#include "mltaln.h"
#include "dp.h"

#define MEMSAVE 1

#define DEBUG 0
#define USE_PENALTY_EX  0
#define STOREWM 1

#define DPTANNI 10

#define LOCAL 0

static int reccycle = 0;

static double localthr;

static void match_ribosum( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
	int j, k, l;
	double scarr[38];
	double **cpmxpd = doublework;
	int **cpmxpdn = intwork;
	int count = 0;
	double *matchpt;
	double **cpmxpdpt;
	int **cpmxpdnpt;
	int cpkd;

	if( initialize )
	{
		for( j=0; j<lgth2; j++ )
		{
			count = 0;
			for( l=0; l<37; l++ )
			{
				if( cpmx2[j][l] )
				{
					cpmxpd[j][count] = cpmx2[j][l];
					cpmxpdn[j][count] = l;
					count++;
				}
			}
			cpmxpdn[j][count] = -1;
		}
	}

	for( l=0; l<37; l++ )
	{
		scarr[l] = 0.0;
		for( k=0; k<37; k++ )
		{
			scarr[l] += ribosumdis[k][l] * cpmx1[i1][k];
		}
	}
#if 0 /* これを使うときはdoubleworkのアロケートを逆にする */
	{
		double *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++;
		} 
	}
	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];
	} 
#else
	matchpt = match;
	cpmxpdnpt = cpmxpdn;
	cpmxpdpt = cpmxpd;
	while( lgth2-- )
	{
		*matchpt = 0.0;
		for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
			*matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
		matchpt++;
		cpmxpdnpt++;
		cpmxpdpt++;
	}
#endif
}

static void match_calc( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
	int j, k, l;
//	double scarr[26];
	double **cpmxpd = doublework;
	int **cpmxpdn = intwork;
	int count = 0;
	double *matchpt;
	double **cpmxpdpt;
	int **cpmxpdnpt;
	int cpkd;
	double *scarr;
	scarr = calloc( nalphabets, sizeof( double ) );

	if( initialize )
	{
		for( j=0; j<lgth2; j++ )
		{
			count = 0;
			for( l=0; l<nalphabets; l++ )
			{
				if( cpmx2[j][l] )
				{
					cpmxpd[j][count] = cpmx2[j][l];
					cpmxpdn[j][count] = l;
					count++;
				}
			}
			cpmxpdn[j][count] = -1;
		}
	}

	for( l=0; l<nalphabets; l++ )
	{
		scarr[l] = 0.0;
		for( k=0; k<nalphabets; k++ )
		{
			scarr[l] += (n_dis[k][l]-RNAthr) * cpmx1[i1][k];
		}
	}
#if 0 /* これを使うときはdoubleworkのアロケートを逆にする */
	{
		double *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++;
		} 
	}
	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];
	} 
#else
	matchpt = match;
	cpmxpdnpt = cpmxpdn;
	cpmxpdpt = cpmxpd;
	while( lgth2-- )
	{
		*matchpt = 0.0;
		for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
			*matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
		matchpt++;
		cpmxpdnpt++;
		cpmxpdpt++;
	}
#endif
	free( scarr );
}

#if 0
static void match_add( double *match, double **cpmx1, double **cpmx2, int i1, int lgth2, double **doublework, int **intwork, int initialize )
{
	int j, k, l;
	double scarr[nalphabets];
	double **cpmxpd = doublework;
	int **cpmxpdn = intwork;
	int count = 0;
	double *matchpt;
	double **cpmxpdpt;
	int **cpmxpdnpt;
	int cpkd;


	if( initialize )
	{
		for( j=0; j<lgth2; j++ )
		{
			count = 0;
			for( l=0; l<nalphabets; l++ )
			{
				if( cpmx2[j][l] )
				{
					cpmxpd[j][count] = cpmx2[j][l];
					cpmxpdn[j][count] = l;
					count++;
				}
			}
			cpmxpdn[j][count] = -1;
		}
	}

	for( l=0; l<nalphabets; l++ )
	{
		scarr[l] = 0.0;
		for( k=0; k<nalphabets; k++ )
		{
			scarr[l] += n_dis[k][l] * cpmx1[i1][k];
		}
	}
#if 0 /* これを使うときはdoubleworkのアロケートを逆にする */
	{
		double *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++;
		} 
	}
	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];
	} 
#else
	matchpt = match;
	cpmxpdnpt = cpmxpdn;
	cpmxpdpt = cpmxpd;
	while( lgth2-- )
	{
//		*matchpt = 0.0; // add dakara
		for( k=0; (cpkd=(*cpmxpdnpt)[k])>-1; k++ )
			*matchpt += scarr[cpkd] * (*cpmxpdpt)[k];
		matchpt++;
		cpmxpdnpt++;
		cpmxpdpt++;
	}
#endif
}
#endif

