text: #include "mltaln.h"
  #include "dp.h"
  
  #define DEBUG 0
  #define DEBUG2 0
  #define XXXXXXX    0
  #define USE_PENALTY_EX  1
  
  static int localstop;
  
  #if 1
  static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 ) 
  {
  	char tmpc = s1[0][i1];
  	char *seq2 = s2[0];
  
  	while( lgth2-- )
  		*match++ = amino_dis[(int)tmpc][(int)*seq2++];
  }
  #else
  static void match_calc( float *match, char **s1, char **s2, int i1, int lgth2 )
  {
  	int j;
  
  	for( j=0; j<lgth2; j++ )
  		match[j] = amino_dis[(*s1)[i1]][(*s2)[j]];
  }
  #endif
  
  #if 0
  static void match_calc_bk( 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[l][j] )
  				{
  					cpmxpd[count][j] = cpmx2[l][j];
  					cpmxpdn[count][j] = l;
  					count++;
  				}
  			}
  			cpmxpdn[count][j] = -1;
  		}
  	}
  
  	for( l=0; l<26; l++ )
  	{
  		scarr[l] = 0.0;
  		for( k=0; k<26; k++ )
  			scarr[l] += n_dis[k][l] * cpmx1[k][i1];
  	}
  #if 0 
  	{
  		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[k][j]>-1; k++ )
  			match[j] += scarr[cpmxpdn[k][j]] * cpmxpd[k][j];
  	} 
  #endif
  }
  #endif
  
  static float gentracking( float *lasthorizontalw, float *lastverticalw, 
  						char **seq1, char **seq2, 
                          char **mseq1, char **mseq2, 
                          float **cpmx1, float **cpmx2, 
                          int **ijpi, int **ijpj, int *off1pt, int *off2pt, int endi, int endj )
  {
  	int i, j, l, iin, jin, lgth1, lgth2, k, limk;
  	int ifi=0, jfi=0; // by D.Mathog
  	char gap[] = "-";
  	lgth1 = strlen( seq1[0] );
  	lgth2 = strlen( seq2[0] );
  
  #if 0
  	for( i=0; i<lgth1; i++ ) 
  	{
  		fprintf( stderr, "lastverticalw[%d] = %f\n", i, lastverticalw[i] );
  	}
  #endif
   
      for( i=0; i<lgth1+1; i++ ) 
      {
          ijpi[i][0] = localstop;
          ijpj[i][0] = localstop;
      }
      for( j=0; j<lgth2+1; j++ ) 
      {
          ijpi[0][j] = localstop;
          ijpj[0][j] = localstop;
      }
  
  	mseq1[0] += lgth1+lgth2;
  	*mseq1[0] = 0;
  	mseq2[0] += lgth1+lgth2;
  	*mseq2[0] = 0;
  	iin = endi; jin = endj;
  	limk = lgth1+lgth2;
  	for( k=0; k<=limk; k++ ) 
  	{
  
  		ifi = ( ijpi[iin][jin] );
  		jfi = ( ijpj[iin][jin] );
  		l = iin - ifi;
  //		if( ijpi[iin][jin] < 0 || ijpj[iin][jin] < 0 )
  //		{
  //			fprintf( stderr, "skip! %d-%d\n", ijpi[iin][jin], ijpj[iin][jin] );
  //			fprintf( stderr, "1: %c-%c\n", seq1[0][iin], seq1[0][ifi] );
  //			fprintf( stderr, "2: %c-%c\n", seq2[0][jin], seq2[0][jfi] );
  //		}
  		while( --l ) 
  		{
  			*--mseq1[0] = seq1[0][ifi+l];
  			*--mseq2[0] = *gap;
  			k++;
  		}
  		l= jin - jfi;
  		while( --l )
  		{
  			*--mseq1[0] = *gap;
  			*--mseq2[0] = seq2[0][jfi+l];
  			k++;
  		}
  
  		if( iin <= 0 || jin <= 0 ) break;
  		*--mseq1[0] = seq1[0][ifi];
  		*--mseq2[0] = seq2[0][jfi];
  
  		if( ijpi[ifi][jfi] == localstop ) break;
  		if( ijpj[ifi][jfi] == localstop ) break; 
  		k++;
  		iin = ifi; jin = jfi;
  	}
  	if( ifi == -1 ) *off1pt = 0; else *off1pt = ifi;
  	if( jfi == -1 ) *off2pt = 0; else *off2pt = jfi;
  
