Commit fc205afe authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 7.402

parent 1d5a43ae

core/Galign11.c

+104 −11
Original line number Diff line number Diff line
@@ -5,6 +5,9 @@ 
#define XXXXXXX    0

#define USE_PENALTY_EX  1



#define TERMGAPFAC 0.0

#define TERMGAPFAC_EX 0.0



#if 1

static void match_calc_mtx( double **mtx, double *match, char **s1, char **s2, int i1, int lgth2 ) 

{
@@ -37,7 +40,9 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
	gap = newgapstr;

	lgth1 = strlen( seq1[0] );

	lgth2 = strlen( seq2[0] );

	double wm;

	double wm, g;

	double fpenalty = (double)penalty;

	double fpenalty_ex = (double)penalty_ex;





#if 0
@@ -56,11 +61,41 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
        ijp[0][j] = -( j + 1 );

    }





//	if( tailgp == 1 || ijp[lgth1][lgth2] >= warpbase )

	if( tailgp == 1 )

		;

	else

	{

#if 1

//		reporterr( "lastverticalw[lgth1-1] = %f\n", lastverticalw[lgth1-1] );

//		reporterr( "lasthorizontalw[lgth2-1] = %f\n", lasthorizontalw[lgth2-1] );

		wm = lasthorizontalw[lgth2-1] - 1.0; // lasthorizontalw[lgth2-1] yori kanarazu chiisai.

		for( j=lgth2-2; j>=0; j-- )

		{

			if( (g=lasthorizontalw[j]+ ( fpenalty * TERMGAPFAC + fpenalty_ex * (lgth2-1-j) * TERMGAPFAC_EX ) ) > wm )

			{

				wm = g;

				iin = lgth1-1; jin = j;

				ijp[lgth1][lgth2] = -( lgth2 - j );

			}

		}

		for( i=lgth1-2; i>=0; i-- )

		{

			if( ( g=lastverticalw[i]+ ( fpenalty * TERMGAPFAC + fpenalty_ex * (lgth1-1-i) * TERMGAPFAC_EX ) ) > wm )

			{

				wm = g;

				iin = i; jin = lgth2-1;

				ijp[lgth1][lgth2] = +( lgth1 - i );

			}

		}

		if( lasthorizontalw[lgth2-1] > wm )  // score ga onaji baai erabarenai

		{

			wm = lasthorizontalw[lgth2-1];

			iin = lgth1-1; jin = lgth2-1;

			ijp[lgth1][lgth2] = 0;

		}

#else

		wm = lastverticalw[0];

		for( i=0; i<lgth1; i++ )

		{
@@ -80,6 +115,7 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
				ijp[lgth1][lgth2] = -( lgth2 - j );

			}

		}

#endif

	}
@@ -158,19 +194,20 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 


//	fprintf( stderr, "%s\n", mseq1[0] );

//	fprintf( stderr, "%s\n", mseq2[0] );

	return( 0.0 );

	return( wm );

}





double G__align11( double **n_dynamicmtx, char **seq1, char **seq2, int alloclen, int headgp, int tailgp )

{



//	int k;

	register int i, j;

	int lasti;                      /* outgap == 0 -> lgth1, outgap == 1 -> lgth1+1 */

	int lastj;

	int lgth1, lgth2;

	int resultlen;

	double wm;   /* int ?????? */

	double wm, wmo;   /* int ?????? */

	double g;

	double *currentw, *previousw;

	double fpenalty = (double)penalty;
@@ -178,6 +215,7 @@ double G__align11( double **n_dynamicmtx, char **seq1, char **seq2, int alloclen 
	double fpenalty_tmp;

#if USE_PENALTY_EX

	double fpenalty_ex = (double)penalty_ex;

	double fpenalty_ex_i;

#endif

#if 1

	double *wtmp;
@@ -428,13 +466,41 @@ double G__align11( double **n_dynamicmtx, char **seq1, char **seq2, int alloclen 
		for( i=1; i<lgth1+1; i++ )

		{

			initverticalw[i] += fpenalty;

#if USE_PENALTY_EX

//			initverticalw[i] += fpenalty_ex * i; // ato de fukkatsu

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

			currentw[j] += fpenalty;

