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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/Salignmm.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,2532 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 0
+#define DEBUG 0
+#define XXXXXXX    0
+#define USE_PENALTY_EX  1
+#define FASTMATCHCALC 1
+#define MCD 0
+
+
+static TLS float **impmtx = NULL;
+static TLS int impalloclen = 0;
+float imp_match_out_sc( int i1, int j1 )
+{
+//	fprintf( stderr, "imp+match = %f\n", impmtx[i1][j1] * fastathreshold );
+//	fprintf( stderr, "val = %f\n", impmtx[i1][j1] );
+	return( impmtx[i1][j1] );
+}
+
+static void imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int *gapmap2 )
+{
+#if FASTMATCHCALC
+	float *pt = impmtx[i1];
+	int *gapmappt = gapmap2;
+	while( lgth2-- )
+		*imp++ += pt[*gapmappt++];
+#else
+	int j;
+	float *pt = impmtx[i1];
+	for( j=0; j<lgth2; j++ )
+		*imp++ += pt[gapmap2[j]];
+#endif
+}
+
+
+static void imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int *gapmap1 )
+{
+#if FASTMATCHCALC
+	int *gapmappt = gapmap1;
+	while( lgth1-- )
+		*imp++ += impmtx[*gapmappt++][j1];
+#else
+	int i;
+	for( i=0; i<lgth1; i++ )
+		*imp++ += impmtx[gapmap1[i]][j1];
+#endif
+}
+
+static void imp_match_out_vead( float *imp, int i1, int lgth2 )
+{
+#if FASTMATCHCALC 
+	float *pt = impmtx[i1];
+	while( lgth2-- )
+		*imp++ += *pt++;
+#else
+	int j;
+	float *pt = impmtx[i1];
+	for( j=0; j<lgth2; j++ )
+		*imp++ += pt[j];
+#endif
+}
+static void imp_match_out_vead_tate( float *imp, int j1, int lgth1 )
+{
+	int i;
+	for( i=0; i<lgth1; i++ )
+		*imp++ += impmtx[i][j1];
+}
+
+void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *pair )
+{
+	foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, pair );
+}
+
+void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore )
+{
+	int i, j, k1, k2, tmpint, start1, start2, end1, end2;
+	float effij;
+	float effij_kozo;
+	double effijx;
+	char *pt, *pt1, *pt2;
+	static TLS char *nocount1 = NULL;
+	static TLS char *nocount2 = NULL;
+	LocalHom *tmpptr;
+
+	if( seq1 == NULL )
+	{
+		if( impmtx ) FreeFloatMtx( impmtx );
+		impmtx = NULL;
+		if( nocount1 ) free( nocount1 );
+		nocount1 = NULL;
+		if( nocount2 ) free( nocount2 );
+		nocount2 = NULL;
+		
+		return;
+	}
+
+	if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+	{
+		if( impmtx ) FreeFloatMtx( impmtx );
+		if( nocount1 ) free( nocount1 );
+		if( nocount2 ) free( nocount2 );
+		impalloclen = MAX( lgth1, lgth2 ) + 2;
+		impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+		nocount1 = AllocateCharVec( impalloclen );
+		nocount2 = AllocateCharVec( impalloclen );
+	}
+
+	for( i=0; i<lgth1; i++ )
+	{
+		for( j=0; j<clus1; j++ )
+			if( seq1[j][i] == '-' ) break;
+		if( j != clus1 ) nocount1[i] = 1; 
+		else			 nocount1[i] = 0;
+	}
+	for( i=0; i<lgth2; i++ )
+	{
+		for( j=0; j<clus2; j++ )
+			if( seq2[j][i] == '-' ) break;
+		if( j != clus2 ) nocount2[i] = 1;
+		else			 nocount2[i] = 0;
+	}
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+	fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+
+
+#if 0
+	fprintf( stderr, "eff1 in _init_strict = \n" );
+	for( i=0; i<clus1; i++ )
+		fprintf( stderr, "eff1[] = %f\n", eff1[i] );
+	for( i=0; i<clus2; i++ )
+		fprintf( stderr, "eff2[] = %f\n", eff2[i] );
+#endif
+
+	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+		impmtx[i][j] = 0.0;
+	effijx =  fastathreshold;
+	for( i=0; i<clus1; i++ )
+	{
+		for( j=0; j<clus2; j++ )
+		{
+			effij = (float)( eff1[i] * eff2[j] * effijx );
+			effij_kozo = (float)( eff1_kozo[i] * eff2_kozo[j] * effijx );
+			tmpptr = localhom[i][j];
+			while( tmpptr )
+			{
+//				fprintf( stderr, "start1 = %d\n", tmpptr->start1 );
+//				fprintf( stderr, "end1   = %d\n", tmpptr->end1   );
+//				fprintf( stderr, "i = %d, seq1 = \n%s\n", i, seq1[i] );
+//				fprintf( stderr, "j = %d, seq2 = \n%s\n", j, seq2[j] );
+				pt = seq1[i];
+				tmpint = -1;
+				while( *pt != 0 )
+				{
+					if( *pt++ != '-' ) tmpint++;
+					if( tmpint == tmpptr->start1 ) break;
+				}
+				start1 = pt - seq1[i] - 1;
+	
+				if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+				else
+				{
+#if MACHIGAI
+					while( *pt != 0 )
+					{
+//						fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+						if( tmpint == tmpptr->end1 ) break;
+						if( *pt++ != '-' ) tmpint++;
+					}
+					end1 = pt - seq1[i] - 0;
+#else
+					while( *pt != 0 )
+					{
+//						fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, tmpptr->end1, pt-seq1[i] );
+						if( *pt++ != '-' ) tmpint++;
+						if( tmpint == tmpptr->end1 ) break;
+					}
+					end1 = pt - seq1[i] - 1;
+#endif
+				}
+	
+				pt = seq2[j];
+				tmpint = -1;
+				while( *pt != 0 )
+				{
+					if( *pt++ != '-' ) tmpint++;
+					if( tmpint == tmpptr->start2 ) break;
+				}
+				start2 = pt - seq2[j] - 1;
+				if( tmpptr->start2 == tmpptr->end2 ) end2 = start2;
+				else
+				{
+#if MACHIGAI
+					while( *pt != 0 )
+					{
+						if( tmpint == tmpptr->end2 ) break;
+						if( *pt++ != '-' ) tmpint++;
+					}
+					end2 = pt - seq2[j] - 0;
+#else
+					while( *pt != 0 )
+					{
+						if( *pt++ != '-' ) tmpint++;
+						if( tmpint == tmpptr->end2 ) break;
+					}
+					end2 = pt - seq2[j] - 1;
+#endif
+				}
+//				fprintf( stderr, "start1 = %d (%c), end1 = %d (%c), start2 = %d (%c), end2 = %d (%c)\n", start1, seq1[i][start1], end1, seq1[i][end1], start2, seq2[j][start2], end2, seq2[j][end2] );
+//				fprintf( stderr, "step 0\n" );
+				if( end1 - start1 != end2 - start2 )
+				{
+//					fprintf( stderr, "CHUUI!!, start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+				}
+
+#if 1
+				k1 = start1; k2 = start2;
+				pt1 = seq1[i] + k1;
+				pt2 = seq2[j] + k2;
+				while( *pt1 && *pt2 )
+				{
+					if( *pt1 != '-' && *pt2 != '-' )
+					{
+// 重みを二重にかけないように注意して下さい。
+//						impmtx[k1][k2] += tmpptr->wimportance * fastathreshold;
+//						impmtx[k1][k2] += tmpptr->importance * effij;
+//						impmtx[k1][k2] += tmpptr->fimportance * effij;
+						if( tmpptr->korh == 'k' )
+							impmtx[k1][k2] += tmpptr->fimportance * effij_kozo;
+						else
