MultiSource/Benchmarks/mafft/Calignm1.c - third_party/llvm-test-suite - Git at Google

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

 #define DEBUG 0

 void tracking( char **nseq, char **aseq, char *seq, int **ijp, int icyc )
 {
 	int i, k, l;
 	int iin, ifi, jin, jfi;
 	int lgth = strlen( aseq[0] );
 	int lgth1 = strlen( seq );
 	char gap[] = "-";

 	for( i=0; i<=icyc+1; i++ )
 	{
 		nseq[i] += lgth+lgth1;
 		*nseq[i] = 0;
 	}

 	iin = lgth; jin = lgth1;
 	for( k=0; k<=lgth+lgth1; )
 	{
 		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;
 			/*
 			if( ifi < 0 ) jfi = -1;
 			if( jfi < 0 ) ifi = -1;
 			*/
 		}
 		for( l=1; l<iin-ifi; l++ )
 		{
 			for( i=0; i<icyc+1; i++ )
 				*--nseq[i] = aseq[i][iin-l];
 			*--nseq[icyc+1] = *gap;
 			k++;
 		}
 		for( l=1; l<jin-jfi; l++ )
 		{
 			for( i=0; i<icyc+1; i++ )
 				*--nseq[i] = *gap;
 			nseq[icyc+1]--;
 			*nseq[icyc+1] = seq[jin-l];
 			k++;
 		}
 		if( iin <= 0 || jin <= 0 ) break;
 		for( i=0; i<icyc+1; i++ )
 			*--nseq[i] = aseq[i][ifi];
 		*--nseq[icyc+1] = seq[jfi];
 		k++;
 		iin = ifi; jin = jfi;
 	}
 }


 char **Calignm1( float *wm, char **aseq, char *seq, double *effarr, int icyc, int ex )
 {
 	register int i, j, k, l;
 	float tmpfloat;
 	int inttmp;
 	static float mi, *m;
 	static int mpi, *mp;
 	static float ***g;
 	int gb1, gc1;
 	static int **ijp;
 	static float **v, **w;
 	static float *gvsa;
 	static char **mseq;
 	static char **nseq;
 	static float **scmx;
 	float wmax;
 	int lgth, lgth1;
 	static int orlgth = 0, orlgth1 = 0;
 	float x;
 	float efficient;
 	float *AllocateFloatVec( int );
 	float totaleff;
 	static float **gl;
 	static float **gs;
 	float **AllocateFloatTri( int );
 	void FreeFloatTri( float ** );

 #if DEBUG
 	FILE *fp;
 #endif


 	totaleff = 0.0;
 	for( i=0; i<icyc+1; i++ ) totaleff += effarr[i];
 	lgth = strlen( aseq[0] );
 	lgth1 = strlen( seq );


 #if DEBUG
 	fprintf( stdout, "effarr in Calignm1 s = \n", ex  );
 	for( i=0; i<icyc+1; i++ )
 		fprintf( stdout, " %f", effarr[i] );
 	printf( "\n" );
 #endif

 	if( orlgth > 0 && orlgth1 > 0 ) for( i=0; i<njob+1; i++ ) nseq[i] = mseq[i];
 /*
  *     allocate
  */

 	if( lgth > orlgth || lgth1 > orlgth1 )
 	{
 		int ll1, ll2;

 		if( orlgth > 0 && orlgth1 > 0 )
 		{
 			FreeFloatMtx( v );

 			FreeFloatCub( g );
 			FreeFloatTri( gl );
 			FreeFloatTri( gs );

 			FreeFloatVec( m );
 			FreeIntVec( mp );

 #if 0
 			FreeCharMtx( nseq );
 #endif
 			FreeCharMtx( mseq );

 			FreeFloatVec( gvsa );
 			FreeFloatMtx( scmx );
 		}

 		ll1 = MAX( (int)(1.1*lgth), orlgth );
 		ll2 = MAX( (int)(1.1*lgth1), orlgth1 );
 		ll1 = MAX( ll1, ll2 );

 #if DEBUG
 		fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 #endif

 		v = AllocateFloatMtx( ll1+2, ll2+2 );

 		g = AllocateFloatCub( ll1+2, 3, 3 );

 		gl = AllocateFloatTri( MAX( ll1, ll2 ) + 3 );
 		gs = AllocateFloatTri( MAX( ll1, ll2 ) + 3 );

 		m = AllocateFloatVec( ll1+2 );
 		mp = AllocateIntVec( ll1+2 );

 		mseq = AllocateCharMtx( njob+1, 1 );
 		nseq = AllocateCharMtx( njob+1, ll1+ll2 );
 		for( i=0; i<njob+1; i++ ) mseq[i] = nseq[i];

 		gvsa = AllocateFloatVec( ll1+2 );

 		scmx = AllocateFloatMtx( 26, ll1+2 );