#if 0
static double Atracking( 
						char **seq1, char **seq2, 
                        char **mseq1, char **mseq2, 
                        int **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 *gaptable1, *gt1bk;
	char *gaptable2, *gt2bk;
	lgth1 = ien-ist+1;
	lgth2 = jen-jst+1;

	gt1bk = AllocateCharVec( lgth1+lgth2+1 );
	gt2bk = AllocateCharVec( lgth1+lgth2+1 );

#if 0
	for( i=0; i<lgth1; i++ ) 
	{
		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
	}
#endif


//	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 );
    }


	gaptable1 = gt1bk + lgth1+lgth2;
	*gaptable1 = 0;
	gaptable2 = gt2bk + lgth1+lgth2;
	*gaptable2 = 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 ) 
		{
			*--gaptable1 = 'o';
			*--gaptable2 = '-';
			k++;
		}
		l= jin - jfi;
		while( --l )
		{
			*--gaptable1 = '-';
			*--gaptable2 = 'o';
			k++;
		}
		if( iin <= 0 || jin <= 0 ) break;
		*--gaptable1 = 'o';
		*--gaptable2 = 'o';
		k++;
		iin = ifi; jin = jfi;

	}

	for( i=0; i<icyc; i++ ) gapireru( mseq1[i], seq1[i]+ist, gaptable1 );
	for( j=0; j<jcyc; j++ ) gapireru( mseq2[j], seq2[j]+jst, gaptable2 );

	free( gt1bk );
	free( gt2bk );

//	fprintf( stderr, "in Atracking (owari), mseq1 = %s\n", mseq1[0] );
//	fprintf( stderr, "in Atracking (owari), mseq2 = %s\n", mseq2[0] );
	return( 0.0 );
}
#endif


static double MSalign2m2m_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, double **cpmx1, double **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, double **gapinfo, double **map )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
	double value = 0.0;
	register int i, j;
	char **aseq1, **aseq2;
	int ll1, ll2;
	int lasti, lastj, imid, jmid = 0;
	double wm = 0.0;   /* int ?????? */
	double g;
	double *currentw, *previousw;
#if USE_PENALTY_EX
	double fpenalty_ex = (double)penalty_ex;
#endif
//	double fpenalty = (double)penalty;
	double *wtmp;
//	short *ijppt;
	int *mpjpt;
//	short **ijp;
	int *mp;
	int mpi;
	double *mjpt, *prept, *curpt;
	double mi;
	double *m;
	double *w1, *w2;
//	double *match;
	double *initverticalw;    /* kufuu sureba iranai */
	double *lastverticalw;    /* kufuu sureba iranai */
	int **intwork;
	double **doublework;
//	short **shortmtx;
#if STOREWM
	double **WMMTX;
	double **WMMTX2;
#endif
	double *midw;
	double *midm;
	double *midn;
	int lgth1, lgth2;
	double maxwm = 0.0;
	int *jumpforwi;
	int *jumpforwj;
	int *jumpbacki;
	int *jumpbackj;
	int *jumpdummi; //muda
	int *jumpdummj; //muda
	int jumpi, jumpj = 0;
	char *gaps;
	int ijpi, ijpj;
	double *ogcp1;
	double *fgcp1;
	double *ogcp2;
	double *fgcp2;
	double firstm;
	int firstmp;
#if 0
	static char ttt1[50000];
	static char ttt2[50000];
#endif

	localthr = -offset + 500; // 0?