+							impmtx[k1][k2] += tmpptr->fimportance * effij;
+							
+//						fprintf( stderr, "#### impmtx[k1][k2] = %f, tmpptr->fimportance=%f, effij=%f\n", impmtx[k1][k2], tmpptr->fimportance, effij );
+//						fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+//						fprintf( stderr, "%d (%c) - %d (%c)  - %f\n", k1, *pt1, k2, *pt2, tmpptr->fimportance * effij );
+						k1++; k2++;
+						pt1++; pt2++;
+					}
+					else if( *pt1 != '-' && *pt2 == '-' )
+					{
+//						fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+						k2++; pt2++;
+					}
+					else if( *pt1 == '-' && *pt2 != '-' )
+					{
+//						fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+						k1++; pt1++;
+					}
+					else if( *pt1 == '-' && *pt2 == '-' )
+					{
+//						fprintf( stderr, "skip, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+						k1++; pt1++;
+						k2++; pt2++;
+					}
+					if( k1 > end1 || k2 > end2 ) break;
+				}
+#else
+				while( k1 <= end1 && k2 <= end2 )
+				{
+					fprintf( stderr, "k1,k2=%d,%d - ", k1, k2 );
+					if( !nocount1[k1] && !nocount2[k2] )
+					{
+						impmtx[k1][k2] += tmpptr->wimportance * eff1[i] * eff2[j]  * fastathreshold;
+						fprintf( stderr, "marked\n" );
+					}
+					else
+						fprintf( stderr, "no count\n" );
+					k1++; k2++;
+				}
+#endif
+				tmpptr = tmpptr->next;
+			}
+		}
+	}
+
+#if 0
+	if( clus1 == 1 && clus2 == 1 )
+	{
+		fprintf( stderr, "writing impmtx\n" );
+		fprintf( stderr, "\n" );
+		fprintf( stderr, "seq1[0] =  %s\n", seq1[0] );
+		fprintf( stderr, "seq2[0] =  %s\n", seq2[0] );
+		fprintf( stderr, "impmtx = \n" );
+		for( k2=0; k2<lgth2; k2++ )
+			fprintf( stderr, "%6.3f ", (double)k2 );
+		fprintf( stderr, "\n" );
+		for( k1=0; k1<lgth1; k1++ )
+		{
+			fprintf( stderr, "%d ", k1 );
+			for( k2=0; k2<30; k2++ )
+				fprintf( stderr, "%2.1f ", impmtx[k1][k2] );
+			fprintf( stderr, "\n" );
+		}
+//		exit( 1 );
+	}
+#endif
+}
+
+#if 0
+void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom )
+{
+	int dif, i, j, k1, k2, tmpint, start1, start2, end1, end2;
+	static TLS int impalloclen = 0;
+	char *pt;
+	int allgap;
+	static TLS char *nocount1 = NULL;
+	static TLS char *nocount2 = NULL;
+
+	if( impalloclen < lgth1 + 2 || impalloclen < lgth2 + 2 )
+	{
+		if( impmtx ) FreeFloatMtx( impmtx );
+		if( nocount1 ) free( nocount1 );
+		if( nocount2 ) free( nocount2 );
+		impalloclen = MAX( lgth1, lgth2 ) + 2;
+		impmtx = AllocateFloatMtx( impalloclen, impalloclen );
+		nocount1 = AllocateCharVec( impalloclen );
+		nocount2 = AllocateCharVec( impalloclen );
+	}
+
+	for( i=0; i<lgth1; i++ )
+	{
+		for( j=0; j<clus1; j++ )
+			if( seq1[j][i] == '-' ) break;
+		if( j != clus1 ) nocount1[i] = 1; 
+		else			 nocount1[i] = 0;
+	}
+	for( i=0; i<lgth2; i++ )
+	{
+		for( j=0; j<clus2; j++ )
+			if( seq2[j][i] == '-' ) break;
+		if( j != clus2 ) nocount2[i] = 1;
+		else			 nocount2[i] = 0;
+	}
+
+#if 0
+fprintf( stderr, "nocount2 =\n" );
+for( i = 0; i<impalloclen; i++ )
+{
+	fprintf( stderr, "nocount2[%d] = %d (%c)\n", i, nocount2[i], seq2[0][i] );
+}
+#endif
+
+	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
+		impmtx[i][j] = 0;
+	for( i=0; i<clus1; i++ )
+	{
+		fprintf( stderr, "i = %d, seq1 = %s\n", i, seq1[i] );
+		for( j=0; j<clus2; j++ )
+		{
+			fprintf( stderr, "start1 = %d\n", localhom[i][j]->start1 );
+			fprintf( stderr, "end1   = %d\n", localhom[i][j]->end1   );
+			fprintf( stderr, "j = %d, seq2 = %s\n", j, seq2[j] );
+			pt = seq1[i];
+			tmpint = -1;
+			while( *pt != 0 )
+			{
+				if( *pt++ != '-' ) tmpint++;
+				if( tmpint == localhom[i][j]->start1 ) break;
+			}
+			start1 = pt - seq1[i] - 1;
+
+			while( *pt != 0 )
+			{
+//				fprintf( stderr, "tmpint = %d, end1 = %d pos = %d\n", tmpint, localhom[i][j].end1, pt-seq1[i] );
+				if( *pt++ != '-' ) tmpint++;
+				if( tmpint == localhom[i][j]->end1 ) break;
+			}
+			end1 = pt - seq1[i] - 1;
+
+			pt = seq2[j];
+			tmpint = -1;
+			while( *pt != 0 )
+			{
+				if( *pt++ != '-' ) tmpint++;
+				if( tmpint == localhom[i][j]->start2 ) break;
+			}
+			start2 = pt - seq2[j] - 1;
+			while( *pt != 0 )
+			{
+				if( *pt++ != '-' ) tmpint++;
+				if( tmpint == localhom[i][j]->end2 ) break;
+			}
+			end2 = pt - seq2[j] - 1;
+//			fprintf( stderr, "start1 = %d, end1 = %d, start2 = %d, end2 = %d\n", start1, end1, start2, end2 );
+			k1 = start1;
+			k2 = start2;
+			fprintf( stderr, "step 0\n" );
+			while( k1 <= end1 && k2 <= end2 )
+			{
+#if 0
+				if( !nocount1[k1] && !nocount2[k2] )
+					impmtx[k1][k2] += localhom[i][j].wimportance * eff1[i] * eff2[j];
+				k1++; k2++;
+#else
+				if( !nocount1[k1] && !nocount2[k2] )
+					impmtx[k1][k2] += localhom[i][j]->wimportance * eff1[i] * eff2[j];
+				k1++; k2++;
+#endif
+			}
+
+			dif = ( end1 - start1 ) - ( end2 - start2 );
+			fprintf( stderr, "dif = %d\n", dif );
+			if( dif > 0 )
+			{
+				do
+				{
+					fprintf( stderr, "dif = %d\n", dif );
+					k1 = start1;
+					k2 = start2 - dif;
+					while( k1 <= end1 && k2 <= end2 )
+					{
+						if( 0 <= k2 && start2 <= k2 && !nocount1[k1] && !nocount2[k2] )
+							impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+						k1++; k2++;
+					}
+				}
+				while( dif-- );
+			}
+			else
+			{
+				do
+				{
+					k1 = start1 + dif;
+					k2 = start2;
+					while( k1 <= end1 )
+					{
+						if( k1 >= 0 && k1 >= start1 && !nocount1[k1] && !nocount2[k2] )
+							impmtx[k1][k2] = localhom[i][j]->wimportance * eff1[i] * eff2[j];
+						k1++; k2++;
+					}
+				}
+				while( dif++ );
+			}
+		}
+	}
+#if 0
+	fprintf( stderr, "impmtx = \n" );
+	for( k2=0; k2<lgth2; k2++ )
+		fprintf( stderr, "%6.3f ", (double)k2 );
+	fprintf( stderr, "\n" );
+	for( k1=0; k1<lgth1; k1++ )
+	{
+		fprintf( stderr, "%d", k1 );
+		for( k2=0; k2<lgth2; k2++ )
+			fprintf( stderr, "%6.3f ", impmtx[k1][k2] );
+		fprintf( stderr, "\n" );
+	}
+#endif
+}
+#endif
+
+#if MCD
+static void match_calc_dynamicmtx( double **pairoffset, double **n_dynamicmtx, float *match, int n1, char **seq1, double *eff1, int n2, char **seq2, double *eff2, int i1, int lgth2, float **floatwork, int **intwork, int initialize, int flip ) 
+{
+// osoi!
