		myfgets( tmpname, N-1, fp );
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		tmp = countnogaplen( tmpseq );
+		if( tmp > nlenmax ) nlenmax  = tmp;
+		if( tmp < *nlenminpt ) *nlenminpt  = tmp;
+		atgcnum += countATGC( tmpseq, &nsite );
+		total += nsite;
+		free( tmpseq );
+	}
+	free( tmpname );
+	atgcfreq = (double)atgcnum / total;
+	fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+	if( dorp == NOTSPECIFIED )
+	{
+		if( atgcfreq > 0.75 ) 	
+		{
+			dorp = 'd';
+			upperCase = -1;
+		}
+		else                  
+		{
+			dorp = 'p';
+			upperCase = 0;
+		}
+	}
+}
+
+
+void getnumlen_nogap_outallreg( FILE *fp, int *nlenminpt )
+{
+	int total;
+	int nsite = 0;
+	int atgcnum;
+	int i, tmp;
+	char *tmpseq, *tmpname;
+	double atgcfreq;
+	tmpname = AllocateCharVec( N );
+	njob = countKUorWA( fp );
+	searchKUorWA( fp );
+	nlenmax = 0;
+	*nlenminpt = 99999999;
+	atgcnum = 0;
+	total = 0;
+	for( i=0; i<njob; i++ )
+	{
+		myfgets( tmpname, N-1, fp );
+		fprintf( stdout, "%s\n", tmpname );
+		tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+		tmp = countnogaplen( tmpseq );
+		fprintf( stdout, "%d\n", tmp );
+		if( tmp > nlenmax ) nlenmax  = tmp;
+		if( tmp < *nlenminpt ) *nlenminpt  = tmp;
+		atgcnum += countATGC( tmpseq, &nsite );
+		total += nsite;
+		free( tmpseq );
+	}
+	free( tmpname );
+	atgcfreq = (double)atgcnum / total;
+	fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+	if( dorp == NOTSPECIFIED )
+	{
+		if( atgcfreq > 0.75 ) 	
+		{
+			dorp = 'd';
+			upperCase = -1;
+		}
+		else                  
+		{
+			dorp = 'p';
+			upperCase = 0;
+		}
+	}
+}
+
+static void escapehtml( char *res, char *ori, int maxlen )
+{
+	char *res0 = res;
+	while( *ori )
+	{
+		if( *ori == '<' ) 
+		{
+			strcpy( res, "&lt;" );
+			res += 3;
+		}
+		else if( *ori == '>' ) 
+		{
+			strcpy( res, "&gt;" );
+			res += 3;
+		}
+		else if( *ori == '&' ) 
+		{
+			strcpy( res, "&amp;" );
+			res += 4;
+		}
+		else if( *ori == '"' ) 
+		{
+			strcpy( res, "&quot;" );
+			res += 5;
+		}
+		else if( *ori == ' ' ) 
+		{
+			strcpy( res, "&nbsp;" );
+			res += 5;
+		}
+		else
+		{
+			*res = *ori;
+		}
+		res++;
+		ori++;
+
+		if( res - res0 -10 > N ) break;
+	}
+	*res = 0;
+}
+
+void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt )
+{
+	int total;
+	int nsite = 0;
+	int atgcnum;
+	int alnlen = 0, alnlen_prev;
+	int i, tmp, lennormalchar;
+	char *tmpseq, *tmpname, *tmpname2;
+	double atgcfreq;
+	tmpname = AllocateCharVec( N );
+	tmpname2 = AllocateCharVec( N );
+	njob = countKUorWA( fp );
+	searchKUorWA( fp );
+	nlenmax = 0;
+	*nlenminpt = 99999999;
+	atgcnum = 0;
+	total = 0;
+	alnlen_prev = -1;
+	*isalignedpt = 1;
+	for( i=0; i<njob; i++ )
+	{
+		myfgets( tmpname, N-1, fp );
+		tmpname2[0] = tmpname[0];
+		escapehtml( tmpname2+1, tmpname+1, N );
+//		fprintf( stdout, "%s\n", tmpname );
+//		fprintf( stdout, "%s\n", tmpname2 );
+//		exit(1);
+		tmpseq = load1SeqWithoutName_realloc_casepreserve( fp );
+		tmp = countnogaplen( tmpseq );
+//		fprintf( stdout, "%d\n", tmp );
+		if( tmp > nlenmax ) nlenmax  = tmp;
+		if( tmp < *nlenminpt ) *nlenminpt  = tmp;
+		atgcnum += countATGC( tmpseq, &nsite );
+		total += nsite;
+
+		alnlen = strlen( tmpseq );
+//		fprintf( stdout, "##### alnlen, alnlen_prev = %d, %d\n", alnlen, alnlen_prev );
+		if( i>0 && alnlen_prev != alnlen ) *isalignedpt = 0;
+		alnlen_prev = alnlen;
+
+		atgcfreq = (double)atgcnum / total;
+//		fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+//		if( dorp == NOTSPECIFIED ) // you kentou
+		{
+			if( atgcfreq > 0.75 ) 	
+			{
+				dorp = 'd';
+				upperCase = -1;
+			}
+			else                  
+			{
+				dorp = 'p';
+				upperCase = 0;
+			}
+		}
+	
+		if( dorp == 'd' ) lennormalchar = countnormalletters( tmpseq, "atgcuATGCU" );
+		else              lennormalchar = countnormalletters( tmpseq, "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv" );
+		free( tmpseq );
+
+		fprintf( ofp, " <label for='s%d'><span id='ss%d'><input type='checkbox' id='s%d' name='s%d' checked></span> <input type='text' class='ll' id='ll%d' style='display:none' size='6' value='%d' readonly='readonly'>%s</label>\n", i, i, i, i, i, lennormalchar, tmpname2 );
+		fprintf( ofp, "<span id='t%d-0' style='display:none'>", i );
+		fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"t%d\")'>+reg</a>", i );
+		fprintf( ofp, " Begin:<input type='text' name='b%d-0' size='8' value='1' class='ie'> End:<input type='text' name='e%d-0' size='8' value='%d' class='ie'>", i, i, tmp );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-0'><input type='checkbox' name='r%d-0' id='r%d-0'>Reverse</label>", i, i, i );
+//		fprintf( ofp, "  Sequence Length:<input type='text' name='l%d' size='8' value='%d' readonly='readonly'>", i, tmp );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='t%d-1' style='display:none'>", i );
+		fprintf( ofp, "      Begin:<input type='text' name='b%d-1' size='8' value='' class='ie'> End:<input type='text' name='e%d-1' size='8' value='' class='ie'>", i, i );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-1'><input type='checkbox' name='r%d-1' id='r%d-1'>Reverse</label>", i, i, i );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='t%d-2' style='display:none'>", i );
+		fprintf( ofp, "      Begin:<input type='text' name='b%d-2' size='8' value='' class='ie'> End:<input type='text' name='e%d-2' size='8' value='' class='ie'>", i, i );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-2'><input type='checkbox' name='r%d-2' id='r%d-2'>Reverse</label>", i, i, i );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='t%d-3' style='display:none'>", i );
+		fprintf( ofp, "      Begin:<input type='text' name='b%d-3' size='8' value='' class='ie'> End:<input type='text' name='e%d-3' size='8' value='' class='ie'>", i, i );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-3'><input type='checkbox' name='r%d-3' id='r%d-3'>Reverse</label>", i, i, i );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='t%d-4' style='display:none'>", i );
+		fprintf( ofp, "      Begin:<input type='text' name='b%d-4' size='8' value='' class='ie'> End:<input type='text' name='e%d-4' size='8' value='' class='ie'>", i, i );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='r%d-4'><input type='checkbox' name='r%d-4' id='r%d-4'>Reverse</label>", i, i, i );
+		fprintf( ofp, "\n</span>" );
+	}
+	free( tmpname );
+	free( tmpname2 );
+	atgcfreq = (double)atgcnum / total;
+	fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+//	if( dorp == NOTSPECIFIED ) // you kentou
+	{
+		if( atgcfreq > 0.75 ) 	
+		{
+			dorp = 'd';
+			upperCase = -1;
+		}
+		else                  
+		{
+			dorp = 'p';
+			upperCase = 0;
+		}
+	}
+	fprintf( ofp, "\n" );
+	if( *isalignedpt )
+	{
+		fprintf( ofp, "<span id='tall-0' style='display:none'>" );
+		fprintf( ofp, "Cut the alignment\n" );
+		fprintf( ofp, " <a href='javascript:void(0)' onclick='ddcycle(this.form,\"tall\")'>+reg</a>" );
+		fprintf( ofp, " Begin:<input type='text' name='ball-0' size='8' value='1'> End:<input type='text' name='eall-0' size='8' value='%d'>", alnlen );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='rall-0'><input type='checkbox' name='rall-0' id='rall-0'>Reverse</label>" );
+		fprintf( ofp, "  Alignment length:<input type='text' name='lall' size='8' value='%d' readonly='readonly'>", alnlen );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='tall-1' style='display:none'>" );
+		fprintf( ofp, "      Begin:<input type='text' name='ball-1' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='rall-1'><input type='checkbox' name='rall-1' id='rall-1'>Reverse</label>" );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='tall-2' style='display:none'>" );
+		fprintf( ofp, "      Begin:<input type='text' name='ball-2' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='rall-2'><input type='checkbox' name='rall-2' id='rall-2'>Reverse</label>" );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='tall-3' style='display:none'>" );
+		fprintf( ofp, "      Begin:<input type='text' name='ball-3' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='rall-3'><input type='checkbox' name='rall-3' id='rall-3'>Reverse</label>" );
+		fprintf( ofp, "\n</span>" );
+		fprintf( ofp, "<span id='tall-4' style='display:none'>" );
+		fprintf( ofp, "      Begin:<input type='text' name='ball-4' size='8' value=''> End:<input type='text' name='eall-1' size='8' value=''>" );
+		if( dorp == 'd' ) fprintf( ofp, " <label for='rall-4'><input type='checkbox' name='rall-4' id='rall-4'>Reverse</label>" );
+		fprintf( ofp, "\n</span>" );
+	}
+
+}
+
+void getnumlen( FILE *fp )
+{
+	int total;
+	int nsite = 0;
+	int atgcnum;
+	int i, tmp;
+	char *tmpseq;
+	char *tmpname;
+	double atgcfreq;
+	tmpname = AllocateCharVec( N );
+	njob = countKUorWA( fp );
+	searchKUorWA( fp );
+	nlenmax = 0;
+	atgcnum = 0;
+	total = 0;
+	for( i=0; i<njob; i++ )
+	{
+		myfgets( tmpname, N-1, fp );
+		tmpseq = load1SeqWithoutName_realloc( fp );
+		tmp = strlen( tmpseq );
+		if( tmp > nlenmax ) nlenmax  = tmp;
+		atgcnum += countATGC( tmpseq, &nsite );
+		total += nsite;
+//		fprintf( stderr, "##### total = %d\n", total );
+		free( tmpseq );
+	}
+
+
+	atgcfreq = (double)atgcnum / total;
+//	fprintf( stderr, "##### atgcfreq = %f\n", atgcfreq );
+	if( dorp == NOTSPECIFIED )
+	{
+		if( atgcfreq > 0.75 ) 	
+		{
+			dorp = 'd';
+			upperCase = -1;
+		}
+		else                  
+		{
+			dorp = 'p';
+			upperCase = 0;
+		}
+	}
+	free( tmpname );
+}
+	
+
+
