MPI/Makefile

+PREFIX = /usr/local
+LIBDIR = $(PREFIX)/libexec/mafft
+BINDIR = $(PREFIX)/bin
+MANDIR = $(PREFIX)/share/man/man1
+DESTDIR = 
+
+
+#CC :=  mpicc -cc=gcc
+CC :=  mpicc
+#CC :=  /u33/app/openmpi/bin/mpicc
+#CFLAGS := -O3 -ipo -no-prec-div -xHost -std=c99
+#CFLAGS := -O3 -std=c99
+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?
+
+
+ENABLE_MULTITHREAD := -Denablemultithread
+#ENABLE_ATOMIC := -Denableatomic
+VPATH := ../core
+
+ifdef ENABLE_ATOMIC
+STDF = -std=c11
+else
+STDF = -std=c99
+endif
+
+CFLAGS := $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS) -I../core -MMD -MP
+
+OBJDIR := ./obj
+ifeq "$(strip $(OBJDIR))" ""
+  OBJDIR := .
+endif
+
+INSTALL = install
+
+PROGS := nodepair_mpi
+SCRIPTS := mpiscript
+OBJNODPAIR := mtxutl.o io.o mltaln9_mpi.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \
+			nodepair_mpi.o defs.o fft.o fftFunctions.o addfunctions.o \
+			pairlocalalign_mpi.o MSalign11.o
+OBJNODPAIR := $(addprefix $(OBJDIR)/, $(OBJNODPAIR))
+DEPSNODPAIR := $(OBJNODPAIR:%.o=%.d) 
+
+
+all : $(PROGS) $(SCRIPTS)
+	cp $(PROGS) $(SCRIPTS) ../binaries
+	chmod 755 ../binaries/*
+	@echo done.
+
+install : all
+	mkdir -p $(DESTDIR)$(LIBDIR)
+	chmod 755 $(DESTDIR)$(LIBDIR)
+	chmod 755 $(PROGS) ||:     # in MinGW, it's ok if this fails
+	$(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR)
+	$(INSTALL) $(SCRIPTS) $(DESTDIR)$(LIBDIR)
+	@echo done.
+
+nodepair_mpi : $(OBJNODPAIR)
+	$(CC) $(LDFLAGS) $(TARGET_ARCH) $^ $(LOADLIBES) $(LDLIBS) -o $@
+
+shmclear : shmclear.c
+	$(CC) $(LDFLAGS) $(TARGET_ARCH) $^ $(LOADLIBES) $(LDLIBS) -o $@
+
+mpiscript : mpiscript.tmpl
+	cp mpiscript.tmpl mpiscript
+
+$(OBJDIR)/%.o : %.c
+	-@mkdir -p $(OBJDIR)
+	@[ -d $(OBJDIR) ]
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -o $@ -c $<
+
+clean :
+	rm -f $(OBJNODPAIR) $(DEPSNODPAIR) $(PROGS) $(SCRIPTS) *.o *.a *.exe *~
+	rm -rf obj/
+
+-include $(DEPSNODPAIR)

MPI/mpiscript.tmpl

+trap "echo 'Cancel' 1>&2" 0 15
+
+if [ ! $MAFFT_N_THREADS_PER_PROCESS ]; then
+	echo "set MAFFT_N_THREADS_PER_PROCESS, the number of cores to be used by a process." 1>&2
+	exit 1
+fi
+
+if [ ! "$MAFFT_MPIRUN" ]; then
+	MAFFT_MPIRUN="mpirun"
+fi
+
+
+
+command="$* -C $MAFFT_N_THREADS_PER_PROCESS"
+
+#rm -rf hat3dir # To avoid cache, don't touch hat3dir here
+
+$MAFFT_MPIRUN $command 1>&2
+sync;
+
+if [ -s hat3dir/tree ]; then
+#if [ -s infile.tree ]; then
+	val=0
+else
+	echo "error in MPI" 1>&2
+	val=1
+fi
+
+trap - 0 15
+exit $val