+	int i, j, k;
+	int c1, c2;
+	double po;
+//	fprintf( stderr, "\nmatch_calc_dynamicmtx... %d", i1 );
+//	fprintf( stderr, "\nseq1[0]=%s\n", seq1[0] );
+//	fprintf( stderr, "\nseq2[0]=%s\n", seq2[0] );
+	for( k=0; k<lgth2; k++ )
+	{
+		match[k] = 0.0;
+		for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
+		{
+			if( flip ) po = pairoffset[j][i];
+			else       po = pairoffset[i][j];
+//			if( k==0 ) fprintf( stderr, "pairoffset[%d][%d] = %f\n", i, j, po );
+			c1 = amino_n[(int)seq1[i][i1]];
+			c2 = amino_n[(int)seq2[j][k]];
+			if( seq1[i][i1] == '-' || seq2[j][k] == '-' ) continue;
+			if( c1 < 0 || c2 < 0 ) continue;
+//			fprintf( stderr, "c1=%d, c2=%d\n", c1, c2 );
+			if( flip ) 
+				match[k] += ( n_dynamicmtx[c1][c2] + po * 600 ) * eff1[i] * eff2[j];
+			else
+				match[k] += ( n_dynamicmtx[c1][c2] + po * 600 ) * eff1[i] * eff2[j];
+//			fprintf( stderr, "match[k] = %f\n", match[k] );
+//			fprintf( stderr, "pairoffset[i][j] = %f\n", pairoffset[i][j] );
+		}
+	}
+//	fprintf( stderr, "done\n" );
+	return;
+}
+#endif
+
+static void fillzero( float *s, int l )
+{
+	while( l-- ) *s++ = 0.0;
+}
+
+static void match_calc_add( double **scoreingmtx, float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+//	fprintf( stderr, "\nmatch_calc... %d", i1 );
+	int j, l;
+//	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+	int *cpmxpdnpt, **cpmxpdnptpt;
+	float *scarr;
+	scarr = calloc( nalphabets, sizeof( float ) );
+	if( initialize )
+	{
+		int count = 0;
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<nalphabets; l++ )
+			{
+				if( cpmx2[l][j] )
+				{
+					cpmxpd[j][count] = cpmx2[l][j];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	{
+		for( l=0; l<nalphabets; l++ )
+		{
+			scarr[l] = 0.0;
+			for( j=0; j<nalphabets; j++ )
+//				scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+//				scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+				scarr[l] += scoreingmtx[j][l] * cpmx1[j][i1];
+		}
+		matchpt = match;
+		cpmxpdnptpt = cpmxpdn;
+		cpmxpdptpt = cpmxpd;
+		while( lgth2-- )
+		{
+//			*matchpt = 0.0;
+			cpmxpdnpt = *cpmxpdnptpt++;
+			cpmxpdpt = *cpmxpdptpt++;
+			while( *cpmxpdnpt>-1 )
+				*matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+			matchpt++;
+		} 
+	}
+	free( scarr );
+//	fprintf( stderr, "done\n" );
+#else
+	int j, k, l;
+//	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	float *scarr;
+	scarr = calloc( nalphabets, sizeof( float ) );
+// simple
+	if( initialize )
+	{
+		int count = 0;
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<nalphabets; l++ )
+			{
+				if( cpmx2[l][j] )
+				{
+					cpmxpd[count][j] = cpmx2[l][j];
+					cpmxpdn[count][j] = l;
+					count++;
+				}
+			}
+			cpmxpdn[count][j] = -1;
+		}
+	}
+	for( l=0; l<nalphabets; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<nalphabets; k++ )
+//			scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+//			scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+			scarr[l] += scoreingmtx[k][l] * cpmx1[k][i1];
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		match[j] = 0.0;
+		for( k=0; cpmxpdn[k][j]>-1; k++ )
+			match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+	} 
+	free( scarr );
+#endif
+}
+static void match_calc( double **n_dynamicmtx, float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+//	fprintf( stderr, "\nmatch_calc... %d", i1 );
+	int j, l;
+//	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+	int *cpmxpdnpt, **cpmxpdnptpt;
+	float *scarr;
+	scarr = calloc( nalphabets, sizeof( float ) );
+	if( initialize )
+	{
+		int count = 0;
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<nalphabets; l++ )
+			{
+				if( cpmx2[l][j] )
+				{
+					cpmxpd[j][count] = cpmx2[l][j];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	{
+		for( l=0; l<nalphabets; l++ )
+		{
+			scarr[l] = 0.0;
+			for( j=0; j<nalphabets; j++ )
+//				scarr[l] += n_dis[j][l] * cpmx1[j][i1];
+//				scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+				scarr[l] += n_dynamicmtx[j][l] * cpmx1[j][i1];
+		}
+		matchpt = match;
+		cpmxpdnptpt = cpmxpdn;
+		cpmxpdptpt = cpmxpd;
+		while( lgth2-- )
+		{
+			*matchpt = 0.0;
+			cpmxpdnpt = *cpmxpdnptpt++;
+			cpmxpdpt = *cpmxpdptpt++;
+			while( *cpmxpdnpt>-1 )
+				*matchpt += scarr[*cpmxpdnpt++] * *cpmxpdpt++;
+			matchpt++;
+		} 
+	}
+	free( scarr );
+//	fprintf( stderr, "done\n" );
+#else
+	int j, k, l;
+//	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	float *scarr;
+	scarr = calloc( nalphabets, sizeof( float ) );
+// simple
+	if( initialize )
+	{
+		int count = 0;
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<nalphabets; l++ )
+			{
+				if( cpmx2[l][j] )
+				{
+					cpmxpd[count][j] = cpmx2[l][j];
+					cpmxpdn[count][j] = l;
+					count++;
+				}
+			}
+			cpmxpdn[count][j] = -1;
+		}
+	}
+	for( l=0; l<nalphabets; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<nalphabets; k++ )
+//			scarr[l] += n_dis[k][l] * cpmx1[k][i1];
+//			scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+			scarr[l] += n_dynamicmtx[k][l] * cpmx1[k][i1];
+	}
+	for( j=0; j<lgth2; j++ )
+	{
+		match[j] = 0.0;
+		for( k=0; cpmxpdn[k][j]>-1; k++ )
+			match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
+	} 
+	free( scarr );
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw, 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        int **ijp, int icyc, int jcyc,
+						int *warpis, int *warpjs, int warpbase )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+	float wm;
+	char *gaptable1, *gt1bk;
+	char *gaptable2, *gt2bk;
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+	gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+	gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+	{
+		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+	}
+#endif
+ 
+	if( outgap == 1 )
+		;
+	else
+	{
+		wm = lastverticalw[0];
+		for( i=0; i<lgth1; i++ )
+		{
+			if( lastverticalw[i] >= wm )
+			{
+				wm = lastverticalw[i];
+				iin = i; jin = lgth2-1;
+				ijp[lgth1][lgth2] = +( lgth1 - i );
+			}
+		}
+		for( j=0; j<lgth2; j++ )
+		{
+			if( lasthorizontalw[j] >= wm )
+			{
+				wm = lasthorizontalw[j];
+				iin = lgth1-1; jin = j;
+				ijp[lgth1][lgth2] = -( lgth2 - j );
+			}
+		}
+	}
+
+    for( i=0; i<lgth1+1; i++ ) 
+    {
+        ijp[i][0] = i + 1;
+    }
+    for( j=0; j<lgth2+1; j++ ) 
+    {
+        ijp[0][j] = -( j + 1 );
+    }
+
+	gaptable1 = gt1bk + lgth1+lgth2;
+	*gaptable1 = 0;
+	gaptable2 = gt2bk + lgth1+lgth2;
+	*gaptable2 = 0;
+
+	iin = lgth1; jin = lgth2;
+	limk = lgth1+lgth2 + 1;
+	*impwmpt = 0.0;
+	for( k=0; k<limk; k++ ) 
+	{
+		if( ijp[iin][jin] >= warpbase )
+		{
+			ifi = warpis[ijp[iin][jin]-warpbase];
+			jfi = warpjs[ijp[iin][jin]-warpbase];
+		}
+		else if( ijp[iin][jin] < 0 ) 
+		{
+			ifi = iin-1; jfi = jin+ijp[iin][jin];
+		}
+		else if( ijp[iin][jin] > 0 )
+		{
+			ifi = iin-ijp[iin][jin]; jfi = jin-1;
+		}
+		else
+		{
+			ifi = iin-1; jfi = jin-1;
+		}
+		if( ifi == -warpbase && jfi == -warpbase )
+		{
+			l = iin;
+			while( --l >= 0 )
+			{
+				*--gaptable1 = 'o';
+				*--gaptable2 = '-';
+				k++;
+			}
+			l= jin;
+			while( --l >= 0 )
+			{
+				*--gaptable1 = '-';
+				*--gaptable2 = 'o';
+			}
+			break;
+		}
+		else
+		{
+			l = iin - ifi;
+			while( --l ) 
+			{
+				*--gaptable1 = 'o';
+				*--gaptable2 = '-';
+				k++;
+			}
+			l= jin - jfi;
+			while( --l )
+			{
+				*--gaptable1 = '-';
+				*--gaptable2 = 'o';
+				k++;
+			}
+		}
+		if( iin == lgth1 || jin == lgth2 )
+			;
+		else
+		{
+			*impwmpt += imp_match_out_sc( iin, jin );
+
+//		fprintf( stderr, "impwm = %f (iin=%d, jin=%d) seq1=%c, seq2=%c\n", *impwmpt, iin, jin, seq1[0][iin], seq2[0][jin] );
+		}
+		if( iin <= 0 || jin <= 0 ) break;
+		*--gaptable1 = 'o';
+		*--gaptable2 = 'o';
+		k++;
+		iin = ifi; jin = jfi;
+	}
+
+	for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+	for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+	free( gt1bk );
