X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fmafft%2Fcore%2FMSalignmm.c.bkbk;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Fmafft%2Fcore%2FMSalignmm.c.bkbk;h=10621be00a936ec18b2b8773536b5eabe8d750c7;hb=dbde3fb6f00b9bb770343631a517c0e599db8528;hp=0000000000000000000000000000000000000000;hpb=85f830bbd51a7277994bd4233141016304e210c9;p=jabaws.git

diff --git a/website/archive/binaries/mac/src/mafft/core/MSalignmm.c.bkbk b/website/archive/binaries/mac/src/mafft/core/MSalignmm.c.bkbk
new file mode 100644
index 0000000..10621be
--- /dev/null
+++ b/website/archive/binaries/mac/src/mafft/core/MSalignmm.c.bkbk
@@ -0,0 +1,1410 @@
+#include "mltaln.h"
+#include "dp.h"
+
+#define DEBUG 0
+#define XXXXXXX    0
+#define USE_PENALTY_EX  0
+#define STOREWM 0
+
+#define DPTANNI 10
+
+
+static reccycle = 0;
+
+static void 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;
+//		gc = ( gappat[j] == '-' );
+		for( i=0; i<len; i++ ) 
+		{
+			gb = gc;
+			gc = ( seq[j][i] == '-' );
+			{
+				if( !gb *  gc ) ogcp[i] += feff;
+			}
+		}
+	}
+//	for( i=0; i<len; i++ ) 
+//	{
+//		fprintf( stderr, "ogcp[%d] = %30.20f\n", i, ogcp[i] );
+//	}
+}
+
+static void 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] == '-' );
+		gc = 0;
+		for( i=1; i<len; i++ ) 
+		{
+			gb = gc;
+			gc = ( seq[j][i] == '-' );
+			{
+				if( gb * !gc ) 
+				{
+					fgcp[i-1] += feff;
+				}
+			}
+		}
+		{
+			gb = gc;
+			gc = 0;
+			{
+//				fprintf( stderr, "changed gc=%d, gb=%d\n", gc, gb );
+				if( gb * !gc ) fgcp[i-1] += feff;
+			}
+		}
+//		fprintf( stderr, "eff[%d] = %30.20f\n", j, eff[j] );
+	}
+//	for( i=0; i<len; i++ ) 
+//	{
+//		fprintf( stderr, "fgcp[%d] = %30.20f\n", i, fgcp[i] );
+//	}
+}
+
+static void match_calc( float *match, float **cpmx1, float **cpmx2, int i1, int lgth2, float **floatwork, int **intwork, int initialize )
+{
+	int j, k, l;
+	float scarr[26];
+	float **cpmxpd = floatwork;
+	int **cpmxpdn = intwork;
+	int count = 0;
+
+	if( initialize )
+	{
+		for( j=0; j<lgth2; j++ )
+		{
+			count = 0;
+			for( l=0; l<26; l++ )
+			{
+				if( cpmx2[j][l] )
+				{
+					cpmxpd[j][count] = cpmx2[j][l];
+					cpmxpdn[j][count] = l;
+					count++;
+				}
+			}
+			cpmxpdn[j][count] = -1;
+		}
+	}
+
+	for( l=0; l<26; l++ )
+	{
+		scarr[l] = 0.0;
+		for( k=0; k<26; k++ )
+		{
+			scarr[l] += n_dis[k][l] * cpmx1[i1][k];
+		}
+	}
+#if 0 /* ¤³¤ì¤ò»È¤¦¤È¤­¤Ïfloatwork¤Î¥¢¥í¥±¡¼¥È¤òµÕ¤Ë¤¹¤ë */
+	{
+		float *fpt, **fptpt, *fpt2;
+		int *ipt, **iptpt;
+		fpt2 = match;
+		iptpt = cpmxpdn;
+		fptpt = cpmxpd;
+		while( lgth2-- )
+		{
+			*fpt2 = 0.0;
+			ipt=*iptpt,fpt=*fptpt;
+			while( *ipt > -1 )
+				*fpt2 += scarr[*ipt++] * *fpt++;
+			fpt2++,iptpt++,fptpt++;
+		} 
+	}
+#else
+	for( j=0; j<lgth2; j++ )
+	{
+		match[j] = 0.0;
+		for( k=0; cpmxpdn[j][k]>-1; k++ )
+			match[j] += scarr[cpmxpdn[j][k]] * cpmxpd[j][k];
+	} 
+#endif
+}
+
+static float Atracking( 
+						char **seq1, char **seq2, 
+                        char **mseq1, char **mseq2, 
+                        short **ijp, int icyc, int jcyc,
+						int ist, int ien, int jst, int jen )
+{
+	int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, klim;
+	char gap[] = "-";
+	float wm;
+	lgth1 = ien-ist+1;
+	lgth2 = jen-jst+1;
+
+#if 0
+	for( i=0; i<lgth1; i++ ) 
+	{
+		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
+	}
+#endif
+
+
+//	fprintf( stderr, "in Atracking, lgth1=%d, lgth2=%d\n", lgth1, lgth2 );
+ 
+    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;
+	}
+
+//	if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+
+	iin = lgth1; jin = lgth2;
+	klim = lgth1+lgth2;
+	for( k=0; k<=klim; 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][ist+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][jst+jfi+l];
+			k++;
+		}
+		if( iin <= 0 || jin <= 0 ) break;