  //	fprintf( stderr, "ifn = %d, jfn = %d\n", ifi, jfi );
  
  
  	return( 0.0 );
  }
  
  
  float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt )
  /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
  {
  //	int k;
  	register int i, j;
  	int lasti, lastj; 
  	int lgth1, lgth2;
  	int resultlen;
  	float wm = 0.0;   /* int ?????? */
  	float g;
  	float *currentw, *previousw;
  #if 1
  	float *wtmp;
  	int *ijpipt;
  	int *ijpjpt;
  	float *mjpt, *Mjpt, *prept, *curpt;
  	int *mpjpt, *Mpjpt;
  #endif
  	static float mi, *m;
  	static float Mi, *largeM;
  	static int **ijpi;
  	static int **ijpj;
  	static int mpi, *mp;
  	static int Mpi, *Mp;
  	static float *w1, *w2;
  	static float *match;
  	static float *initverticalw;    /* kufuu sureba iranai */
  	static float *lastverticalw;    /* kufuu sureba iranai */
  	static char **mseq1;
  	static char **mseq2;
  	static char **mseq;
  	static float **cpmx1;
  	static float **cpmx2;
  	static int **intwork;
  	static float **floatwork;
  	static int orlgth1 = 0, orlgth2 = 0;
  	float maxwm;
  	float tbk;
  	int tbki, tbkj;
  	int endali, endalj;
  //	float localthr = 0.0;
  //	float localthr2 = 0.0;
  	float fpenalty = (float)penalty;
  	float fpenalty_OP = (float)penalty_OP;
  	float fpenalty_ex = (float)penalty_ex;
  //	float fpenalty_EX = (float)penalty_EX;
  	float foffset = (float)offset;
  	float localthr = -foffset;
  	float localthr2 = -foffset;
  
  
  //	fprintf( stderr, "@@@@@@@@@@@@@ penalty_OP = %f, penalty_EX = %f, pelanty = %f\n", fpenalty_OP, fpenalty_EX, fpenalty );
  
  	if( orlgth1 == 0 )
  	{
  		mseq1 = AllocateCharMtx( njob, 0 );
  		mseq2 = AllocateCharMtx( njob, 0 );
  	}
  
  
  	lgth1 = strlen( seq1[0] );
  	lgth2 = strlen( seq2[0] );
  
  	if( lgth1 > orlgth1 || lgth2 > orlgth2 )
  	{
  		int ll1, ll2;
  
  		if( orlgth1 > 0 && orlgth2 > 0 )
  		{
  			FreeFloatVec( w1 );
  			FreeFloatVec( w2 );
  			FreeFloatVec( match );
  			FreeFloatVec( initverticalw );
  			FreeFloatVec( lastverticalw );
  
  			FreeFloatVec( m );
  			FreeIntVec( mp );
  			FreeFloatVec( largeM );
  			FreeIntVec( Mp );
  
  			FreeCharMtx( mseq );
  
  			FreeFloatMtx( cpmx1 );
  			FreeFloatMtx( cpmx2 );
  
  			FreeFloatMtx( floatwork );
  			FreeIntMtx( intwork );
  		}
  
  		ll1 = MAX( (int)(1.3*lgth1), orlgth1 ) + 100;
  		ll2 = MAX( (int)(1.3*lgth2), orlgth2 ) + 100;
  