MPI/nodepair_mpi.c

+#include "mltaln.h"
+#include "mpi.h"
+#include <errno.h>
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 0
+#define SHISHAGONYU 0 // for debug
+
+
+// from tbfast
+static int treein;
+static int treeout;
+
+
+// from pairlocalalign
+static int stdout_dist;
+
+
+static void arguments( int argc, char *argv[] )
+{
+    int c;
+
+	nthread = 1;
+	nadd = 0;
+	inputfile = NULL;
+	fftkeika = 0;
+	pslocal = -1000.0;
+	nblosum = 62;
+	fmodel = 0;
+	calledByXced = 0;
+	devide = 0;
+	use_fft = 0;
+	fftscore = 1;
+	fftRepeatStop = 0;
+	fftNoAnchStop = 0;
+    weight = 3;
+    utree = 1;
+	tbutree = 1;
+    refine = 0;
+    check = 1;
+    cut = 0.0;
+    disp = 0;
+    outgap = 1;
+    alg = 'A';
+    mix = 0;
+	tbitr = 0;
+	scmtd = 5;
+	tbweight = 0;
+	tbrweight = 3;
+	checkC = 0;
+	treemethod = 'x';
+	contin = 0;
+	scoremtx = 1;
+	kobetsubunkatsu = 0;
+	divpairscore = 0;
+	stdout_dist = 0;
+//	dorp = NOTSPECIFIED;
+	ppenalty = NOTSPECIFIED;
+	ppenalty_OP = NOTSPECIFIED;
+	ppenalty_ex = NOTSPECIFIED;
+	ppenalty_EX = NOTSPECIFIED;
+	penalty_shift_factor = 1000.0;
+	poffset = NOTSPECIFIED;
+	kimuraR = NOTSPECIFIED;
+	pamN = NOTSPECIFIED;
+	geta2 = GETA2;
+	fftWinSize = NOTSPECIFIED;
+	fftThreshold = NOTSPECIFIED;
+	RNAppenalty = NOTSPECIFIED;
+	RNApthr = NOTSPECIFIED;
+	specificityconsideration = 0.0;
+	usenaivescoreinsteadofalignmentscore = 0;
+	specifictarget = 0;
+	nwildcard = 0;
+	compacttree = 2; // tsuneni!
+	treein = 0;
+	treeout = 0;
+	fastathreshold = 2.7;
+	constraint = 2;
+
+//	localhomfile = 0; // tbfast.c no wo tsukaunode comment out
+
+//	reporterr( "argc=%d\n", argc );
+//	reporterr( "*argv=%s\n", *argv );
+//	reporterr( "(*argv)[0]=%c\n", (*argv)[0] );
+    while( --argc > 0 && (*++argv)[0] == '-' )
+	{
+//		reporterr( "(*argv)[0] in while loop = %s\n", (*argv) );
+        while ( ( c = *++argv[0] ) )
+		{
+            switch( c )
+            {
+				case 'i':
+					inputfile = *++argv;
+//					fprintf( stderr, "inputfile = %s\n", inputfile );
+					--argc;
+					goto nextoption;
+				case 'f':
+					ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'g':
+					ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'O':
+					ppenalty_OP = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'E':
+					ppenalty_EX = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'Q':
+					penalty_shift_factor = atof( *++argv );
+					--argc;
+					goto nextoption;
+				case 'h':
+					poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'k':
+					kimuraR = myatoi( *++argv );
+//					fprintf( stderr, "kimuraR = %d\n", kimuraR );
+					--argc;
+					goto nextoption;
+				case 'b':
+					nblosum = myatoi( *++argv );
+					scoremtx = 1;
+//					fprintf( stderr, "blosum %d\n", nblosum );
+					--argc;
+					goto nextoption;
+				case 'j':
+					pamN = myatoi( *++argv );
+					scoremtx = 0;
+					TMorJTT = JTT;
+//					fprintf( stderr, "jtt %d\n", pamN );
+					--argc;
+					goto nextoption;