	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( lgth1 < 5 )
//		fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
//	if( lgth2 < 5 )
//		fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
//

#if 0
	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 );
	}

#if MEMSAVE
	aseq1 = AllocateCharMtx( icyc, 0 );
	aseq2 = AllocateCharMtx( jcyc, 0 );
	for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
	for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
#else
	aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
	aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
#endif

//  if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai 
//    if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
    if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
	{
//		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 );	


#if MEMSAVE
		free( aseq1 );
		free( aseq2 );
#else
		for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
		for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );

		FreeCharMtx( aseq1 );
		FreeCharMtx( aseq2 );
#endif

//		fprintf( stderr, "value = %f\n", value );

		return( value );
	}
//	fprintf( stderr, "Trying to divide the mtx\n" );

	ll1 = ( (int)(lgth1) ) + 100;
	ll2 = ( (int)(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 );

	doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets ); 
	intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets ); 

#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_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, 0, lgth1, doublework, intwork, 1 );

	match_ribosum( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 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 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] + 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_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );
		currentw[0] = initverticalw[i];

		m[0] = ogcp1[i];
#if STOREM
		WMMTX2[i][0] = m[0];
#endif
		if( i == imid ) midm[0] = m[0];

		mi = previousw[0] + 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 + fgcp2[j-1];
//			g = mi + fpenalty;
#if 0
			fprintf( stderr, "%5.0f?", g );
#endif
			if( g > wm )
			{
				wm = g;
//				*ijppt = -( j - mpi );
			}
			g = *prept + ogcp2[j];
//			g = *prept;
			if( g >= mi )
			{
				mi = g;
				mpi = j-1;
			}
#if USE_PENALTY_EX
			mi += fpenalty_ex;
#endif

			g = *mjpt + fgcp1[i-1];
//			g = *mjpt + fpenalty;
#if 0 
			fprintf( stderr, "%5.0f?", g );
#endif
			if( g > wm )
			{
				wm = g;
//				*ijppt = +( i - *mpjpt );
			}


			g = *prept + ogcp1[i];
//			g = *prept;
			if( g >= *mjpt )
			{
				*mjpt = g;
				*mpjpt = i-1;
			}
#if USE_PENALTY_EX
			m[j] += fpenalty_ex;
#endif
#if LOCAL
            if( wm < localthr )
            {       
//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
				wm = 0;
            }       
#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_ribosum( initverticalw, cpmx2+jst, cpmx1+ist, lgth2-1, lgth1, doublework, intwork, 1 );
	match_ribosum( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, doublework, intwork, 1 );

	for( i=0; i<lgth1-1; i++ )
	{
		initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
//		initverticalw[i] += fpenalty;
	}
	for( j=0; j<lgth2-1; j++ )
	{
		currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
//		currentw[j] += fpenalty;
	}

#if STOREWM
	for( i=0; i<lgth1-1; i++ )
	{
		WMMTX[i][lgth2-1] += ( 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] += ( 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] + 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_ribosum( currentw, cpmx1+ist, cpmx2+jst, i, lgth2, doublework, intwork, 0 );

		currentw[lgth2-1] = initverticalw[i];

//		m[lgth2] = fgcp1[i];
//		WMMTX2[i][lgth2] += m[lgth2];
//		fprintf( stderr, "m[] = %f\n", m[lgth2] );

		mi = previousw[lgth2-1] + 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 + ogcp2[j+1];
//			g = mi + fpenalty;
			if( g > wm )
			{
				wm = g;
				ijpj = mpi;
				ijpi = i+1;
			}

			g = *prept + 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 + 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 + 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 LOCAL
            if( wm < localthr )
            {       
//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
				wm = 0;
            }       
#endif

#if STOREWM
			WMMTX[i][j] += wm;
//			WMMTX2[i][j+1] += *mjpt + fpenalty;
			WMMTX2[i][j] += *curpt;
#endif
			*curpt += wm;

			mjpt--;
			prept--;
			mpjpt--;
			curpt--;
		}
//		fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
		g = *prept + 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( jmid > 0 && midn[jmid-1] > wm ) //060413
			{
				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 0
			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;
			}

#if 0
			else if( jmid == lgth2 ) 
			{
				fprintf( stderr, "CHUI1!\n" );
				jumpi=0; jumpj=0;
				imid=jumpforwi[0]; jmid=lgth2-1;
			}
#else // 060414
			else if( jmid >= lgth2 ) 
			{
//				fprintf( stderr, "CHUI1!\n" );
				jumpi=imid-1; jmid=lgth2;
				jumpj = lgth2-1;
			}
#endif
			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];



	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
		map[i][j] = WMMTX[i][j] / maxwm;
//		map[i][j] = WMMTX2[i][j] / maxwm;