#if USE_PENALTY_EX

//			currentw[j] += fpenalty_ex * j; // ato de fukkatsu

//			reporterr( "added _ex\n" );

#endif

		}

	}

	else

	{

		for( i=1; i<lgth1+1; i++ )

		{

			initverticalw[i] += fpenalty * TERMGAPFAC;

#if USE_PENALTY_EX // 2018/Apr/22

			initverticalw[i] += fpenalty_ex * i * TERMGAPFAC_EX;

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

			currentw[j] += fpenalty * TERMGAPFAC;

#if USE_PENALTY_EX // 2018/Apr/22

			currentw[j] += fpenalty_ex * j * TERMGAPFAC_EX;

//			reporterr( "added _ex\n" );

#endif

		}

	}





	for( j=1; j<lgth2+1; ++j ) 

	{

		m[j] = currentw[j-1]; mp[j] = 0;
@@ -510,6 +576,9 @@ fprintf( stderr, "\n" ); 
			warpjpt = warpj + 1;

		}



		if( i < lgth1 ) fpenalty_ex_i = fpenalty_ex;

		else fpenalty_ex_i = 0.0; // 2018/May/11



		for( j=1; j<lastj; j++ )

		{
@@ -528,12 +597,14 @@ fprintf( stderr, "\n" ); 
				*ijppt = -( j - mpi );

			}

			if( (g=*prept) >= mi )

//			if( (g=*prept) > mi )

			{

				mi = g;

				mpi = j-1;

			}

#if USE_PENALTY_EX

			mi += fpenalty_ex;

			mi += fpenalty_ex_i;

//			mi += fpenalty_ex;

#endif



#if 0
@@ -545,11 +616,13 @@ fprintf( stderr, "\n" ); 
				*ijppt = +( i - *mpjpt );

			}

			if( (g=*prept) >= *mjpt )

//			if( (g=*prept) > *mjpt )

			{

				*mjpt = g;

				*mpjpt = i-1;

			}

#if USE_PENALTY_EX

			if( j < lgth2 ) // 2018/May/11

				m[j] += fpenalty_ex;

#endif

#if 1
@@ -647,6 +720,7 @@ fprintf( stderr, "\n" ); 
		}

	}





	if( trywarp )

	{

//		fprintf( stderr, "\nwm = %f\n", wm );
@@ -659,7 +733,10 @@ fprintf( stderr, "\n" ); 
		free( prevwarpj );

	}



	Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp, warpis, warpjs, warpbase );

	wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, tailgp, warpis, warpjs, warpbase );

	if( !tailgp ) wm = wmo;



//	reporterr( "wm (after tracking) = %f\n", wm );

	if( warpis ) free( warpis );

	if( warpjs ) free( warpjs );
@@ -698,6 +775,7 @@ double G__align11_noalign( double **n_dynamicmtx, int penal, int penal_ex, char 
	double fpenalty = (double)penal;

#if USE_PENALTY_EX

	double fpenalty_ex = (double)penal_ex;

	double fpenalty_ex_i;

#endif

#if 1

	double *wtmp;
@@ -831,10 +909,18 @@ double G__align11_noalign( double **n_dynamicmtx, int penal, int penal_ex, char 
		for( i=1; i<lgth1+1; i++ )

		{

			initverticalw[i] += fpenalty;

#if USE_PENALTY_EX // 2018/Apr/23

//			initverticalw[i] += fpenalty_ex * i; // ato de fukkatsu

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

			currentw[j] += fpenalty;

#if USE_PENALTY_EX // 2018/Apr/23

//			currentw[j] += fpenalty_ex * j; // ato de fukkatsu

//			reporterr( "added _ex\n" );

#endif

		}

	}
@@ -901,6 +987,10 @@ fprintf( stderr, "\n" ); 
		mjpt = m + 1;

		prept = previousw;

		curpt = currentw + 1;



		if( i < lgth1 ) fpenalty_ex_i = fpenalty_ex;

		else fpenalty_ex_i = 0.0; // 2018/May/11



		for( j=1; j<lgth2+1; j++ )

		{

			wm = *prept;
@@ -915,12 +1005,13 @@ fprintf( stderr, "\n" ); 
			{

				wm = g;