+	free( gt2bk );
+}
+
+static float Atracking( float *lasthorizontalw, float *lastverticalw, 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        int **ijp, int icyc, int jcyc,
+						int tailgp,
+						int *warpis, int *warpjs, int warpbase )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, limk;
+	float wm;
+	char *gaptable1, *gt1bk;
+	char *gaptable2, *gt2bk;
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+	gt1bk = AllocateCharVec( lgth1+lgth2+1 );
+	gt2bk = AllocateCharVec( lgth1+lgth2+1 );
+
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+	{
+		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+	}
+#endif
+ 
+	if( tailgp == 1 )
+		;
+	else
+	{
+		wm = lastverticalw[0];
+		for( i=0; i<lgth1; i++ )
+		{
+			if( lastverticalw[i] >= wm )
+			{
+				wm = lastverticalw[i];
+				iin = i; jin = lgth2-1;
+				ijp[lgth1][lgth2] = +( lgth1 - i );
+			}
+		}
+		for( j=0; j<lgth2; j++ )
+		{
+			if( lasthorizontalw[j] >= wm )
+			{
+				wm = lasthorizontalw[j];
+				iin = lgth1-1; jin = j;
+				ijp[lgth1][lgth2] = -( lgth2 - j );
+			}
+		}
+	}
+
+    for( i=0; i<lgth1+1; i++ ) 
+    {
+        ijp[i][0] = i + 1;
+    }
+    for( j=0; j<lgth2+1; j++ ) 
+    {
+        ijp[0][j] = -( j + 1 );
+    }
+
+	gaptable1 = gt1bk + lgth1+lgth2;
+	*gaptable1 = 0;
+	gaptable2 = gt2bk + lgth1+lgth2;
+	*gaptable2 = 0;
+
+	iin = lgth1; jin = lgth2;
+	limk = lgth1+lgth2 + 1;
+	for( k=0; k<limk; k++ ) 
+	{
+		if( ijp[iin][jin] >= warpbase )
+		{
+			ifi = warpis[ijp[iin][jin]-warpbase];
+			jfi = warpjs[ijp[iin][jin]-warpbase];
+		}
+		else if( ijp[iin][jin] < 0 ) 
+		{
+			ifi = iin-1; jfi = jin+ijp[iin][jin];
+		}
+		else if( ijp[iin][jin] > 0 )
+		{
+			ifi = iin-ijp[iin][jin]; jfi = jin-1;
+		}
+		else
+		{
+			ifi = iin-1; jfi = jin-1;
+		}
+
+		if( ifi == -warpbase && jfi == -warpbase )
+		{
+			l = iin;
+			while( --l >= 0 )
+			{
+				*--gaptable1 = 'o';
+				*--gaptable2 = '-';
+				k++;
+			}
+			l= jin;
+			while( --l >= 0 )
+			{
+				*--gaptable1 = '-';
+				*--gaptable2 = 'o';
+			}
+			break;
+		}
+		else
+		{
+			l = iin - ifi;
+			while( --l ) 
+			{
+				*--gaptable1 = 'o';
+				*--gaptable2 = '-';
+				k++;
+			}
+			l= jin - jfi;
+			while( --l )
+			{
+				*--gaptable1 = '-';
+				*--gaptable2 = 'o';
+				k++;
+			}
+		}
+		if( iin <= 0 || jin <= 0 ) break;
+		*--gaptable1 = 'o';
+		*--gaptable2 = 'o';
+		k++;
+		iin = ifi; jin = jfi;
+	}
+
+	for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i], gaptable1 );
+	for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j], gaptable2 );
+
+	free( gt1bk );
+	free( gt2bk );
+
+	return( 0.0 );
+}
+
+float A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	register int i, j;
+	int lasti, lastj;      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+	int lgth1, lgth2;
+	int resultlen;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+//	float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+	float *wtmp;
+	int *ijppt;
+	float *mjpt, *prept, *curpt;
+	int *mpjpt;
+#endif
+	static TLS float mi, *m;
+	static TLS int **ijp;
+	static TLS int mpi, *mp;
+	static TLS float *w1, *w2;
+	static TLS float *match;
+	static TLS float *initverticalw;    /* kufuu sureba iranai */
+	static TLS float *lastverticalw;    /* kufuu sureba iranai */
+	static TLS char **mseq1;
+	static TLS char **mseq2;
+	static TLS char **mseq;
+	static TLS float *ogcp1;
+	static TLS float *ogcp2;
+	static TLS float *fgcp1;
+	static TLS float *fgcp2;
+	static TLS float **cpmx1;
+	static TLS float **cpmx2;
+	static TLS int **intwork;
+	static TLS float **floatwork;
+	static TLS int orlgth1 = 0, orlgth2 = 0;
+	static TLS float *gapfreq1;
+	static TLS float *gapfreq2;
+	float fpenalty = (float)penalty;
+	float fpenalty_shift = (float)penalty_shift;
+	float *fgcp2pt;
+	float *ogcp2pt;
+	float fgcp1va;
+	float ogcp1va;
+	float *gf2pt;
+	float *gf2ptpre;
+	float gf1va;
+	float gf1vapre;
+	float headgapfreq1;
+	float headgapfreq2;
+
+	int *warpis = NULL;
+	int *warpjs = NULL;
+	int *warpi = NULL;
+	int *warpj = NULL;
+	int *prevwarpi = NULL;
+	int *prevwarpj = NULL;
+	float *wmrecords = NULL;
+	float *prevwmrecords = NULL;
+	int warpn = 0;
+	int warpbase;
+	float curm = 0.0;
+	float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+	int *warpipt, *warpjpt;
+
+
+	if( seq1 == NULL )
+	{
+		if( orlgth1 )
+		{
+//			fprintf( stderr, "## Freeing local arrays in A__align\n" );
+			orlgth1 = 0;
+			orlgth2 = 0;
+
+			imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+
+			free( mseq1 );
+			free( mseq2 );
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+
+			FreeCharMtx( mseq );
+
+			FreeFloatVec( ogcp1 );
+			FreeFloatVec( ogcp2 );
+			FreeFloatVec( fgcp1 );
+			FreeFloatVec( fgcp2 );
+
+
+			FreeFloatMtx( cpmx1 );
+			FreeFloatMtx( cpmx2 );
+
+			FreeFloatVec( gapfreq1 );
+			FreeFloatVec( gapfreq2 );
+
+			FreeFloatMtx( floatwork );
+			FreeIntMtx( intwork );
+
+		}
+		else
+		{
+//			fprintf( stderr, "## Not allocated\n" );
+		}
+		return( 0.0 );
+	}
+
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+#if 0
+	if( lgth1 == 0 || lgth2 == 0 )
+	{
+		fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+	}
+#endif
+	if( lgth1 == 0 && lgth2 == 0 )
+		return( 0.0 );
+
+	if( lgth1 == 0 )
+	{
+		for( i=0; i<icyc; i++ )
+		{
+			j = lgth2;
+			seq1[i][j] = 0;
+			while( j ) seq1[i][--j] = *newgapstr;
+//			fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+		}
+		return( 0.0 );
+	}
+
+	if( lgth2 == 0 )
+	{
+		for( i=0; i<jcyc; i++ )
+		{
+			j = lgth1;
+			seq2[i][j] = 0;
+			while( j ) seq2[i][--j] = *newgapstr;
+//			fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+		}
+		return( 0.0 );
+	}
+
+	warpbase = lgth1 + lgth2;
+	warpis = NULL;
+	warpjs = NULL;
+	warpn = 0;
+
+
+
+	if( trywarp )
+	{
+//		fprintf( stderr, "IN A__align, penalty_shift = %d\n", penalty_shift );
+		if( headgp == 0 || tailgp == 0 )
+		{
+			fprintf( stderr, "At present, headgp and tailgp must be 1 to allow shift.\n" );
+			exit( 1 );
+		}
+		wmrecords = AllocateFloatVec( lgth2+1 );
+		warpi = AllocateIntVec( lgth2+1 );
+		warpj = AllocateIntVec( lgth2+1 );
+		prevwmrecords = AllocateFloatVec( lgth2+1 );
+		prevwarpi = AllocateIntVec( lgth2+1 );
+		prevwarpj = AllocateIntVec( lgth2+1 );
+		for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
+		for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
+		for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
+		for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
+		for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
+		for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
+	}
+
+
+#if 0
+	fprintf( stderr, "####  eff in SA+++align\n" );
+	fprintf( stderr, "####  seq1[0] = %s\n", seq1[0] );
+	fprintf( stderr, "####  strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+	fprintf( stderr, "####  seq2[0] = %s\n", seq2[0] );
+	fprintf( stderr, "####  strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
+	for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
+#endif
+	if( orlgth1 == 0 )
+	{
+		mseq1 = AllocateCharMtx( njob, 0 );
+		mseq2 = AllocateCharMtx( njob, 0 );
+	}
+
+
+
+	if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+	{
+		int ll1, ll2;
+
+
+		if( orlgth1 > 0 && orlgth2 > 0 )
+		{
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+
+			FreeCharMtx( mseq );
+
+			FreeFloatVec( ogcp1 );
+			FreeFloatVec( ogcp2 );
+			FreeFloatVec( fgcp1 );
+			FreeFloatVec( fgcp2 );
+
+
+			FreeFloatMtx( cpmx1 );
+			FreeFloatMtx( cpmx2 );
+
+			FreeFloatVec( gapfreq1 );
+			FreeFloatVec( gapfreq2 );
+
+			FreeFloatMtx( floatwork );
+			FreeIntMtx( intwork );
+		}
+
+		ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+		ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+		fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+		w1 = AllocateFloatVec( ll2+2 );