+		for( i=0; i<icyc; i++ ) 
+			*--mseq1[i] = seq1[i][ist+ifi];
+		for( j=0; j<jcyc; j++ ) 
+			*--mseq2[j] = seq2[j][jst+jfi];
+		k++;
+		iin = ifi; jin = jfi;
+
+//		if( lgth2 == 1 ) fprintf( stderr, "in Atracking, mseq1 = %s, mseq2 = %s\n", mseq1[0], mseq2[0] );
+	}
+//	fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
+//	fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
+	return( 0.0 );
+}
+
+static float MSalignmm_tanni( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	register int i, j;
+	int ll1, ll2;
+	int lasti, lastj;
+	int resultlen;
+	float wm;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+	float fpenalty = (float)penalty;
+	float fpenalty_ex = (float)penalty_ex;
+#if 1
+	float *wtmp;
+	short *ijppt;
+	float *mjpt, *prept, *curpt;
+	int *mpjpt;
+#endif
+	float mi, *m;
+	short **ijp;
+	int mpi, *mp;
+	float *w1, *w2;
+	float *initverticalw;    /* kufuu sureba iranai */
+	float *lastverticalw;    /* kufuu sureba iranai */
+	int **intwork;
+	float **floatwork;
+	short **shortmtx;
+	float dumfl;
+	int lgth1, lgth2;
+	float *ogcp1;
+	float *fgcp1;
+	float *ogcp2;
+	float *fgcp2;
+	char **aseq1;
+	char **aseq2;
+	char **aseq1bk, **aseq2bk;
+
+	ogcp1 = gapinfo[0] + ist;
+	fgcp1 = gapinfo[1] + ist;
+	ogcp2 = gapinfo[2] + jst;
+	fgcp2 = gapinfo[3] + jst;
+
+#if STOREWM
+	char ttt1[10000], ttt2[10000];
+#endif
+
+
+	lgth1 = ien-ist+1;
+	lgth2 = jen-jst+1;
+
+#if STOREWM
+	strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;
+	strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
+
+	fprintf( stderr, "in _tanni ist,ien = %d,%d, lgth1=%d\n", ist, ien, lgth1 );
+	fprintf( stderr, "in _tanni jst,jen = %d,%d, lgth2=%d\n", jst, jen, lgth2 );
+	fprintf( stderr, "ttt1 = %s\n", ttt1 );
+	fprintf( stderr, "ttt2 = %s\n", ttt2 );
+#endif
+
+
+	ll1 = ( (int)(1.3*lgth1) ) + 100;
+	ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+	aseq1 = AllocateCharMtx( icyc, 0 );
+	aseq2 = AllocateCharMtx( jcyc, 0 );
+	aseq1bk = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+	aseq2bk = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+	for( i=0; i<icyc; i++ ) aseq1[i] = aseq1bk[i];
+	for( i=0; i<jcyc; i++ ) aseq2[i] = aseq2bk[i];
+
+	w1 = AllocateFloatVec( ll2+2 );
+	w2 = AllocateFloatVec( ll2+2 );
+
+	initverticalw = AllocateFloatVec( ll1+2 );
+	lastverticalw = AllocateFloatVec( ll1+2 );
+
+	m = AllocateFloatVec( ll2+2 );
+	mp = AllocateIntVec( ll2+2 );
+
+	floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 27 ); 
+	intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 27 ); 
+
+
+	shortmtx = AllocateShortMtx( ll1+1, ll2+1 );
+
+	ijp = shortmtx;
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+	match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+	for( i=1; i<lgth1+1; i++ )
+	{
+		initverticalw[i] += fpenalty * ( ogcp1[0] + fgcp1[i-1] );
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+	}
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+		m[j] = currentw[j-1] + fpenalty * ogcp1[1]; mp[j] = 0;;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+
+
+	lasti = lgth1+1;
+	for( i=1; i<lasti; i++ )
+	{
+
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+		currentw[0] = initverticalw[i];
+
+		mi = previousw[0] + fpenalty * ogcp2[1]; 
+		mpi = 0;
+
+		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+		lastj = lgth2+1;
+		for( j=1; j<lastj; j++ )
+		{
+			wm = *prept;
+			*ijppt = 0;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + fpenalty * fgcp2[j-1];
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijppt = -( j - mpi );
+			}
+			g = *prept + fpenalty * ogcp2[j];
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fpenalty * fgcp1[i-1];
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+				*ijppt = +( i - *mpjpt );
+			}
+			g = *prept + fpenalty * ogcp1[i];