+void WriteGapFill( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq )
+{
+	static char b[N];
+	int i, j;
+	int nalen[M];
+	static char gap[N];
+	static char buff[N];
+
+#if IODEBUG
+	fprintf( stderr, "IMAKARA KAKU\n" );
+#endif
+	nlenmax = 0;
+	for( i=0; i<locnjob; i++ )
+	{
+		int len = strlen( aseq[i] );
+		if( nlenmax < len ) nlenmax = len;
+	}
+
+	for( i=0; i<nlenmax; i++ ) gap[i] = '-';
+	gap[nlenmax] = 0;
+
+	fprintf( fp, "%5d", locnjob );
+	fprintf( fp, "\n" );
+
+	for( i=0; i<locnjob; i++ )
+	{
+		strcpy( buff, aseq[i] );
+		strncat( buff, gap, nlenmax-strlen( aseq[i] ) );
+		buff[nlenmax] = 0;
+		nalen[i] = strlen( buff );
+		fprintf( fp, "%s\n", name[i] );
+		fprintf( fp, "%5d\n", nalen[i] );
+		for( j=0; j<nalen[i]; j=j+C )
+		{
+			strncpy_caseC( b, buff+j, C ); b[C] = 0;
+			fprintf( fp, "%s\n",b );
+		}
+	}
+#if DEBUG
+	fprintf( stderr, "nalen[0] = %d\n", nalen[0] );
+#endif
+#if IODEBUG
+	fprintf( stderr, "KAKIOWATTA\n" );
+#endif
+}
+
+void writeDataforgaln( FILE *fp, int locnjob, char **name, int *nlen, char **aseq )
+{
+	int i, j;
+	int nalen;
+
+	for( i=0; i<locnjob; i++ )
+	{
+		nalen = strlen( aseq[i] );
+		fprintf( fp, ">%s\n", name[i]+1 );
+		for( j=0; j<nalen; j=j+C )
+		{
+#if 0
+			strncpy( b, aseq[i]+j, C ); b[C] = 0;
+			fprintf( fp, "%s\n",b );
+#else
+			fprintf( fp, "%.*s\n", C, aseq[i]+j );
+#endif
+		}
+	}
+}
+
+void writeData_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq )
+{
+	int i, j;
+	int nalen;
+
+	for( i=0; i<locnjob; i++ )
+	{
+#if DEBUG
+		fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+		nalen = strlen( aseq[i] );
+		fprintf( fp, ">%s\n", name[i]+1 );
+		for( j=0; j<nalen; j=j+C )
+		{
+#if 0
+			strncpy( b, aseq[i]+j, C ); b[C] = 0;
+			fprintf( fp, "%s\n",b );
+#else
+			fprintf( fp, "%.*s\n", C, aseq[i]+j );
+#endif
+		}
+	}
+}
+
+void writeData( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq )
+{
+	int i, j;
+	int nalen;
+
+	for( i=0; i<locnjob; i++ )
+	{
+#if DEBUG
+		fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+		nalen = strlen( aseq[i] );
+		fprintf( fp, ">%s\n", name[i]+1 );
+		for( j=0; j<nalen; j=j+C )
+		{
+#if 0
+			strncpy( b, aseq[i]+j, C ); b[C] = 0;
+			fprintf( fp, "%s\n",b );
+#else
+			fprintf( fp, "%.*s\n", C, aseq[i]+j );
+#endif
+		}
+	}
+}
+
+
+void write1seq( FILE *fp, char *aseq )
+{
+	int j;
+	int nalen;
+
+	nalen = strlen( aseq );
+	for( j=0; j<nalen; j=j+C )
+		fprintf( fp, "%.*s\n", C, aseq+j );
+}
+
+void readhat2_floathalf_part_pointer( FILE *fp, int nseq, int nadd, char **name, float **mtx )
+{
+    int i, j, nseq0, norg;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) 
+	{
+		fprintf( stderr, "%d != %d\n", nseq, nseq0 );
+		ErrorExit( "hat2 is wrong." );
+	}
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+	norg = nseq-nadd;
+    for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ )
+    {
+        mtx[i][j] = ( input_new( fp, D ) );
+    }
+}
+
+void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx )
+{
+    int i, j, nseq0;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) 
+	{
+		fprintf( stderr, "%d != %d\n", nseq, nseq0 );
+		ErrorExit( "hat2 is wrong." );
+	}
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+    for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+    {
+        mtx[i][j-i] = ( input_new( fp, D ) );
+    }
+}
+void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx )
+{
+    int i, j, nseq0;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+    for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+    {
+        mtx[i][j-i] = ( input_new( fp, D ) );
+    }
+}
+void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx )
+{
+    int i, j, nseq0;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+    for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+    {
+        mtx[i][j] = ( input_new( fp, D ) );
+    }
+}
+void readhat2_int( FILE *fp, int nseq, char name[M][B], int **mtx )
+{
+    int i, j, nseq0;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+    for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+    {
+        mtx[i][j] = (int)( input_new( fp, D ) * INTMTXSCALE + 0.5 );
+    }
+}
+
+void readhat2_pointer( FILE *fp, int nseq, char **name, double **mtx )
+{
+    int i, j, nseq0;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+    for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+    {
+        mtx[i][j] = (double)input_new( fp, D);
+    }
+}
+void readhat2( FILE *fp, int nseq, char name[M][B], double **mtx )
+{
+    int i, j, nseq0;
+    char b[B];
+
+    fgets( b, B, fp );
+    fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
+    fgets( b, B, fp );
+    for( i=0; i<nseq; i++ )
+    {
+#if 0
+        getaline_fp_eof( b, B, fp ); 
+#else
+		myfgets( b, B-2, fp );
+#endif
+#if 0
+		j = MIN( strlen( b+6 ), 10 );
+        if( strncmp( name[i], b+6 , j ) ) 
+		{
+			fprintf( stderr, "Error in hat2\n" );
+			fprintf( stderr, "%s != %s\n", b, name[i] );
+			exit( 1 );
+		}
+#endif
+    }
+    for( i=0; i<nseq-1; i++ ) for( j=i+1; j<nseq; j++ )
+    {
+        mtx[i][j] = (double)input_new( fp, D);
+    }
+}
+
+void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx )
+{
+	int i, j, ijsa;
+	double max = 0.0;
+	for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<locnjob; i++ )
+	{
+		for( j=i+1; j<njob; j++ )
+		{
+			fprintf( hat2p, "%#6.3f", mtx[i][j-i] );
+			ijsa = j-i;
+			if( ijsa % 12 == 0 || ijsa == locnjob-i-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+void WriteFloatHat2_pointer( FILE *hat2p, int locnjob, char **name, float **mtx )
+{
+	int i, j;
+	double max = 0.0;
+	for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<locnjob; i++ )
+	{
+		for( j=1; j<locnjob-i; j++ ) 
+		{
+			fprintf( hat2p, "%#6.3f", mtx[i][j] );
+			if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx )
+{
+	int i, j;
+	double max = 0.0;
+	for( i=0; i<locnjob-1; i++ ) for( j=1; j<locnjob-i; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<locnjob; i++ )
+	{
+		for( j=1; j<locnjob-i; j++ ) 
+		{
+			fprintf( hat2p, "%#6.3f", mtx[i][j] );
+			if( j % 12 == 0 || j == locnjob-i-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+void WriteHat2_int( FILE *hat2p, int locnjob, char name[M][B], int **mtx )
+{
+	int i, j;
+	double max = 0.0;
+	for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+	max /= INTMTXSCALE;
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<locnjob-1; i++ )
+	{
+		for( j=i+1; j<locnjob; j++ ) 
+		{
+			fprintf( hat2p, "%#6.3f", (float)mtx[i][j] / INTMTXSCALE );
+			if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+void WriteHat2_part_pointer( FILE *hat2p, int locnjob, int nadd, char **name, double **mtx )
+{
+	int i, j;
+	int norg = locnjob-nadd;
+	double max = 0.0;
+//	for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<norg; i++ )
+	{
+		for( j=0; j<nadd; j++ ) 
+		{
+			fprintf( hat2p, "%#6.3f", mtx[i][j] );
+			if( (j+1) % 12 == 0 || j == nadd-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx )
+{
+	int i, j;
+	double max = 0.0;
+	for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<locnjob-1; i++ )
+	{
+		for( j=i+1; j<locnjob; j++ ) 
+		{
+			fprintf( hat2p, "%#6.3f", mtx[i][j] );
+			if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx )
+{
+	int i, j;
+	double max = 0.0;
+	for( i=0; i<locnjob-1; i++ ) for( j=i+1; j<locnjob; j++ ) if( mtx[i][j] > max ) max = mtx[i][j];
+
+	fprintf( hat2p, "%5d\n", 1 );
+	fprintf( hat2p, "%5d\n", locnjob );
+	fprintf( hat2p, " %#6.3f\n", max * 2.5 );
+
+	for( i=0; i<locnjob; i++ ) fprintf( hat2p, "%4d. %s\n", i+1, name[i] );
+	for( i=0; i<locnjob-1; i++ )
+	{
+		for( j=i+1; j<locnjob; j++ ) 
+		{
+			fprintf( hat2p, "%#6.3f", mtx[i][j] );
+			if( (j-i) % 12 == 0 || j == locnjob-1 ) fprintf( hat2p, "\n" );
+		}
+	}
+}
+
+#if 0
+void WriteHat2plain( FILE *hat2p, int locnjob, double **mtx )
+{
+	int i, j, ilim;
+
+	ilim = locnjob-1;
+	for( i=0; i<ilim; i++ )
+	{
+		fprintf( hat2p, "%d-%d d=%.3f\n", i+1, i+1, 0.0 );
+		for( j=i+1; j<locnjob; j++ ) 
+		{
+			fprintf( hat2p, "%d-%d d=%.3f\n", i+1, j+1, mtx[i][j] );
+		}
+	}
+}
+#endif
+
+int ReadFasta_sub( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+    int i, count=0;
+    char b[B];
+    int junban[M];
+
+    count = 0;
+    for( i=0; i<10000000 && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+            count++;
+        }
+    }
+
+	for( i=0; i<nseq; i++ ) dis[i] = 0.0;
+    count = 0;
+    for( i=0; i<100000 && count<nseq; i++ )
+    {
+		if( fgets( b, B-1, fp ) ) break;
+        if( !strncmp( name[junban[count]], b, 20  ) )
+        {
+            fgets( b, B-1, fp );
+            dis[junban[count]] = atof( b );
+            count++;
+        }
+    }
+    return 0;
+}
+
+
+int ReadSsearch( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+    int i, count=0;
+    char b[B];
+    int junban[M];
+	int opt;
+
+    count = 0;
+    for( i=0; i<10000000 && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+			sscanf( b+75, "%d", &opt ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+        }
+    }
+
+/*
+    count = 0;
+    for( i=0; i<100000 && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( name[junban[count]], b, 20  ) )
+        {
+            dis[junban[count]] = atof( b+65 );
+            count++;
+        }
+    }
+*/
+    return 0;
+}
+
+int ReadBlastm7_avscore( FILE *fp, double *dis, int nin )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    int *junban;
+	double score, sumscore;
+	double len, sumlen;
+	int qstart, qend, tstart, tend;