 #if DEBUG
 		fprintf( stderr, "succeeded\n\n" );
 #endif

 		orlgth = ll1;
 		orlgth1 = ll2;
 #if DEBUG
 		fprintf( stderr, "orlgth   ==  %d\n", orlgth );
 #endif
 	}

 	if( orlgth > commonAlloc1 || orlgth1 > commonAlloc2 )
 	{
 		int ll1, ll2;

 		if( commonAlloc1 && commonAlloc2 )
 		{
 			FreeIntMtx( commonIP );
 		}

 		ll1 = MAX( commonAlloc1, orlgth );
 		ll2 = MAX( commonAlloc2, orlgth1 );

 #if DEBUG
 		fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
 #endif

 		commonIP = AllocateIntMtx( ll1+10, ll2+10 );

 #if DEBUG
 		fprintf( stderr, "succeeded\n\n" );
 #endif

 		commonAlloc1 = ll1;
 		commonAlloc2 = ll2;
 	}

 	ijp = commonIP;

 	scmx_calc( icyc, aseq, effarr, scmx );

 	for( i=0; i<lgth; i++ )
 	{
 		float scarr[26];
 		for( l=0; l<26; l++ )
 		{
 			scarr[l] = 0.0;
 			for( k=0; k<26; k++ )
 				scarr[l] += n_dis[k][l] * scmx[k][i];
 		}
 		for( j=0; j<lgth1; j++ )
 		{
 			v[i][j] = scarr[(int)amino_n[(int)seq[j]]];
 		}
 		gvsa[i] = scarr[24];
 	}
 	for( i=0; i<lgth+1; i++ ) v[i][lgth1] = 0.0;
 	for( j=0; j<lgth1+1; j++ ) v[lgth][j] = 0.0;
 	gvsa[lgth] = 0.0;

 	for( j=0; j<lgth+1; j++ ) for( k=0; k<3; k++ ) for( l=0; l<3; l++ )
 		g[j][k][l] = 0;


 	for( i=0; i<icyc+1; i++ )
 	{
 		efficient = (float)effarr[i];

 		gc1 = 0; /* 1? */
 		for( j=0; j<lgth+1; j++ )
 		{
 			gb1 = gc1;

 			gc1 = ( aseq[i][j] == '-' );
 			if( j == lgth )  gc1 = 0; /*  0? */
 							/* continue; */

 			g[j][0][0] += ( !gb1 *  gc1 ) * efficient * penalty;
 			g[j][1][0] += ( 0 ) * efficient * penalty;
 			g[j][2][0] += ( 0 ) * efficient * penalty;
 			g[j][0][1] += ( gb1 * !gc1 + !gb1 * !gc1 ) * efficient * penalty;
 			g[j][1][1] += ( 0 ) * efficient * penalty;
 			g[j][0][2] += ( !gb1 ) * efficient * penalty;  /* ??? */
 			g[j][2][2] += ( 0 ) * efficient * penalty;
 		}
 	}

 	for( i=0; i<lgth+2; i++ ) for( j=0; j<=i+1; j++ )
 	{
 		gs[i][j] = gl[i][j] = 0.0;
 	}

 	for( i=0; i<icyc+1; i++ )
 	{
 		efficient = (float)effarr[i];
 		inttmp = 0;
 		for( j=0; j<lgth+1; j++ )
 		{
 			if( aseq[i][j] == '-' )
 			{
 				inttmp++;
 				gs[j][inttmp] += (float)efficient * penalty;

 				if( aseq[i][j+1] != '-' )
 					gl[j][inttmp] += (float)efficient * penalty;
 			}
 			else inttmp = 0;
 		}

 	}
 	/*

 	for( i=0; i<lgth+1; i++ )
 	{
 		fprintf( stderr, "gl[%d][] = ", i );
 		fprintf( stderr, "\n" );
 		for( j=0; j<=i+1; j++ )
 			fprintf( stderr, " %.0f", i, j, gl[i][j] );
 		fprintf( stderr, "\n" );
 	}
 	*/

 	for( i=0; i<lgth+1; i++ )
 	{
 		for( j=1; j<=i; j++ )
 			gs[i][j+1] += gs[i][j];
 		for( j=i; j>0; j-- )
 			gl[i][j] += gl[i][j+1];
 	}

 /*
 	for( i=0; i<lgth+1; i++ )
 	{
 	j = 5;
 		fprintf( stderr, "gs[%d][%d] = %f, gl[%d][%d] = %f\n", i, j, gs[i][j], i, j, gl[i][j] );
 	}