+		w2 = AllocateFloatVec( ll2+2 );
+		match = AllocateFloatVec( ll2+2 );
+
+		initverticalw = AllocateFloatVec( ll1+2 );
+		lastverticalw = AllocateFloatVec( ll1+2 );
+
+		m = AllocateFloatVec( ll2+2 );
+		mp = AllocateIntVec( ll2+2 );
+
+		mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+		ogcp1 = AllocateFloatVec( ll1+2 );
+		ogcp2 = AllocateFloatVec( ll2+2 );
+		fgcp1 = AllocateFloatVec( ll1+2 );
+		fgcp2 = AllocateFloatVec( ll2+2 );
+
+		cpmx1 = AllocateFloatMtx( nalphabets, ll1+2 );
+		cpmx2 = AllocateFloatMtx( nalphabets, ll2+2 );
+
+		gapfreq1 = AllocateFloatVec( ll1+2 );
+		gapfreq2 = AllocateFloatVec( ll2+2 );
+
+#if FASTMATCHCALC
+		floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets ); 
+		intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets+1 ); 
+#else
+		floatwork = AllocateFloatMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+		intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
+#endif
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n" );
+#endif
+
+		orlgth1 = ll1 - 100;
+		orlgth2 = ll2 - 100;
+	}
+
+
+	for( i=0; i<icyc; i++ )
+	{
+		mseq1[i] = mseq[i];
+		seq1[i][lgth1] = 0;
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		mseq2[j] = mseq[icyc+j];
+		seq2[j][lgth2] = 0;
+	}
+
+
+	if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+	{
+		int ll1, ll2;
+
+		if( commonAlloc1 && commonAlloc2 )
+		{
+			FreeIntMtx( commonIP );
+		}
+
+		ll1 = MAX( orlgth1, commonAlloc1 );
+		ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+		fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+		commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n\n" );
+#endif
+
+		commonAlloc1 = ll1;
+		commonAlloc2 = ll2;
+	}
+	ijp = commonIP;
+
+#if 0
+	{
+		float t = 0.0;
+		for( i=0; i<icyc; i++ )
+			t += eff1[i];
+	fprintf( stderr, "## totaleff = %f\n", t );
+	}
+#endif
+
+	cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+	cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+	if( sgap1 )
+	{
+		new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+		new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+		new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
+		new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+		outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
+		outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
+		outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
+		outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
+	}
+	else
+	{
+		st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+		st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+		st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+		st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+		headgapfreq1 = 0.0;
+		headgapfreq2 = 0.0;
+		gapfreq1[lgth1] = 0.0;
+		gapfreq2[lgth2] = 0.0;
+	}
+
+	if( legacygapcost == 0 )
+	{
+		gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
+		gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
+		for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
+		for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
+		headgapfreq1 = 1.0 - headgapfreq1;
+		headgapfreq2 = 1.0 - headgapfreq2;
+	}
+	else
+	{
+		for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
+		for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
+		headgapfreq1 = 1.0;
+		headgapfreq2 = 1.0;
+	}
+
+#if 0
+	fprintf( stderr, "\ngapfreq1[] =" );
+	for( i=0; i<lgth1; i++ ) fprintf( stderr, "%5.2f ", gapfreq1[i] );
+	fprintf( stderr, "\n" );
+
+	fprintf( stderr, "\ngapfreq2[] =" );
+	for( i=0; i<lgth2; i++ ) fprintf( stderr, "%5.2f ", gapfreq2[i] );
+	fprintf( stderr, "\n" );
+#endif
+	
+
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
+		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
+	}
+
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
+		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
+	}
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc( n_dynamicmtx, initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+	if( localhom )
+		imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
+
+	match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+	if( localhom )
+		imp_match_out_vead( currentw, 0, lgth2 ); // 060306
+#if 0 // -> tbfast.c
+	if( localhom )
+		imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+	if( headgp == 1 )
+	{
+		for( i=1; i<lgth1+1; i++ )
+		{
+//			initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+			initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
+		}
+		for( j=1; j<lgth2+1; j++ )
+		{
+//			currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+			currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
+		}
+	}
+#if OUTGAP0TRY
+	else
+	{
+		fprintf( stderr, "offset = %d\n", offset );
+		for( j=1; j<lgth2+1; j++ )
+			currentw[j] -= offset * j / 2.0;
+		for( i=1; i<lgth1+1; i++ )
+			initverticalw[i] -= offset * i / 2.0;
+	}
+#endif
+#if 0
+	fprintf( stderr, "\n   " );
+	for( j=0; j<lgth2+1; j++ ) fprintf( stderr, "    %c ", seq2[0][j] );
+	fprintf( stderr, "\n%c ", seq1[0][0]  );
+	for( j=0; j<lgth2+1; j++ )
+	{
+		fprintf( stderr, "%5.0f ", currentw[j] );
+	}
+	fprintf( stderr, "\n"  );
+#endif
+
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+//		m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+		m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
+	}
+	if( lgth2 == 0 )
+		lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+	else
+		lastverticalw[0] = currentw[lgth2-1];
+
+	if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+	lastj = lgth2+1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+	fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+	fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ ) 
+	fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ ) 
+	fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+	for( i=1; i<lasti; i++ )
+	{
+
+#ifdef enablemultithread
+//		fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+		if( chudanpt && *chudanpt != chudanref ) 
+		{
+//			fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+			*chudanres = 1;
+			return( -1.0 );
+		}
+#endif
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, i, lgth2, floatwork, intwork, 0 );
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+	fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+		if( localhom )
+		{
+//			fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if  0
+			imp_match_out_vead( currentw, i, lgth2 );
+#else
+			imp_match_out_vead( currentw, i, lgth2 );
+#endif
+		}
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+	fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+		currentw[0] = initverticalw[i];
+
+#if 0
+		fprintf( stderr, "%c ", seq1[0][i] );
+		for( j=0; j<lgth2+1; j++ )
+		{
+			fprintf( stderr, "%5.0f ", currentw[j] );
+		}
+		fprintf( stderr, "\n"  );
+#endif
+	
+//		mi = previousw[0] + ogcp2[1]; mpi = 0;
+		mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
+		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+		fgcp2pt = fgcp2;
+		ogcp2pt = ogcp2 + 1;
+		fgcp1va = fgcp1[i-1];
+		ogcp1va = ogcp1[i];
+		gf1va = gapfreq1[i];
+		gf1vapre = gapfreq1[i-1];
+		gf2pt = gapfreq2+1;
+		gf2ptpre = gapfreq2;
+
+		if( trywarp )
+		{
+			prevwmrecordspt = prevwmrecords;
+			wmrecordspt = wmrecords+1;
+			wmrecords1pt = wmrecords;
+			warpipt = warpi + 1;
+			warpjpt = warpj + 1;
+		}
+
+
+		for( j=1; j<lastj; j++ )
+		{
+#ifdef xxxenablemultithread
+//			fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+			if( chudanpt && *chudanpt != chudanref ) 
+			{
+//				fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+				*chudanres = 1;
+				return( -1.0 );
+			}
+#endif
+			wm = *prept;
+			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "\n i=%d, j=%d %c, %c", i, j, seq1[0][i], seq2[0][j] );
+			fprintf( stderr, "%5.0f->", wm );
+			fprintf( stderr, "%5.0f? (penal=%5.2f)", g=mi+*fgcp2pt*(1.0-gapfreq1[i]), *fgcp2pt*(1.0-gapfreq1[i]) );