+	double scorepersite;
+	static char qal[N], tal[N], al[N];
+	int nlocalhom;
+
+	junban = calloc( nin, sizeof( int ) );
+
+	count = 0;
+	sumscore = 0.0;
+	sumlen = 0.0;
+	score = 0.0;
+	len = 0.0;
+	scorepersite = 0.0; // by D.Mathog, a guess
+    while( 1 )
+	{
+
+		if( feof( fp ) ) break;
+
+		while( fgets( b, B-1, fp ) )
+		{
+			if( !strncmp( "          <Hit_def>", b, 19 ) || !strncmp( "              <Hsp_num>", b, 23 ) ) break;
+		}
+
+		if( !strncmp( "          <Hit_def>", b, 19 ) )
+		{
+			junban[count] = atoi( b+31 );
+			nlocalhom = 0;
+		}
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_score>", b, 25 ) ) break;
+		pt = b + 25;
+		score = atof( pt );
+		sumscore += score;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_query-from>", b, 30 ) ) break;
+		pt = b + 30;
+		qstart = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_query-to>", b, 28 ) ) break;
+		pt = b + 28;
+		qend = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_hit-from>", b, 28 ) ) break;
+		pt = b + 28;
+		tstart = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_hit-to>", b, 26 ) ) break;
+		pt = b + 26;
+		tend = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_align-len>", b, 29 ) ) break;
+		pt = b + 29;
+		len = atoi( pt );
+		sumlen += len;
+
+
+		while( fgets( al, N-100, fp ) )
+			if( !strncmp( "              <Hsp_qseq>", al, 24 ) ) break;
+
+		strcpy( qal, al+24 );
+		pt = qal;
+		while( *++pt != '<' )
+			;
+		*pt = 0;
+
+
+		while( fgets( al, N-100, fp ) )
+			if( !strncmp( "              <Hsp_hseq>", al, 24 ) ) break;
+
+		strcpy( tal, al+24 );
+		pt = tal;
+		while( *++pt != '<' )
+			;
+		*pt = 0;
+
+
+//		fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "            </Hsp>:", b, 18 ) ) break;
+
+
+		fgets( b, B-1, fp );
+
+
+		if( !strncmp( "          </Hit_hsps>", b, 21 ) )
+		{
+			dis[junban[count++]] = sumscore;
+			sumscore = 0.0;
+			fgets( b, B-1, fp );
+			fgets( b, B-1, fp );
+			scorepersite = sumscore / sumlen;
+			if( scorepersite != (int)scorepersite )
+			{
+				fprintf( stderr, "ERROR! sumscore=%f, sumlen=%f, and scorepersite=%f\n", sumscore, sumlen, scorepersite );
+				exit( 1 );
+			}
+
+			if( !strncmp( "      </Iteration_hits>", b, 23 ) ) break;
+		}
+	}
+
+	free( junban );
+
+    return (int)scorepersite;
+}
+int ReadBlastm7_scoreonly( FILE *fp, double *dis, int nin )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    int *junban;
+	int overlapaa;
+	double score, sumscore;
+	int qstart, qend, tstart, tend;
+	static char qal[N], tal[N], al[N];
+	int nlocalhom;
+
+	junban = calloc( nin, sizeof( int ) );
+
+	count = 0;
+	sumscore = 0.0;
+	score = 0.0;
+    while( 1 )
+	{
+
+		if( feof( fp ) ) break;
+
+		while( fgets( b, B-1, fp ) )
+		{
+			if( !strncmp( "          <Hit_def>", b, 19 ) || !strncmp( "              <Hsp_num>", b, 23 ) ) break;
+		}
+
+		if( !strncmp( "          <Hit_def>", b, 19 ) )
+		{
+			junban[count] = atoi( b+31 );
+			nlocalhom = 0;
+		}
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_score>", b, 25 ) ) break;
+		pt = b + 25;
+		score = atof( pt );
+		sumscore += score;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_query-from>", b, 30 ) ) break;
+		pt = b + 30;
+		qstart = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_query-to>", b, 28 ) ) break;
+		pt = b + 28;
+		qend = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_hit-from>", b, 28 ) ) break;
+		pt = b + 28;
+		tstart = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_hit-to>", b, 26 ) ) break;
+		pt = b + 26;
+		tend = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_align-len>", b, 29 ) ) break;
+		pt = b + 29;
+		overlapaa = atoi( pt );
+
+
+		while( fgets( al, N-100, fp ) )
+			if( !strncmp( "              <Hsp_qseq>", al, 24 ) ) break;
+
+		strcpy( qal, al+24 );
+		pt = qal;
+		while( *++pt != '<' )
+			;
+		*pt = 0;
+
+
+		while( fgets( al, N-100, fp ) )
+			if( !strncmp( "              <Hsp_hseq>", al, 24 ) ) break;
+
+		strcpy( tal, al+24 );
+		pt = tal;
+		while( *++pt != '<' )
+			;
+		*pt = 0;
+
+
+//		fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
+
+//		nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "            </Hsp>:", b, 18 ) ) break;
+
+
+		fgets( b, B-1, fp );
+
+
+		if( !strncmp( "          </Hit_hsps>", b, 21 ) )
+		{
+			dis[junban[count++]] = sumscore;
+			sumscore = 0.0;
+			fgets( b, B-1, fp );
+			fgets( b, B-1, fp );
+			if( !strncmp( "      </Iteration_hits>", b, 23 ) ) break;
+		}
+	}
+
+	free( junban );
+
+    return count;
+}
+
+int ReadBlastm7( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    static int junban[M];
+	int overlapaa;
+	double score, sumscore;
+	int qstart, qend, tstart, tend;
+	static char qal[N], tal[N], al[N];
+	int nlocalhom;
+
+
+
+	count = 0;
+	sumscore = 0.0;
+	score = 0.0;
+	nlocalhom = 0;
+    while( 1 )
+	{
+
+		if( feof( fp ) ) break;
+
+		while( fgets( b, B-1, fp ) )
+		{
+			if( !strncmp( "          <Hit_def>", b, 19 ) || !strncmp( "              <Hsp_num>", b, 23 ) ) break;
+		}
+
+		if( !strncmp( "          <Hit_def>", b, 19 ) )
+		{
+			junban[count] = atoi( b+31 );
+			nlocalhom = 0;
+		}
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_score>", b, 25 ) ) break;
+		pt = b + 25;
+		score = atof( pt );
+		sumscore += score;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_query-from>", b, 30 ) ) break;
+		pt = b + 30;
+		qstart = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_query-to>", b, 28 ) ) break;
+		pt = b + 28;
+		qend = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_hit-from>", b, 28 ) ) break;
+		pt = b + 28;
+		tstart = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_hit-to>", b, 26 ) ) break;
+		pt = b + 26;
+		tend = atoi( pt ) - 1;
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "              <Hsp_align-len>", b, 29 ) ) break;
+		pt = b + 29;
+		overlapaa = atoi( pt );
+
+
+		while( fgets( al, N-100, fp ) )
+			if( !strncmp( "              <Hsp_qseq>", al, 24 ) ) break;
+
+		strcpy( qal, al+24 );
+		pt = qal;
+		while( *++pt != '<' )
+			;
+		*pt = 0;
+
+
+		while( fgets( al, N-100, fp ) )
+			if( !strncmp( "              <Hsp_hseq>", al, 24 ) ) break;
+
+		strcpy( tal, al+24 );
+		pt = tal;
+		while( *++pt != '<' )
+			;
+		*pt = 0;
+
+
+//		fprintf( stderr, "t=%d, score = %f, qstart=%d, qend=%d, tstart=%d, tend=%d, overlapaa=%d\n", junban[count], score, qstart, qend, tstart, tend, overlapaa );
+
+		nlocalhom += addlocalhom_r( qal, tal, localhomlist+junban[count], qstart, tstart, score, overlapaa, nlocalhom );
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "            </Hsp>:", b, 18 ) ) break;
+
+
+		fgets( b, B-1, fp );
+
+
+		if( !strncmp( "          </Hit_hsps>", b, 21 ) )
+		{
+			dis[junban[count++]] = sumscore;
+			sumscore = 0.0;
+			fgets( b, B-1, fp );
+			fgets( b, B-1, fp );
+			if( !strncmp( "      </Iteration_hits>", b, 23 ) ) break;
+		}
+	}
+    return count;
+}
+
+int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    static int junban[M];
+	int opt;
+	double z, bits;
+
+
+    count = 0;
+#if 0
+    for( i=0; i<10000000 && count<nseq; i++ )
+#else
+    while( !feof( fp ) )
+#endif
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+
+			pt = strchr( b, ')' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+
+        }
+    }
+
+    return count;
+}
+int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    static int junban[M];
+	int overlapaa;
+	int opt, qstart, qend, tstart, tend;
+	double z, bits;
+	int qal_display_start, tal_display_start;
+	static char qal[N], tal[N];
+	char *qal2, *tal2;
+	int c;
+
+
+    count = 0;
+#if 0
+    for( i=0; i<10000000 && count<nseq; i++ )
+#else
+    while( !feof( fp ) )
+#endif
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+
+			if( strchr( b, 'r' ) ) continue;
+
+			pt = strchr( b, ']' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+
+        }
+		else if( 0 == strncmp( ">>+==========+", b, 14 ) )
+		{
+			break;
+		}
+
+    }
+	if( !count ) return -1;
+
+	count = 0;
+    while( 1 )
+	{
+		if( strncmp( ">>+==========+", b, 14 ) )
+		{
+			fgets( b, B-1, fp );
+			if( feof( fp ) ) break;
+			continue;
+		}
+		junban[count++] = atoi( b+14 );
+//		fprintf( stderr, "t = %d\n", atoi( b+14 ) );
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "; fa_opt:", b, 9 ) || !strncmp( "; sw_s-w opt:", b, 13 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		opt = atoi( pt );
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_overlap:", b+4, 9 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		overlapaa = atoi( pt );
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_start:", b+4, 7 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		qstart = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_stop:", b+4, 6 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		qend = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		qal_display_start = atoi( pt ) - 1;
+
+		pt = qal;
+		while( (c = fgetc( fp )) )
+		{
+			if( c == '>' ) 
+			{
+				ungetc( c, fp );
+				break;
+			}
+			if( isalpha( c ) || c == '-' ) 
+			*pt++ = c;
+		}
+		*pt = 0;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_start:", b+4, 7 ) ) break;
+		pt = strstr( b, ":" ) + 1;
+		tstart = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_stop:", b+4, 6 ) ) break;
+		pt = strstr( b, ":" ) + 1;
+		tend = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+		pt = strstr( b, ":" ) + 1;
+		tal_display_start = atoi( pt ) - 1;
+
+		pt = tal;
+		while( ( c = fgetc( fp ) ) )