			}

			if( (g=*prept) >= mi )

//			if( (g=*prept) >= mi )

			if( (g=*prept) > mi ) // onaji hazu

			{

				mi = g;

			}

#if USE_PENALTY_EX

			mi += fpenalty_ex;

			mi += fpenalty_ex_i;

#endif



#if 0
@@ -930,11 +1021,13 @@ fprintf( stderr, "\n" ); 
			{

				wm = g;

			}

			if( (g=*prept) >= *mjpt )

//			if( (g=*prept) >= *mjpt )

			if( (g=*prept) > *mjpt ) // onaji hazu

			{

				*mjpt = g;

			}

#if USE_PENALTY_EX

			if( j < lgth2 ) // 2018/May/11

				m[j] += fpenalty_ex;

#endif
@@ -952,7 +1045,7 @@ fprintf( stderr, "\n" ); 
	fprintf( stderr, "\n" );

	fprintf( stderr, ">\n%s\n", mseq1[0] );

	fprintf( stderr, ">\n%s\n", mseq2[0] );

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

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

#endif



	return( wm );

core/Salignmm.c

+112 −5
Original line number Diff line number Diff line
@@ -9,6 +9,9 @@ 
#define FASTMATCHCALC 1

#define SLOW 0



#define TERMGAPFAC 0.0

#define TERMGAPFAC_EX 0.0





static TLS double **impmtx = NULL;

static TLS int impalloclen = 0;
@@ -872,6 +875,38 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
		;

	else

	{

#if 1

		double fpenalty = (double)penalty;

		double fpenalty_ex = (double)penalty_ex;

		double g;

//		reporterr( "in S, lastverticalw[lgth1-1] = %f\n", lastverticalw[lgth1-1] );

//		reporterr( "in S, lasthorizontalw[lgth2-1] = %f\n", lasthorizontalw[lgth2-1] );

		wm = lasthorizontalw[lgth2-1] - 1.0; // lasthorizontalw[lgth2-1] yori kanarazu chiisai.

		for( j=lgth2-2; j>=0; j-- )

		{

			if( (g=lasthorizontalw[j]+ ( fpenalty * TERMGAPFAC + fpenalty_ex * (lgth2-1-j) * TERMGAPFAC_EX ) ) > wm )

			{

				wm = g;

				iin = lgth1-1; jin = j;

				ijp[lgth1][lgth2] = -( lgth2 - j );

			}

		}

		for( i=lgth1-2; i>=0; i-- )

		{

			if( ( g=lastverticalw[i]+ ( fpenalty * TERMGAPFAC + fpenalty_ex * (lgth1-1-i) * TERMGAPFAC_EX ) ) > wm )

			{

				wm = g;

				iin = i; jin = lgth2-1;

				ijp[lgth1][lgth2] = +( lgth1 - i );

			}

		}

		if( lasthorizontalw[lgth2-1] > wm )  // score ga onaji baai erabarenai

		{

			wm = lasthorizontalw[lgth2-1];

			iin = lgth1-1; jin = lgth2-1;

			ijp[lgth1][lgth2] = 0;

		}

#else

		wm = lastverticalw[0];

		for( i=0; i<lgth1; i++ )

		{
@@ -891,6 +926,7 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
				ijp[lgth1][lgth2] = -( lgth2 - j );

			}

		}

#endif

	}



    for( i=0; i<lgth1+1; i++ )
@@ -1027,7 +1063,7 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
		*gt2 = gaptable2;

	}



	return( 0.0 );

	return( wm );

}



double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp, int firstmem, int calledbyfulltreebase, double **cpmxchild0, double **cpmxchild1, double ***cpmxresult, double orieff1, double orieff2 )
@@ -1046,6 +1082,7 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
	int lgth1, lgth2;

	int resultlen;

	double wm = 0.0;   /* int ?????? */

	double wmo = 0.0;

	double g;

	double *currentw, *previousw;

//	double fpenalty = (double)penalty;
@@ -1663,20 +1700,48 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
		imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );



#endif



	if( headgp == 1 )

	{

		for( i=1; i<lgth1+1; i++ )

		{

//			initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;

			initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2pt[0] ) ;

#if USE_PENALTY_EX // 2018/Apr/23

			initverticalw[i] += fpenalty_ex * i;

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

//			currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;

			currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1pt[0] ) ;

#if USE_PENALTY_EX // 2018/Apr/23

			currentw[j] += fpenalty_ex * j;

//			reporterr( "added _ex\n" );

#endif

		}

	}

	else

	{

		for( i=1; i<lgth1+1; i++ )

		{

			initverticalw[i] += fpenalty * TERMGAPFAC; // motto tanjun de yoi?