#if STOREWM

#if 0
	for( i=0; i<lgth1; i++ )
	{
		double maxpairscore = -9999.9;
		double tmpscore;

		for( j=0; j<lgth2; j++ )
		{
			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
			{
				map12[i].pos = j;
				map12[i].score = tmpscore;
				maxpairscore = tmpscore;
			}
		}

		for( k=0; k<lgth1; k++ )
		{
			if( i == k ) continue;
			if( map12[i].score <= WMMTX[k][map12[i].pos] )
				break;
		}
		if( k != lgth1 )
		{
			map12[i].pos = -1;
			map12[i].score = -1.0;
		}
		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
	}
	for( j=0; j<lgth2; j++ )
	{
		double maxpairscore = -9999.9;
		double tmpscore;

		for( i=0; i<lgth1; i++ )
		{
			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
			{
				map21[j].pos = i;
				map21[j].score = tmpscore;
				maxpairscore = tmpscore;
			}
		}

		for( k=0; k<lgth2; k++ )
		{
			if( j == k ) continue;
			if( map21[j].score <= WMMTX[map21[j].pos][k] )
				break;
		}
		if( k != lgth2 )
		{
			map21[j].pos = -1;
			map21[j].score = -1.0;
		}
		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
	}

	for( i=0; i<lgth1; i++ )
	{
		if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i ) 
			fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
	}
#endif

#if 0
	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" );
    }
#endif

#if 0
    fprintf( stdout, "#WMMTX = \n" );
    for( i=0; i<lgth1; i++ )
    {
//        fprintf( stdout, "%d ", i ); 
        for( j=0; j<lgth2; j++ )
        {
//          if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
                fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
			if( WMMTX[i][j] == maxwm )
                fprintf( stdout, "selected \n" );
			else
                fprintf( stdout, "\n" );
        }
        fprintf( stdout, "\n" );
    }
#endif

#if 0

	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


#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( doublework );
	FreeIntMtx( intwork );

#if STOREWM
	FreeFloatMtx( WMMTX );
	FreeFloatMtx( WMMTX2 );
#endif

	return( value );

}
static double MSalignmm_rec( int icyc, int jcyc, double *eff1, double *eff2, char **seq1, char **seq2, double **cpmx1, double **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, int depth, double **gapinfo, double **map )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
	double value = 0.0;
	register int i, j;
	char **aseq1, **aseq2;
	int ll1, ll2;
	int lasti, lastj, imid, jmid=0;
	double wm = 0.0;   /* int ?????? */
	double g;
	double *currentw, *previousw;
#if USE_PENALTY_EX
	double fpenalty_ex = (double)RNApenalty_ex;
#endif
//	double fpenalty = (double)penalty;
	double *wtmp;
//	short *ijppt;
	int *mpjpt;
//	short **ijp;
	int *mp;
	int mpi;
	double *mjpt, *prept, *curpt;
	double mi;
	double *m;
	double *w1, *w2;
//	double *match;
	double *initverticalw;    /* kufuu sureba iranai */
	double *lastverticalw;    /* kufuu sureba iranai */
	int **intwork;
	double **doublework;
//	short **shortmtx;
#if STOREWM
	double **WMMTX;
	double **WMMTX2;
#endif
	double *midw;
	double *midm;
	double *midn;
	int lgth1, lgth2;
	double maxwm = 0.0;
	int *jumpforwi;
	int *jumpforwj;
	int *jumpbacki;
	int *jumpbackj;
	int *jumpdummi; //muda
	int *jumpdummj; //muda
	int jumpi, jumpj = 0;
	char *gaps;
	int ijpi, ijpj;
	double *ogcp1;
	double *fgcp1;
	double *ogcp2;
	double *fgcp2;
	double firstm;
	int firstmp;
#if 0
	static char ttt1[50000];
	static char ttt2[50000];
#endif

	localthr = -offset + 500; // 0?

	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( lgth1 < 5 )
//		fprintf( stderr, "\nWARNING: lgth1 = %d\n", lgth1 );
//	if( lgth2 < 5 )
//		fprintf( stderr, "\nWARNING: lgth2 = %d\n", lgth2 );
//

#if 0
	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 );
	}

#if MEMSAVE
	aseq1 = AllocateCharMtx( icyc, 0 );
	aseq2 = AllocateCharMtx( jcyc, 0 );
	for( i=0; i<icyc; i++ ) aseq1[i] = mseq1[i];
	for( i=0; i<jcyc; i++ ) aseq2[i] = mseq2[i];
#else
	aseq1 = AllocateCharMtx( icyc, lgth1+lgth2+100 );
	aseq2 = AllocateCharMtx( jcyc, lgth1+lgth2+100 );
#endif