+			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++;
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+	}
+
+//	fprintf( stderr, "wm = %f\n", wm );
+
+	Atracking( seq1, seq2, aseq1, aseq2, ijp, icyc, jcyc, ist, ien, jst, jen );
+
+	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+	for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+//	fprintf( stderr, "in _tanni, aseq1 = %s\n", aseq1[0] );
+//	fprintf( stderr, "in _tanni, mseq1 = %s\n", mseq1[0] );
+
+	FreeFloatVec( w1 );
+	FreeFloatVec( w2 );
+	FreeFloatVec( initverticalw );
+	FreeFloatVec( lastverticalw );
+
+	FreeFloatVec( m );
+	FreeIntVec( mp );
+
+
+	FreeFloatMtx( floatwork );
+	FreeIntMtx( intwork );
+
+	FreeShortMtx( shortmtx );
+
+	FreeCharMtx( aseq1bk );
+	FreeCharMtx( aseq2bk );
+
+	free( aseq1 );
+	free( aseq2 );
+
+	return( wm );
+
+}
+
+static float MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, float **cpmx1, float **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, float **gapinfo )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	float value = 0.0;
+	register int i, j;
+	char **aseq1, **aseq2;
+	int ll1, ll2, l, len;
+	int lasti, lastj, imid, jmid;
+	int resultlen;
+	float wm;   /* int ?????? */
+	float g;
+	float *currentw, *previousw;
+	float fpenalty = (float)penalty;
+	float fpenalty_ex = (float)penalty_ex;
+	float *wtmp;
+//	short *ijppt;
+	int *mpjpt;
+//	short **ijp;
+	int *mp;
+	int mpi;
+	float *mjpt, *prept, *curpt;
+	float mi;
+	float *m;
+	float *w1, *w2;
+//	float *match;
+	float *initverticalw;    /* kufuu sureba iranai */
+	float *lastverticalw;    /* kufuu sureba iranai */
+	int **intwork;
+	float **floatwork;
+//	short **shortmtx;
+#if STOREWM
+	float **WMMTX;
+	float **WMMTX2;
+#endif
+	float *midw;
+	float *midm;
+	float *midn;
+	float dumfl;
+	int lgth1, lgth2;
+	float maxwm;
+	int *jumpforwi;
+	int *jumpforwj;
+	int *jumpbacki;
+	int *jumpbackj;
+	int *jumpdummi; //muda
+	int *jumpdummj; //muda
+	int jumpi, jumpj;
+	char *gaps;
+	int ijpi, ijpj;
+	float *ogcp1;
+	float *fgcp1;
+	float *ogcp2;
+	float *fgcp2;
+#if STOREWM
+	static char ttt1[50000];
+	static char ttt2[50000];
+#endif
+
+
+	ogcp1 = gapinfo[0] + ist;
+	fgcp1 = gapinfo[1] + ist;
+	ogcp2 = gapinfo[2] + jst;
+	fgcp2 = gapinfo[3] + jst;
+
+
+	depth++;
+	reccycle++;
+
+	lgth1 = ien-ist+1;
+	lgth2 = jen-jst+1;
+
+
+#if STOREWM
+	fprintf( stderr, "==== MSalign (depth=%d, reccycle=%d), ist=%d, ien=%d, jst=%d, jen=%d\n", depth, reccycle, ist, ien, jst, jen );
+	strncpy( ttt1, seq1[0]+ist, lgth1 );
+	strncpy( ttt2, seq2[0]+jst, lgth2 );
+	ttt1[lgth1] = 0;
+	ttt2[lgth2] = 0;
+	fprintf( stderr, "seq1 = %s\n", ttt1 );
+	fprintf( stderr, "seq2 = %s\n", ttt2 );
+#endif
+	if( lgth2 <= 0 )
+	{
+		fprintf( stderr, "==== jimei\n" );
+//		exit( 1 );
+		for( i=0; i<icyc; i++ ) 
+		{
+			strncpy( mseq1[i], seq1[i]+ist, lgth1 );
+			mseq1[i][lgth1] = 0;
+		}
+		for( i=0; i<jcyc; i++ ) 
+		{
+			mseq2[i][0] = 0;
+			for( j=0; j<lgth1; j++ )
+				strcat( mseq2[i], "-" );
+		}
+
+//		fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+//		fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+		return( (float)offset * lgth1 );
+	}
+
+	aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
+	aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
+
+	if( lgth1 < DPTANNI || lgth2 < DPTANNI )
+	{
+//		fprintf( stderr, "==== Going to _tanni\n" );
+
+		value = MSalignmm_tanni( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ien, jst, jen, alloclen, aseq1, aseq2, gapinfo );	
+
+
+		for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+		for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+//		fprintf( stderr, "==== mseq1[0] (%d) = %s\n", depth, mseq1[0] );
+//		fprintf( stderr, "==== mseq2[0] (%d) = %s\n", depth, mseq2[0] );
+
+//		fprintf( stderr, "freeing aseq\n" );
+		FreeCharMtx( aseq1 );