+#endif
+			if( (g=mi+*fgcp2pt*gf1va) > wm )
+			{
+				wm = g;
+				*ijppt = -( j - mpi );
+//				fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );
+			}
+			if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+#if 0 
+			fprintf( stderr, "%5.0f->", wm );
+			fprintf( stderr, "%5.0f? (penal=%5.2f)", g=*mjpt+fgcp1va*(1.0-gapfreq2[j]), fgcp1va*(1.0-gapfreq2[j]) );
+#endif
+			if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
+			{
+				wm = g;
+				*ijppt = +( i - *mpjpt );
+//				fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );
+			}
+			if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+
+			if( trywarp )
+			{
+#if USE_PENALTY_EX
+				if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
+#else
+				if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
+#endif
+				{
+//					fprintf( stderr, "WARP!!\n" );
+					if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
+					{
+						*ijppt = warpbase + warpn - 1;
+					}
+					else
+					{
+						*ijppt = warpbase + warpn;
+						warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
+						warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
+						warpis[warpn] = prevwarpi[j-1];
+						warpjs[warpn] = prevwarpj[j-1];
+						warpn++;
+					}
+					wm = g;
+				}
+	
+#if 0
+				fprintf( stderr, "%5.0f ", wm );
+#endif
+				curm = *curpt + wm;
+	
+				if( *wmrecords1pt > *wmrecordspt )
+				{
+					*wmrecordspt = *wmrecords1pt;
+					*warpipt  = *(warpipt-1);
+					*warpjpt  = *(warpjpt-1);
+				}
+				if( curm > *wmrecordspt )
+				{
+					*wmrecordspt = curm;
+					*warpipt = i;
+					*warpjpt = j;
+				}
+				wmrecordspt++;
+				wmrecords1pt++;
+				warpipt++;
+				warpjpt++;
+			}
+
+			*curpt++ += wm;
+			ijppt++;
+			mjpt++;
+			prept++;
+			mpjpt++;
+			fgcp2pt++;
+			ogcp2pt++;
+			gf2ptpre++;
+			gf2pt++;
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+
+		if( trywarp )
+		{
+			fltncpy( prevwmrecords, wmrecords, lastj );
+			intncpy( prevwarpi, warpi, lastj );
+			intncpy( prevwarpj, warpj, lastj );
+		}
+	}
+
+	if( trywarp )
+	{
+//		fprintf( stderr, "wm = %f\n", wm );
+//		fprintf( stderr, "warpn = %d\n", warpn );
+		free( wmrecords );
+		free( prevwmrecords );
+		free( warpi );
+		free( warpj );
+		free( prevwarpi );
+		free( prevwarpj );
+	}
+
+#if OUTGAP0TRY
+	if( !outgap )
+	{
+		for( j=1; j<lgth2+1; j++ )
+			currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+		for( i=1; i<lgth1+1; i++ )
+			lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
+	}
+#endif
+		
+	/*
+	fprintf( stderr, "\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+	fprintf( stderr, "#####\n" );
+	for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+	fprintf( stderr, "====>" );
+	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+	for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+	*/
+	if( localhom )
+	{
+		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
+	}
+	else
+		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase );
+
+	if( warpis ) free( warpis );
+	if( warpjs ) free( warpjs );
+
+//	fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+	resultlen = strlen( mseq1[0] );
+	if( alloclen < resultlen || resultlen > N )
+	{
+		fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+		ErrorExit( "LENGTH OVER!\n" );
+	}
+
+
+	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+	for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+#if 0
+	fprintf( stderr, "\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+	fprintf( stderr, "#####\n" );
+	for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+#endif
+
+//	fprintf( stderr, "wm = %f\n", wm );
+
+	return( wm );
+}
+
+float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+	fprintf( stderr, "Unexpected error.  Please contact [e-mail]\n" );
+	exit( 1 );
+}
+
+
+float A__align_variousdist( double **pairoffset, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+
+//	int k;
+	register int i, j, c;
+	int lasti, lastj;      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */
+	int lgth1, lgth2;
+	int resultlen;
+	float wm = 0.0;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+//	float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)penalty_ex;
+#endif
+#if 1
+	float *wtmp;
+	int *ijppt;
+	float *mjpt, *prept, *curpt;
+	int *mpjpt;
+#endif
+	static TLS float mi, *m;
+	static TLS int **ijp;
+	static TLS int mpi, *mp;
+	static TLS float *w1, *w2;
+	static TLS float *match;
+	static TLS float *initverticalw;    /* kufuu sureba iranai */
+	static TLS float *lastverticalw;    /* kufuu sureba iranai */
+	static TLS char **mseq1;
+	static TLS char **mseq2;
+	static TLS char **mseq;
+	static TLS float *ogcp1;
+	static TLS float *ogcp2;
+	static TLS float *fgcp1;
+	static TLS float *fgcp2;
+	static TLS float ***cpmx1s;
+	static TLS float ***cpmx2s;
+	static TLS int ***intwork;
+	static TLS float ***floatwork;
+	static TLS int orlgth1 = 0, orlgth2 = 0;
+	static TLS float *gapfreq1;
+	static TLS float *gapfreq2;
+	float fpenalty = (float)penalty;
+	float fpenalty_shift = (float)penalty_shift;
+	float *fgcp2pt;
+	float *ogcp2pt;
+	float fgcp1va;
+	float ogcp1va;
+	float *gf2pt;
+	float *gf2ptpre;
+	float gf1va;
+	float gf1vapre;
+	float headgapfreq1;
+	float headgapfreq2;
+
+	int *warpis = NULL;
+	int *warpjs = NULL;
+	int *warpi = NULL;
+	int *warpj = NULL;
+	int *prevwarpi = NULL;
+	int *prevwarpj = NULL;
+	float *wmrecords = NULL;
+	float *prevwmrecords = NULL;
+	int warpn = 0;
+	int warpbase;
+	float curm = 0.0;
+	float *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
+	int *warpipt, *warpjpt;
+
+
+	if( seq1 == NULL )
+	{
+		if( orlgth1 )
+		{
+//			fprintf( stderr, "## Freeing local arrays in A__align\n" );
+			orlgth1 = 0;
+			orlgth2 = 0;
+
+			imp_match_init_strict( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0 );
+
+			free( mseq1 );
+			free( mseq2 );
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+
+			FreeCharMtx( mseq );
+
+			FreeFloatVec( ogcp1 );
+			FreeFloatVec( ogcp2 );
+			FreeFloatVec( fgcp1 );
+			FreeFloatVec( fgcp2 );
+
+
+			FreeFloatCub( cpmx1s );
+			FreeFloatCub( cpmx2s );
+
+			FreeFloatVec( gapfreq1 );
+			FreeFloatVec( gapfreq2 );
+
+			FreeFloatCub( floatwork );
+			FreeIntCub( intwork );
+
+		}
+		else
+		{
+//			fprintf( stderr, "## Not allocated\n" );
+		}
+		return( 0.0 );
+	}
+
+
+
+//	fprintf( stderr, "\npairoffset = \n" );
+//	for( i=0; i<icyc; i ++ ) for( j=0; j<jcyc; j ++ )
+//		fprintf( stderr, "%d-%d, %f\n", i, j, pairoffset[i][j] );
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+#if 0
+	if( lgth1 == 0 || lgth2 == 0 )
+	{
+		fprintf( stderr, "WARNING (Aalignmm): lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+	}
+#endif
+	if( lgth1 == 0 && lgth2 == 0 )
+		return( 0.0 );
+
+	if( lgth1 == 0 )
+	{
+		for( i=0; i<icyc; i++ )
+		{
+			j = lgth2;
+			seq1[i][j] = 0;
+			while( j ) seq1[i][--j] = *newgapstr;
+//			fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+		}
+		return( 0.0 );
+	}
+
+	if( lgth2 == 0 )
+	{
+		for( i=0; i<jcyc; i++ )
+		{
+			j = lgth1;
+			seq2[i][j] = 0;
+			while( j ) seq2[i][--j] = *newgapstr;
+//			fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+		}
+		return( 0.0 );
+	}
+
+	warpbase = lgth1 + lgth2;
+	warpis = NULL;
+	warpjs = NULL;
+	warpn = 0;
+
+	if( trywarp )
+	{
+//		fprintf( stderr, "In A__align_variousdist !!!!!\n" );
+		if( headgp == 0 || tailgp == 0 )
+		{
+			fprintf( stderr, "At present, headgp and tailgp must be 1.\n" );
+			exit( 1 );
+		}
+		wmrecords = AllocateFloatVec( lgth2+1 );
+		warpi = AllocateIntVec( lgth2+1 );
+		warpj = AllocateIntVec( lgth2+1 );
+		prevwmrecords = AllocateFloatVec( lgth2+1 );
+		prevwarpi = AllocateIntVec( lgth2+1 );
+		prevwarpj = AllocateIntVec( lgth2+1 );
+		for( i=0; i<lgth2+1; i++ ) wmrecords[i] = 0.0;
+		for( i=0; i<lgth2+1; i++ ) prevwmrecords[i] = 0.0;
