X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2FpartSalignmm.c;fp=binaries%2Fsrc%2Fmafft%2Fcore%2FpartSalignmm.c;h=b670b73d22105ff9991208587bd20935d6fb9e62;hb=063b30bb5e8161134ae764742636ab538e10eea7;hp=0000000000000000000000000000000000000000;hpb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;p=jabaws.git

diff --git a/binaries/src/mafft/core/partSalignmm.c b/binaries/src/mafft/core/partSalignmm.c
new file mode 100644
index 0000000..b670b73
--- /dev/null
+++ b/binaries/src/mafft/core/partSalignmm.c
@@ -0,0 +1,1266 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define MACHIGAI 0
+#define OUTGAP0TRY 1
+#define DEBUG 0
+#define XXXXXXX    0
+#define USE_PENALTY_EX  0
+#define FASTMATCHCALC 1
+
+#if 0
+static void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len )
+{
+	int i, j, gc, gb; 
+	float feff;
+	
+	for( i=0; i<len; i++ ) ogcp[i] = 0.0;
+	for( j=0; j<clus; j++ ) 
+	{
+		feff = (float)eff[j];
+		gc = 0;
+		for( i=0; i<len; i++ ) 
+		{
+			gb = gc;
+			gc = ( seq[j][i] == '-' );
+			{
+				if( !gb *  gc ) ogcp[i] += feff;
+			}
+		}
+	}
+}
+
+static void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len )
+{
+	int i, j, gc, gb; 
+	float feff;
+	
+	for( i=0; i<len; i++ ) fgcp[i] = 0.0;
+	for( j=0; j<clus; j++ ) 
+	{
+		feff = (float)eff[j];
+		gc = ( seq[j][0] == '-' );
+		for( i=1; i<len+1; i++ ) 
+		{
+			gb = gc;
+			gc = ( seq[j][i] == '-' );
+			{
+				if( gb * !gc ) fgcp[i-1] += feff;
+			}
+		}
+	}
+}
+#endif
+
+
+			
+		
+
+static TLS int impalloclen = 0;
+static TLS float **impmtx = NULL;
+float part_imp_match_out_sc( int i1, int j1 )
+{
+//	fprintf( stderr, "impalloclen = %d\n", impalloclen );
+//	fprintf( stderr, "i1,j1=%d,%d -> impmtx=%f\n", i1, j1, impmtx[i1][j1] );
+	return( impmtx[i1][j1] );
+#if 0
+	if( i1 == l1 || j1 == l2 ) return( 0.0 );
+	return( impmtx[i1+start1][j1+start2] );
+#endif
+}
+static void part_imp_match_out_vead_gapmap( float *imp, int i1, int lgth2, int start2, int *gapmap2 )
+{
+#if FASTMACHCALC
+	float *pt = imp;
+	int *gapmappt = gapmap2;
+	while( lgth2-- )
+		*pt++ += impmtx[i1][start2+*gapmappt++];
+#else
+	int j;
+	for( j=0; j<lgth2; j++ )
+	{
+		imp[j] += impmtx[i1][start2+gapmap2[j]];
+	}
+#endif
+}
+
+static void part_imp_match_out_vead_tate_gapmap( float *imp, int j1, int lgth1, int start1, int *gapmap1 )
+{
+#if FASTMACHCALC
+	float *pt = imp;
+	int *gapmappt = gapmap1;
+	while( lgth1-- )
+		*pt++ = impmtx[start1+*gapmappt++][j1];
+#else
+	int i;
+	for( i=0; i<lgth1; i++ )
+	{
+		imp[i] += impmtx[start1+gapmap1[i]][j1];
+	}
+#endif
+}
+
+void part_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;
+	double effij, effijx, effij_kozo; 
+	char *pt, *pt1, *pt2;
+	LocalHom *tmpptr;
+
+	if( seq1 == NULL )
+	{
+		if( impmtx ) FreeFloatMtx( impmtx );
+		impmtx = NULL;
+		return;
+	}
+
+	if( impalloclen <= lgth1 + 2 || impalloclen <= lgth2 + 2 )
+	{
+		if( impmtx ) FreeFloatMtx( impmtx );
+		impalloclen = MAX( lgth1, lgth2 ) + 2;
+		impmtx = AllocateFloatMtx( impalloclen+100, impalloclen+100 );
+	}
+
+
+#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 = 1.0 * fastathreshold;
+	for( i=0; i<clus1; i++ )
+	{
+		for( j=0; j<clus2; j++ )
+		{
+			effij = eff1[i] * eff2[j] * effijx;
+			effij_kozo = 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 = (int)( pt - seq1[i] ) - 1;
+	
+				if( tmpptr->start1 == tmpptr->end1 ) end1 = start1;
+				else
+				{
+#if MACHIGAI
+					while( *pt != 0 )
+					{
+						if( tmpint == tmpptr->end1 ) break;
+						if( *pt++ != '-' ) tmpint++;
+					}
+					end1 = (int)( pt - seq1[i] ) - 1;
+#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 = (int)( pt - seq1[i] ) - 1;
+#endif