//  if( lgth1 < DPTANNI && lgth2 < DPTANNI ) // & dato lgth ==1 no kanousei ga arunode yokunai 
//    if( lgth1 < DPTANNI ) // kore mo lgth2 ga mijikasugiru kanousei ari
    if( lgth1 < DPTANNI || lgth2 < DPTANNI ) // zettai ni anzen ka?
	{
//		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 );	


#if MEMSAVE
		free( aseq1 );
		free( aseq2 );
#else
		for( i=0; i<icyc; i++ ) strcpy( mseq1[i], aseq1[i] );
		for( i=0; i<jcyc; i++ ) strcpy( mseq2[i], aseq2[i] );

		FreeCharMtx( aseq1 );
		FreeCharMtx( aseq2 );
#endif

//		fprintf( stderr, "value = %f\n", value );

		return( value );
	}
//	fprintf( stderr, "Trying to divide the mtx\n" );

	ll1 = ( (int)(lgth1) ) + 100;
	ll2 = ( (int)(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 );

	doublework = AllocateFloatMtx( MAX( ll1, ll2 )+2, nalphabets ); 
	intwork = AllocateIntMtx( MAX( ll1, ll2 )+2, nalphabets ); 

#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, doublework, intwork, 1 );

	match_calc( currentw, cpmx1+ist, cpmx2+jst, 0, lgth2, doublework, intwork, 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 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] + 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, doublework, intwork, 0 );
		currentw[0] = initverticalw[i];

		m[0] = ogcp1[i];
#if STOREM
		WMMTX2[i][0] = m[0];
#endif
		if( i == imid ) midm[0] = m[0];

		mi = previousw[0] + 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 + fgcp2[j-1];
//			g = mi + fpenalty;
#if 0
			fprintf( stderr, "%5.0f?", g );
#endif
			if( g > wm )
			{
				wm = g;
//				*ijppt = -( j - mpi );
			}
			g = *prept + ogcp2[j];
//			g = *prept;
			if( g >= mi )
			{
				mi = g;
				mpi = j-1;
			}
#if USE_PENALTY_EX
			mi += fpenalty_ex;
#endif

			g = *mjpt + fgcp1[i-1];
//			g = *mjpt + fpenalty;
#if 0 
			fprintf( stderr, "%5.0f?", g );
#endif
			if( g > wm )
			{
				wm = g;
//				*ijppt = +( i - *mpjpt );
			}


			g = *prept + ogcp1[i];
//			g = *prept;
			if( g >= *mjpt )
			{
				*mjpt = g;
				*mpjpt = i-1;
			}
#if USE_PENALTY_EX
			m[j] += fpenalty_ex;
#endif
#if LOCAL
            if( wm < localthr )
            {       
//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
				wm = 0;
            }       
#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, doublework, intwork, 1 );
	match_calc( currentw, cpmx1+ist, cpmx2+jst, lgth1-1, lgth2, doublework, intwork, 1 );

	for( i=0; i<lgth1-1; i++ )
	{
		initverticalw[i] += ( fgcp1[lgth1-1] + ogcp1[i+1] );
//		initverticalw[i] += fpenalty;
	}
	for( j=0; j<lgth2-1; j++ )
	{
		currentw[j] += ( fgcp2[lgth2-1] + ogcp2[j+1] );
//		currentw[j] += fpenalty;
	}

#if STOREWM
	for( i=0; i<lgth1-1; i++ )
	{
		WMMTX[i][lgth2-1] += ( 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] += ( 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] + 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, doublework, intwork, 0 );

		currentw[lgth2-1] = initverticalw[i];

//		m[lgth2] = fgcp1[i];
//		WMMTX2[i][lgth2] += m[lgth2];
//		fprintf( stderr, "m[] = %f\n", m[lgth2] );

		mi = previousw[lgth2-1] + 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 + ogcp2[j+1];
//			g = mi + fpenalty;
			if( g > wm )
			{
				wm = g;
				ijpj = mpi;
				ijpi = i+1;
			}

			g = *prept + 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 + 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 + 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 LOCAL
            if( wm < localthr )
            {       
//				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
				wm = 0;
            }       
#endif