 */

 /*
 	printf( "%d\n", lgth  );
 	for( i=0; i<lgth; i++ )
 	{
 		printf( "%f %f %f %f %f %f %f\n", g[i][0][0], g[i][1][0], g[i][2][0], g[i][0][1], g[i][1][1], g[i][0][2], g[i][2][2] );
 	}
 	printf( "\n\n\n\n\n" );
 */
 /*
 	for( i=0; i<lgth; i++ ) for( j=0; j<3; j++ ) for( k=0; k<3; k++ )
 	{
 		g[i][j][k] /= ( (float)icyc + 1.0 );
 	}
 */

 /*
 fp = fopen( "gapp", "a" );
 fprintf( fp, "gapmatrix g[i][][] except for %d\n", ex+1 );
 for( i=0; i<100; i++ )
 {
 	fprintf( fp, "site No.%#3d  ", i+1 );
 	fprintf( fp, "00:%#5d ", -(int)g[i][0][0] );
 	fprintf( fp, "10:%#5d ", -(int)g[i][1][0] );
 	fprintf( fp, "20:%#5d ", -(int)g[i][2][0] );
 	fprintf( fp, "01:%#5d ", -(int)g[i][0][1] );
 	fprintf( fp, "11:%#5d ", -(int)g[i][1][1] );
 	fprintf( fp, "02:%#5d ", -(int)g[i][0][2] );
 	fprintf( fp, "22:%#5d ", -(int)g[i][2][2] );
 	fprintf( fp, "\n" );
 }
 fprintf( fp, "\n" );
 fclose ( fp );
 */

 	w = v;

 	w[0][0] += /* scmx[24][0] * penalty */ g[0][0][0];  /* [0][0] ? */
 	w[1][0] += g[0][0][1] + g[1][1][0] + gs[1][2] + gvsa[0];  /*  ??? */
 	tmpfloat = 0.0;
 	for( i=2; i<lgth+2; i++ )
 	{
 		tmpfloat += g[i-1][1][1] + gl[i-2][i-1] + gvsa[i-1];
 		w[i][0] += g[0][0][1] + gvsa[0] + tmpfloat + g[i][1][0] + gs[i][i+1];
 	}

 	w[0][1] += penalty * totaleff + n_dis[24][0] * totaleff;
 	tmpfloat = 0.0;
 	for( j=2; j<lgth1+1; j++ )
 	{
 		tmpfloat += n_dis[24][0] * totaleff;
 		w[0][j] += penalty * totaleff + tmpfloat;
 	}

 	for( j=0; j<lgth1+1; ++j )
 	{
 		m[j] = 0; mp[j] = 0;
 	}
 	for( i=1; i<lgth+1; i++ )
 	{
 		mi = 0; mpi = 0;
 		for( j=1; j<lgth1+1; j++ )
 		{
 			if( j > 1 )
 			{
 				x = w[i-1][j-2] + g[i-0][0][2] + n_dis[24][0] * totaleff;
 				mi += g[i-1][2][2] + n_dis[24][0] * totaleff;
 				if( mi < x )
 				{
 					mi = x;
 					mpi = j-2;
 				}
 			}
 			else
 			{
 				mi = w[i-1][0] + g[i-0][0][2]/* + n_dis[24][0] * totaleff */;  /* 0.0? */
 				/*
 				fprintf( stderr, " i == %d j == 1, w[i][0] == %f, mi == %f, g[i][0][2] == %f\n", i, w[i][0], mi, g[i][0][2] );
 				*/
 			/*
 				mi = 0.0 + g[i-0][0][2];  * 0.0? *
 			*/
 				mpi = 0;
 			}

 			if( i > 1 )
 			{
 				x = w[i-2][j-1] + g[i-1][0][1] + gvsa[i-1];
 				m[j] += g[i-1][1][1] + gl[i-2][i-mp[j]-2] + gvsa[i-1];      /* ??? */
 				if( m[j] < x )
 				{
 					m[j] = x;
 					mp[j] = i-2;
 				}

 			}
 			else
 			{
 				m[j] = w[0][j-1]+ g[i][0][1]/* + gvsa[1] */;  /* 0.0? */
 				mp[j] = 0;
 			}

 			wmax = w[i-1][j-1] + g[i][0][0];
 			/*
 			ip[i][j]=i-1;
 			jp[i][j]=j-1;
 			*/
 			ijp[i][j] = 0;

 			x = mi + g[i][2][0];
 			if( x > wmax )
 			{
 				wmax = x;
 				/*
 				ip[i][j] = i-1;
 				jp[i][j] = mpi;
 				*/
 				ijp[i][j] = -( j - mpi );    /* ijp[][] < 0 -> j ni gap */
 			}

 			x = m[j] + g[i][1][0] + gs[i][i-mp[j]];
 			if( x > wmax )
 			{
 				wmax = x;
 				/*
 				ip[i][j] = mp[j];
 				jp[i][j] = j-1;
 				*/
 				ijp[i][j] = +( i - mp[j] );
 			}
 			w[i][j] += wmax;
 		}
 	}
 	if( cnst )
 	{
 		w[lgth][lgth1] = w[lgth-1][lgth1-1] + g[lgth][0][0];
 		/*
 		ip[lgth][lgth1] = lgth-1;
 		jp[lgth][lgth1] = lgth1-1;
 		*/
 		ijp[lgth][lgth1] = 0;
 	}