+				}
+	
+				pt = seq2[j];
+				tmpint = -1;
+				while( *pt != 0 )
+				{
+					if( *pt++ != '-' ) tmpint++;
+					if( tmpint == tmpptr->start2 ) break;
+				}
+				start2 = (int)( 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 = (int)( pt - seq2[j] ) - 1;
+#else
+					while( *pt != 0 )
+					{
+						if( *pt++ != '-' ) tmpint++;
+						if( tmpint == tmpptr->end2 ) break;
+					}
+					end2 = (int)( 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 );
+				}
+
+				k1 = start1; k2 = start2;
+				pt1 = seq1[i] + k1;
+				pt2 = seq2[j] + k2;
+				while( *pt1 && *pt2 )
+				{
+					if( *pt1 != '-' && *pt2 != '-' )
+					{
+// ½Å¤ß¤òÆó½Å¤Ë¤«¤±¤Ê¤¤¤è¤¦¤ËÃí°Õ¤·¤Æ²¼¤µ¤¤¡£
+//						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, "k1=%d, k2=%d, impalloclen=%d\n", k1, k2, impalloclen );
+//						fprintf( stderr, "mark, %d (%c) - %d (%c) \n", k1, *pt1, k2, *pt2 );
+						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;
+				}
+				tmpptr = tmpptr->next;
+			}
+		}
+	}
+#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, "%2.1f ", impmtx[k1][k2] );
+		fprintf( stderr, "\n" );
+	}
+	exit( 1 );
+#endif
+}
+
+
+void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, int *gapmap1, int *gapmap2, RNApair *additionalpair )
+{
+	foldrna( nseq1, nseq2, seq1, seq2, eff1, eff2, grouprna1, grouprna2, impmtx, gapmap1, gapmap2, additionalpair );
+}
+
+
+void part_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;
+	static TLS char *nocount1 = NULL;
+	static TLS char *nocount2 = NULL;
+
+	if( impalloclen < lgth1 || impalloclen < lgth2 )
+	{
+		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 );
+		impalloclen -= 2;
+	}
+
+	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] = 0.0;
+	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" );
+	}
+	exit( 1 );
+#endif
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+#if FASTMATCHCALC
+	int j, l;
+	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	float *matchpt, *cpmxpdpt, **cpmxpdptpt;
+	int *cpmxpdnpt, **cpmxpdnptpt;
+	if( initialize )
+	{
+		int count = 0;
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<26; l++ )
+			{
+				if( cpmx2[l][j] )
+				{
+					cpmxpd[j][count] = cpmx2[l][j];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	{
+		for( l=0; l<26; l++ )
+		{
+			scarr[l] = 0.0;
+			for( j=0; j<26; j++ )
+				scarr[l] += n_dis_consweight_multi[j][l] * cpmx1[j][i1];
+//				scarr[l] += n_dis[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++;
+		} 
+	}
+#else
+	int j, k, l;
+	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	// simple
+	if( initialize )
+	{
+		int count = 0;
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<26; l++ )
+			{
+				if( cpmx2[l][j] )
+				{
+					cpmxpd[count][j] = cpmx2[l][j];
+					cpmxpdn[count][j] = l;
+					count++;
+				}
+			}
+			cpmxpdn[count][j] = -1;
+		}
+	}
+	for( l=0; l<26; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<26; k++ )
+			scarr[l] += n_dis_consweight_multi[k][l] * cpmx1[k][i1];
+//			scarr[l] += n_dis[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];
+	} 
+#endif
+}
+
+static void Atracking_localhom( float *impwmpt, float *lasthorizontalw, float *lastverticalw, 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        float **cpmx1, float **cpmx2, 
+                        int **ijp, int icyc, int jcyc,
+						int start1, int end1, int start2, int end2,
+						int *gapmap1, int *gapmap2 )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k;
+//	char gap[] = "-";
+	char *gap;
+	float wm;
+	gap = newgapstr;
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+#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 );
+    }