+		FreeCharMtx( aseq2 );
+
+//		fprintf( stderr, "value = %f\n", value );
+
+		return( value );
+	}
+//	fprintf( stderr, "Trying to divide the mtx\n" );
+
+	ll1 = ( (int)(1.3*lgth1) ) + 100;
+	ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+//	fprintf( stderr, "ll1,ll2=%d,%d\n", ll1, ll2 );
+
+	w1 = AllocateFloatVec( ll2+2 );
+	w2 = AllocateFloatVec( ll2+2 );
+//	match = AllocateFloatVec( ll2+2 );
+	midw = AllocateFloatVec( ll2+2 );
+	midn = AllocateFloatVec( ll2+2 );
+	midm = AllocateFloatVec( ll2+2 );
+	jumpbacki = AllocateIntVec( ll2+2 );
+	jumpbackj = AllocateIntVec( ll2+2 );
+	jumpforwi = AllocateIntVec( ll2+2 );
+	jumpforwj = AllocateIntVec( ll2+2 );
+	jumpdummi = AllocateIntVec( ll2+2 );
+	jumpdummj = AllocateIntVec( ll2+2 );
+
+	initverticalw = AllocateFloatVec( ll1+2 );
+	lastverticalw = AllocateFloatVec( ll1+2 );
+
+	m = AllocateFloatVec( ll2+2 );
+	mp = AllocateIntVec( ll2+2 );
+	gaps = AllocateCharVec( MAX( ll1, ll2 ) + 2 );
+
+	floatwork = AllocateFloatMtx( MAX( ll1, ll2 )+2, 26 ); 
+	intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, 26 ); 
+
+#if DEBUG
+	fprintf( stderr, "succeeded\n" );
+#endif
+
+#if STOREWM
+	WMMTX = AllocateFloatMtx( ll1, ll2 );
+	WMMTX2 = AllocateFloatMtx( ll1, ll2 );
+#endif
+#if 0
+	shortmtx = AllocateShortMtx( ll1, ll2 );
+
+#if DEBUG
+	fprintf( stderr, "succeeded\n\n" );
+#endif
+
+	ijp = shortmtx;
+#endif
+
+	currentw = w1;
+	previousw = w2;
+
+	match_calc( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, floatwork, intwork, 1 );
+
+	match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, floatwork, intwork, 1 );
+
+	for( i=1; i<lgth1+1; i++ )
+	{
+		initverticalw[i] += fpenalty  * ( ogcp1[0] + fgcp1[i-1] );
+//		initverticalw[i] += fpenalty;
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		currentw[j] += fpenalty * ( ogcp2[0] + fgcp2[j-1] );
+//		currentw[j] += fpenalty;
+	}
+
+#if STOREWM
+	WMMTX[0][0] = initverticalw[0];
+	for( i=1; i<lgth1+1; i++ )
+	{
+		WMMTX[i][0] = initverticalw[i];
+	}
+	for( j=1; j<lgth2+1; j++ )
+	{
+		WMMTX[0][j] = currentw[j];
+	}
+#endif
+
+	for( j=1; j<lgth2+1; ++j ) 
+	{
+		m[j] = currentw[j-1] + fpenalty * ogcp1[1];
+//		m[j] = currentw[j-1];
+		mp[j] = 0;
+	}
+
+	lastverticalw[0] = currentw[lgth2-1];
+
+	imid = lgth1 * 0.5;
+
+	jumpi = 0; // atode kawaru.
+	lasti = lgth1+1;
+#if STOREWM
+	for( i=1; i<lasti; i++ )
+#else
+	for( i=1; i<=imid; i++ )
+#endif
+	{
+		wtmp = previousw; 
+		previousw = currentw;
+		currentw = wtmp;
+
+		previousw[0] = initverticalw[i-1];
+
+		match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+		currentw[0] = initverticalw[i];
+
+
+		mi = previousw[0] + fpenalty * ogcp2[1]; 
+//		mi = previousw[0];
+		mpi = 0;
+
+//		ijppt = ijp[i] + 1;
+		mjpt = m + 1;
+		prept = previousw;
+		curpt = currentw + 1;
+		mpjpt = mp + 1;
+
+
+		lastj = lgth2+1;
+		for( j=1; j<lastj; j++ )
+		{
+
+			wm = *prept;
+
+#if 0
+			fprintf( stderr, "%5.0f->", wm );
+#endif
+			g = mi + fpenalty * fgcp2[j-1];
+//			g = mi + fpenalty;
+#if 0
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijppt = -( j - mpi );
+			}
+			g = *prept + fpenalty * ogcp2[j];
+//			g = *prept;
+			if( g >= mi )
+			{
+				mi = g;
+				mpi = j-1;
+			}
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+			g = *mjpt + fpenalty  * fgcp1[i-1];
+//			g = *mjpt + fpenalty;
+#if 0 
+			fprintf( stderr, "%5.0f?", g );
+#endif
+			if( g > wm )
+			{
+				wm = g;
+//				*ijppt = +( i - *mpjpt );
+			}
+
+
+			g = *prept + fpenalty * ogcp1[i];
+//			g = *prept;
+			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;
+
+#if STOREWM
+			WMMTX[i][j] = *curpt;
+			WMMTX2[i][j] = *mjpt;
+#endif
+
+			if( i == imid ) //muda
+			{	
+				jumpbackj[j] = *mpjpt; // muda atode matomeru
+				jumpbacki[j] = mpi; // muda atode matomeru