 	*wm = w[lgth][lgth1];

 	for( i=0; i<lgth+1; i++ )
 	{
 	/*
 		ip[i][0] = -1; jp[i][0] = -1;
 	*/
 		ijp[i][0] = i + 1;
 	}
 	for( j=0; j<lgth1+1; j++ )
 	{
 	/*
 		ip[0][j] = -1; jp[0][j] = -1;
 	*/
 		ijp[0][j] = -( j + 1 );
 	}
 	/*
 	ip[lgth][lgth1]=iin; jp[lgth][lgth1]=jin;
 	ip[lgth+1][lgth1+1]=lgth; jp[lgth+1][lgth1+1]=lgth1;
 	*/
 	/*
 	tracking( nseq, aseq, seq, ip, jp, icyc );
 	*/
 	tracking( nseq, aseq, seq, ijp, icyc );
 /*
 fp = fopen( "matrx", "a" );
 fprintf( fp, "matrix v\n" );
 fprintf( fp, "%#5d", 0 );
 for( j=0; j<20; j++ ) fprintf( fp, "%#5d", j );
 fprintf( fp, "\n" );
 for( i=0; i<lgth+1; i++ )
 {
 	fprintf( fp, "%#5d", i );
 	for( j=0; j<20; j++ )
 	{
 		fprintf( fp, "%#5d", (int)( w[i][j]/(icyc+1) ) );
 	}
 	fprintf( fp, "\n" );
 }
 fclose( fp );
 */
 #if DEBUG
 	printf( "seq1[0] = %s\n", nseq[0] );
 	printf( "seq2[0] = %s\n", nseq[icyc+1] );
 #endif
 	*wm = w[lgth][lgth1];
 	return( nseq );
 }

 double Cscore_m_1( char **seq, int locnjob, int ex, double **eff )
 {
     int i, k;
     int len = strlen( seq[0] );
     int gb1, gb2, gc1, gc2;
     int cob;
     int nglen;
     double score;
 	double pen;
 	double tmpscore;
 	int *glen1, *glen2;

 	int tmp1, tmp2;


 	glen1 = AllocateIntVec( locnjob );
 	glen2 = AllocateIntVec( locnjob );
     score = 0.0;
     nglen = 0;
 	/*
 	printf( "in Cscore_m_1\n" );
 	for( i=0; i<locnjob; i++ )
 	{
 		if( i == ex ) continue;
 		fprintf( stdout, "%d-%d:%f\n", ex, i, eff[ex][i] );
 	}
 	*/
    	for( k=0; k<len; k++ )
     {

 		tmpscore = pen = 0;
    		for( i=0; i<locnjob; i++ )
         {
  	 		double efficient = eff[ex][i];
         	if( i == ex ) continue;
 			if( k > 0 )
 			{
          		 gb1 = ( seq[i][k-1] == '-' );
            		 gb2 = ( seq[ex][k-1] == '-' );
 			}
 			else
 			{
 				gb1 = 0;
 				gb2 = 0;
 			}

 			if( gb1 ) glen1[i]++; else glen1[i] = 0;
 			if( gb2 ) glen2[i]++; else glen2[i] = 0;

             gc1 = ( seq[i][k] == '-' );
             gc2 = ( seq[ex][k] == '-' );

 			if( glen1[i] >= glen2[i] ) tmp1 = 1; else tmp1 = 0;
 			if( glen1[i] <= glen2[i] ) tmp2 = 1; else tmp2 = 0;
             cob =
                    !gb1  *  gc1
                  * !gb2  * !gc2

                  + !gb1  * !gc1
                  * !gb2  *  gc2

                  + !gb1  *  gc1
                  *  gb2  * !gc2

                  +  gb1  * !gc1
                  * !gb2  *  gc2

                  +  gb1  * !gc1
                  *  gb2  *  gc2      * tmp1

                  +  gb1  *  gc1
                  *  gb2  * !gc2      * tmp2
                  ;

             pen += (double)cob * penalty * efficient;
             tmpscore += (double)amino_dis[(int)seq[i][k]][(int)seq[ex][k]] * efficient;
             /*
             nglen += ( !gc1 * !gc2 );
             */
 			/*
 			if( k == 0 )
 			{
 				printf( "%c<->%c * %f = %f\n", seq[ex][k], seq[i][k], efficient, amino_dis[seq[i][k]][seq[ex][k]] * efficient );
 			}
 			*/
         }
 		score += tmpscore;
 		score += pen;
 		/*
         if( 1 ) fprintf( stdout, "%c   %f    ", seq[ex][k], score / (locnjob-1) );
         if( 1 ) fprintf( stdout, "penalty  %f\n", (double)pen / (locnjob - 1 ) );
 		*/
     }
 	/*
     fprintf( stdout, "in Cscore_m_1 %f\n", score );
 	*/
 	/*
 	fprintf( stdout, "%s\n", seq[ex] );
 	*/
 	free( glen1 );
 	free( glen2 );
     return( (double)score /*/ nglen + 400.0*/ );
 }
	#include "mltaln.h"
	#include "dp.h"