+				case 'm':
+					pamN = myatoi( *++argv );
+					scoremtx = 0;
+					TMorJTT = TM;
+//					fprintf( stderr, "TM %d\n", pamN );
+					--argc;
+					goto nextoption;
+				case 'l':
+					fastathreshold = atof( *++argv );
+					constraint = 2;
+					--argc;
+					goto nextoption;
+#if 0
+				case 'l':
+					ppslocal = (int)( atof( *++argv ) * 1000 + 0.5 );
+					pslocal = (int)( 600.0 / 1000.0 * ppslocal + 0.5);
+//					fprintf( stderr, "ppslocal = %d\n", ppslocal );
+//					fprintf( stderr, "pslocal = %d\n", pslocal );
+					--argc;
+					goto nextoption;
+#else
+#endif
+				case 'C':
+					nthread = myatoi( *++argv );
+					if( nthread == 0 ) nthread = 1;
+//					fprintf( stderr, "nthread = %d\n", nthread );
+					--argc; 
+#ifndef enablemultithread
+					nthread = 0;
+#endif
+					goto nextoption;
+				case 'I':
+					nadd = myatoi( *++argv );
+//					fprintf( stderr, "nadd = %d\n", nadd );
+					--argc;
+					goto nextoption;
+				case 'u':
+					specificityconsideration = (double)myatof( *++argv );
+//					fprintf( stderr, "specificityconsideration = %f\n", specificityconsideration );
+					--argc; 
+					goto nextoption;
+				case 'c':
+					stdout_dist = 1;
+					break;
+#if 1
+				case 'a':
+					fmodel = 1;
+					break;
+#endif
+				case 'K':
+					addprofile = 0;
+					break;
+#if 0
+				case 'r':
+					fmodel = -1;
+					break;
+#endif
+				case 'D':
+					dorp = 'd';
+					break;
+				case 'P':
+					dorp = 'p';
+					break;
+#if 0
+				case 'e':
+					fftscore = 0;
+					break;
+				case 'O':
+					fftNoAnchStop = 1;
+					break;
+#endif
+#if 0
+				case 'Q':
+					calledByXced = 1;
+					break;
+				case 'x':
+					disp = 1;
+					break;
+				case 'a':
+					alg = 'a';
+					break;
+				case 'S':
+					alg = 'S';
+					break;
+#endif
+				case 'N':
+					alg = 'N';
+					break;
+				case 'A':
+					alg = 'A';
+					break;
+				case 'L':
+					alg = 'L';
+					break;
+				case 'Z':
+					usenaivescoreinsteadofalignmentscore = 1;
+					break;
+				case 'B': // hitsuyou! memopt -M -B no tame
+					break;
+#if 0
+				case 'Y':
+					alg = 'Y'; // nadd>0 no toki nomi. moto no hairetsu to atarashii hairetsuno alignmnt -> L;
+					break;
+				case 's':
+					alg = 's';
+					break;
+				case 'G':
+					alg = 'G';
+					break;
+				case 'B': // hitsuyou! memopt -M -B no tame
+					break;
+				case 'T':
+					alg = 'T';
+					break;
+				case 'H':
+					alg = 'H';
+					break;
+				case 'M':
+					alg = 'M';
+					break;
+				case 'R':
+					alg = 'R';
+					break;
+				case 'r':
+					alg = 'r'; // nadd>0 no toki nomi. moto no hairetsu to atarashii hairetsuno alignmnt -> R, last
+					break;
+				case 'V':
+					alg = 'V';
+					break;
+#endif
+				case 'T': // tbfast.c no noalign ni taiou
+					break;
+				case 'F':
+					use_fft = 1;
+					break;
+				case 'U':
+					treein = 1;
+					break;
+				case 't':
+					treeout = 1;
+					break;
+				case 'y':
+					divpairscore = 1;
+					break;
+				case '=':