+//				fprintf( stderr, "jumpbackj[%d] in forward dp is %d\n", j, *mpjpt );
+//				fprintf( stderr, "jumpbacki[%d] in forward dp is %d\n", j, mpi );
+				midw[j] = *curpt;
+				midm[j] = *mjpt;
+				midn[j] = mi;
+			}
+
+			mjpt++;
+			prept++;
+			mpjpt++;
+			curpt++;
+
+		}
+		lastverticalw[i] = currentw[lgth2-1];
+#if 0  // ue
+		if( i == imid )
+		{
+			for( j=0; j<lgth2; j++ ) midw[j] = currentw[j];
+			for( j=0; j<lgth2; j++ ) midm[j] = m[j];
+		}
+#endif
+	}
+//	for( j=0; j<lgth2; j++ ) midw[j] = WMMTX[imid][j];
+//	for( j=0; j<lgth2; j++ ) midm[j] = WMMTX2[imid][j];
+
+#if 0
+    for( i=0; i<lgth1; i++ )
+    {
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 10.2f ", WMMTX[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "WMMTX2 = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 10.2f ", WMMTX2[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "\n" );
+#endif
+
+// gyakudp
+
+	match_calc( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, floatwork, intwork, 1 );
+	match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, floatwork, intwork, 1 );
+
+	for( i=0; i<lgth1-1; i++ )
+	{
+		initverticalw[i] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+//		initverticalw[i] += fpenalty;
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		currentw[j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+//		currentw[j] += fpenalty;
+	}
+
+#if STOREWM
+	for( i=0; i<lgth1-1; i++ )
+	{
+		WMMTX[i][lgth2-1] += fpenalty * ( fgcp1[lgth1-1] + ogcp1[i+1] );
+		fprintf( stderr, "fgcp1[lgth1-1] + ogcp1[i+1] = %f\n", fgcp1[lgth1-1] + ogcp1[i+1] );
+	}
+	for( j=0; j<lgth2-1; j++ )
+	{
+		WMMTX[lgth1-1][j] += fpenalty * ( fgcp2[lgth2-1] + ogcp2[j+1] );
+		fprintf( stderr, "fgcp2[lgth2-1] + ogcp2[j+1] = %f\n", fgcp2[lgth2-1] + ogcp2[j+1] );
+	}
+#endif
+
+	for( j=lgth2-1; j>0; --j )
+	{
+		m[j-1] = currentw[j] + fpenalty * fgcp2[lgth2-2];
+//		m[j-1] = currentw[j];
+		mp[j] = lgth1-1;
+	}
+
+//	for( j=0; j<lgth2; j++ ) m[j] = 0.0;
+	// m[lgth2-1] ha irunoka?
+
+//	for( i=lgth1-2; i>=imid; i-- )
+	for( i=lgth1-2; i>-1; i-- )
+	{
+		wtmp = previousw;
+		previousw = currentw;
+		currentw = wtmp;
+		previousw[lgth2-1] = initverticalw[i+1];
+//		match_calc( currentw, seq1, seq2, i, lgth2 );
+		match_calc( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, floatwork, intwork, 0 );
+
+		currentw[lgth2-1] = initverticalw[i];
+
+		mi = previousw[lgth2-1] + fpenalty * fgcp2[lgth2-2];
+//		mi = previousw[lgth2-1];
+		mpi = lgth2 - 1;
+
+		mjpt = m + lgth2 - 2;
+		prept = previousw + lgth2 - 1;
+		curpt = currentw + lgth2 - 2;
+		mpjpt = mp + lgth2 - 2;
+
+
+		for( j=lgth2-2; j>-1; j-- )
+		{
+			wm = *prept;
+			ijpi = i+1;
+			ijpj = j+1;
+
+			g = mi + fpenalty * ogcp2[j+1];
+//			g = mi + fpenalty;
+			if( g > wm )
+			{
+				wm = g;
+				ijpj = mpi;
+			}
+
+			g = *prept + fpenalty * fgcp2[j];
+//			g = *prept;
+			if( g >= mi )
+			{
+//				fprintf( stderr, "i,j=%d,%d - renewed! mpi = %d\n", i, j, j+1 );
+				mi = g;
+				mpi = j + 1;
+			}
+
+#if USE_PENALTY_EX
+			mi += fpenalty_ex;
+#endif
+
+//			fprintf( stderr, "i,j=%d,%d *mpjpt = %d\n", i, j, *mpjpt );
+			g = *mjpt + fpenalty * ogcp1[i+1];
+//			g = *mjpt + fpenalty;
+			if( g > wm )
+			{
+				wm = g;
+				ijpi = *mpjpt;
+			}
+
+//			if( i == imid )fprintf( stderr, "i,j=%d,%d \n", i, j );
+			g = *prept + fpenalty * fgcp1[i];
+//			g = *prept;
+			if( g >= *mjpt )
+			{
+				*mjpt = g;
+				*mpjpt = i + 1;
+			}
+
+#if USE_PENALTY_EX
+			m[j] += fpenalty_ex;
+#endif
+
+			if( i == jumpi || i == imid - 1 )
+			{
+				jumpforwi[j] = ijpi; //muda
+				jumpforwj[j] = ijpj; //muda
+//				fprintf( stderr, "jumpfori[%d] = %d\n", j, ijpi );
+//				fprintf( stderr, "jumpforj[%d] = %d\n", j, ijpj );
+			}
+			if( i == imid ) // muda
+			{
+				midw[j] += wm;
+//				midm[j+1] += *mjpt + fpenalty; //??????