	#define DEBUG 0

	void tracking( char nseq, char aseq, char seq, int *ijp, int icyc )
	{
	int i, k, l;
	int iin, ifi, jin, jfi;
	int lgth = strlen( aseq[0] );
	int lgth1 = strlen( seq );
	char gap[] = "-";

	for( i=0; i<=icyc+1; i++ )
	{
	nseq[i] += lgth+lgth1;
	*nseq[i] = 0;
	}

	iin = lgth; jin = lgth1;
	for( k=0; k<=lgth+lgth1; )
	{
	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;
	/*
	if( ifi < 0 ) jfi = -1;
	if( jfi < 0 ) ifi = -1;
	*/
	}
	for( l=1; l<iin-ifi; l++ )
	{
	for( i=0; i<icyc+1; i++ )
	*--nseq[i] = aseq[i][iin-l];
	--nseq[icyc+1] = gap;
	k++;
	}
	for( l=1; l<jin-jfi; l++ )
	{
	for( i=0; i<icyc+1; i++ )
	--nseq[i] = gap;
	nseq[icyc+1]--;
	*nseq[icyc+1] = seq[jin-l];
	k++;
	}
	if( iin <= 0 \|\| jin <= 0 ) break;
	for( i=0; i<icyc+1; i++ )
	*--nseq[i] = aseq[i][ifi];
	*--nseq[icyc+1] = seq[jfi];
	k++;
	iin = ifi; jin = jfi;
	}
	}


	char *Calignm1( float wm, char *aseq, char seq, double *effarr, int icyc, int ex )
	{
	register int i, j, k, l;
	float tmpfloat;
	int inttmp;
	static float mi, *m;
	static int mpi, *mp;
	static float ***g;
	int gb1, gc1;
	static int **ijp;
	static float v, w;
	static float *gvsa;
	static char **mseq;
	static char **nseq;
	static float **scmx;
	float wmax;
	int lgth, lgth1;
	static int orlgth = 0, orlgth1 = 0;
	float x;
	float efficient;
	float *AllocateFloatVec( int );
	float totaleff;
	static float **gl;
	static float **gs;
	float **AllocateFloatTri( int );
	void FreeFloatTri( float ** );

	#if DEBUG
	FILE *fp;
	#endif


	totaleff = 0.0;
	for( i=0; i<icyc+1; i++ ) totaleff += effarr[i];
	lgth = strlen( aseq[0] );
	lgth1 = strlen( seq );


	#if DEBUG
	fprintf( stdout, "effarr in Calignm1 s = \n", ex );
	for( i=0; i<icyc+1; i++ )
	fprintf( stdout, " %f", effarr[i] );
	printf( "\n" );
	#endif

	if( orlgth > 0 && orlgth1 > 0 ) for( i=0; i<njob+1; i++ ) nseq[i] = mseq[i];
	/*
	* allocate
	*/

	if( lgth > orlgth \|\| lgth1 > orlgth1 )
	{
	int ll1, ll2;

	if( orlgth > 0 && orlgth1 > 0 )
	{
	FreeFloatMtx( v );

	FreeFloatCub( g );
	FreeFloatTri( gl );
	FreeFloatTri( gs );

	FreeFloatVec( m );
	FreeIntVec( mp );

	#if 0
	FreeCharMtx( nseq );
	#endif
	FreeCharMtx( mseq );

	FreeFloatVec( gvsa );
	FreeFloatMtx( scmx );
	}

	ll1 = MAX( (int)(1.1*lgth), orlgth );
	ll2 = MAX( (int)(1.1*lgth1), orlgth1 );
	ll1 = MAX( ll1, ll2 );

	#if DEBUG
	fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
	#endif

	v = AllocateFloatMtx( ll1+2, ll2+2 );

	g = AllocateFloatCub( ll1+2, 3, 3 );

	gl = AllocateFloatTri( MAX( ll1, ll2 ) + 3 );
	gs = AllocateFloatTri( MAX( ll1, ll2 ) + 3 );

	m = AllocateFloatVec( ll1+2 );
	mp = AllocateIntVec( ll1+2 );

	mseq = AllocateCharMtx( njob+1, 1 );
	nseq = AllocateCharMtx( njob+1, ll1+ll2 );
	for( i=0; i<njob+1; i++ ) mseq[i] = nseq[i];

	gvsa = AllocateFloatVec( ll1+2 );

	scmx = AllocateFloatMtx( 26, ll1+2 );

