Commit 500ceb1b authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 7.453

parent b6517578

MPI/Makefile

+1 −1
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ CFLAGS := -O3 
#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind

# CFLAGS := -O0 -g -ipo -no-prec-div -xHost -std=c99

TARGET_ARCH := 

LDLIBS := -lm -lrt   # -lrt?

LDLIBS := -lm -lrt -lpthread  # -lrt?





ENABLE_MULTITHREAD := -Denablemultithread

core/Falign.c

+1363 −205

File changed.

Preview size limit exceeded, changes collapsed.

core/MSalignmm.c

+3 −0
Original line number Diff line number Diff line
@@ -719,6 +719,7 @@ static double MSalignmm_tanni( double **n_dynamicmtx, int icyc, int jcyc, double 
	lgth1 = ien-ist+1;

	lgth2 = jen-jst+1;





#if STOREWM

	strncpy( ttt1, seq1[0]+ist, lgth1 ); ttt1[lgth1] = 0;

	strncpy( ttt2, seq2[0]+jst, lgth2 ); ttt2[lgth2] = 0;
@@ -2124,6 +2125,7 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
	nglen1 = seqlen( seq1[0] );

	nglen2 = seqlen( seq2[0] );





#if 0

	fprintf( stderr, "\n" );

	for( i=0; i<icyc; i++ ) fprintf( stderr, "seq1[%d] at root = %s\n", i, seq1[i] );
@@ -2134,6 +2136,7 @@ double MSalignmm( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
	lgth1 = strlen( seq1[0] );

	lgth2 = strlen( seq2[0] );





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

	ll2 = ( (int)(lgth2) ) + 100;

core/Salignmm.c

+11 −10
Original line number Diff line number Diff line
@@ -819,6 +819,7 @@ static void createfgresult( double **gapfresult, int limk, double eff1, double e 
}



static double Atracking( double *lasthorizontalw, double *lastverticalw, 

						double fpenalty, double fpenalty_ex,

						char **seq1, char **seq2, 

                        char **mseq1, char **mseq2, 

                        int **ijp, int icyc, int jcyc,
@@ -876,8 +877,8 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
	else

	{

#if 1

		double fpenalty = (double)penalty;

		double fpenalty_ex = (double)penalty_ex;

//		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] );
@@ -1066,7 +1067,7 @@ static double Atracking( double *lasthorizontalw, double *lastverticalw, 
	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 )

double A__align( double **n_dynamicmtx, int penalty_l, int penalty_ex_l, 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 )

/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */

{
@@ -1087,7 +1088,7 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
	double *currentw, *previousw;

//	double fpenalty = (double)penalty;

#if USE_PENALTY_EX

	double fpenalty_ex = (double)penalty_ex;

	double fpenalty_ex = (double)penalty_ex_l;

#endif

#if 1

	double *wtmp;
@@ -1121,7 +1122,7 @@ double A__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, 
	double *gapfreq1pt;

	static TLS double *gapfreq2;

	double *gapfreq2pt;

	double fpenalty = (double)penalty;

	double fpenalty = (double)penalty_l;

	double fpenalty_shift = (double)penalty_shift;

	double *fgcp2pt;

	double *ogcp2pt;
@@ -2050,7 +2051,7 @@ fprintf( stderr, "\n" ); 
	else

	{

//		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 );

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

		if( !tailgp ) wm = wmo;

	}
@@ -2194,7 +2195,7 @@ double A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, in 
}





double A__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, 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 )

double A__align_variousdist( int **which, double ***matrices, double **n_dynamicmtx, int penalty_l, int penalty_ex_l, char **seq1, char **seq2, double *eff1, double *eff2, double **eff1s, double **eff2s, 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 )

/* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */

{
@@ -2211,7 +2212,7 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic 
	double *currentw, *previousw;

//	double fpenalty = (double)penalty;

#if USE_PENALTY_EX

	double fpenalty_ex = (double)penalty_ex;

	double fpenalty_ex = (double)penalty_ex_l;

#endif

#if 1

	double *wtmp;
@@ -2240,7 +2241,7 @@ double A__align_variousdist( int **which, double ***matrices, double **n_dynamic 
	static TLS int orlgth1 = 0, orlgth2 = 0;

	static TLS double *gapfreq1;

	static TLS double *gapfreq2;

	double fpenalty = (double)penalty;

	double fpenalty = (double)penalty_l;

	double fpenalty_shift = (double)penalty_shift;

	double *fgcp2pt;

	double *ogcp2pt;
@@ -3041,7 +3042,7 @@ fprintf( stderr, "\n" ); 
	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.

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

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

		if( !tailgp ) wm = wmo;

	}

core/addfunctions.c

+2 −2
Original line number Diff line number Diff line
@@ -86,7 +86,7 @@ void profilealignment2( int n0, int n2, char **aln0, char **aln2, int alloclen, 
	if( alg == 'M' )

		MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1

	else

		A__align( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1

		A__align( n_dis_consweight_multi, penalty, penalty_ex, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1



	newlen = strlen( aln0[0] );
@@ -211,7 +211,7 @@ static void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1, 
	if( alg == 'M' )

		MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1

	else

		A__align( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1

		A__align( n_dis_consweight_multi, penalty, penalty_ex, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); //outgap=1, 2014/Dec/1



	newlen = strlen( aln0[0] );