#if STOREWM
			WMMTX[i][j] += wm;
//			WMMTX2[i][j+1] += *mjpt + fpenalty;
			WMMTX2[i][j] += *curpt;
#endif
			*curpt += wm;

			mjpt--;
			prept--;
			mpjpt--;
			curpt--;
		}
//		fprintf( stderr, "adding *mjpt (=%f) to WMMTX2[%d][%d]\n", *mjpt, i, j+1 );
		g = *prept + 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( jmid > 0 && midn[jmid-1] > wm ) //060413
			{
				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 0
			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;
			}

#if 0
			else if( jmid == lgth2 ) 
			{
				fprintf( stderr, "CHUI1!\n" );
				jumpi=0; jumpj=0;
				imid=jumpforwi[0]; jmid=lgth2-1;
			}
#else // 060414
			else if( jmid >= lgth2 ) 
			{
//				fprintf( stderr, "CHUI1!\n" );
				jumpi=imid-1; jmid=lgth2;
				jumpj = lgth2-1;
			}
#endif
			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];



	for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
		map[i][j] = WMMTX[i][j] / maxwm;
//		map[i][j] = WMMTX2[i][j] / maxwm;

#if STOREWM

#if 0
	for( i=0; i<lgth1; i++ )
	{
		double maxpairscore = -9999.9;
		double tmpscore;

		for( j=0; j<lgth2; j++ )
		{
			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
			{
				map12[i].pos = j;
				map12[i].score = tmpscore;
				maxpairscore = tmpscore;
			}
		}

		for( k=0; k<lgth1; k++ )
		{
			if( i == k ) continue;
			if( map12[i].score <= WMMTX[k][map12[i].pos] )
				break;
		}
		if( k != lgth1 )
		{
			map12[i].pos = -1;
			map12[i].score = -1.0;
		}
		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, map12[i].pos, map12[i].score, seq1[0][i], seq2[0][map12[i].pos] );
	}
	for( j=0; j<lgth2; j++ )
	{
		double maxpairscore = -9999.9;
		double tmpscore;

		for( i=0; i<lgth1; i++ )
		{
			if( maxpairscore < (tmpscore=WMMTX[i][j]) )
			{
				map21[j].pos = i;
				map21[j].score = tmpscore;
				maxpairscore = tmpscore;
			}
		}

		for( k=0; k<lgth2; k++ )
		{
			if( j == k ) continue;
			if( map21[j].score <= WMMTX[map21[j].pos][k] )
				break;
		}
		if( k != lgth2 )
		{
			map21[j].pos = -1;
			map21[j].score = -1.0;
		}
		fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", j, map21[j].pos, map21[j].score, seq2[0][j], seq1[0][map21[j].pos] );
	}

	for( i=0; i<lgth1; i++ )
	{
		if( map12[i].pos != -1 ) if( map21[map12[i].pos].pos != i ) 
			fprintf( stderr, "ERROR i=%d, but map12[i].pos=%d and map21[map12[i].pos]=%d\n", i, map12[i].pos, map21[map12[i].pos].pos );
	}
#endif

#if 0
	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" );
    }
	exit( 1 );
#endif

#if 0
    fprintf( stdout, "#WMMTX = \n" );
    for( i=0; i<lgth1; i++ )
    {
//        fprintf( stdout, "%d ", i ); 
        for( j=0; j<lgth2; j++ )
        {
//          if( WMMTX[i][j] > amino_dis['a']['g'] -1 )
                fprintf( stdout, "%d %d %8.1f", i, j, WMMTX[i][j] );
			if( WMMTX[i][j] == maxwm )
                fprintf( stdout, "selected \n" );
			else
                fprintf( stdout, "\n" );
        }
        fprintf( stdout, "\n" );
    }
	exit( 1 );
#endif

#if 0

	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


#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( doublework );
	FreeIntMtx( intwork );

#if STOREWM
	FreeFloatMtx( WMMTX );
	FreeFloatMtx( WMMTX2 );
#endif


	free( gaps );
#if MEMSAVE
	free( aseq1 );
	free( aseq2 );
#else
	FreeCharMtx( aseq1 );
	FreeCharMtx( aseq2 );
#endif
	
	return( value );
}



double Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, double **map )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
//	int k;
	int i, j;
	int ll1, ll2;
	int lgth1, lgth2;
	double wm = 0.0;   /* int ?????? */
	char **mseq1;
	char **mseq2;
//	char **mseq;
	double *ogcp1;
	double *ogcp2;
	double *fgcp1;
	double *fgcp2;
	double **cpmx1;
	double **cpmx2;
	double **gapinfo;
//	double fpenalty;
	double fpenalty = (double)RNApenalty;
	int nglen1, nglen2;