  #if DEBUG
  		fprintf( stderr, "\ntrying to allocate (%d+%d)xn matrices ... ", ll1, ll2 );
  #endif
  
  		w1 = AllocateFloatVec( ll2+2 );
  		w2 = AllocateFloatVec( ll2+2 );
  		match = AllocateFloatVec( ll2+2 );
  
  		initverticalw = AllocateFloatVec( ll1+2 );
  		lastverticalw = AllocateFloatVec( ll1+2 );
  
  		m = AllocateFloatVec( ll2+2 );
  		mp = AllocateIntVec( ll2+2 );
  		largeM = AllocateFloatVec( ll2+2 );
  		Mp = AllocateIntVec( ll2+2 );
  
  		mseq = AllocateCharMtx( njob, ll1+ll2 );
  
  		cpmx1 = AllocateFloatMtx( 26, ll1+2 );
  		cpmx2 = AllocateFloatMtx( 26, ll2+2 );
  
  		floatwork = AllocateFloatMtx( 26, MAX( ll1, ll2 )+2 ); 
  		intwork = AllocateIntMtx( 26, MAX( ll1, ll2 )+2 ); 
  
  #if DEBUG
  		fprintf( stderr, "succeeded\n" );
  #endif
  
  		orlgth1 = ll1 - 100;
  		orlgth2 = ll2 - 100;
  	}
  
  
  	mseq1[0] = mseq[0];
  	mseq2[0] = mseq[1];
  
  
  	if( orlgth1 > commonAlloc1 || orlgth2 > commonAlloc2 )
  	{
  		int ll1, ll2;
  
  		if( commonAlloc1 && commonAlloc2 )
  		{
  			FreeIntMtx( commonIP );
  			FreeIntMtx( commonJP );
  		}
  
  		ll1 = MAX( orlgth1, commonAlloc1 );
  		ll2 = MAX( orlgth2, commonAlloc2 );
  
  #if DEBUG
  		fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
  #endif
  
  		commonIP = AllocateIntMtx( ll1+10, ll2+10 );
  		commonJP = AllocateIntMtx( ll1+10, ll2+10 );
  
  #if DEBUG
  		fprintf( stderr, "succeeded\n\n" );
  #endif
  
  		commonAlloc1 = ll1;
  		commonAlloc2 = ll2;
  	}
  	ijpi = commonIP;
  	ijpj = commonJP;
  
  
  #if 0
  	for( i=0; i<lgth1; i++ ) 
  		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );
  #endif
  
  	currentw = w1;
  	previousw = w2;
  
  	match_calc( initverticalw, seq2, seq1, 0, lgth1 );
  
  	match_calc( currentw, seq1, seq2, 0, lgth2 );
  
  
  	lasti = lgth2+1;
  	for( j=1; j<lasti; ++j ) 
  	{
  		m[j] = currentw[j-1]; mp[j] = 0;
  		largeM[j] = currentw[j-1]; Mp[j] = 0;
  	}
  
  	lastverticalw[0] = currentw[lgth2-1];
  
  
  #if 0
  fprintf( stderr, "currentw = \n" );
  for( i=0; i<lgth1+1; i++ )
  {
  	fprintf( stderr, "%5.2f ", currentw[i] );
  }
  fprintf( stderr, "\n" );
  fprintf( stderr, "initverticalw = \n" );
  for( i=0; i<lgth2+1; i++ )
  {
  	fprintf( stderr, "%5.2f ", initverticalw[i] );
  }
  fprintf( stderr, "\n" );
  #endif
  #if DEBUG2
  	fprintf( stderr, "\n" );
  	fprintf( stderr, "       " );
  	for( j=0; j<lgth2+1; j++ )
  		fprintf( stderr, "%c     ", seq2[0][j] );
  	fprintf( stderr, "\n" );
  #endif
  
  	localstop = lgth1+lgth2+1;
  	maxwm = -999999999.9;
  	endali = endalj = 0;
  #if DEBUG2
  	fprintf( stderr, "\n" );
  	fprintf( stderr, "%c   ", seq1[0][0] );
  
