Commit b6517578 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 7.429

parent f5b755f2

MPI/Makefile

+2 −2
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ else 
STDF = -std=c99

endif



CFLAGS := $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS) -I../core -MMD -MP

MYCFLAGS := $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS) -I../core -MMD -MP



OBJDIR := ./obj

ifeq "$(strip $(OBJDIR))" ""
@@ -71,7 +71,7 @@ mpiscript : mpiscript.tmpl 
$(OBJDIR)/%.o : %.c

	-@mkdir -p $(OBJDIR)

	@[ -d $(OBJDIR) ]

	$(CC) $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -o $@ -c $<

	$(CC) $(MYCFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -o $@ -c $<



clean :

	rm -f $(OBJNODPAIR) $(DEPSNODPAIR) $(PROGS) $(SCRIPTS) *.o *.a *.exe *~

MPI/mltaln9_mpi.c

+0 −81
Original line number Diff line number Diff line
@@ -12006,87 +12006,6 @@ void commongappick_record( int nseq, char **seq, int *map ) 
}





void commongappick( int nseq, char **seq )

{

	int i, j, count;

	int len = strlen( seq[0] );

#if 1



	int *mapfromnewtoold;



	mapfromnewtoold = calloc( len+1, sizeof( int ) );



	for( i=0, count=0; i<=len; i++ ) 

	{

		for( j=0; j<nseq; j++ )

			if( seq[j][i] != '-' ) break;

		if( j != nseq )

		{

			mapfromnewtoold[count++] = i;

	 	}

	}

//	mapfromnewtoold[count] = -1; // iranai

	for( j=0; j<nseq; j++ )

	{

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

		{

			seq[j][i] = seq[j][mapfromnewtoold[i]];

		}

	}

	free( mapfromnewtoold );

#else

--------------------------



	int *mapfromoldtonew;

	int pos;



	mapfromoldtonew = calloc( len+1, sizeof( int ) );

	for( i=0; i<=len; i++ ) mapfromoldtonew[i] = -1;



	for( i=0, count=0; i<=len; i++ ) 

	{

		for( j=0; j<nseq; j++ )

			if( seq[j][i] != '-' ) break;

		if( j != nseq )

		{

			mapfromoldtonew[i] = count;

			count++;

	 	}

	}

	for( j=0; j<nseq; j++ )

	{

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

		{

			if( (pos=mapfromoldtonew[i]) != -1 )

				seq[j][pos] = seq[j][i];

		}

	}

	free( mapfromoldtonew );

--------------------------



	for( i=0, count=0; i<=len; i++ ) 

	{

	/*

		allgap = 1;

		for( j=0; j<nseq; j++ ) 

			allgap *= ( seq[j][i] == '-' );

		if( !allgap )

	*/

		for( j=0; j<nseq; j++ )

			if( seq[j][i] != '-' ) break;

		if( j != nseq )

		{

			for( j=0; j<nseq; j++ )

			{

				seq[j][count] = seq[j][i];

			}

			count++;

	 	}

	}



#endif

}



#if 0

void commongaprecord( int nseq, char **seq, char *originallygapped )

{

core/Dalignmm.c

+1 −1
Original line number Diff line number Diff line
@@ -4280,7 +4280,7 @@ fprintf( stderr, "\n" ); 
	reporterr( "diff = %f\n\n", (pairscore - wm + *impmatch ) / fpenalty );



#if 1

	if( ( !trywarp && abs( pairscore - wm +*impmatch ) > 0.01 ) || PFACERROR )

	if( ( !trywarp && fabs( pairscore - wm +*impmatch ) > 0.01 ) || PFACERROR ) // abs() -> fabs(), 2019/Jan/25

//	if( abs( pairscore - wm +*impmatch ) > 0.01 )

#else

	if( abs( pairscore - wm +*impmatch ) > 0.01 )

core/Makefile

+10 −2
Original line number Diff line number Diff line
@@ -14,6 +14,10 @@ ENABLE_MULTITHREAD = -Denablemultithread 
# Comment out the above line if your compiler 

# does not support "atomic_int".



#DASH_CLIENT = dash_client

# Uncomment the above line to use protein 3D 

# structural information.  Go language is required.



CC = gcc

#CC = icc

CFLAGS = -O3
@@ -50,7 +54,8 @@ INSTALL = install 
PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \

		multi2hat3s pairash addsingle maffttext2hex hex2maffttext \

        splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \

		seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version

		seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version \

		$(DASH_CLIENT)

SOS = libdisttbfast.so

DLLS = libdisttbfast.dll

DYLIBS = libdisttbfast.dylib
@@ -152,6 +157,9 @@ sos : $(SOS) 
dylibs : $(DYLIBS)

dlls : $(DLLS)



$(DASH_CLIENT): dash_client.go

	go build dash_client.go



univscript: univscript.tmpl Makefile

	sed "s:_PROGS:$(PROGS):" univscript.tmpl  > univscript
@@ -537,7 +545,7 @@ score.o : score.c $(HEADER) 
	$(CC) $(MYCFLAGS) -c score.c



clean :

	rm -f *.o *.a *.exe *~ $(PERLPROGS) $(PROGS) $(SCRIPTS) $(SOS) $(DYLIBS) $(DLLS) *.gcda *.gcno

	rm -f *.o *.a *.exe *~ $(PERLPROGS) $(PROGS) $(SCRIPTS) $(SOS) $(DYLIBS) $(DLLS) *.gcda *.gcno $(DASH_CLIENT)

#	rm -f ../binaries/* ../scripts/*



install : all

core/README

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+1 −0
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SUPPORT environments without Pthreads