#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

	nglen1 = seqlen( seq1[0] );
	nglen2 = seqlen( seq2[0] );

	lgth1 = strlen( seq1[0] );
	lgth2 = strlen( seq2[0] );

	ll1 = ( (int)(lgth1) ) + 100;
	ll2 = ( (int)(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, nalphabets+1 );
	cpmx2 = AllocateFloatMtx( ll2+2, nalphabets+1 );

	for( i=0; i<icyc; i++ ) 
	{
		if( strlen( seq1[i] ) != lgth1 )
		{
			fprintf( stderr, "i = %d / %d\n", i, icyc );
			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
			exit( 1 );
		}
	}
	for( j=0; j<jcyc; j++ )
	{
		if( strlen( seq2[j] ) != lgth2 )
		{
			fprintf( stderr, "j = %d / %d\n", j, jcyc );
			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
			exit( 1 );
		}
	}

	MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
	MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );


#if 1

	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, egap2 );
		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 );
	}

#if 1
	for( i=0; i<lgth1; i++ ) 
	{
		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
//		fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
	}
	for( i=0; i<lgth2; i++ ) 
	{
		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
//		fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
	}
#else
	for( i=0; i<lgth1; i++ ) 
	{
		ogcp1[i] = 0.5 * fpenalty;
		fgcp1[i] = 0.5 * fpenalty;
	}
	for( i=0; i<lgth2; i++ ) 
	{
		ogcp2[i] = 0.5 * fpenalty;
		fgcp2[i] = 0.5 * fpenalty;
	}
#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, map );
#if DEBUG
		fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
		fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
		fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
		fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
#endif

//	fprintf( stderr, "wm = %f\n", wm );

#if 0

	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
	for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );

	if( seqlen( seq1[0] ) != nglen1 )
	{
		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
		fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
		exit( 1 );
	}
	if( seqlen( seq2[0] ) != nglen2 )
	{
		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
		exit( 1 );
	}
#endif

	FreeFloatVec( ogcp1 );
	FreeFloatVec( ogcp2 );
	FreeFloatVec( fgcp1 );
	FreeFloatVec( fgcp2 );
	FreeFloatMtx( cpmx1 );
	FreeFloatMtx( cpmx2 );
	free( (void *)gapinfo );

	FreeCharMtx( mseq1 );
	FreeCharMtx( mseq2 );

	lgth1 = strlen( seq1[0] );
	lgth2 = strlen( seq2[0] );
	for( i=0; i<icyc; i++ ) 
	{
		if( strlen( seq1[i] ) != lgth1 )
		{
			fprintf( stderr, "i = %d / %d\n", i, icyc );
			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
			exit( 1 );
		}
	}
	for( j=0; j<jcyc; j++ )
	{
		if( strlen( seq2[j] ) != lgth2 )
		{
			fprintf( stderr, "j = %d / %d\n", j, jcyc );
			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
			exit( 1 );
		}
	}

	return( wm );
}

double Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *sgap1, char *sgap2, char *egap1, char *egap2, double **map )
/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
{
//	int k;
	int i, j;
	int ll1, ll2;
	int lgth1, lgth2;
	double wm = 0.0;   /* int ?????? */
	char **mseq1;
	char **mseq2;
	double *ogcp1;
	double *ogcp2;
	double *fgcp1;
	double *fgcp2;
	double **cpmx1;
	double **cpmx2;
	double **gapinfo;
	double fpenalty = (double)penalty;
	int nglen1, nglen2;

#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

	nglen1 = seqlen( seq1[0] );
	nglen2 = seqlen( seq2[0] );

	lgth1 = strlen( seq1[0] );
	lgth2 = strlen( seq2[0] );

	ll1 = ( (int)(lgth1) ) + 100;
	ll2 = ( (int)(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, 39 );
	cpmx2 = AllocateFloatMtx( ll2+2, 39 );

	for( i=0; i<icyc; i++ ) 
	{
		if( strlen( seq1[i] ) != lgth1 )
		{
			fprintf( stderr, "i = %d / %d\n", i, icyc );
			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
			exit( 1 );
		}
	}
	for( j=0; j<jcyc; j++ )
	{
		if( strlen( seq2[j] ) != lgth2 )
		{
			fprintf( stderr, "j = %d / %d\n", j, jcyc );
			fprintf( stderr, "bug! hairetsu ga kowareta!\n" );
			exit( 1 );
		}
	}