+		{
+			if( c == '>' ) 
+			{
+				ungetc( c, fp );
+				break;
+			}
+			if( isalpha( c ) || c == '-' ) 
+			*pt++ = c;
+		}
+		*pt = 0;
+
+//		fprintf( stderr, "(%d-%d:%d-%d)\n", qstart, qend, tstart, tend );
+//		fprintf( stderr, "qal_display_start = %d, tal_display_start = %d\n", qal_display_start, tal_display_start );
+
+//		fprintf( stderr, "qal = %s\n", qal );
+//		fprintf( stderr, "tal = %s\n", tal );
+
+		qal2 = cutal( qal, qal_display_start, qstart, qend );
+		tal2 = cutal( tal, tal_display_start, tstart, tend );
+
+//		fprintf( stderr, "qal2 = %s\n", qal2 );
+//		fprintf( stderr, "tal2 = %s\n", tal2 );
+
+//		fprintf( stderr, "putting   %d - %d, opt = %d\n", qmem, junban[count-1], opt );
+		putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
+	}
+//	fprintf( stderr, "count = %d\n", count );
+    return count;
+}
+int ReadFasta34m10( FILE *fp, double *dis, int qmem, char **name, LocalHom *localhomlist )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    static int junban[M];
+	int overlapaa;
+	int opt, qstart, qend, tstart, tend;
+	double z, bits;
+	int qal_display_start, tal_display_start;
+	static char qal[N], tal[N];
+	char *qal2, *tal2;
+	int c;
+
+
+    count = 0;
+#if 0
+    for( i=0; i<10000000 && count<nseq; i++ )
+#else
+    while( !feof( fp ) )
+#endif
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+
+			pt = strchr( b, ')' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+
+        }
+		else if( 0 == strncmp( ">>+==========+", b, 14 ) )
+		{
+			break;
+		}
+
+    }
+	if( !count ) return -1;
+
+	count = 0;
+    while( 1 )
+	{
+		if( strncmp( ">>+==========+", b, 14 ) )
+		{
+			fgets( b, B-1, fp );
+			if( feof( fp ) ) break;
+			continue;
+		}
+		junban[count++] = atoi( b+14 );
+//		fprintf( stderr, "t = %d\n", atoi( b+14 ) );
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "; fa_opt:", b, 9 ) || !strncmp( "; sw_s-w opt:", b, 13 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		opt = atoi( pt );
+
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_overlap:", b+4, 9 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		overlapaa = atoi( pt );
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_start:", b+4, 7 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		qstart = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_stop:", b+4, 6 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		qend = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+		pt = strstr( b, ":" ) +1;
+		qal_display_start = atoi( pt ) - 1;
+
+		pt = qal;
+		while( (c = fgetc( fp )) )
+		{
+			if( c == '>' ) 
+			{
+				ungetc( c, fp );
+				break;
+			}
+			if( isalpha( c ) || c == '-' ) 
+			*pt++ = c;
+		}
+		*pt = 0;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_start:", b+4, 7 ) ) break;
+		pt = strstr( b, ":" ) + 1;
+		tstart = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_stop:", b+4, 6 ) ) break;
+		pt = strstr( b, ":" ) + 1;
+		tend = atoi( pt ) - 1;
+
+		while( fgets( b, B-1, fp ) )
+			if( !strncmp( "_display_start:", b+4, 15 ) ) break;
+		pt = strstr( b, ":" ) + 1;
+		tal_display_start = atoi( pt ) - 1;
+
+		pt = tal;
+		while( ( c = fgetc( fp ) ) )
+		{
+			if( c == '>' ) 
+			{
+				ungetc( c, fp );
+				break;
+			}
+			if( isalpha( c ) || c == '-' ) 
+			*pt++ = c;
+		}
+		*pt = 0;
+
+//		fprintf( stderr, "(%d-%d:%d-%d)\n", qstart, qend, tstart, tend );
+//		fprintf( stderr, "qal_display_start = %d, tal_display_start = %d\n", qal_display_start, tal_display_start );
+
+//		fprintf( stderr, "qal = %s\n", qal );
+//		fprintf( stderr, "tal = %s\n", tal );
+
+		qal2 = cutal( qal, qal_display_start, qstart, qend );
+		tal2 = cutal( tal, tal_display_start, tstart, tend );
+
+//		fprintf( stderr, "qal2 = %s\n", qal2 );
+//		fprintf( stderr, "tal2 = %s\n", tal2 );
+
+//		fprintf( stderr, "putting   %d - %d, opt = %d\n", qmem, junban[count-1], opt );
+		putlocalhom( qal2, tal2, localhomlist+junban[count-1], qstart, tstart, opt, overlapaa );
+	}
+//	fprintf( stderr, "count = %d\n", count );
+    return count;
+}
+int ReadFasta34m10_scoreonly_nucbk( FILE *fp, double *dis, int nin )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    int pos;
+	int opt;
+	double z, bits;
+
+    count = 0;
+    while( !feof( fp ) )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+===========+", b, 13 ) )
+        {
+            pos = atoi( b+13 );
+
+			if( strchr( b, 'r' ) ) continue;
+
+//			pt = strchr( b, ')' ) + 1;
+			pt = strchr( b, ']' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+            dis[pos] += (double)opt;
+            count++;
+#if 0
+			fprintf( stderr, "b=%s\n", b );
+			fprintf( stderr, "opt=%d\n", opt );
+			fprintf( stderr, "pos=%d\n", pos );
+			fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
+#endif
+
+        }
+		else if( 0 == strncmp( ">>><<<", b, 6 ) )
+		{
+			break;
+		}
+
+    }
+	if( !count ) return -1;
+
+    return count;
+}
+
+int ReadFasta34m10_scoreonly_nuc( FILE *fp, double *dis, int nin )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    int pos;
+	int opt;
+	double z, bits;
+	int c;
+	int *yonda;
+
+
+	yonda = AllocateIntVec( nin );
+	for( c=0; c<nin; c++ ) yonda[c] = 0;
+	for( c=0; c<nin; c++ ) dis[c] = 0.0;
+
+    count = 0;
+    while( !feof( fp ) )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+===========+", b, 13 ) )
+        {
+            pos = atoi( b+13 );
+
+			if( strchr( b, 'r' ) ) continue;
+
+//			pt = strchr( b, ')' ) + 1;
+			pt = strchr( b, ']' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+			if( yonda[pos] == 0 )
+			{
+	            dis[pos] += (double)opt;
+				yonda[pos] = 1;
+			}
+            count++;
+#if 0
+			fprintf( stderr, "b=%s\n", b );
+			fprintf( stderr, "opt=%d\n", opt );
+			fprintf( stderr, "pos=%d\n", pos );
+			fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
+#endif
+
+        }
+        else if( !strncmp( ">>>", b, 3 ) )
+		{
+			for( c=0; c<nin; c++ ) yonda[c] = 0;
+		}
+		else if( 0 == strncmp( ">>><<<", b, 6 ) )
+		{
+			break;
+		}
+
+    }
+
+	free( yonda );
+
+	if( !count ) return -1;
+
+    return count;
+}
+
+int ReadFasta34m10_scoreonly( FILE *fp, double *dis, int nin )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    int pos;
+	int opt;
+	double z, bits;
+	int c;
+	int *yonda;
+
+
+	yonda = AllocateIntVec( nin );
+	for( c=0; c<nin; c++ ) yonda[c] = 0;
+	for( c=0; c<nin; c++ ) dis[c] = 0.0;
+
+    count = 0;
+    while( !feof( fp ) )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+===========+", b, 13 ) )
+        {
+            pos = atoi( b+13 );
+
+			pt = strchr( b, ')' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+			if( yonda[pos] == 0 )
+			{
+	            dis[pos] += (double)opt;
+				yonda[pos] = 1;
+			}
+            count++;
+#if 0
+			fprintf( stderr, "b=%s\n", b );
+			fprintf( stderr, "opt=%d\n", opt );
+			fprintf( stderr, "pos=%d\n", pos );
+			fprintf( stderr, "dis[pos]=%f\n", dis[pos] );
+#endif
+
+        }
+        else if( !strncmp( ">>>", b, 3 ) )
+		{
+			for( c=0; c<nin; c++ ) yonda[c] = 0;
+		}
+		else if( 0 == strncmp( ">>><<<", b, 6 ) )
+		{
+			break;
+		}
+
+    }
+
+	free( yonda );
+
+	if( !count ) return -1;
+
+    return count;
+}
+int ReadFasta34( FILE *fp, double *dis, int nseq, char name[M][B], LocalHom *localhomlist )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    static int junban[M];
+	int overlapaa;
+	int opt, qstart, qend, tstart, tend;
+	double z, bits;
+
+
+    count = 0;
+#if 0
+    for( i=0; i<10000000 && count<nseq; i++ )
+#else
+    while( !feof( fp ) )
+#endif
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+
+			pt = strchr( b, ')' ) + 1;
+			sscanf( pt, "%d %lf %lf",  &opt, &bits, &z ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+
+        }
+		else if( 0 == strncmp( ">>+==========+", b, 14 ) )
+		{
+			break;
+		}
+
+    }
+	if( !count ) return -1;
+
+	count = 0;
+    while( !feof( fp ) )
+	{
+		if( !strncmp(">>+==========+", b, 14 ) )
+		{
+            junban[count] = atoi( b+14 );
+            count++;
+        	fgets( b, B-1, fp ); // initn:
+			pt = strstr( b, "opt: " ) + 5;
+			localhomlist[junban[count-1]].opt = atof( pt );
+        	fgets( b, B-1, fp ); // Smith-Waterman score
+			pt = strstr( b, "ungapped) in " ) + 13;
+			sscanf( pt, "%d", &overlapaa ); 
+			fprintf( stderr, "pt = %s, overlapaa = %d\n", pt, overlapaa );
+			pt = strstr( b, "overlap (" ) + 8;
+			sscanf( pt, "(%d-%d:%d-%d)", &qstart, &qend, &tstart, &tend ); 
+			localhomlist[junban[count-1]].overlapaa = overlapaa;
+			localhomlist[junban[count-1]].start1 = qstart-1;
+			localhomlist[junban[count-1]].end1   = qend-1;
+			localhomlist[junban[count-1]].start2 = tstart-1;
+			localhomlist[junban[count-1]].end2   = tend-1;
+		}
+        fgets( b, B-1, fp );
+	}
+	fprintf( stderr, "count = %d\n", count );
+    return count;
+}
+
+int ReadFasta3( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+    int count=0;
+    char b[B];
+	char *pt;
+    int junban[M];
+	int initn, init1, opt;
+	double z;
+
+    count = 0;
+#if 0
+    for( i=0; i<10000000 && count<nseq; i++ )
+#else
+    while( !feof( fp ) )
+#endif
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+
+			pt = strchr( b, ')' ) + 1;
+			sscanf( pt, "%d %d %d %lf", &initn, &init1, &opt, &z ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+        }
+    }
+    return 0;
+}
+
+int ReadFasta( FILE *fp, double *dis, int nseq, char name[M][B] )
+{
+    int i, count=0;
+    char b[B];
+    int junban[M];
+	int initn, init1, opt;