+
+	for( i=0; i<icyc; i++ )
+	{
+		mseq1[i] += lgth1+lgth2;
+		*mseq1[i] = 0;
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		mseq2[j] += lgth1+lgth2;
+		*mseq2[j] = 0;
+	}
+	iin = lgth1; jin = lgth2;
+	*impwmpt = 0.0;
+	for( k=0; k<=lgth1+lgth2; k++ ) 
+	{
+		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;
+		}
+		l = iin - ifi;
+		while( --l ) 
+		{
+			for( i=0; i<icyc; i++ )
+				*--mseq1[i] = seq1[i][ifi+l];
+			for( j=0; j<jcyc; j++ ) 
+				*--mseq2[j] = *gap;
+			k++;
+		}
+		l= jin - jfi;
+		while( --l )
+		{
+			for( i=0; i<icyc; i++ ) 
+				*--mseq1[i] = *gap;
+			for( j=0; j<jcyc; j++ ) 
+				*--mseq2[j] = seq2[j][jfi+l];
+			k++;
+		}
+		if( iin != lgth1 && jin != lgth2 ) // ??
+		{
+			*impwmpt += part_imp_match_out_sc( gapmap1[iin]+start1, gapmap2[jin]+start2 );
+//			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;
+		for( i=0; i<icyc; i++ ) 
+			*--mseq1[i] = seq1[i][ifi];
+		for( j=0; j<jcyc; j++ ) 
+			*--mseq2[j] = seq2[j][jfi];
+		k++;
+		iin = ifi; jin = jfi;
+	}
+}
+static float Atracking( float *lasthorizontalw, float *lastverticalw, 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        float **cpmx1, float **cpmx2, 
+                        int **ijp, int icyc, int jcyc )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk;
+//	char gap[] = "-";
+	char *gap;
+	gap = newgapstr;
+	float wm = 0.0;
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+#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 );
+    }
+
+	for( i=0; i<icyc; i++ )
+	{
+		mseq1[i] += lgth1+lgth2;
+		*mseq1[i] = 0;
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		mseq2[j] += lgth1+lgth2;
+		*mseq2[j] = 0;
+	}
+	iin = lgth1; jin = lgth2;
+	lastk = lgth1+lgth2;
+	for( k=0; k<=lastk; k++ ) 
+	{
+		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;
+		}
+		l = iin - ifi;
+		while( --l ) 
+		{
+			for( i=0; i<icyc; i++ )
+				*--mseq1[i] = seq1[i][ifi+l];
+			for( j=0; j<jcyc; j++ ) 
+				*--mseq2[j] = *gap;
+			k++;
+		}
+		l= jin - jfi;
+		while( --l )
+		{
+			for( i=0; i<icyc; i++ ) 
+				*--mseq1[i] = *gap;
+			for( j=0; j<jcyc; j++ ) 
+				*--mseq2[j] = seq2[j][jfi+l];
+			k++;
+		}
+		if( iin <= 0 || jin <= 0 ) break;
+		for( i=0; i<icyc; i++ ) 
+			*--mseq1[i] = seq1[i][ifi];
+		for( j=0; j<jcyc; j++ ) 
+			*--mseq2[j] = seq2[j][jfi];
+		k++;
+		iin = ifi; jin = jfi;
+	}
+	return( 0.0 );
+}
+
+float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres )
+/* 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;
+#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;
+	float fpenalty = (float)penalty;
+#if USE_PENALTY_EX
+	float fpenalty_ex = (float)penalty_ex;
+#endif
+	float *fgcp2pt;
+	float *ogcp2pt;
+	float fgcp1va;
+	float ogcp1va;
+
+
+	if( seq1 == NULL )
+	{
+		if( orlgth1 )
+		{
+//			fprintf( stderr, "## Freeing local arrays in A__align\n" );
+			orlgth1 = 0;
+			orlgth2 = 0;
+
+			part_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 );
+
+			FreeFloatMtx( floatwork );
+			FreeIntMtx( intwork );
+
+		}
+		else
+		{
+//			fprintf( stderr, "## Not allocated\n" );
+		}
+		return( 0.0 );
+	}
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+#if 1
+	if( lgth1 == 0 ) fprintf( stderr, "WARNING: lgth1=0 in partA__align\n" );
+	if( lgth2 == 0 ) fprintf( stderr, "WARNING: lgth2=0 in partA__align\n" );
+
+	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] = '-';
+//			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] = '-';
+//			fprintf( stderr, "seq2[i] = %s\n", seq2[i] );
+		}
+		return( 0.0 );
+	}
+#endif
+
+#if 0
+	fprintf( stderr, "eff in SA+++align\n" );
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "eff1[%d] = %f\n", i, eff1[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 );