  	for( j=0; j<lgth2+1; j++ )
  		fprintf( stderr, "%5.0f ", currentw[j] );
  	fprintf( stderr, "\n" );
  #endif
  
  	lasti = lgth1+1;
  	for( i=1; i<lasti; i++ )
  	{
  		wtmp = previousw; 
  		previousw = currentw;
  		currentw = wtmp;
  
  		previousw[0] = initverticalw[i-1];
  
  		match_calc( currentw, seq1, seq2, i, lgth2 );
  #if DEBUG2
  		fprintf( stderr, "%c   ", seq1[0][i] );
  		fprintf( stderr, "%5.0f ", currentw[0] );
  #endif
  
  #if XXXXXXX
  fprintf( stderr, "\n" );
  fprintf( stderr, "i=%d\n", i );
  fprintf( stderr, "currentw = \n" );
  for( j=0; j<lgth2; j++ )
  {
  	fprintf( stderr, "%5.2f ", currentw[j] );
  }
  fprintf( stderr, "\n" );
  #endif
  #if XXXXXXX
  fprintf( stderr, "\n" );
  fprintf( stderr, "i=%d\n", i );
  fprintf( stderr, "currentw = \n" );
  for( j=0; j<lgth2; j++ )
  {
  	fprintf( stderr, "%5.2f ", currentw[j] );
  }
  fprintf( stderr, "\n" );
  #endif
  		currentw[0] = initverticalw[i];
  
  		mi = previousw[0]; mpi = 0;
  		Mi = previousw[0]; Mpi = 0;
  
  #if 0
  		if( mi < localthr ) mi = localthr2;
  #endif
  
  		ijpipt = ijpi[i] + 1;
  		ijpjpt = ijpj[i] + 1;
  		mjpt = m + 1;
  		Mjpt = largeM + 1;
  		prept = previousw;
  		curpt = currentw + 1;
  		mpjpt = mp + 1;
  		Mpjpt = Mp + 1;
  		tbk = -999999.9;
  		tbki = 0;
  		tbkj = 0;
  		lastj = lgth2+1;
  		for( j=1; j<lastj; j++ )
  		{
  			wm = *prept;
  			*ijpipt = i-1;
  			*ijpjpt = j-1;
  
  
  //			fprintf( stderr, "i,j=%d,%d %c-%c\n", i, j, seq1[0][i], seq2[0][j] );
  //			fprintf( stderr, "wm=%f\n", wm );
  #if 0
  			fprintf( stderr, "%5.0f->", wm );
  #endif
  			g = mi + fpenalty;
  #if 0
  			fprintf( stderr, "%5.0f?", g );
  #endif
  			if( g > wm )
  			{
  				wm = g;
  //				*ijpipt = i - 1; 
  				*ijpjpt = mpi;
  			}
  			g = *prept;
  			if( g > mi )
  			{
  				mi = g;
  				mpi = j-1;
  			}
  
  #if USE_PENALTY_EX
  			mi += fpenalty_ex;
  #endif
  
  #if 0
  			fprintf( stderr, "%5.0f->", wm );
  #endif
  			g = *mjpt + fpenalty;
  #if 0
  			fprintf( stderr, "m%5.0f?", g );
  #endif
  			if( g > wm )
  			{
  				wm = g;
  				*ijpipt = *mpjpt;
  				*ijpjpt = j - 1; //IRU!
  			}
  			g = *prept;
  			if( g > *mjpt )
  			{
  				*mjpt = g;
  				*mpjpt = i-1;
  			}
  #if USE_PENALTY_EX
  			*mjpt += fpenalty_ex;
  #endif
  
  
  			g =  tbk + fpenalty_OP; 
  //			g =  tbk; 
  			if( g > wm )
  			{
  				wm = g;
  				*ijpipt = tbki;
  				*ijpjpt = tbkj;
  //				fprintf( stderr, "hit! i%d, j%d, ijpi = %d, ijpj = %d\n", i, j, *ijpipt, *ijpjpt );
  			}
  //			g = Mi;
  			if( Mi > tbk )
  			{
  				tbk = Mi; //error desu.
  				tbki = i-1;
  				tbkj = Mpi;
  			}
  //			g = *Mjpt;
  			if( *Mjpt > tbk )
  			{
  				tbk = *Mjpt;
  				tbki = *Mpjpt;
  				tbkj = j-1;
  			}
  //			tbk += fpenalty_EX;// + foffset;
  