+
+    count = 0;
+	for( i=0; i<nseq; i++ ) dis[i] = 0.0;
+    for( i=0; !feof( fp ) && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+
+			sscanf( b+50, "%d %d %d", &initn, &init1, &opt ); 
+            dis[junban[count]] = (double)opt;
+            count++;
+        }
+    }
+
+/*
+    count = 0;
+    for( i=0; i<100000 && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( name[junban[count]], b, 20  ) )
+        {
+            dis[junban[count]] = atof( b+65 );
+            count++;
+        }
+    }
+*/
+    return 0;
+}
+
+
+int ReadOpt( FILE *fp, int opt[M], int nseq, char name[M][B] )
+{
+    int i, count=0;
+    char b[B];
+    int junban[M];
+	int optt, initn, init1;
+
+    count = 0;
+    for( i=0; i<10000000 && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+			sscanf( b+50, "%d %d %d", &initn, &init1, &optt ); 
+            opt[junban[count]] = (double)optt;
+            count++;
+        }
+    }
+    return 0;
+}
+
+int ReadOpt2( FILE *fp, int opt[M], int nseq, char name[M][B] )
+{
+    int i, count=0;
+    char b[B];
+    int junban[M];
+
+    count = 0;
+    for( i=0; i<10000000 && count<nseq; i++ )
+    {
+        fgets( b, B-1, fp );
+        if( !strncmp( "+==========+", b, 12 ) )
+        {
+            junban[count] = atoi( b+12 );
+            opt[junban[count]] = atoi( b+65 );
+            count++;
+        }
+    }
+    return 0;
+}
+
+
+
+int writePre( int nseq, char **name, int nlen[M], char **aseq, int force )
+{
+#if USE_XCED
+	int i, value;
+	if( !signalSM )
+	{
+		if( force ) 
+		{
+			rewind( prep_g );
+			if( devide ) dvWrite( prep_g, nseq, name, nlen, aseq );
+#if 0
+			else    WriteGapFill( prep_g, nseq, name, nlen, aseq );
+#else
+			else    writeData( prep_g, nseq, name, nlen, aseq );
+#endif
+		}
+		return( 0 );
+	}
+	for( i=0; i<10; i++ )
+	{
+#if IODEBUG
+		fprintf( stderr, "SEMAPHORE = %d\n", signalSM[SEMAPHORE] );
+#endif
+		if( signalSM[SEMAPHORE]-- > 0 )
+		{
+#if 0 /* /tmp/pre の関係ではずした */
+			if( ferror( prep_g ) ) prep_g = fopen( "pre", "w" );
+			if( !prep_g ) ErrorExit( "Cannot re-open pre." ); 
+#endif
+			rewind( prep_g );
+			signalSM[STATUS] = IMA_KAITERU;
+#if IODEBUG
+			if( force ) fprintf( stderr, "FINAL " );
+#endif
+			if( devide ) dvWrite( prep_g, nseq, name, nlen, aseq );
+			else    WriteGapFill( prep_g, nseq, name, nlen, aseq );
+			/*
+			fprintf( prep_g, '\EOF' );
+			*/
+			fflush( prep_g );
+			if( force ) signalSM[STATUS] = OSHIMAI;
+			else        signalSM[STATUS] = KAKIOWATTA;
+			value = 1;
+			signalSM[SEMAPHORE]++;
+#if IODEBUG
+			fprintf( stderr, "signalSM[STATUS] = %c\n", signalSM[STATUS] );
+#endif
+			break;
+		}
+		else
+		{
+#if IODEBUG
+			fprintf( stderr, "YONDERUKARA_AKIRAMERU\n" );
+#endif
+			value = 0;
+			signalSM[SEMAPHORE]++;
+			if( !force ) break;
+#if IODEBUG
+			fprintf( stderr, "MATSU\n" );
+#endif
+			sleep( 1 );
+		}
+	}
+	if( force && !value ) ErrorExit( "xced ga pre wo hanasanai \n" );
+	return( value );
+#else
+	if( force ) 
+	{
+		rewind( prep_g );
+		writeData_pointer( prep_g, nseq, name, nlen, aseq );
+	}
+#endif
+	return( 0 );
+}
+
+
+void readOtherOptions( int *ppidptr, int *fftThresholdptr, int *fftWinSizeptr )
+{
+	if( calledByXced )
+	{
+		FILE *fp = fopen( "pre", "r" );
+		char b[B];
+		if( !fp ) ErrorExit( "Cannot open pre.\n" );
+		fgets( b, B-1, fp );
+		sscanf( b, "%d %d %d", ppidptr, fftThresholdptr, fftWinSizeptr );
+		fclose( fp );
+#if IODEBUG
+	fprintf( stderr, "b = %s\n", b );
+	fprintf( stderr, "ppid = %d\n", ppid );
+	fprintf( stderr, "fftThreshold = %d\n", fftThreshold );
+	fprintf( stderr, "fftWinSize = %d\n", fftWinSize );
+#endif
+	}
+	else
+	{
+		*ppidptr = 0;
+		*fftThresholdptr = FFT_THRESHOLD;
+		if( dorp == 'd' )
+			*fftWinSizeptr = FFT_WINSIZE_D;
+		else
+			*fftWinSizeptr = FFT_WINSIZE_P;
+	}
+#if 0
+	fprintf( stderr, "fftThresholdptr=%d\n", *fftThresholdptr );
+	fprintf( stderr, "fftWinSizeptr=%d\n", *fftWinSizeptr );
+#endif
+}
+
+void initSignalSM( void )
+{
+//	int signalsmid;
+
+#if IODEBUG
+	if( ppid ) fprintf( stderr, "PID of xced = %d\n", ppid );
+#endif
+	if( !ppid )
+	{
+		signalSM = NULL;
+		return;
+	}
+
+#if 0
+	signalsmid = shmget( (key_t)ppid, 3, IPC_ALLOC | 0666 );
+	if( signalsmid == -1 ) ErrorExit( "Cannot get Shared memory for signal.\n" );
+	signalSM = shmat( signalsmid, 0, 0 );
+	if( (int)signalSM == -1 ) ErrorExit( "Cannot attatch Shared Memory for signal!\n" );
+	signalSM[STATUS] = IMA_KAITERU;
+	signalSM[SEMAPHORE] = 1;
+#endif
+}
+
+void initFiles( void )
+{
+	char pname[100];
+	if( ppid )
+		sprintf( pname, "/tmp/pre.%d", ppid );
+	else
+		sprintf( pname, "pre" );
+	prep_g = fopen( pname, "w" );
+	if( !prep_g ) ErrorExit( "Cannot open pre" );
+
+	trap_g = fopen( "trace", "w" );
+	if( !trap_g ) ErrorExit( "cannot open trace" );
+	fprintf( trap_g, "PID = %d\n", getpid() );
+	fflush( trap_g );
+}
+
+void closeFiles( void )
+{
+	fclose( prep_g );
+	fclose( trap_g );
+}
+
+
+void WriteForFasta( FILE *fp, int locnjob, char **name, int nlen[M], char **aseq )
+{
+    static char b[N];
+    int i, j;
+    int nalen[M];
+
+    for( i=0; i<locnjob; i++ )
+    {
+        nalen[i] = strlen( aseq[i] );
+        fprintf( fp, ">%s\n", name[i] );
+        for( j=0; j<nalen[i]; j=j+C ) 
+        {
+            strncpy( b, aseq[i]+j, C ); b[C] = 0;
+            fprintf( fp, "%s\n",b );
+        }
+    }
+}
+
+void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+	double opt;
+	static char buff[B];
+	char infor[100];
+	int i, j, overlapaa, start1, end1, start2, end2;
+	LocalHom *tmpptr1, *tmpptr2;
+
+//	for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+	while ( NULL != fgets( buff, B-1, fp ) )
+	{
+//		fprintf( stderr, "\n" );
+		sscanf( buff, "%d %d %d %lf %d %d %d %d %s",  &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+		if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+		if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+//		if( i < j )
+		{
+			if( localhomtable[i][j].nokori++ > 0 )
+			{
+				tmpptr1 = localhomtable[i][j].last;
+//				fprintf( stderr, "reallocating, localhomtable[%d][%d].nokori = %d\n", i, j, localhomtable[i][j].nokori );
+				tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr1 = tmpptr1->next;
+				tmpptr1->extended = -1;
+				tmpptr1->next = NULL;
+				localhomtable[i][j].last = tmpptr1;
+//				fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
+			}
+			else
+			{
+				tmpptr1 = localhomtable[i]+j;
+//				fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", i, j, localhomtable[i][j].nokori );
+			}
+	
+			tmpptr1->start1 = start1;
+			tmpptr1->start2 = start2;
+			tmpptr1->end1 = end1;
+			tmpptr1->end2 = end2;
+//			tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr1->opt = opt;
+			tmpptr1->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr1->overlapaa = overlapaa;
+			tmpptr1->korh = *infor;
+		}
+//		else
+		{
+			if( localhomtable[j][i].nokori++ > 0 )
+			{
+				tmpptr2 = localhomtable[j][i].last;
+				tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr2 = tmpptr2->next;
+				tmpptr2->extended = -1;
+				tmpptr2->next = NULL;
+				localhomtable[j][i].last = tmpptr2;
+//				fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
+			}
+			else
+			{
+				tmpptr2 = localhomtable[j]+i;
+//				fprintf( stderr, "### i,j = %d,%d, nokori=%d\n", j, i, localhomtable[j][i].nokori );
+			}
+	
+			tmpptr2->start2 = start1;
+			tmpptr2->start1 = start2;
+			tmpptr2->end2 = end1;
+			tmpptr2->end1 = end2;
+//			tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr2->opt = opt;
+			tmpptr2->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr2->overlapaa = overlapaa;
+			tmpptr2->korh = *infor;
+	
+//			fprintf( stderr, "i=%d, j=%d, st1=%d, en1=%d, opt = %f\n", i, j, tmpptr1->start1, tmpptr1->end1, opt );
+		}
+
+	}
+}
+void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec )
+{
+	double opt;
+	static char buff[B];
+	char infor[100];
+	int i, j, overlapaa, start1, end1, start2, end2;
+	int **nlocalhom = NULL;
+	LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
+
+	nlocalhom = AllocateIntMtx( njob, njob );
+	for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) nlocalhom[i][j] = 0;
+
+	while ( NULL != fgets( buff, B-1, fp ) )
+	{
+//		fprintf( stderr, "\n" );
+		sscanf( buff, "%d %d %d %lf %d %d %d %d %s",  &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+		if( *infor == 'k' ) kozoarivec[i] = kozoarivec[j] = 1;
+
+#if 0
+		if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+//		if( i < j )
+		{
+			if( nlocalhom[i][j]++ > 0 )
+			{
+//				fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+				tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr1 = tmpptr1->next;
+				tmpptr1->next = NULL;
+			}
+			else
+			{
+				tmpptr1 = localhomtable[i]+j;
+//				fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+			}
+	
+			tmpptr1->start1 = start1; // CHUUI!!!!
+			tmpptr1->start2 = start2;
+			tmpptr1->end1 = end1; // CHUUI!!!!
+			tmpptr1->end2 = end2;
+//			tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr1->opt = opt;
+			tmpptr1->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr1->overlapaa = overlapaa;
+			tmpptr1->korh = *infor;
+	
+//			fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+		}
+//		else
+		{
+			if( nlocalhom[j][i]++ > 0 )
+			{
+				tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr2 = tmpptr2->next;
+				tmpptr2->next = NULL;
+			}
+			else
+				tmpptr2 = localhomtable[j]+i;
+	
+			tmpptr2->start2 = start1; // CHUUI!!!!