+		for( i=0; i<lgth2+1; i++ ) prevwarpi[i] = -warpbase;
+		for( i=0; i<lgth2+1; i++ ) prevwarpj[i] = -warpbase;
+		for( i=0; i<lgth2+1; i++ ) warpi[i] = -warpbase;
+		for( i=0; i<lgth2+1; i++ ) warpj[i] = -warpbase;
+	}
+
+#if 0
+	fprintf( stderr, "####  eff in SA+++align\n" );
+	fprintf( stderr, "####  seq1[0] = %s\n", seq1[0] );
+	fprintf( stderr, "####  strlen( seq1[0] ) = %d\n", strlen( seq1[0] ) );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[i] );
+	fprintf( stderr, "####  seq2[0] = %s\n", seq2[0] );
+	fprintf( stderr, "####  strlen( seq2[0] ) = %d\n", strlen( seq2[0] ) );
+	for( i=0; i<jcyc; i++ ) fprintf( stderr, "eff2[%d] = %f\n", i, eff2[i] );
+#endif
+	if( orlgth1 == 0 )
+	{
+		mseq1 = AllocateCharMtx( njob, 0 );
+		mseq2 = AllocateCharMtx( njob, 0 );
+	}
+
+
+
+	if( lgth1 > orlgth1 || lgth2 > orlgth2 )
+	{
+		int ll1, ll2;
+
+
+		if( orlgth1 > 0 && orlgth2 > 0 )
+		{
+			FreeFloatVec( w1 );
+			FreeFloatVec( w2 );
+			FreeFloatVec( match );
+			FreeFloatVec( initverticalw );
+			FreeFloatVec( lastverticalw );
+
+			FreeFloatVec( m );
+			FreeIntVec( mp );
+
+			FreeCharMtx( mseq );
+
+			FreeFloatVec( ogcp1 );
+			FreeFloatVec( ogcp2 );
+			FreeFloatVec( fgcp1 );
+			FreeFloatVec( fgcp2 );
+
+
+			FreeFloatCub( cpmx1s );
+			FreeFloatCub( cpmx2s );
+
+			FreeFloatVec( gapfreq1 );
+			FreeFloatVec( gapfreq2 );
+
+			FreeFloatCub( floatwork );
+			FreeIntCub( intwork );
+		}
+
+		ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
+		ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
+
+#if DEBUG
+		fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
+#endif
+
+		w1 = AllocateFloatVec( ll2+2 );
+		w2 = AllocateFloatVec( ll2+2 );
+		match = AllocateFloatVec( ll2+2 );
+
+		initverticalw = AllocateFloatVec( ll1+2 );
+		lastverticalw = AllocateFloatVec( ll1+2 );
+
+		m = AllocateFloatVec( ll2+2 );
+		mp = AllocateIntVec( ll2+2 );
+
+		mseq = AllocateCharMtx( njob, ll1+ll2 );
+
+		ogcp1 = AllocateFloatVec( ll1+2 );
+		ogcp2 = AllocateFloatVec( ll2+2 );
+		fgcp1 = AllocateFloatVec( ll1+2 );
+		fgcp2 = AllocateFloatVec( ll2+2 );
+
+		cpmx1s = AllocateFloatCub( maxdistclass, nalphabets, ll1+2 );
+		cpmx2s = AllocateFloatCub( maxdistclass, nalphabets, ll2+2 );
+
+		gapfreq1 = AllocateFloatVec( ll1+2 );
+		gapfreq2 = AllocateFloatVec( ll2+2 );
+
+		floatwork = AllocateFloatCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets ); 
+		intwork = AllocateIntCub( maxdistclass, MAX( ll1, ll2 )+2, nalphabets+1 ); 
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n" );
+#endif
+
+		orlgth1 = ll1 - 100;
+		orlgth2 = ll2 - 100;
+	}
+
+
+	for( i=0; i<icyc; i++ )
+	{
+		mseq1[i] = mseq[i];
+		seq1[i][lgth1] = 0;
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		mseq2[j] = mseq[icyc+j];
+		seq2[j][lgth2] = 0;
+	}
+
+
+	if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
+	{
+		int ll1, ll2;
+
+		if( commonAlloc1 && commonAlloc2 )
+		{
+			FreeIntMtx( commonIP );
+		}
+
+		ll1 = MAX( orlgth1, commonAlloc1 );
+		ll2 = MAX( orlgth2, commonAlloc2 );
+
+#if DEBUG
+		fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
+#endif
+
+		commonIP = AllocateIntMtx( ll1+10, ll2+10 );
+
+#if DEBUG
+		fprintf( stderr, "succeeded\n\n" );
+#endif
+
+		commonAlloc1 = ll1;
+		commonAlloc2 = ll2;
+	}
+	ijp = commonIP;
+
+#if 0
+	{
+		float t = 0.0;
+		for( i=0; i<icyc; i++ )
+			t += eff1[i];
+	fprintf( stderr, "## totaleff = %f\n", t );
+	}
+#endif
+
+//	cpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+//	cpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+	for( c=0; c<maxdistclass; c++ )
+	{
+//		fprintf( stderr, "c=%d\n", c );
+		cpmx_calc_new( seq1, cpmx1s[c], eff1s[c], lgth1, icyc );
+		cpmx_calc_new( seq2, cpmx2s[c], eff2s[c], lgth2, jcyc );
+	}
+
+	if( sgap1 )
+	{
+		new_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1, sgap1 );
+		new_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2, sgap2 );
+		new_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1, egap1 );
+		new_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2, egap2 );
+		outgapcount( &headgapfreq1, icyc, sgap1, eff1 );
+		outgapcount( &headgapfreq2, jcyc, sgap2, eff2 );
+		outgapcount( gapfreq1+lgth1, icyc, egap1, eff1 );
+		outgapcount( gapfreq2+lgth2, jcyc, egap2, eff2 );
+	}
+	else
+	{
+		st_OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+		st_OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+		st_FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+		st_FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+		headgapfreq1 = 0.0;
+		headgapfreq2 = 0.0;
+		gapfreq1[lgth1] = 0.0;
+		gapfreq2[lgth2] = 0.0;
+	}
+
+	if( legacygapcost == 0 )
+	{
+		gapcountf( gapfreq1, seq1, icyc, eff1, lgth1 );
+		gapcountf( gapfreq2, seq2, jcyc, eff2, lgth2 );
+		for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0 - gapfreq1[i];
+		for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0 - gapfreq2[i];
+		headgapfreq1 = 1.0 - headgapfreq1;
+		headgapfreq2 = 1.0 - headgapfreq2;
+	}
+	else
+	{
+		for( i=0; i<lgth1+1; i++ ) gapfreq1[i] = 1.0;
+		for( i=0; i<lgth2+1; i++ ) gapfreq2[i] = 1.0;
+		headgapfreq1 = 1.0;
+		headgapfreq2 = 1.0;
+	}
+
+#if 0
+	fprintf( stderr, "\ngapfreq1[] =" );
+	for( i=0; i<lgth1; i++ ) fprintf( stderr, "%5.2f ", gapfreq1[i] );
+	fprintf( stderr, "\n" );
+
+	fprintf( stderr, "\ngapfreq2[] =" );
+	for( i=0; i<lgth2; i++ ) fprintf( stderr, "%5.2f ", gapfreq2[i] );
+	fprintf( stderr, "\n" );
+#endif
+	
+
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty * ( gapfreq1[i] );
+		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty * ( gapfreq1[i] );
+	}
+
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty * ( gapfreq2[i] );
+		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty * ( gapfreq2[i] );
+	}
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+//	for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[i] = %s\n", seq1[i] );
+//	for( j=0; j<jcyc; j++ ) fprintf( stderr, "seq2[j] = %s\n", seq2[j] );
+
+#if MCD
+	match_calc_dynamicmtx( pairoffset, n_dynamicmtx, initverticalw, jcyc, seq2, eff2, icyc, seq1, eff1, 0, lgth1, *floatwork, *intwork, 1, 1 );
+//	for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
+#else
+	fillzero( initverticalw, lgth1 );
+	for( c=0; c<maxdistclass; c++ )
+	{
+//		fprintf( stderr, "c=%d matrices[c][W][W] = %f\n", c, matrices[c][amino_n['W']][amino_n['W']] );
+//		for( i=0; i<lgth1; i++ ) fprintf( stderr, "seq1[i] = %c, cpmx1s[c][3][%d] = %f\n", seq1[0][i], i, cpmx1s[c][3][i] );
+//		for( i=0; i<lgth2; i++ ) fprintf( stderr, "seq2[i] = %c, cpmx2s[c][3][%d] = %f\n", seq2[0][i], i, cpmx2s[c][3][i] );
+		match_calc_add( matrices[c], initverticalw, cpmx2s[c], cpmx1s[c], 0, lgth1, floatwork[c], intwork[c], 1 );
+//		for( i=0; i<lgth1; i++ ) fprintf( stderr, "c=%d, %d - %f\n", c, i, initverticalw[i] );
+	}
+//	for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
+#endif
+
+//	exit( 1 );
+
+	if( localhom )
+		imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
+
+#if MCD
+	match_calc_dynamicmtx( pairoffset, n_dynamicmtx, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, 0, lgth2, *floatwork, *intwork, 1, 0 );
+//	for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
+//	exit( 1 );
+#else
+	fillzero( currentw, lgth2 );
+	for( c=0; c<maxdistclass; c++ )
+		match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], 0, lgth2, floatwork[c], intwork[c], 1 );
+//	for( i=0; i<lgth2; i++ ) fprintf( stderr, "%d - %f\n", i, currentw[i] );
+//	exit( 1 );
+#endif
+
+	if( localhom )
+		imp_match_out_vead( currentw, 0, lgth2 ); // 060306
+#if 0 // -> tbfast.c
+	if( localhom )
+		imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+	if( headgp == 1 )
+	{
+		for( i=1; i<lgth1+1; i++ )
+		{
+//			initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+			initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;
+		}
+		for( j=1; j<lgth2+1; j++ )