  //			g = *prept;
  			if( *prept > *Mjpt )
  			{
  				*Mjpt = *prept;
  				*Mpjpt = i-1;
  			}
  //			*Mjpt += fpenalty_EX;// + foffset;
  
  //			g = *prept;
  			if( *prept > Mi )
  			{
  				Mi = *prept;
  				Mpi = j-1;
  			}
  //			Mi += fpenalty_EX;// + foffset;
  
  
  //			fprintf( stderr, "wm=%f, tbk=%f(%c-%c), mi=%f, *mjpt=%f\n", wm, tbk, seq1[0][tbki], seq2[0][tbkj], mi, *mjpt );
  //			fprintf( stderr, "ijp = %c,%c\n", seq1[0][abs(*ijpipt)], seq2[0][abs(*ijpjpt)] );
  
  
  			if( maxwm < wm )
  			{
  				maxwm = wm;
  				endali = i;
  				endalj = j;
  			}
  #if 1
  			if( wm < localthr )
  			{
  //				fprintf( stderr, "stop i=%d, j=%d, curpt=%f\n", i, j, *curpt );
  				*ijpipt = localstop;
  //				*ijpjpt = localstop; 
  				wm = localthr2;
  			}
  #endif
  #if 0
  			fprintf( stderr, "%5.0f ", *curpt );
  #endif
  #if DEBUG2
  			fprintf( stderr, "%5.0f ", wm );
  //			fprintf( stderr, "%c-%c *ijppt = %d, localstop = %d\n", seq1[0][i], seq2[0][j], *ijppt, localstop );
  #endif
  
  			*curpt += wm;
  			ijpipt++;
  			ijpjpt++;
  			mjpt++;
  			Mjpt++;
  			prept++;
  			mpjpt++;
  			Mpjpt++;
  			curpt++;
  		}
  #if DEBUG2
  		fprintf( stderr, "\n" );
  #endif
  
  		lastverticalw[i] = currentw[lgth2-1];
  	}
  
  
  #if DEBUG2
  	fprintf( stderr, "maxwm = %f\n", maxwm );
  	fprintf( stderr, "endali = %d\n", endali );
  	fprintf( stderr, "endalj = %d\n", endalj );
  #endif
  
  	if( ijpi[endali][endalj] == localstop ) // && ijpj[endali][endalj] == localstop )
  	{
  		strcpy( seq1[0], "" );
  		strcpy( seq2[0], "" );
  		*off1pt = *off2pt = 0;
  		return( 0.0 );
  	}
  
  
  	gentracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, cpmx1, cpmx2, ijpi, ijpj, off1pt, off2pt, endali, endalj );
  
  //	fprintf( stderr, "### impmatch = %f\n", *impmatch );
  
  	resultlen = strlen( mseq1[0] );
  	if( alloclen < resultlen || resultlen > N )
  	{
  		fprintf( stderr, "alloclen=%d, resultlen=%d, N=%d\n", alloclen, resultlen, N );
  		ErrorExit( "LENGTH OVER!\n" );
  	}
  
  
  	strcpy( seq1[0], mseq1[0] );
  	strcpy( seq2[0], mseq2[0] );
  
  #if 0
  	fprintf( stderr, "\n" );
  	fprintf( stderr, ">\n%s\n", mseq1[0] );
  	fprintf( stderr, ">\n%s\n", mseq2[0] );
  #endif
  
  
  	return( maxwm );
  }
  
  