+
+			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( 26, ll1+2 );
+		cpmx2 = AllocateFloatMtx( 26, ll2+2 );
+
+#if FASTMATCHCALC
+		floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); 
+		intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 ); 
+#else
+		floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); 
+		intwork = AllocateIntMtx( 26, 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];
+	for( j=0; j<jcyc; j++ ) mseq2[j] = mseq[icyc+j];
+
+
+	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;
+
+	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 );
+	}
+	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 );
+	}
+
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
+		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
+		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
+	}
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+
+	match_calc( initverticalw, cpmx2, cpmx1, 0, lgth1, floatwork, intwork, 1 );
+	if( localhom )
+		part_imp_match_out_vead_tate_gapmap( initverticalw, gapmap2[0]+start2, lgth1, start1, gapmap1 );
+
+
+	match_calc( currentw, cpmx1, cpmx2, 0, lgth2, floatwork, intwork, 1 );
+	if( localhom )
+		part_imp_match_out_vead_gapmap( currentw, gapmap1[0]+start1, lgth2, start2, gapmap2 );
+#if 0 // -> tbfast.c
+	if( localhom )
+		imp_match_calc( currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
+
+#endif
+
+	if( outgap == 1 )
+	{
+		for( i=1; i<lgth1+1; i++ )
+		{
+			initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;
+		}
+		for( j=1; j<lgth2+1; j++ )
+		{
+			currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;
+		}
+	}
+#if OUTGAP0TRY
+	else
+	{
+		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
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+		m[j] = currentw[j-1] + ogcp1[1]; mp[j] = 0;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	if( outgap ) 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!!! i\n" );
+			*chudanres = 1;
+			return( -1.0 );
+		}
+#endif
+
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc( 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 );
+//			imp_match_out_vead( currentw, i, lgth2 );
+			part_imp_match_out_vead_gapmap( currentw, gapmap1[i]+start1, lgth2, start2, gapmap2 );
+		}
+#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];
+
+
+		mi = previousw[0] + ogcp2[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];
+		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!!! j\n" );
+				*chudanres = 1;
+				return( -1.0 );
+			}
+#endif
+			wm = *prept;
+			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + *fgcp2pt;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijppt = -( j - mpi );
+			}
+			g = *prept + *ogcp2pt;
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fgcp1va;
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijppt = +( i - *mpjpt );
+			}
+			g = *prept + ogcp1va;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i-1;
+			}
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+#if 0
+			fprintf( stderr, "%5.0f ", wm );
+#endif
+			*curpt += wm;
+			ijppt++;
+			mjpt++;
+			prept++;
+			mpjpt++;
+			curpt++;
+			fgcp2pt++;
+			ogcp2pt++;
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+
+	}
+
+#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, cpmx1, cpmx2, ijp, icyc, jcyc, start1, end1, start2, end2, gapmap1, gapmap2 );
+	}
+	else
+		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+//	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] );
+	/*
+	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] );
+	*/
+
+
+	return( wm );
+}
+