+					specifictarget = 1;
+					break;
+				case ':':
+					nwildcard = 1;
+					break;
+				case 'q':
+					lhlimit = myatoi( *++argv );
+					--argc; 
+					goto nextoption;
+/* Modified 01/08/27, default: user tree */
+				case 'J':
+					tbutree = 0;
+					break;
+/* modification end. */
+                default:
+                    fprintf( stderr, "illegal option %c\n", c );
+                    argc = 0;
+                    break;
+            }
+		}
+		nextoption:
+			;
+	}
+    if( argc == 1 )
+    {
+        cut = atof( (*argv) );
+        argc--;
+    }
+    if( argc != 0 ) 
+    {
+        fprintf( stderr, "pairlocalalign options: Check source file !\n" );
+        exit( 1 );
+    }
+	if( tbitr == 1 && outgap == 0 )
+	{
+		fprintf( stderr, "conflicting options : o, m or u\n" );
+		exit( 1 );
+	}
+}
+
+int main( int argc, char *argv[] )
+{
+	static int  *nlen = NULL;	
+	static int *selfscore = NULL;
+	static char **name = NULL, **seq = NULL;
+	static double *eff = NULL;
+	int i;
+	static int ***topol = NULL;
+	static Treedep *dep = NULL;
+	static double **len = NULL;
+	FILE *infp = NULL;
+
+	char c;
+
+
+#if 1
+//	int required = MPI_THREAD_MULTIPLE;
+	int required = MPI_THREAD_FUNNELED;
+	int provided;
+	MPI_Init_thread(&argc, &argv, required, &provided);
+#else
+	MPI_Init(&argc,&argv);
+#endif
+
+	int my_rank;
+	int num_of_processes;
+	MPI_Comm_rank(MPI_COMM_WORLD,&my_rank);
+	MPI_Comm_size(MPI_COMM_WORLD,&num_of_processes);
+
+
+	if (provided < required) {
+#if 0
+		if (my_rank == 0) {
+			reporterr( "MPI_THREAD_MULTIPLE (mpi thread support level) is required\n");
+			reporterr( "required level is %d and provided level is %d\n", required, provided );
+		}
+		MPI_Finalize();
+		exit( 1 );
+#else
+		if (my_rank == 0) reporterr( "WARNING: mpi thread support level %d is required, but provided level is %d.\n", required, provided );
+#endif
+	} else {
+		if (my_rank == 0) reporterr( "mpi thread support level : required level is %d and provided level is %d\n", required, provided );
+	}
+
+
+	arguments( argc, argv );
+
+	if( alg != 'A' && alg != 'L' && alg != 'N' )
+	{
+		reporterr( "alg %c is not yet supported\n", alg );
+		exit( 1 );
+	}
+	if( alg != 'N' && usenaivescoreinsteadofalignmentscore == 1 )
+	{
+		reporterr( "The combination of usenaivescoreinsteadofalignmentscore and alg %c is not yet supported\n", alg );
+		exit( 1 );
+	}
+
+	if( fastathreshold < 0.0001 )
+	{
+		constraint = 0; 
+		lhlimit = 0;
+	}
+
+
+
+	if(my_rank==0){
+		if( inputfile )
+		{
+			infp = fopen( inputfile, "r" );
+			if( !infp ) 
+			{
+				fprintf( stderr, "Cannot open %s\n", inputfile );
+				exit( 1 );
+			}
+		}
+		else    
+			infp = stdin;
+
+		getnumlen( infp );
+		rewind( infp );
+	}
+	// getnumlen
+	MPI_Bcast(&njob,1, MPI_INT, 0, MPI_COMM_WORLD);
+	MPI_Bcast(&nlenmax,1, MPI_INT, 0, MPI_COMM_WORLD);
+	MPI_Bcast(&dorp,1, MPI_INT, 0, MPI_COMM_WORLD);
+	fprintf( stderr, "my_rank: %d, njob: %d, nlenmax: %d\n", my_rank, njob, nlenmax);
