X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2FMSalignmm.c.algLargeA;fp=binaries%2Fsrc%2Fmafft%2Fcore%2FMSalignmm.c.algLargeA;h=0000000000000000000000000000000000000000;hb=6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce;hp=fd773559d1a0a01577370d66cd434ca6f3a386f6;hpb=48f0451143441afce738d887b0cde1fb5cdbc02e;p=jabaws.git

diff --git a/binaries/src/mafft/core/MSalignmm.c.algLargeA b/binaries/src/mafft/core/MSalignmm.c.algLargeA
deleted file mode 100644
index fd77355..0000000
--- a/binaries/src/mafft/core/MSalignmm.c.algLargeA
+++ /dev/null
@@ -1,1461 +0,0 @@
-#include "mltaln.h"
-#include "dp.h"
-
-#define DEBUG 0
-#define XXXXXXX    0
-#define USE_PENALTY_EX  0
-#define STOREWM 0
-
-#define DPTANNI 1000
-
-
-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;
-	float firstm;
-	int firstmp;
-#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 ) // lgth1 <= 0 ha?
-	{
-		fprintf( stderr, "\n\n==== jimei\n\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( 0.0 );
-	}
-
-	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];
-
-		m[0] = fpenalty * ogcp1[i];
-#if STOREM
-		WMMTX2[i][0] = m[0];
-#endif
-		if( i == imid ) midm[0] = m[0];
-
-		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;
-			}
-
-//			fprintf( stderr, "m[%d] = %f\n", j, m[j] );
-			mjpt++;
-			prept++;
-			mpjpt++;
-			curpt++;
-
-		}
-		lastverticalw[i] = currentw[lgth2-1];
-
-#if STOREWM
-		WMMTX2[i][lgth2] = m[lgth2-1];
-#endif
-
-#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-- )
-	firstm = -9999999.9;
-	firstmp = lgth1-1;
-	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];
-
-//		m[lgth2] = fpenalty * fgcp1[i];
-//		WMMTX2[i][lgth2] += m[lgth2];
-//		fprintf( stderr, "m[] = %f\n", m[lgth2] );
-
-		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;
-				ijpi = i+1;
-			}
-
-			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;
-				ijpj = j+1;
-			}
-
-//			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--;
-		}
-//		fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
-		g = *prept + fpenalty * fgcp1[i];
-		if( firstm < g ) 
-		{
-			firstm = g;
-			firstmp = i + 1;
-		}
-#if STOREWM
-		WMMTX2[i][j+1] += firstm;
-#endif
-		if( i == imid ) midm[j+1] += firstm;
-
-		if( i == imid - 1 )	
-		{
-			maxwm = midw[1];
-			jmid = 0;
-//			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;
-				}
-//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
-			}
-			for( j=0; j<lgth2+1; j++ )
-			{
-				wm = midm[j];
-				if( wm > maxwm )
-				{
-					jmid = j;
-					maxwm = wm;
-				}
-//				if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
-			}
-
-//			if( depth == 1 ) fprintf( stderr, "maxwm!! = %f\n", maxwm );
-
-
-//			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 );
-			}
-
-
-//			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 );
-			if( jmid == 0 )
-			{
-//				fprintf( stderr, "CHUI2!\n" );
-				jumpj = 0; jmid = 1;
-				jumpi = firstmp - 1;
-				imid = firstmp;
-			}
-			else if( jmid == lgth2 )
-			{
-//				fprintf( stderr, "CHUI1!\n" );
-				jumpi=0; jumpj=0;
-				imid=jumpforwi[0]; jmid=lgth2-1;
-			}
-			else
-			{
-				imid = jumpforwi[jumpj];
-				jmid = jumpforwj[jumpj];
-			}
-#if 0
-			fprintf( stderr, "jumpi -> %d\n", jumpi );
-			fprintf( stderr, "jumpj -> %d\n", jumpj );
-			fprintf( stderr, "imid -> %d\n", imid );
-			fprintf( stderr, "jmid -> %d\n", jmid );
-#endif
-
-#if STOREWM
-			break;
-#else
-			break;
-#endif
-		}
-	}
-#if 0
-		jumpi=0; jumpj=0;
-		imid=lgth1-1; jmid=lgth2-1;
-	}
-#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+1; 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 DEBUG
-	if( value - maxwm > 1 || maxwm - value > 1 )
-	{
-		fprintf( stderr, "WARNING value  = %f, but maxwm = %f penalty = %f\n", value, maxwm, fpenalty );
-		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] );
-		}
-
-//		exit( 1 );
-	}
-	else
-	{
-		fprintf( stderr, "value = %.0f, maxwm = %.0f -> ok\n", value, maxwm );
-	}
-#endif
-
-	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 );
-}