+				midm[j+1] += *mjpt; //??????
+			}
+			if( i == imid - 1 )
+			{
+//				midn[j] += mi + fpenalty;  //????
+				midn[j] += mi;  //????
+			}
+#if STOREWM
+			WMMTX[i][j] += wm;
+//			WMMTX2[i][j+1] += *mjpt + fpenalty;
+			WMMTX2[i][j+1] += *mjpt;
+#endif
+			*curpt += wm;
+
+			mjpt--;
+			prept--;
+			mpjpt--;
+			curpt--;
+		}
+
+		if( i == imid - 1 )	
+		{
+			maxwm = midw[1];
+//			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			for( j=2; j<lgth2-1; j++ )
+			{
+				wm = midw[j];
+				if( wm > maxwm )
+				{
+					jmid = j;
+					maxwm = wm;
+					jumpi = imid-1;
+					jumpj = jmid-1;
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+			for( j=1; j<lgth2; j++ )
+			{
+				wm = midm[j];
+				if( wm > maxwm )
+				{
+					jmid = j;
+					maxwm = wm;
+					jumpi = jumpbackj[jmid];
+					jumpj = jmid-1;
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+			for( j=2; j<lgth2; j++ )
+			{
+				wm = midn[j-1];
+				if( wm > maxwm )
+				{
+					jmid = j-1;
+					maxwm = wm;
+					jumpi = imid-1;
+					jumpj = jumpbacki[jmid];
+				}
+//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+			}
+
+			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
+
+#if 0
+			fprintf( stderr, "### imid=%d, jmid=%d\n", imid, jmid );
+			wm = midw[jmid];
+			jumpi = imid-1;
+			jumpj = jmid-1;
+			if( midn[jmid-1] > wm )
+			{
+				jumpi = imid-1;
+				jumpj = jumpbacki[jmid];
+				wm = midn[jmid-1];
+				fprintf( stderr, "rejump (n)\n" );
+			}
+			if( midm[jmid] > wm )
+			{
+				jumpi = jumpbackj[jmid];
+				jumpj = jmid-1;
+				wm = midm[jmid];
+				fprintf( stderr, "rejump (m) jumpi=%d\n", jumpi );
+			}
+#endif
+
+			fprintf( stderr, "--> imid=%d, jmid=%d\n", imid, jmid );
+			fprintf( stderr, "--> jumpi=%d, jumpj=%d\n", jumpi, jumpj );
+#if STOREWM
+			fprintf( stderr, "imid = %d\n", imid );
+			fprintf( stderr, "midn = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midn[j] );
+			}
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "midw = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midw[j] );
+			}
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "midm = \n" );
+			for( j=0; j<lgth2; j++ )
+			{
+				fprintf( stderr, "% 7.1f ", midm[j] );
+			}
+			fprintf( stderr, "\n" );
+#endif
+//			fprintf( stderr, "maxwm = %f\n", maxwm );
+		}
+
+		if( i == jumpi ) //saki?
+		{
+//			fprintf( stderr, "imid, jumpi = %d,%d\n", imid, jumpi );
+//			fprintf( stderr, "jmid, jumpj = %d,%d\n", jmid, jumpj );
+			imid = jumpforwi[jumpj];
+			jmid = jumpforwj[jumpj];
+			fprintf( stderr, "imid -> %d\n", imid );
+			fprintf( stderr, "jmid -> %d\n", jmid );
+#if STOREWM
+#else
+			break;
+#endif
+		}
+	}
+//	fprintf( stderr, "imid = %d, but jumpi = %d\n", imid, jumpi );
+//	fprintf( stderr, "jmid = %d, but jumpj = %d\n", jmid, jumpj );
+
+//	for( j=0; j<lgth2; j++ ) midw[j] += currentw[j];
+//	for( j=0; j<lgth2; j++ ) midm[j] += m[j+1];
+//	for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+//	for( j=0; j<lgth2; j++ ) midw[j] += WMMTX[imid][j];
+
+
+#if STOREWM
+	fprintf( stderr, "WMMTX = \n" );
+    for( i=0; i<lgth1; i++ )
+    {
+        fprintf( stderr, "%d ", i );
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 7.2f ", WMMTX[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+	fprintf( stderr, "WMMTX2 = (p = %f)\n", fpenalty );
+    for( i=0; i<lgth1; i++ )
+    {
+        fprintf( stderr, "%d ", i );
+        for( j=0; j<lgth2; j++ )
+        {
+            fprintf( stderr, "% 7.2f ", WMMTX2[i][j] );
+        }
+        fprintf( stderr, "\n" );
+    }
+