+
+
+
+	if( njob < 2 )
+	{
+		fprintf( stderr, "At least 2 sequences should be input!\n"
+						 "Only %d sequence found.\n", njob ); 
+		exit( 1 );
+	}
+
+
+#ifndef mingw
+	setstacksize( 200 * njob ); // topolorder() de ookime no stack wo shiyou.
+#endif
+
+
+	seq = AllocateCharMtx( njob, nlenmax+1 );
+
+	name = AllocateCharMtx( njob, B+1 );
+	nlen = AllocateIntVec( njob );
+	selfscore = AllocateIntVec( njob );
+
+	topol = AllocateIntCub( njob, 2, 0 );
+	len = AllocateFloatMtx( njob, 2 );
+	eff = AllocateDoubleVec( njob );
+
+
+	dep = (Treedep *)calloc( njob, sizeof( Treedep ) );
+
+
+	if(my_rank==0){
+#if 0
+		readData( infp, name, nlen, seq );
+#else
+		readData_pointer( infp, name, nlen, seq );
+		fclose( infp );
+#endif
+	}
+	for(i=0;i<njob;i++){
+		MPI_Bcast(name[i], B+1, MPI_CHAR, 0, MPI_COMM_WORLD);
+		MPI_Bcast(seq[i], nlenmax+1, MPI_CHAR, 0, MPI_COMM_WORLD);
+	}
+	MPI_Bcast(nlen, njob, MPI_INT, 0, MPI_COMM_WORLD);
+
+
+	constants( njob, seq );
+
+#if 0
+	fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+	initSignalSM();
+	initFiles();
+
+//	WriteOptions( trap_g );
+
+	c = seqcheck( seq );
+	if( c )
+	{
+		fprintf( stderr, "Illegal character %c\n", c );
+		exit( 1 );
+	}
+
+//	writePre( njob, name, nlen, seq, 0 );
+
+	if( treein ) loadtree( njob, topol, len, name, nlen, dep, treeout );
+	pairalign_node( njob, nlenmax, name, seq, topol, len, dep, treein, treeout );
+
+
+	FreeCharMtx( seq ); seq = NULL;
+
+	FreeCharMtx( name ); name = NULL;
+	free( nlen ); nlen = NULL;
+	free( selfscore ); selfscore = NULL;
+
+	for( i=0; i<njob; i++ ) 
+	{
+		free( topol[i][0] ); topol[i][0] = NULL;
+		free( topol[i][1] ); topol[i][1] = NULL;
+		free( topol[i] ); topol[i] = NULL;
+		free( len[i] ); len[i] = NULL;
+	}
+	free( topol ); topol = NULL;
+	free( len ); len = NULL;
+	free( eff ); eff = NULL;
+	free( dep ); dep = NULL;
+
+
+	freeconstants();
+	closeFiles();
+	FreeCommonIP();
+
+	MPI_Finalize();
+
+//	reporterr( "nodepair_mpi used " );
+//	use_getrusage();
+	return( 0 );
+
+#if 0 // gui mitaiou
+chudan:
+	if( seq ) FreeCharMtx( seq ); seq = NULL;
+
+	if( name ) FreeCharMtx( name ); name = NULL;
+	if( nlen ) free( nlen ); nlen = NULL;
+	if( selfscore ) free( selfscore ); selfscore = NULL;
+
+
+
+	if( topol ) FreeIntCub( topol ); topol = NULL;
+	if( dep ) free( dep ); dep = NULL;
+
+	freeconstants();
+	closeFiles();
+	FreeCommonIP();
+
+	if( topol )
+	{
+		for( i=0; i<njob; i++ ) 
+		{
+			if( topol[i] )
+			{
+				if( topol[i][0] ) free( topol[i][0] ); topol[i][0] = NULL;
+				if( topol[i][1] ) free( topol[i][1] ); topol[i][1] = NULL;
+			}
+			free( topol[i] ); topol[i] = NULL;
+		}
+		free( topol ); topol = NULL;
+	}
+	if( len ) 
+	{
+		for( i=0; i<njob; i++ ) 
+		{
+			if( len[i] ) free( len[i] ); len[i] = 0;
+		}
+		free( len ); len = NULL;
+	}
+	if( eff ) free( eff ); eff = NULL;
+	if( dep ) free( dep ); dep = NULL;
+
+
+
+	MPI_Finalize();
+
+
+	return( 0 );
+#endif
+
+}