#if USE_PENALTY_EX // 2018/Apr/22

			initverticalw[i] += fpenalty_ex * i * TERMGAPFAC_EX;

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

			currentw[j] += fpenalty * TERMGAPFAC; // motto tanjun de yoi?

#if USE_PENALTY_EX // 2018/Apr/22

			currentw[j] += fpenalty_ex * j * TERMGAPFAC_EX;

//			reporterr( "added _ex\n" );

#endif

		}

	}





#if OUTGAP0TRY

	else

	{
@@ -1687,6 +1752,8 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
			initverticalw[i] -= offset * i / 2.0;

	}

#endif





#if 0

	fprintf( stderr, "\n   " );

	for( j=0; j<lgth2+1; j++ ) fprintf( stderr, "    %c ", seq2[0][j] );
@@ -1843,6 +1910,7 @@ fprintf( stderr, "\n" ); 
//				fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );

			}

			if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )

//			if( (g=*prept+*ogcp2pt*gf1vapre) > mi )

			{

				mi = g;

				mpi = j-1;
@@ -1862,6 +1930,7 @@ fprintf( stderr, "\n" ); 
//				fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );

			}

			if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )

//			if( (g=*prept+ ogcp1va* *gf2ptpre) > *mjpt )

			{

				*mjpt = g;

				*mpjpt = i-1;
@@ -1980,10 +2049,13 @@ fprintf( stderr, "\n" ); 
	}

	else

	{

//		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, eff1, eff2, cpmxresult, cpmx1pt, cpmx2pt, gapfreq1pt, gapfreq2pt, ogcp1opt, ogcp2opt, fgcp1opt, fgcp2opt, orieff1, orieff2, (cpmx1pt!=cpmx1), (cpmx2pt!=cpmx2) );

		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, &gt1, &gt2 );

//		wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, eff1, eff2, cpmxresult, cpmx1pt, cpmx2pt, gapfreq1pt, gapfreq2pt, ogcp1opt, ogcp2opt, fgcp1opt, fgcp2opt, orieff1, orieff2, (cpmx1pt!=cpmx1), (cpmx2pt!=cpmx2) );

		wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, reuseprofiles, &gt1, &gt2 );

		if( !tailgp ) wm = wmo;

	}



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



#if 1

	if( cpmxresult )

	{
@@ -2134,6 +2206,7 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic 
	int lgth1, lgth2;

	int resultlen;

	double wm = 0.0;   /* int ?????? */

	double wmo = 0.0;   /* int ?????? */

	double g;

	double *currentw, *previousw;

//	double fpenalty = (double)penalty;
@@ -2610,13 +2683,42 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic 
		{

//			initverticalw[i] += ( ogcp1[0] + fgcp1[i-1] ) ;

			initverticalw[i] += ( ogcp1[0] * headgapfreq2 + fgcp1[i-1] * gapfreq2[0] ) ;

#if USE_PENALTY_EX // 2018/Apr/23

			initverticalw[i] += fpenalty_ex * i;

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

//			currentw[j] += ( ogcp2[0] + fgcp2[j-1] ) ;

			currentw[j] += ( ogcp2[0] * headgapfreq1 + fgcp2[j-1] * gapfreq1[0] ) ;

#if USE_PENALTY_EX // 2018/Apr/23

			currentw[j] += fpenalty_ex * j;

//			reporterr( "added _ex\n" );

#endif

		}

	}

	else

	{

		for( i=1; i<lgth1+1; i++ )

		{

			initverticalw[i] += fpenalty * TERMGAPFAC; // motto tanjun de yoi?