+	fprintf( stderr, "jumpbacki = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpbacki[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpbackj = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpbackj[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpforwi = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpforwi[j] );
+	}
+	fprintf( stderr, "\n" );
+	fprintf( stderr, "jumpforwj = \n" );
+	for( j=0; j<lgth2; j++ )
+	{
+		fprintf( stderr, "% 7d ", jumpforwj[j] );
+	}
+	fprintf( stderr, "\n" );
+
+
+#endif
+
+//	Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijp, icyc, jcyc );
+
+#if 0 // irukamo
+	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" );
+	}
+#endif
+
+
+
+#if 0
+	fprintf( stderr, "jumpi = %d, imid = %d\n", jumpi, imid );
+	fprintf( stderr, "jumpj = %d, jmid = %d\n", jumpj, jmid );
+
+	fprintf( stderr, "imid = %d\n", imid );
+	fprintf( stderr, "jmid = %d\n", jmid );
+#endif
+
+
+	FreeFloatVec( w1 );
+	FreeFloatVec( w2 );
+	FreeFloatVec( initverticalw );
+	FreeFloatVec( lastverticalw );
+	FreeFloatVec( midw );
+	FreeFloatVec( midm );
+	FreeFloatVec( midn );
+
+	FreeIntVec( jumpbacki );
+	FreeIntVec( jumpbackj );
+	FreeIntVec( jumpforwi );
+	FreeIntVec( jumpforwj );
+	FreeIntVec( jumpdummi );
+	FreeIntVec( jumpdummj );
+
+	FreeFloatVec( m );
+	FreeIntVec( mp );
+
+	FreeFloatMtx( floatwork );
+	FreeIntMtx( intwork );
+
+#if STOREWM
+	FreeFloatMtx( WMMTX );
+	FreeFloatMtx( WMMTX2 );
+#endif
+
+//	fprintf( stderr, "==== calling myself (first)\n" );
+
+	fprintf( stderr, "jumpi = %d\n", jumpi );
+	value = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist, ist+jumpi, jst, jst+jumpj, alloclen, aseq1, aseq2, depth, gapinfo );	
+	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
+	for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );
+
+//	fprintf( stderr, "====(f) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+//	fprintf( stderr, "====(f) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+	len = strlen( mseq1[0] );
+//	fprintf( stderr, "len = %d\n", len );
+	l = jmid - jumpj - 1;
+//	fprintf( stderr, "l=%d\n", l );
+	if( l > 0 )
+	{
+		for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+		for( i=0; i<icyc; i++ ) 
+		{
+			strcat( mseq1[i], gaps );
+			mseq1[i][len+l] = 0;
+		}
+		for( j=0; j<jcyc; j++ )
+		{
+			strncat( mseq2[j], seq2[j]+jst+jumpj+1, l );
+			mseq2[j][len+l] = 0;
+		}
+		fprintf( stderr, "penalizing (2) .. %f(%d), %f(%d)\n", ogcp2[jumpj+1], jumpj+1, fgcp2[jmid-1], jmid-1 );
+		value += fpenalty * ( ogcp2[jumpj+1] + fgcp2[jmid-1] );
+//		value += fpenalty;
+	}
+	len = strlen( mseq1[0] );
+	l = imid - jumpi - 1;
+//	fprintf( stderr, "l=%d\n", l );
+	if( l > 0 )
+	{
+		for( i=0; i<l; i++ ) gaps[i] = '-'; gaps[i] = 0;
+		for( i=0; i<icyc; i++ )
+		{
+			strncat( mseq1[i], seq1[i]+ist+jumpi+1, l );
+			mseq1[i][len+l] = 0;
+		}
+		for( j=0; j<jcyc; j++ ) 
+		{
+			strcat( mseq2[j], gaps );
+			mseq2[j][len+l] = 0;
+		}
+
+//		for( i=0; i<lgth1; i++ ) fprintf( stderr, "ogcp1[%d] = %f\n", i, ogcp1[i] );
+//		for( i=0; i<lgth1; i++ ) fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+
+
+		fprintf( stderr, "penalizing (1) .. ogcp1[%d] = %f, fgcp1[%d] = %f\n", jumpi+1, ogcp1[jumpi+1], imid-1, fgcp1[imid-1] );
+		value += fpenalty * ( ogcp1[jumpi+1] + fgcp1[imid-1] );
+//		value += fpenalty;
+	}
+#if 0
+	for( i=0; i<icyc; i++ ) fprintf( stderr, "after gapfill mseq1[%d]=%s\n", i, mseq1[i] );
+	for( i=0; i<jcyc; i++ ) fprintf( stderr, "after gapfill mseq2[%d]=%s\n", i, mseq2[i] );
+#endif
+
+//	fprintf( stderr, "==== calling myself (second)\n" );
+
+	value += MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, ist+imid, ien, jst+jmid, jen, alloclen, aseq1, aseq2, depth, gapinfo );	
+
+
+
+	if( value - maxwm > 1 || maxwm - value > 1 )