	#if DEBUG
	fprintf( stderr, "succeeded\n\n" );
	#endif

	orlgth = ll1;
	orlgth1 = ll2;
	#if DEBUG
	fprintf( stderr, "orlgth == %d\n", orlgth );
	#endif
	}

	if( orlgth > commonAlloc1 \|\| orlgth1 > commonAlloc2 )
	{
	int ll1, ll2;

	if( commonAlloc1 && commonAlloc2 )
	{
	FreeIntMtx( commonIP );
	}

	ll1 = MAX( commonAlloc1, orlgth );
	ll2 = MAX( commonAlloc2, orlgth1 );

	#if DEBUG
	fprintf( stderr, "\n\ntrying to allocate %dx%d matrices ... ", ll1+1, ll2+1 );
	#endif

	commonIP = AllocateIntMtx( ll1+10, ll2+10 );

	#if DEBUG
	fprintf( stderr, "succeeded\n\n" );
	#endif

	commonAlloc1 = ll1;
	commonAlloc2 = ll2;
	}

	ijp = commonIP;

	scmx_calc( icyc, aseq, effarr, scmx );

	for( i=0; i<lgth; i++ )
	{
	float scarr[26];
	for( l=0; l<26; l++ )
	{
	scarr[l] = 0.0;
	for( k=0; k<26; k++ )
	scarr[l] += n_dis[k][l] * scmx[k][i];
	}
	for( j=0; j<lgth1; j++ )
	{
	v[i][j] = scarr[(int)amino_n[(int)seq[j]]];
	}
	gvsa[i] = scarr[24];
	}
	for( i=0; i<lgth+1; i++ ) v[i][lgth1] = 0.0;
	for( j=0; j<lgth1+1; j++ ) v[lgth][j] = 0.0;
	gvsa[lgth] = 0.0;

	for( j=0; j<lgth+1; j++ ) for( k=0; k<3; k++ ) for( l=0; l<3; l++ )
	g[j][k][l] = 0;


	for( i=0; i<icyc+1; i++ )
	{
	efficient = (float)effarr[i];

	gc1 = 0; /* 1? */
	for( j=0; j<lgth+1; j++ )
	{
	gb1 = gc1;

	gc1 = ( aseq[i][j] == '-' );
	if( j == lgth ) gc1 = 0; /* 0? */
	/* continue; */

	g[j][0][0] += ( !gb1 * gc1 ) * efficient * penalty;
	g[j][1][0] += ( 0 ) * efficient * penalty;
	g[j][2][0] += ( 0 ) * efficient * penalty;
	g[j][0][1] += ( gb1 * !gc1 + !gb1 * !gc1 ) * efficient * penalty;
	g[j][1][1] += ( 0 ) * efficient * penalty;
	g[j][0][2] += ( !gb1 ) * efficient * penalty; /* ??? */
	g[j][2][2] += ( 0 ) * efficient * penalty;
	}
	}

	for( i=0; i<lgth+2; i++ ) for( j=0; j<=i+1; j++ )
	{
	gs[i][j] = gl[i][j] = 0.0;
	}

	for( i=0; i<icyc+1; i++ )
	{
	efficient = (float)effarr[i];
	inttmp = 0;
	for( j=0; j<lgth+1; j++ )
	{
	if( aseq[i][j] == '-' )
	{
	inttmp++;
	gs[j][inttmp] += (float)efficient * penalty;

	if( aseq[i][j+1] != '-' )
	gl[j][inttmp] += (float)efficient * penalty;
	}
	else inttmp = 0;
	}

	}
	/*

	for( i=0; i<lgth+1; i++ )
	{
	fprintf( stderr, "gl[%d][] = ", i );
	fprintf( stderr, "\n" );
	for( j=0; j<=i+1; j++ )
	fprintf( stderr, " %.0f", i, j, gl[i][j] );
	fprintf( stderr, "\n" );
	}
	*/

	for( i=0; i<lgth+1; i++ )
	{
	for( j=1; j<=i; j++ )
	gs[i][j+1] += gs[i][j];
	for( j=i; j>0; j-- )
	gl[i][j] += gl[i][j+1];
	}

	/*
	for( i=0; i<lgth+1; i++ )
	{
	j = 5;
	fprintf( stderr, "gs[%d][%d] = %f, gl[%d][%d] = %f\n", i, j, gs[i][j], i, j, gl[i][j] );
	}