+		{
+//			currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+			currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;
+		}
+	}
+#if OUTGAP0TRY
+	else
+	{
+		fprintf( stderr, "offset = %d\n", offset );
+		for( j=1; j<lgth2+1; j++ )
+			currentw[j] -= offset * j / 2.0;
+		for( i=1; i<lgth1+1; i++ )
+			initverticalw[i] -= offset * i / 2.0;
+	}
+#endif
+#if 0
+	fprintf( stderr, "\n   " );
+	for( j=0; j<lgth2+1; j++ ) fprintf( stderr, "    %c ", seq2[0][j] );
+	fprintf( stderr, "\n%c ", seq1[0][0]  );
+	for( j=0; j<lgth2+1; j++ )
+	{
+		fprintf( stderr, "%5.0f ", currentw[j] );
+	}
+	fprintf( stderr, "\n"  );
+#endif
+
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+//		m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+		m[j] = currentw[j-1] + ogcp1[1] * gapfreq2[j-1]; mp[j] = 0;;
+	}
+	if( lgth2 == 0 )
+		lastverticalw[0] = 0.0; // Falign kara yobaretatoki kounarukanousei ari
+	else
+		lastverticalw[0] = currentw[lgth2-1];
+
+	if( tailgp ) lasti = lgth1+1; else lasti = lgth1;
+	lastj = lgth2+1;
+
+#if XXXXXXX
+fprintf( stderr, "currentw = \n" );
+for( i=0; i<lgth1+1; i++ )
+{
+	fprintf( stderr, "%5.2f ", currentw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "initverticalw = \n" );
+for( i=0; i<lgth2+1; i++ )
+{
+	fprintf( stderr, "%5.2f ", initverticalw[i] );
+}
+fprintf( stderr, "\n" );
+fprintf( stderr, "fcgp\n" );
+for( i=0; i<lgth1; i++ ) 
+	fprintf( stderr, "fgcp1[%d]=%f\n", i, ogcp1[i] );
+for( i=0; i<lgth2; i++ ) 
+	fprintf( stderr, "fgcp2[%d]=%f\n", i, ogcp2[i] );
+#endif
+
+	for( i=1; i<lasti; i++ )
+	{
+
+#ifdef enablemultithread
+//		fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+		if( chudanpt && *chudanpt != chudanref ) 
+		{
+//			fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+			*chudanres = 1;
+			return( -1.0 );
+		}
+#endif
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+#if MCD
+		match_calc_dynamicmtx( pairoffset, n_dynamicmtx, currentw, icyc, seq1, eff1, jcyc, seq2, eff2, i, lgth2, *floatwork, *intwork, 0, 0 );
+#else
+		fillzero( currentw, lgth2 );
+		for( c=0; c<maxdistclass; c++ )
+			match_calc_add( matrices[c], currentw, cpmx1s[c], cpmx2s[c], i, lgth2, floatwork[c], intwork[c], 0 );
+#endif
+#if 0
+		if( i == 1 )
+		{
+			fprintf( stderr, "\n" );
+			for( j=0; j<lgth2; j++ ) fprintf( stderr, "%d - %f\n", j, currentw[j] );
+			exit( 1 );
+		}
+#endif
+
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+	fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+		if( localhom )
+		{
+//			fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
+#if  0
+			imp_match_out_vead( currentw, i, lgth2 );
+#else
+			imp_match_out_vead( currentw, i, lgth2 );
+#endif
+		}
+#if XXXXXXX
+fprintf( stderr, "\n" );
+fprintf( stderr, "i=%d\n", i );
+fprintf( stderr, "currentw = \n" );
+for( j=0; j<lgth2; j++ )
+{
+	fprintf( stderr, "%5.2f ", currentw[j] );
+}
+fprintf( stderr, "\n" );
+#endif
+		currentw[0] = initverticalw[i];
+
+#if 0
+		fprintf( stderr, "%c ", seq1[0][i] );
+		for( j=0; j<lgth2+1; j++ )
+		{
+			fprintf( stderr, "%5.0f ", currentw[j] );
+		}
+		fprintf( stderr, "\n"  );
+#endif
+	
+//		mi = previousw[0] + ogcp2[1]; mpi = 0;
+		mi = previousw[0] + ogcp2[1] * gapfreq1[i-1]; mpi=0;
+		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+		fgcp2pt = fgcp2;
+		ogcp2pt = ogcp2 + 1;
+		fgcp1va = fgcp1[i-1];
+		ogcp1va = ogcp1[i];
+		gf1va = gapfreq1[i];
+		gf1vapre = gapfreq1[i-1];
+		gf2pt = gapfreq2+1;
+		gf2ptpre = gapfreq2;
+
+		if( trywarp )
+		{
+			prevwmrecordspt = prevwmrecords;
+			wmrecordspt = wmrecords+1;
+			wmrecords1pt = wmrecords;
+			warpipt = warpi + 1;
+			warpjpt = warpj + 1;
+		}
+
+		for( j=1; j<lastj; j++ )
+		{
+#ifdef xxxenablemultithread
+//			fprintf( stderr, "chudan = %d, %d\n", *chudanpt, chudanref );
+			if( chudanpt && *chudanpt != chudanref ) 
+			{
+//				fprintf( stderr, "\n\n## CHUUDAN!!! S\n" );
+				*chudanres = 1;
+				return( -1.0 );
+			}
+#endif
+			wm = *prept;
+			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "\n i=%d, j=%d %c, %c", i, j, seq1[0][i], seq2[0][j] );
+			fprintf( stderr, "%5.0f->", wm );
+			fprintf( stderr, "%5.0f? (penal=%5.2f)", g=mi+*fgcp2pt*(1.0-gapfreq1[i]), *fgcp2pt*(1.0-gapfreq1[i]) );
+#endif
+			if( (g=mi+*fgcp2pt*gf1va) > wm )
+			{
+				wm = g;
+				*ijppt = -( j - mpi );
+//				fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );
+			}
+			if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+#if 0 
+			fprintf( stderr, "%5.0f->", wm );
+			fprintf( stderr, "%5.0f? (penal=%5.2f)", g=*mjpt+fgcp1va*(1.0-gapfreq2[j]), fgcp1va*(1.0-gapfreq2[j]) );
+#endif
+			if( (g=*mjpt+ fgcp1va* *gf2pt) > wm )
+			{
+				wm = g;
+				*ijppt = +( i - *mpjpt );
+//				fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );
+			}
+			if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+			if( trywarp )
+			{
+#if USE_PENALTY_EX
+				if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
+#else
+				if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
+#endif
+				{
+					if( warpn && prevwarpi[j-1] == warpis[warpn-1] && prevwarpj[j-1] == warpjs[warpn-1] )
+					{
+						*ijppt = warpbase + warpn - 1;
+					}
+					else
+					{
+						*ijppt = warpbase + warpn;
+						warpis = realloc( warpis, sizeof(int) * ( warpn+1 ) );
+						warpjs = realloc( warpjs, sizeof(int) * ( warpn+1 ) );
+						warpis[warpn] = prevwarpi[j-1];
+						warpjs[warpn] = prevwarpj[j-1];
+						warpn++;
+					}
+					wm = g;
+				}
+				curm = *curpt + wm;
+
+				if( *wmrecords1pt > *wmrecordspt )
+				{
+					*wmrecordspt = *wmrecords1pt;
+					*warpipt  = *(warpipt-1);
+					*warpjpt  = *(warpjpt-1);
+				}
+				if( curm > *wmrecordspt )
+				{
+					*wmrecordspt = curm;
+					*warpipt = i;
+					*warpjpt = j;
+				}
+				wmrecordspt++;
+				wmrecords1pt++;
+				warpipt++;
+				warpjpt++;
+			}
+
+#if 0
+			fprintf( stderr, "%5.0f ", wm );
+#endif
+			*curpt++ += wm;
+			ijppt++;
+			mjpt++;
+			prept++;
+			mpjpt++;
+			fgcp2pt++;
+			ogcp2pt++;
+			gf2ptpre++;
+			gf2pt++;
+
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+
+		if( trywarp )
+		{
+			fltncpy( prevwmrecords, wmrecords, lastj );
+			intncpy( prevwarpi, warpi, lastj );
+			intncpy( prevwarpj, warpj, lastj );
+		}
+	}
+	if( trywarp )
+	{
+//		fprintf( stderr, "wm = %f\n", wm );
+//		fprintf( stderr, "warpn = %d\n", warpn );
+		free( wmrecords );
+		free( prevwmrecords );
+		free( warpi );
+		free( warpj );
+		free( prevwarpi );
+		free( prevwarpj );
+	}
+
+
+#if OUTGAP0TRY
+	if( !outgap )
+	{
+		for( j=1; j<lgth2+1; j++ )
+			currentw[j] -= offset * ( lgth2 - j ) / 2.0;
+		for( i=1; i<lgth1+1; i++ )
+			lastverticalw[i] -= offset * ( lgth1 - i  / 2.0);
+	}
+#endif
+		
+	/*
+	fprintf( stderr, "\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr,"%s\n", seq1[i] );
+	fprintf( stderr, "#####\n" );
+	for( j=0; j<jcyc; j++ ) fprintf( stderr,"%s\n", seq2[j] );
+	fprintf( stderr, "====>" );
+	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
+	for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
+	*/
+	if( localhom )
+	{
+		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
+	}
+	else
+		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase );
+
+	if( warpis ) free( warpis );
+	if( warpjs ) free( warpjs );
+
+//	fprintf( stderr, "### impmatch = %f\n", *impmatch );
+
+	resultlen = strlen( mseq1[0] );
+	if( alloclen < resultlen || resultlen > N )
+	{
+		fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
+		ErrorExit( "LENGTH OVER!\n" );
+	}
+
+
+	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+	for( j=0; j<jcyc; j++ ) strcpy( seq2[j], mseq2[j] );
+#if 0
+	fprintf( stderr, "\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "%s\n", mseq1[i] );
+	fprintf( stderr, "#####\n" );
+	for( j=0; j<jcyc; j++ ) fprintf( stderr, "%s\n", mseq2[j] );
+#endif
+
+//	fprintf( stderr, "wm = %f\n", wm );
+
+	return( wm );
+}