+			tmpptr2->start1 = start2;
+			tmpptr2->end2 = end1; // CHUUI!!!!
+			tmpptr2->end1 = end2;
+//			tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr2->opt = opt;
+			tmpptr2->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr2->overlapaa = overlapaa;
+			tmpptr2->korh = *infor;
+
+//			fprintf( stderr, "j=%d, i=%d, opt = %f\n", j, i, opt );
+		}
+
+	}
+	FreeIntMtx( nlocalhom );
+}
+
+
+void readlocalhomtable_two( FILE*fp, int norg, int nadd, LocalHom **localhomtable, LocalHom **localhomtablex, char *kozoarivec ) // for test only
+{
+	double opt;
+	static char buff[B];
+	char infor[100];
+	int i, j, overlapaa, start1, end1, start2, end2;
+	int **nlocalhom = NULL;
+	int **nlocalhomx = NULL;
+	LocalHom *tmpptr1=NULL, *tmpptr2=NULL; // by D.Mathog, a guess
+
+	nlocalhom = AllocateIntMtx( norg, nadd );
+	for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ ) nlocalhom[i][j] = 0;
+	nlocalhomx = AllocateIntMtx( nadd, norg );
+	for( i=0; i<nadd; i++ ) for( j=0; j<norg; j++ ) nlocalhomx[i][j] = 0;
+
+	while ( NULL != fgets( buff, B-1, fp ) )
+	{
+//		fprintf( stderr, "\n" );
+		sscanf( buff, "%d %d %d %lf %d %d %d %d %s",  &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+		if( *infor == 'k' ) 
+		{
+			fprintf( stderr, "Not supported!\n" );
+			exit( 1 );
+		}
+		j -= norg;
+
+#if 0
+		if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+//		if( i < j )
+		{
+			if( nlocalhom[i][j]++ > 0 )
+			{
+//				fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+				tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr1 = tmpptr1->next;
+				tmpptr1->next = NULL;
+			}
+			else
+			{
+				tmpptr1 = localhomtable[i]+j;
+//				fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+			}
+	
+			tmpptr1->start1 = start1; // CHUUI!!!!
+			tmpptr1->start2 = start2;
+			tmpptr1->end1 = end1; // CHUUI!!!!
+			tmpptr1->end2 = end2;
+//			tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr1->opt = opt;
+			tmpptr1->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr1->overlapaa = overlapaa;
+			tmpptr1->korh = *infor;
+	
+//			fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+		}
+
+		{
+			if( nlocalhomx[j][i]++ > 0 )
+			{
+				tmpptr2->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr2 = tmpptr2->next;
+				tmpptr2->next = NULL;
+			}
+			else
+				tmpptr2 = localhomtablex[j]+i;
+	
+			tmpptr2->start2 = start1+1; // CHUUI!!!!
+			tmpptr2->start1 = start2;
+			tmpptr2->end2 = end1+1; // CHUUI!!!!
+			tmpptr2->end1 = end2;
+//			tmpptr2->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr2->opt = opt;
+			tmpptr2->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr2->overlapaa = overlapaa;
+			tmpptr2->korh = *infor;
+
+//			fprintf( stderr, "j=%d, i=%d, opt = %f\n", j, i, opt );
+		}
+
+	}
+	FreeIntMtx( nlocalhom );
+	FreeIntMtx( nlocalhomx );
+}
+
+void readlocalhomtable_one( FILE*fp, int norg, int nadd, LocalHom **localhomtable, char *kozoarivec ) // for test only
+{
+	double opt;
+	static char buff[B];
+	char infor[100];
+	int i, j, overlapaa, start1, end1, start2, end2;
+	int **nlocalhom = NULL;
+	LocalHom *tmpptr1=NULL; // by D.Mathog, a guess
+
+	nlocalhom = AllocateIntMtx( norg, nadd );
+	for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ ) nlocalhom[i][j] = 0;
+
+	while ( NULL != fgets( buff, B-1, fp ) )
+	{
+//		fprintf( stderr, "\n" );
+		sscanf( buff, "%d %d %d %lf %d %d %d %d %s",  &i, &j, &overlapaa, &opt, &start1, &end1, &start2, &end2, infor );
+		if( *infor == 'k' ) 
+		{
+			fprintf( stderr, "Not supported!\n" );
+			exit( 1 );
+		}
+		j -= norg;
+
+#if 0
+		if( start1 == end1 || start2 == end2 ) continue; //mondai ari
+#endif
+
+
+//		if( i < j )
+		{
+			if( nlocalhom[i][j]++ > 0 )
+			{
+//				fprintf( stderr, "reallocating, nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+				tmpptr1->next = (LocalHom *)calloc( 1, sizeof( LocalHom ) );
+				tmpptr1 = tmpptr1->next;
+				tmpptr1->next = NULL;
+			}
+			else
+			{
+				tmpptr1 = localhomtable[i]+j;
+//				fprintf( stderr, "nlocalhom[%d][%d] = %d\n", i, j, nlocalhom[i][j] );
+			}
+	
+			tmpptr1->start1 = start1; // CHUUI!!!!
+			tmpptr1->start2 = start2;
+			tmpptr1->end1 = end1; // CHUUI!!!!
+			tmpptr1->end2 = end2;
+//			tmpptr1->opt = ( opt / overlapaa + 0.00 ) / 5.8  * 600;
+//			tmpptr1->opt = opt;
+			tmpptr1->opt = ( opt + 0.00 ) / 5.8  * 600;
+			tmpptr1->overlapaa = overlapaa;
+			tmpptr1->korh = *infor;
+	
+//			fprintf( stderr, "i=%d, j=%d, opt = %f\n", i, j, opt );
+		}
+
+	}
+	FreeIntMtx( nlocalhom );
+}
+
+void outlocalhom_part( LocalHom **localhom, int norg, int nadd )
+{
+	int i, j;
+	LocalHom *tmpptr;
+	for( i=0; i<norg; i++ ) for( j=0; j<nadd; j++ )
+	{
+		tmpptr = localhom[i]+j;
+		fprintf( stderr, "%d-%d\n", i, j+norg );
+		do
+		{
+			fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
+		}
+		while( (tmpptr=tmpptr->next) );
+	}
+}
+
+void outlocalhom( LocalHom **localhom, int nseq )
+{
+	int i, j;
+	LocalHom *tmpptr;
+	for( i=0; i<nseq; i++ ) for( j=0; j<nseq; j++ )
+	{
+		tmpptr = localhom[i]+j;
+		fprintf( stderr, "%d-%d\n", i, j );
+		do
+		{
+			fprintf( stderr, "reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f\n", tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt );
+		}
+		while( (tmpptr=tmpptr->next) );
+	}
+}
+
+void outlocalhompt( LocalHom ***localhom, int n1, int n2 )
+{
+	int i, j;
+	LocalHom *tmpptr;
+	for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+	{
+		tmpptr = localhom[i][j];
+//		fprintf( stdout, "%d-%d\n", i, j );
+		do
+		{
+			fprintf( stdout, "%d-%d, reg1=%d-%d, reg2=%d-%d, imp=%f, opt=%f, wimp=%f\n", i, j, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->importance, tmpptr->opt, tmpptr->wimportance );
+		}
+		while( (tmpptr=tmpptr->next) );
+	}
+}
+
+void FreeLocalHomTable_part( LocalHom **localhomtable, int n, int m ) 
+{
+	int i, j;
+	LocalHom *ppp, *tmpptr;
+	for( i=0; i<n; i++ ) 
+	{
+		for( j=0; j<m; j++ )
+		{
+			tmpptr=localhomtable[i]+j;
+			ppp = tmpptr->next;
+			for( ; tmpptr; tmpptr=ppp )
+			{
+#if DEBUG
+				fprintf( stderr, "i=%d, j=%d\n", i, j ); 
+#endif
+				ppp = tmpptr->next;
+				if( tmpptr!=localhomtable[i]+j ) 
+				{
+#if DEBUG
+					fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+					free( tmpptr );
+				}
+			}
+		}
+#if DEBUG
+		fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+		free( localhomtable[i] );
+	}
+#if DEBUG
+	fprintf( stderr, "freeing localhomtable\n" );
+#endif
+	free( localhomtable );
+#if DEBUG
+	fprintf( stderr, "freed\n" );
+#endif
+}
+
+void FreeLocalHomTable_two( LocalHom **localhomtable, int n, int m ) 
+{
+	int i, j;
+	LocalHom *ppp, *tmpptr;
+	for( i=0; i<n; i++ ) 
+	{
+		for( j=0; j<m; j++ )
+		{
+			tmpptr=localhomtable[i]+j;
+			ppp = tmpptr->next;
+			for( ; tmpptr; tmpptr=ppp )
+			{
+#if DEBUG
+				fprintf( stderr, "i=%d, j=%d\n", i, j ); 
+#endif
+				ppp = tmpptr->next;
+				if( tmpptr!=localhomtable[i]+j ) 
+				{
+#if DEBUG
+					fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+					free( tmpptr );
+				}
+			}
+		}
+#if DEBUG
+		fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+		free( localhomtable[i] );
+	}
+
+	for( i=n; i<n+m; i++ ) 
+	{
+		for( j=0; j<n; j++ )
+		{
+			tmpptr=localhomtable[i]+j;
+			ppp = tmpptr->next;
+			for( ; tmpptr; tmpptr=ppp )
+			{
+#if DEBUG
+				fprintf( stderr, "i=%d, j=%d\n", i, j ); 
+#endif
+				ppp = tmpptr->next;
+				if( tmpptr!=localhomtable[i]+j ) 
+				{
+#if DEBUG
+					fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+					free( tmpptr );
+				}
+			}
+		}
+#if DEBUG
+		fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+		free( localhomtable[i] );
+	}
+#if DEBUG
+	fprintf( stderr, "freeing localhomtable\n" );
+#endif
+	free( localhomtable );
+#if DEBUG
+	fprintf( stderr, "freed\n" );
+#endif
+}
+
+void FreeLocalHomTable_one( LocalHom **localhomtable, int n, int m ) 
+{
+	int i, j;
+	LocalHom *ppp, *tmpptr;
+	for( i=0; i<n; i++ ) 
+	{
+		for( j=0; j<m; j++ )
+		{
+			tmpptr=localhomtable[i]+j;
+			ppp = tmpptr->next;
+			for( ; tmpptr; tmpptr=ppp )
+			{
+#if DEBUG
+				fprintf( stderr, "i=%d, j=%d\n", i, j ); 
+#endif
+				ppp = tmpptr->next;
+				if( tmpptr!=localhomtable[i]+j ) 
+				{
+#if DEBUG