	*/

	/*
	printf( "%d\n", lgth );
	for( i=0; i<lgth; i++ )
	{
	printf( "%f %f %f %f %f %f %f\n", g[i][0][0], g[i][1][0], g[i][2][0], g[i][0][1], g[i][1][1], g[i][0][2], g[i][2][2] );
	}
	printf( "\n\n\n\n\n" );
	*/
	/*
	for( i=0; i<lgth; i++ ) for( j=0; j<3; j++ ) for( k=0; k<3; k++ )
	{
	g[i][j][k] /= ( (float)icyc + 1.0 );
	}
	*/

	/*
	fp = fopen( "gapp", "a" );
	fprintf( fp, "gapmatrix g[i][][] except for %d\n", ex+1 );
	for( i=0; i<100; i++ )
	{
	fprintf( fp, "site No.%#3d ", i+1 );
	fprintf( fp, "00:%#5d ", -(int)g[i][0][0] );
	fprintf( fp, "10:%#5d ", -(int)g[i][1][0] );
	fprintf( fp, "20:%#5d ", -(int)g[i][2][0] );
	fprintf( fp, "01:%#5d ", -(int)g[i][0][1] );
	fprintf( fp, "11:%#5d ", -(int)g[i][1][1] );
	fprintf( fp, "02:%#5d ", -(int)g[i][0][2] );
	fprintf( fp, "22:%#5d ", -(int)g[i][2][2] );
	fprintf( fp, "\n" );
	}
	fprintf( fp, "\n" );
	fclose ( fp );
	*/

	w = v;

	w[0][0] += /* scmx[24][0] * penalty / g[0][0][0]; / [0][0] ? */
	w[1][0] += g[0][0][1] + g[1][1][0] + gs[1][2] + gvsa[0]; /* ??? */
	tmpfloat = 0.0;
	for( i=2; i<lgth+2; i++ )
	{
	tmpfloat += g[i-1][1][1] + gl[i-2][i-1] + gvsa[i-1];
	w[i][0] += g[0][0][1] + gvsa[0] + tmpfloat + g[i][1][0] + gs[i][i+1];
	}

	w[0][1] += penalty * totaleff + n_dis[24][0] * totaleff;
	tmpfloat = 0.0;
	for( j=2; j<lgth1+1; j++ )
	{
	tmpfloat += n_dis[24][0] * totaleff;
	w[0][j] += penalty * totaleff + tmpfloat;
	}

	for( j=0; j<lgth1+1; ++j )
	{
	m[j] = 0; mp[j] = 0;
	}
	for( i=1; i<lgth+1; i++ )
	{
	mi = 0; mpi = 0;
	for( j=1; j<lgth1+1; j++ )
	{
	if( j > 1 )
	{
	x = w[i-1][j-2] + g[i-0][0][2] + n_dis[24][0] * totaleff;
	mi += g[i-1][2][2] + n_dis[24][0] * totaleff;
	if( mi < x )
	{
	mi = x;
	mpi = j-2;
	}
	}
	else
	{
	mi = w[i-1][0] + g[i-0][0][2]/* + n_dis[24][0] * totaleff /; / 0.0? */
	/*
	fprintf( stderr, " i == %d j == 1, w[i][0] == %f, mi == %f, g[i][0][2] == %f\n", i, w[i][0], mi, g[i][0][2] );
	*/
	/*
	mi = 0.0 + g[i-0][0][2]; * 0.0? *
	*/
	mpi = 0;
	}

	if( i > 1 )
	{
	x = w[i-2][j-1] + g[i-1][0][1] + gvsa[i-1];
	m[j] += g[i-1][1][1] + gl[i-2][i-mp[j]-2] + gvsa[i-1]; /* ??? */
	if( m[j] < x )
	{
	m[j] = x;
	mp[j] = i-2;
	}

	}
	else
	{
	m[j] = w[0][j-1]+ g[i][0][1]/* + gvsa[1] /; / 0.0? */
	mp[j] = 0;
	}

	wmax = w[i-1][j-1] + g[i][0][0];
	/*
	ip[i][j]=i-1;
	jp[i][j]=j-1;
	*/
	ijp[i][j] = 0;

	x = mi + g[i][2][0];
	if( x > wmax )
	{
	wmax = x;
	/*
	ip[i][j] = i-1;
	jp[i][j] = mpi;
	*/
	ijp[i][j] = -( j - mpi ); /* ijp[][] < 0 -> j ni gap */
	}

	x = m[j] + g[i][1][0] + gs[i][i-mp[j]];
	if( x > wmax )
	{
	wmax = x;
	/*
	ip[i][j] = mp[j];
	jp[i][j] = j-1;
	*/
	ijp[i][j] = +( i - mp[j] );
	}
	w[i][j] += wmax;
	}
	}
	if( cnst )
	{
	w[lgth][lgth1] = w[lgth-1][lgth1-1] + g[lgth][0][0];
	/*
	ip[lgth][lgth1] = lgth-1;
	jp[lgth][lgth1] = lgth1-1;
	*/
	ijp[lgth][lgth1] = 0;
	}