#if 0
	MScpmx_calc_new( seq1, cpmx1, eff1, lgth1, icyc );
	MScpmx_calc_new( seq2, cpmx2, eff2, lgth2, jcyc );
#else
	cpmx_ribosum( seq1, seq1r, dir1, cpmx1, eff1, lgth1, icyc );
	cpmx_ribosum( seq2, seq2r, dir2, cpmx2, eff2, lgth2, jcyc );
#endif


#if 1

	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, egap2 );
		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 );
	}

#if 1
	for( i=0; i<lgth1; i++ ) 
	{
		ogcp1[i] = 0.5 * ( 1.0 - ogcp1[i] ) * fpenalty;
		fgcp1[i] = 0.5 * ( 1.0 - fgcp1[i] ) * fpenalty;
//		fprintf( stderr, "fgcp1[%d] = %f\n", i, fgcp1[i] );
	}
	for( i=0; i<lgth2; i++ ) 
	{
		ogcp2[i] = 0.5 * ( 1.0 - ogcp2[i] ) * fpenalty;
		fgcp2[i] = 0.5 * ( 1.0 - fgcp2[i] ) * fpenalty;
//		fprintf( stderr, "fgcp2[%d] = %f\n", i, fgcp2[i] );
	}
#else
	for( i=0; i<lgth1; i++ ) 
	{
		ogcp1[i] = 0.5 * fpenalty;
		fgcp1[i] = 0.5 * fpenalty;
	}
	for( i=0; i<lgth2; i++ ) 
	{
		ogcp2[i] = 0.5 * fpenalty;
		fgcp2[i] = 0.5 * fpenalty;
	}
#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 = MSalign2m2m_rec( icyc, jcyc, eff1, eff2, seq1, seq2, cpmx1, cpmx2, 0, lgth1-1, 0, lgth2-1, alloclen, mseq1, mseq2, 0, gapinfo, map );
#if DEBUG
		fprintf( stderr, " seq1[0] = %s\n", seq1[0] );
		fprintf( stderr, " seq2[0] = %s\n", seq2[0] );
		fprintf( stderr, "mseq1[0] = %s\n", mseq1[0] );
		fprintf( stderr, "mseq2[0] = %s\n", mseq2[0] );
#endif

//	fprintf( stderr, "wm = %f\n", wm );

#if 0

	for( i=0; i<icyc; i++ ) strcpy( seq1[i], mseq1[i] );
	for( i=0; i<jcyc; i++ ) strcpy( seq2[i], mseq2[i] );

	if( seqlen( seq1[0] ) != nglen1 )
	{
		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen1) seqlen(seq1[0])=%d but nglen1=%d\n", seqlen( seq1[0] ), nglen1 );
		fprintf( stderr, "seq1[0] = %s\n", seq1[0] );
		exit( 1 );
	}
	if( seqlen( seq2[0] ) != nglen2 )
	{
		fprintf( stderr, "bug! hairetsu ga kowareta! (nglen2) seqlen(seq2[0])=%d but nglen2=%d\n", seqlen( seq2[0] ), nglen2 );
		exit( 1 );
	}
#endif

	FreeFloatVec( ogcp1 );
	FreeFloatVec( ogcp2 );
	FreeFloatVec( fgcp1 );
	FreeFloatVec( fgcp2 );
	FreeFloatMtx( cpmx1 );
	FreeFloatMtx( cpmx2 );
	free( (void *)gapinfo );

	FreeCharMtx( mseq1 );
	FreeCharMtx( mseq2 );

	lgth1 = strlen( seq1[0] );
	lgth2 = strlen( seq2[0] );
	for( i=0; i<icyc; i++ ) 
	{
		if( strlen( seq1[i] ) != lgth1 )
		{
			fprintf( stderr, "i = %d / %d\n", i, icyc );
			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
			exit( 1 );
		}
	}
	for( j=0; j<jcyc; j++ )
	{
		if( strlen( seq2[j] ) != lgth2 )
		{
			fprintf( stderr, "j = %d / %d\n", j, jcyc );
			fprintf( stderr, "hairetsu ga kowareta (end of MSalignmm) !\n" );
			exit( 1 );
		}
	}

	return( wm );
}