#if USE_PENALTY_EX // 2018/Apr/22

			initverticalw[i] += fpenalty_ex * i * TERMGAPFAC_EX;

//			reporterr( "added _ex\n" );

#endif

		}

		for( j=1; j<lgth2+1; j++ )

		{

			currentw[j] += fpenalty * TERMGAPFAC; // motto tanjun de yoi?

#if USE_PENALTY_EX // 2018/Apr/22

			currentw[j] += fpenalty_ex * j * TERMGAPFAC_EX;

//			reporterr( "added _ex\n" );

#endif

		}

	}





#if OUTGAP0TRY

	else

	{
@@ -2806,6 +2908,7 @@ fprintf( stderr, "\n" ); 
//				fprintf( stderr, "Jump to %d (%c)!", mpi, seq2[0][mpi] );

			}

			if( (g=*prept+*ogcp2pt*gf1vapre) >= mi )

//			if( (g=*prept+*ogcp2pt*gf1vapre) > mi )

			{

				mi = g;

				mpi = j-1;
@@ -2825,6 +2928,7 @@ fprintf( stderr, "\n" ); 
//				fprintf( stderr, "Jump to %d (%c)!", *mpjpt, seq1[0][*mpjpt] );

			}

			if( (g=*prept+ ogcp1va* *gf2ptpre) >= *mjpt )

//			if( (g=*prept+ ogcp1va* *gf2ptpre) > *mjpt )

			{

				*mjpt = g;

				*mpjpt = i-1;
@@ -2935,8 +3039,11 @@ fprintf( stderr, "\n" ); 
		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL );

	}

	else

	{

//		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.0, 0.0, 1, 1 ); // NULL x 11 ha atode awaseru.

		Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL);

		wmo = Atracking( currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, tailgp, warpis, warpjs, warpbase, &ngap1, &ngap2, 0, NULL, NULL);

		if( !tailgp ) wm = wmo;

	}



	if( warpis ) free( warpis );

	if( warpjs ) free( warpjs );

core/blosum.c

+1 −0
Original line number Diff line number Diff line
@@ -367,6 +367,7 @@ static void overridematrix( double **matrix ) 
		}

		reporterr( "Score(%c=0x%x,%c=0x%x)=%f\n", i1, i1, i2, i2, v );

		matrix[i1][i2] = v;

		matrix[i2][i1] = v; // 2018/May/11

	}

}

core/constants.c

+6 −0
Original line number Diff line number Diff line
@@ -714,6 +714,12 @@ void constants( int nseq, char **seq ) 
		fprintf( stdout, "####### average1  = %f\n", average );

#endif



		if( average < 0.0 )

		{

			reporterr( "\nUnrealistic scoring matrix.  Give larger positive values to matches (A/A, B/B, etc).\n\n" );

			exit( 1 );

		}



		for( i=0; i<nalphabets; i++ ) for( j=0; j<nalphabets; j++ ) 

			n_distmp[i][j] *= 600.0 / average;

#if TEST

core/disttbfast.c

+5 −2
Original line number Diff line number Diff line
@@ -1460,7 +1460,6 @@ static void *treebasethread( void *arg ) 
			pthread_cond_wait( targ->treecond, targ->mutex ); // tabun iranai

		(*nrunpt)++;



// moved, 20187/Mar/10

		m1 = topol[l][0][0];

		m2 = topol[l][1][0];

#if 0
@@ -1503,7 +1502,7 @@ static void *treebasethread( void *arg ) 
		}

#endif





// moved, 2018/Mar/10. Must be after changing memhist[l]

		if( mergeoralign[l] == 'n' )

		{

//			reporterr(       "SKIP!\n" );
@@ -1514,6 +1513,8 @@ static void *treebasethread( void *arg ) 
//			free( topol[l][1] ); topol[l][1] = NULL;

//			free( topol[l] ); topol[l] = NULL;

			pthread_mutex_unlock( targ->mutex );

			free( localmem[0] );

			free( localmem[1] );

			continue;

		}
@@ -1975,6 +1976,8 @@ static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char 
//			free( topol[l][0] ); topol[l][0] = NULL;

//			free( topol[l][1] ); topol[l][1] = NULL;

//			free( topol[l] ); topol[l] = NULL;

			free( localmem[0] );

			free( localmem[1] );

			continue;

		}