	*wm = w[lgth][lgth1];

	for( i=0; i<lgth+1; i++ )
	{
	/*
	ip[i][0] = -1; jp[i][0] = -1;
	*/
	ijp[i][0] = i + 1;
	}
	for( j=0; j<lgth1+1; j++ )
	{
	/*
	ip[0][j] = -1; jp[0][j] = -1;
	*/
	ijp[0][j] = -( j + 1 );
	}
	/*
	ip[lgth][lgth1]=iin; jp[lgth][lgth1]=jin;
	ip[lgth+1][lgth1+1]=lgth; jp[lgth+1][lgth1+1]=lgth1;
	*/
	/*
	tracking( nseq, aseq, seq, ip, jp, icyc );
	*/
	tracking( nseq, aseq, seq, ijp, icyc );
	/*
	fp = fopen( "matrx", "a" );
	fprintf( fp, "matrix v\n" );
	fprintf( fp, "%#5d", 0 );
	for( j=0; j<20; j++ ) fprintf( fp, "%#5d", j );
	fprintf( fp, "\n" );
	for( i=0; i<lgth+1; i++ )
	{
	fprintf( fp, "%#5d", i );
	for( j=0; j<20; j++ )
	{
	fprintf( fp, "%#5d", (int)( w[i][j]/(icyc+1) ) );
	}
	fprintf( fp, "\n" );
	}
	fclose( fp );
	*/
	#if DEBUG
	printf( "seq1[0] = %s\n", nseq[0] );
	printf( "seq2[0] = %s\n", nseq[icyc+1] );
	#endif
	*wm = w[lgth][lgth1];
	return( nseq );
	}

	double Cscore_m_1( char seq, int locnjob, int ex, double eff )
	{
	int i, k;
	int len = strlen( seq[0] );
	int gb1, gb2, gc1, gc2;
	int cob;
	int nglen;
	double score;
	double pen;
	double tmpscore;
	int glen1, glen2;

	int tmp1, tmp2;


	glen1 = AllocateIntVec( locnjob );
	glen2 = AllocateIntVec( locnjob );
	score = 0.0;
	nglen = 0;
	/*
	printf( "in Cscore_m_1\n" );
	for( i=0; i<locnjob; i++ )
	{
	if( i == ex ) continue;
	fprintf( stdout, "%d-%d:%f\n", ex, i, eff[ex][i] );
	}
	*/
	for( k=0; k<len; k++ )
	{

	tmpscore = pen = 0;
	for( i=0; i<locnjob; i++ )
	{
	double efficient = eff[ex][i];
	if( i == ex ) continue;
	if( k > 0 )
	{
	gb1 = ( seq[i][k-1] == '-' );
	gb2 = ( seq[ex][k-1] == '-' );
	}
	else
	{
	gb1 = 0;
	gb2 = 0;
	}

	if( gb1 ) glen1[i]++; else glen1[i] = 0;
	if( gb2 ) glen2[i]++; else glen2[i] = 0;

	gc1 = ( seq[i][k] == '-' );
	gc2 = ( seq[ex][k] == '-' );

	if( glen1[i] >= glen2[i] ) tmp1 = 1; else tmp1 = 0;
	if( glen1[i] <= glen2[i] ) tmp2 = 1; else tmp2 = 0;
	cob =
	!gb1 * gc1
	* !gb2 * !gc2

	+ !gb1 * !gc1
	* !gb2 * gc2

	+ !gb1 * gc1
	* gb2 * !gc2

	+ gb1 * !gc1
	* !gb2 * gc2

	+ gb1 * !gc1
	* gb2 * gc2 * tmp1

	+ gb1 * gc1
	* gb2 * !gc2 * tmp2
	;

	pen += (double)cob * penalty * efficient;
	tmpscore += (double)amino_dis[(int)seq[i][k]][(int)seq[ex][k]] * efficient;
	/*
	nglen += ( !gc1 * !gc2 );
	*/
	/*
	if( k == 0 )
	{
	printf( "%c<->%c * %f = %f\n", seq[ex][k], seq[i][k], efficient, amino_dis[seq[i][k]][seq[ex][k]] * efficient );
	}
	*/
	}
	score += tmpscore;
	score += pen;
	/*
	if( 1 ) fprintf( stdout, "%c %f ", seq[ex][k], score / (locnjob-1) );
	if( 1 ) fprintf( stdout, "penalty %f\n", (double)pen / (locnjob - 1 ) );
	*/
	}
	/*
	fprintf( stdout, "in Cscore_m_1 %f\n", score );
	*/
	/*
	fprintf( stdout, "%s\n", seq[ex] );
	*/
	free( glen1 );
	free( glen2 );
	return( (double)score // nglen + 400.0/ );
	}