+					fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+					free( tmpptr );
+				}
+			}
+		}
+#if DEBUG
+		fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+		free( localhomtable[i] );
+	}
+
+#if DEBUG
+	fprintf( stderr, "freeing localhomtable\n" );
+#endif
+	free( localhomtable );
+#if DEBUG
+	fprintf( stderr, "freed\n" );
+#endif
+}
+
+void FreeLocalHomTable( LocalHom **localhomtable, int n ) 
+{
+	int i, j;
+	LocalHom *ppp, *tmpptr;
+	for( i=0; i<n; i++ ) 
+	{
+		for( j=0; j<n; j++ )
+		{
+			tmpptr=localhomtable[i]+j;
+			ppp = tmpptr->next;
+			for( ; tmpptr; tmpptr=ppp )
+			{
+#if DEBUG
+				fprintf( stderr, "i=%d, j=%d\n", i, j ); 
+#endif
+				ppp = tmpptr->next;
+				if( tmpptr!=localhomtable[i]+j ) 
+				{
+#if DEBUG
+					fprintf( stderr, "freeing %p\n", tmpptr );
+#endif
+					free( tmpptr );
+				}
+			}
+		}
+#if DEBUG
+		fprintf( stderr, "freeing localhomtable[%d]\n", i );
+#endif
+		free( localhomtable[i] );
+	}
+#if DEBUG
+	fprintf( stderr, "freeing localhomtable\n" );
+#endif
+	free( localhomtable );
+#if DEBUG
+	fprintf( stderr, "freed\n" );
+#endif
+}
+
+char *progName( char *str )
+{
+    char *value; 
+    if( ( value = strrchr( str, '/' ) ) != NULL )
+        return( value+1 );
+    else    
+        return( str );
+}
+
+static void tabtospace( char *str )
+{
+	char *p;
+//	fprintf( stderr, "before = %s\n", str );
+	while( NULL != ( p = strchr( str , '\t' ) ) )
+	{
+		*p = ' ';
+	}
+//	fprintf( stderr, "after = %s\n", str );
+}
+
+static char *extractfirstword( char *str )
+{
+	char *val = str;
+
+	tabtospace( str );
+	while( *str )
+	{
+		if( val == str && *str == ' ' )
+		{
+			val++; str++;
+		}
+		else if( *str != ' ' )
+		{
+			str++;
+		}
+		else if( *str == ' ' )
+		{
+			*str = 0;
+		}
+	}
+	return( val );
+}
+
+void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order, int namelen )
+{
+	int pos, pos2, j;
+	if( namelen == -1 ) namelen = 10;
+	pos = 0;
+
+	fprintf( fp, " %d %d\n", nseq, maxlen );
+	
+	while( pos < maxlen )
+	{
+		for( j=0; j<nseq; j++ )
+		{
+			if( pos == 0 )
+				fprintf( fp, "%-*.*s", namelen, namelen, extractfirstword( name[order[j]]+1 ) );
+			else
+				fprintf( fp, "%-*.*s", namelen, namelen, "" );
+
+			pos2 = pos;
+			while( pos2 < pos+41 && pos2 < maxlen )
+			{
+				fprintf( fp, " %.10s", seq[order[j]]+pos2 );
+				pos2 += 10;
+			}
+			fprintf( fp, "\n" );
+		}
+		fprintf( fp, "\n" );
+		pos += 50;
+	}
+}
+
+void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen )
+{
+	int pos, j;
+	if( namelen == -1 ) namelen = 15;
+	pos = 0;
+	if( comment == NULL )
+		fprintf( fp, "CLUSTAL format alignment by MAFFT (v%s)\n\n", VERSION );
+	else
+		fprintf( fp, "CLUSTAL format alignment by MAFFT %s (v%s)\n\n", comment, VERSION );
+	
+	while( pos < maxlen )
+	{
+		fprintf( fp, "\n" );
+		for( j=0; j<nseq; j++ )
+		{
+			fprintf( fp, "%-*.*s ", namelen, namelen, extractfirstword( name[order[j]]+1 ) );
+			fprintf( fp, "%.60s\n", seq[order[j]]+pos ); // 長さが違うとだめ。
+		}
+		if( mark )
+		{
+			fprintf( fp, "%-*.*s ", namelen, namelen, "" );
+			fprintf( fp, "%.60s\n", mark + pos ); // 長さが違うとだめ。
+		}
+		pos += 60;
+	}
+}
+
+
+void writeData_reorder_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq, int *order )
+{
+	int i, j, k;
+	int nalen;
+
+	for( i=0; i<locnjob; i++ )
+	{
+		k = order[i];
+#if DEBUG
+		fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+		nalen = strlen( aseq[k] );
+		fprintf( fp, ">%s\n", name[k]+1 );
+		for( j=0; j<nalen; j=j+C )
+		{
+#if 0
+			strncpy( b, aseq[k]+j, C ); b[C] = 0;
+			fprintf( fp, "%s\n",b );
+#else
+			fprintf( fp, "%.*s\n", C, aseq[k]+j );
+#endif
+		}
+	}
+}
+void writeData_reorder( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq, int *order )
+{
+	int i, j, k;
+	int nalen;
+
+	for( i=0; i<locnjob; i++ )
+	{
+		k = order[i];
+#if DEBUG
+		fprintf( stderr, "i = %d in writeData\n", i );
+#endif
+		nalen = strlen( aseq[k] );
+		fprintf( fp, ">%s\n", name[k]+1 );
+		for( j=0; j<nalen; j=j+C )
+		{
+#if 0
+			strncpy( b, aseq[k]+j, C ); b[C] = 0;
+			fprintf( fp, "%s\n",b );
+#else
+			fprintf( fp, "%.*s\n", C, aseq[k]+j );
+#endif
+		}
+	}
+}
+static void showaamtxexample()
+{
+	fprintf( stderr, "Format error in aa matrix\n" );
+	fprintf( stderr, "# Example:\n" );
+	fprintf( stderr, "# comment\n" );
+	fprintf( stderr, "   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V\n" );
+	fprintf( stderr, "A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0\n" );
+	fprintf( stderr, "R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3\n" );
+	fprintf( stderr, "...\n" );
+	fprintf( stderr, "V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4\n" );
+	fprintf( stderr, "frequency 0.07 0.05 0.04 0.05 0.02 .. \n" );
+	fprintf( stderr, "# Example end\n" );
+	fprintf( stderr, "Only the lower half is loaded\n" );
+	fprintf( stderr, "The last line (frequency) is optional.\n" );
+	exit( 1 );
+}
+
+double *loadaamtx( void )
+{
+	int i, j, k, ii, jj;
+	double *val;
+	double **raw;
+	int *map;
+	char *aaorder = "ARNDCQEGHILKMFPSTWYV";
+	char *inorder;
+	char *line;
+	char *ptr1;
+	char *ptr2;
+	char *mtxfname = "_aamtx";
+	FILE *mf;
+
+	raw = AllocateDoubleMtx( 21, 20 );
+	val = AllocateDoubleVec( 420 );
+	map = AllocateIntVec( 20 );
+
+	if( dorp != 'p' )
+	{
+		fprintf( stderr, "User-defined matrix is not supported for DNA\n" );
+		exit( 1 );
+	}
+
+	mf = fopen( mtxfname, "r" );
+	if( mf == NULL )
+	{
+		fprintf( stderr, "Cannot open the _aamtx file\n" );
+		exit( 1 );
+	}
+
+	inorder = calloc( 1000, sizeof( char ) );
+	line = calloc( 1000, sizeof( char ) );
+	
+
+	while( !feof( mf ) )
+	{
+		fgets( inorder, 999, mf );
+		if( inorder[0] != '#' ) break;
+	}
+	ptr1 = ptr2 = inorder;
+	while( *ptr2 )
+	{
+		if( isalpha( *ptr2 ) )
+		{
+			*ptr1 = toupper( *ptr2 );
+			ptr1++;
+		}
+		ptr2++;
+	}
+	inorder[20] = 0;
+
+	for( i=0; i<20; i++ )
+	{
+		ptr2 = strchr( inorder, aaorder[i] );
+		if( ptr2 == NULL )
+		{
+			fprintf( stderr, "%c: not found in the first 20 letters.\n", aaorder[i] );
+			showaamtxexample();
+		}
+		else
+		{
+			map[i] = ptr2 - inorder;
+		}
+	}
+
+	i = 0;
+	while( !feof( mf ) )
+	{
+		fgets( line, 999, mf );
+//		fprintf( stderr, "line = %s\n", line );
+		if( line[0] == '#' ) continue;
+		ptr1 = line;
+//		fprintf( stderr, "line = %s\n", line );
+		for( j=0; j<=i; j++ )
+		{
+			while( !isdigit( *ptr1 ) && *ptr1 != '-' && *ptr1 != '.' )
+				ptr1++;
+
+			raw[i][j] = atof( ptr1 );
+//			fprintf( stderr, "raw[][]=%f, %c-%c %d-%d\n", raw[i][j], inorder[i], inorder[j], i, j );
+			ptr1 = strchr( ptr1, ' ' );
+			if( ptr1 == NULL && j<i) showaamtxexample();
+		}
+		i++;
+		if( i > 19 ) break;
+	}
+
+	for( i=0; i<20; i++ ) raw[20][i] = -1.0;
+	while( !feof( mf ) )
+	{
+		fgets( line, 999, mf );
+		if( line[0] == 'f' )
+		{
+//			fprintf( stderr, "line = %s\n", line );
+			ptr1 = line;
+			for( j=0; j<20; j++ )
+			{
+				while( !isdigit( *ptr1 ) && *ptr1 != '-' && *ptr1 != '.' )
+					ptr1++;
+	
+				raw[20][j] = atof( ptr1 );
+//				fprintf( stderr, "raw[20][]=%f, %c %d\n", raw[20][j], inorder[i], j );
+				ptr1 = strchr( ptr1, ' ' );
+				if( ptr1 == NULL && j<19) showaamtxexample();
+			}
+			break;
+		}
+	}
+
+	k = 0;
+	for( i=0; i<20; i++ )
+	{
+		for( j=0; j<=i; j++ )
+		{
+			if( i != j )
+			{
+				ii = MAX( map[i], map[j] );
+				jj = MIN( map[i], map[j] );
+			}
+			else ii = jj = map[i];
+			val[k++] = raw[ii][jj];
+//			fprintf( stderr, "%c-%c, %f\n", aaorder[i], aaorder[j], val[k-1] );
+		}
+	}
+	for( i=0; i<20; i++ ) val[400+i] = raw[20][map[i]];
+
+	fprintf( stderr, "inorder = %s\n", inorder );
+	fclose( mf );
+	free( inorder );
+	free( line );
+	FreeDoubleMtx( raw );
+	free( map );
+	return( val );
+}
+
+static void tab2space( char *s ) // nen no tame
+{
+	while( *s )
+	{
+		if( *s == '\t' ) *s = ' ';
+		s++;
+	}
+}
+
+static int readasubalignment( char *s, int *t, int *preservegaps )
+{
+	int v = 0;
+	char status = 's';
+	char *pt = s;
+	*preservegaps = 0;
+	tab2space( s );
+	while( *pt )
+	{
+		if( *pt == ' ' )
+		{
+			status = 's';
+		}
+		else
+		{
+			if( status == 's' ) 
+			{
+				if( *pt == '\n' || *pt == '#' ) break;
+				status = 'n';
+				t[v] = atoi( pt );
+				if( t[v] == 0 )
+				{