+	{
+		fprintf( stderr, "WARNING value  = %f, but maxwm = %f penalty = %f\n", value, maxwm, fpenalty );
+#if 1
+		for( i=0; i<icyc; i++ )
+		{
+			fprintf( stderr, ">1-%d\n%s\n", i, mseq1[i] );
+			fprintf( stderr, "%s\n", aseq1[i] );
+		}
+		for( i=0; i<jcyc; i++ )
+		{
+			fprintf( stderr, ">2-%d\n%s\n", i, mseq2[i] );
+			fprintf( stderr, "%s\n", aseq2[i] );
+		}
+#endif
+
+//		exit( 1 );
+	}
+	else
+	{
+		fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
+	}
+
+	for( i=0; i<icyc; i++ ) strcat( mseq1[i], aseq1[i] );
+	for( i=0; i<jcyc; i++ ) strcat( mseq2[i], aseq2[i] );
+
+//	fprintf( stderr, "====(s) aseq1[0] (%d) = %s (%d-%d)\n", depth, aseq1[0], ist, ien );
+//	fprintf( stderr, "====(s) aseq2[0] (%d) = %s (%d-%d)\n", depth, aseq2[0], jst, jen );
+
+	free( gaps );
+	FreeCharMtx( aseq1 );
+	FreeCharMtx( aseq2 );
+	
+	return( value );
+}
+
+
+
+float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen )
+/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
+{
+//	int k;
+	int i, j;
+	int ll1, ll2;
+	int lgth1, lgth2;
+	float wm;   /* int ?????? */
+	char **mseq1;
+	char **mseq2;
+	char **mseq;
+	float *ogcp1;
+	float *ogcp2;
+	float *fgcp1;
+	float *fgcp2;
+	float **cpmx1;
+	float **cpmx2;
+	float **gapinfo;
+
+#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
+
+	lgth1 = strlen( seq1[0] );
+	lgth2 = strlen( seq2[0] );
+
+	ll1 = ( (int)(1.3*lgth1) ) + 100;
+	ll2 = ( (int)(1.3*lgth2) ) + 100;
+
+	mseq1 = AllocateCharMtx( icyc, ll1+ll2 );
+	mseq2 = AllocateCharMtx( jcyc, ll1+ll2 );
+
+	gapinfo = AllocateFloatMtx( 4, 0 );
+	ogcp1 = AllocateFloatVec( ll1+2 );
+	ogcp2 = AllocateFloatVec( ll2+2 );
+	fgcp1 = AllocateFloatVec( ll1+2 );
+	fgcp2 = AllocateFloatVec( ll2+2 );
+
+
+	cpmx1 = AllocateFloatMtx( ll1+2, 27 );
+	cpmx2 = AllocateFloatMtx( ll2+2, 27 );
+
+	for( i=0; i<icyc; i++ ) 
+	{
+		seq1[i][lgth1] = 0;
+	}
+	for( j=0; j<jcyc; j++ )
+	{
+		seq2[j][lgth2] = 0;
+	}
+
+	MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
+	MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
+
+
+#if 1
+
+	OpeningGapCount( ogcp1, icyc, seq1, eff1, lgth1 );
+	OpeningGapCount( ogcp2, jcyc, seq2, eff2, lgth2 );
+	FinalGapCount( fgcp1, icyc, seq1, eff1, lgth1 );
+	FinalGapCount( fgcp2, jcyc, seq2, eff2, lgth2 );
+
+#if 1
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] );
+		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] );
+//		fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] );
+		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] );
+//		fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
+	}
+#else
+	for( i=0; i<lgth1; i++ ) 
+	{
+		ogcp1[i] = 0.5;
+		fgcp1[i] = 0.5;
+	}
+	for( i=0; i<lgth2; i++ ) 
+	{
+		ogcp2[i] = 0.5;
+		fgcp2[i] = 0.5;
+	}
+#endif
+
+	gapinfo[0] = ogcp1;
+	gapinfo[1] = fgcp1;
+	gapinfo[2] = ogcp2;
+	gapinfo[3] = fgcp2;
+#endif
+
+#if 0
+	fprintf( stdout, "in MSalignmm.c\n" );
+	for( i=0; i<icyc; i++ )
+	{
+		fprintf( stdout, ">%d of GROUP1\n", i );
+		fprintf( stdout, "%s\n", seq1[i] );
+	}
+	for( i=0; i<jcyc; i++ )
+	{
+		fprintf( stdout, ">%d of GROUP2\n", i );
+		fprintf( stdout, "%s\n", seq2[i] );
+	}
+	fflush( stdout );
+#endif
+
+	wm = MSalignmm_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo );
+
+//	fprintf( stderr, "wm = %f\n", wm );
+
+	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
+	for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );
+
+
+	FreeFloatVec( ogcp1 );
+	FreeFloatVec( ogcp2 );
+	FreeFloatVec( fgcp1 );
+	FreeFloatVec( fgcp2 );
+	FreeFloatMtx( cpmx1 );
+	FreeFloatMtx( cpmx2 );
+	free( (void *)gapinfo );
+
+	FreeCharMtx( mseq1 );
+	FreeCharMtx( mseq2 );
+
+	return( wm );
+}