+					fprintf( stderr, "Format error? Sequences must be specified as 1, 2, 3...\n" );
+					exit( 1 );
+				}
+				if( t[v] < 0 ) *preservegaps = 1;
+				t[v] = abs( t[v] );
+				t[v] -= 1;
+				v++;
+			}
+		}
+		pt++;
+	}
+	t[v] = -1;
+	return( v );
+}
+
+static int countspace( char *s )
+{
+	int v = 0;
+	char status = 's';
+	char *pt = s;
+	tab2space( s );
+	while( *pt )
+	{
+		if( *pt == ' ' )
+		{
+			status = 's';
+		}
+		else
+		{
+			if( status == 's' ) 
+			{
+				if( *pt == '\n' || *pt == '#' ) break;
+				v++;
+				status = 'n';
+				if( atoi( pt ) == 0 )
+				{
+					fprintf( stderr, "Format error? Sequences should be specified as 1, 2, 3...\n" );
+					exit( 1 );
+				}
+			}
+		}
+		pt++;
+	}
+	return( v );
+}
+
+
+void readsubalignmentstable( int nseq, int **table, int *preservegaps, int *nsubpt, int *maxmempt )
+{
+	FILE *fp;
+	char *line;
+	int linelen = 1000000;
+	int nmem;
+	int lpos;
+	int i, p;
+	int *tab01;
+
+	line = calloc( linelen, sizeof( char ) );
+	fp = fopen( "_subalignmentstable", "r" );
+	if( !fp )
+	{
+		fprintf( stderr, "Cannot open _subalignmentstable\n" );
+		exit( 1 );
+	}
+	if( table == NULL )
+	{
+		*nsubpt = 0;
+		*maxmempt = 0;
+		while( 1 )
+		{
+			fgets( line, linelen-1, fp );
+			if( feof( fp ) ) break;
+			if( line[strlen(line)-1] != '\n' )
+			{
+				fprintf( stderr, "too long line? \n" );
+				exit( 1 );
+			}
+			if( line[0] == '#' ) continue;
+			if( atoi( line ) == 0 ) continue;
+			nmem = countspace( line );
+			if( nmem > *maxmempt ) *maxmempt = nmem;
+			(*nsubpt)++;
+		}
+	}
+	else
+	{
+		tab01 = calloc( nseq, sizeof( int ) );
+		for( i=0; i<nseq; i++ ) tab01[i] = 0;
+		lpos = 0;
+		while( 1 )
+		{
+			fgets( line, linelen-1, fp );
+			if( feof( fp ) ) break;
+			if( line[strlen(line)-1] != '\n' )
+			{
+				fprintf( stderr, "too long line? \n" );
+				exit( 1 );
+			}
+			if( line[0] == '#' ) continue;
+			if( atoi( line ) == 0 ) continue;
+			readasubalignment( line, table[lpos], preservegaps+lpos );
+			for( i=0; (p=table[lpos][i])!=-1; i++ )
+			{
+				if( tab01[p] )
+				{
+					fprintf( stderr, "\nSequence %d appears in different groups.\n", p+1 );
+					fprintf( stderr, "Hierarchical grouping is not supported.\n\n" );
+					exit( 1 );
+				}
+				tab01[p] = 1;
+				if( p > nseq-1 )
+				{
+					fprintf( stderr, "Sequence %d does not exist in the input sequence file.\n", p+1 );
+					exit( 1 );
+				}
+			}
+			lpos++;
+		}
+		free( tab01 );
+	}
+	fclose( fp );
+	free( line );
+}
+
+
+void readmccaskill( FILE *fp, RNApair **pairprob, int length )
+{
+	char gett[1000];
+	int *pairnum;
+	int i;
+	int left, right;
+	float prob;
+	int c;
+
+	pairnum = (int *)calloc( length, sizeof( int ) );
+	for( i=0; i<length; i++ ) pairnum[i] = 0;
+
+	c = getc( fp );
+	{
+		if( c != '>' )
+		{
+			fprintf( stderr, "format error in hat4 - 1\n" );
+			exit( 1 );
+		}
+	}
+	fgets( gett, 999, fp );
+	while( 1 )
+	{
+		if( feof( fp ) ) break;
+		c = getc( fp );
+		ungetc( c, fp );
+		if( c == '>' || c == EOF )
+		{
+			break;
+		}
+		fgets( gett, 999, fp );
+//		fprintf( stderr, "gett = %s\n", gett );
+		sscanf( gett, "%d %d %f", &left, &right, &prob );
+
+		if( left >= length || right >= length )
+		{
+			fprintf( stderr, "format error in hat4 - 2\n" );
+			exit( 1 );
+		}
+
+		if( prob < 0.01 ) continue; // 080607, mafft ni dake eikyou
+
+		if( left != right && prob > 0.0 )
+		{
+			pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
+			pairprob[left][pairnum[left]].bestscore = prob;
+			pairprob[left][pairnum[left]].bestpos = right;
+			pairnum[left]++;
+			pairprob[left][pairnum[left]].bestscore = -1.0;
+			pairprob[left][pairnum[left]].bestpos = -1;
+//			fprintf( stderr, "%d-%d, %f\n", left, right, prob );
+
+			pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
+			pairprob[right][pairnum[right]].bestscore = prob;
+			pairprob[right][pairnum[right]].bestpos = left;
+			pairnum[right]++;
+			pairprob[right][pairnum[right]].bestscore = -1.0;
+			pairprob[right][pairnum[right]].bestpos = -1;
+//			fprintf( stderr, "%d-%d, %f\n", right, left, prob );
+		}
+	}
+	free( pairnum );
+}
+
+void readpairfoldalign( FILE *fp, char *s1, char *s2, char *aln1, char *aln2, int q1, int q2, int *of1, int *of2, int sumlen )
+{
+	char gett[1000];
+	int *maptoseq1;
+	int *maptoseq2;
+	char dumc;
+	int dumi;
+	char sinseq[100], sinaln[100];
+	int posinseq, posinaln;
+	int alnlen;
+	int i;
+	int pos1, pos2;
+	char *pa1, *pa2;
+	char qstr[1000];
+
+	*of1 = -1;
+	*of2 = -1;
+
+	maptoseq1 = AllocateIntVec( sumlen+1 );
+	maptoseq2 = AllocateIntVec( sumlen+1 );
+
+	posinaln = 0; // foldalign ga alingment wo kaesanaitok no tame.
+
+	while( !feof( fp ) )
+	{
+		fgets( gett, 999, fp );
+		if( !strncmp( gett, "; ALIGNING", 10 ) ) break;
+	}
+	sprintf( qstr, "; ALIGNING            %d against %d\n", q1+1, q2+1 );
+	if( strcmp( gett, qstr ) )
+	{
+		fprintf( stderr, "Error in FOLDALIGN\n" );
+		fprintf( stderr, "qstr = %s, but gett = %s\n", qstr, gett );
+		exit( 1 );
+	}
+
+	while( !feof( fp ) )
+	{
+		fgets( gett, 999, fp );
+		if( !strncmp( gett, "; --------", 10 ) ) break;
+	}
+
+
+	while( !feof( fp ) )
+	{
+		fgets( gett, 999, fp );
+		if( !strncmp( gett, "; ********", 10 ) ) break;
+//		fprintf( stderr, "gett = %s\n", gett );
+		sscanf( gett, "%c %c %s %s %d %d", &dumc, &dumc, sinseq, sinaln, &dumi, &dumi );
+		posinaln = atoi( sinaln );
+		posinseq = atoi( sinseq );
+//		fprintf( stderr, "posinseq = %d\n", posinseq );
+//		fprintf( stderr, "posinaln = %d\n", posinaln );
+		maptoseq1[posinaln-1] = posinseq-1;
+	}
+	alnlen = posinaln;
+
+	while( !feof( fp ) )
+	{
+		fgets( gett, 999, fp );
+		if( !strncmp( gett, "; --------", 10 ) ) break;
+	}
+
+	while( !feof( fp ) )
+	{
+		fgets( gett, 999, fp );
+		if( !strncmp( gett, "; ********", 10 ) ) break;
+//		fprintf( stderr, "gett = %s\n", gett );
+		sscanf( gett, "%c %c %s %s %d %d", &dumc, &dumc, sinseq, sinaln, &dumi, &dumi );
+		posinaln = atof( sinaln );
+		posinseq = atof( sinseq );
+//		fprintf( stderr, "posinseq = %d\n", posinseq );
+//		fprintf( stderr, "posinaln = %d\n", posinaln );
+		maptoseq2[posinaln-1] = posinseq-1;
+	}
+	if( alnlen != posinaln )
+	{
+		fprintf( stderr, "Error in foldalign?\n" );
+		exit( 1 );
+	}
+
+	pa1 = aln1;
+	pa2 = aln2;
+	for( i=0; i<alnlen; i++ )
+	{
+		pos1 = maptoseq1[i];
+		pos2 = maptoseq2[i];
+
+		if( pos1 > -1 )
+			*pa1++ = s1[pos1];
+		else
+			*pa1++ = '-';
+
+		if( pos2 > -1 )
+			*pa2++ = s2[pos2];
+		else
+			*pa2++ = '-';
+	}
+	*pa1 = 0;
+	*pa2 = 0;
+
+	*of1 = 0;
+	for( i=0; i<alnlen; i++ )
+	{
+		*of1 = maptoseq1[i];
+		if( *of1 > -1 ) break;
+	}
+	*of2 = 0;
+	for( i=0; i<alnlen; i++ )
+	{
+		*of2 = maptoseq2[i];
+		if( *of2 > -1 ) break;
+	}
+
+//	fprintf( stderr, "*of1=%d, aln1 = :%s:\n", *of1, aln1 );
+//	fprintf( stderr, "*of2=%d, aln2 = :%s:\n", *of2, aln2 );
+
+	free( maptoseq1 );
+	free( maptoseq2 );
+}
+
+int myatoi( char *in )
+{
+	if( in == NULL )
+	{
+		fprintf( stderr, "Error in myatoi()\n" );
+		exit( 1 );
+	}
+	return( atoi( in ) );
+}
+
+float myatof( char *in )
+{
+	if( in == NULL )
+	{
+		fprintf( stderr, "Error in myatof()\n" );
+		exit( 1 );
+	}
+	return( atof( in ) );
+}
+
+void reporterr( const char *str, ... )
+{
+//	static int loglen = 0;
+	va_list args;
+
+	if( gmsg )
+	{
+# if 1  // ato de sakujo
+		static FILE *errtmpfp = NULL;
+		if( errtmpfp == NULL )
+			errtmpfp = fopen( "maffterr", "w" );
+		else
+			errtmpfp = fopen( "maffterr", "a" );
+		va_start( args, str );
+		vfprintf( errtmpfp, str, args );
+		va_end( args );
+		fclose( errtmpfp );
+#endif
+
+#if 0
+		char *tmpptr;
+		tmpptr = (char *)realloc( *gmsg, (loglen+10000) * sizeof( char ) );
+		if( tmpptr == NULL )
+		{
+			fprintf( stderr, "Cannot relloc *gmsg\n" );
+			exit( 1 );
+		}
+		*gmsg = tmpptr;
+		va_start( args, str );
+		loglen += vsprintf( *gmsg + loglen, str, args );
+		va_end( args );
+
+
+		va_start( args, str );
+		loglen += vsprintf( *gmsg + loglen, str, args );
+		va_end( args );
+		*(*gmsg + loglen) = 0;
+		if( loglen > gmsglen - 100 ) loglen = 0; // tekitou
+#endif
+
+	}
+	else
+	{
+		va_start( args, str );
+		vfprintf( stderr, str, args );
+		va_end( args );
+//		fflush( stderr ); // iru?
+	}
+	return;
+}