core/Dalignmm.c

@@ -116,7 +116,7 @@ void imp_rnaD( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, dou
 }
 
 
-void imp_match_init_strictD( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, char *swaplist, int forscore, int *orinum1, int *orinum2 )
+void imp_match_init_strictD( double *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, char *swaplist, int forscore, int *orinum1, int *orinum2, int *uselh, int *seedinlh1, int *seedinlh2, int nodeid, int nfiles )
 {
 //	int i, j, k1, k2, tmpint, start1, start2, end1, end2;
 //	double effij;
@@ -150,7 +150,10 @@ void imp_match_init_strictD( double *imp, int clus1, int clus2, int lgth1, int l
 //		nocount2 = AllocateCharVec( impalloclen );
 	}
 
+	if( nodeid == -1 )
 		fillimp( impmtx, imp, clus1, clus2, lgth1, lgth2, seq1, seq2, eff1, eff2, eff1_kozo, eff2_kozo, localhom, swaplist, forscore, orinum1, orinum2 );
+	else
+		fillimp_file( impmtx, imp, clus1, clus2, lgth1, lgth2, seq1, seq2, eff1, eff2, eff1_kozo, eff2_kozo, localhom, swaplist, forscore, orinum1, orinum2, uselh, seedinlh1, seedinlh2, nodeid, nfiles );
 }
 
 
@@ -2508,7 +2511,7 @@ static void freegaplenpartly( Gaplen **mtx, int startpos, int endpos )
 #endif
 
 
-double D__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+double D__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 )
 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 {
 
@@ -2610,7 +2613,7 @@ double D__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,
 			orlgth1 = 0;
 			orlgth2 = 0;
 
-			imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
+			imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, 0, 0 );
 
 			free( mseq1 );
 			free( mseq2 );
@@ -3241,13 +3244,13 @@ double D__align( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1,
 	previousw = w2;
 
 	match_calc( n_dynamicmtx, initverticalw, cpmx2, cpmx1, 0, lgth1, doublework, intwork, 1 );
-	if( localhom )
+	if( constraint )
 		imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
 
 	match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
-	if( localhom )
+	if( constraint )
 		imp_match_out_vead( currentw, 0, lgth2 ); // 060306
-#if 0 // -> tbfast.c
+#if 0 // -> tbfast.c // impossible
 	if( localhom )
 		imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
 
@@ -3403,7 +3406,7 @@ for( j=0; j<lgth2; j++ )
 }
 fprintf( stderr, "\n" );
 #endif
-		if( localhom )
+		if( constraint )
 		{
 //			fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
 #if  0
@@ -4151,7 +4154,7 @@ fprintf( stderr, "\n" );
 	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
 	for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
 	*/
-	if( localhom )
+	if( constraint )
 	{
 		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
 	}
@@ -4311,7 +4314,7 @@ fprintf( stderr, "\n" );
 }
 
 
-double D__align_ls( double **n_dynamicmtx, char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+double D__align_ls( 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 v1, v2;
 	double val;
@@ -4329,26 +4332,26 @@ double D__align_ls( double **n_dynamicmtx, char **seq1, char **seq2, double *eff
 
 	if( v1 >= v2 )
 	{
-		val = D__align( n_dynamicmtx, seq1, seq2, eff1, eff2, icyc, jcyc, alloclen, localhom, impmatch, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+		val = D__align( n_dynamicmtx, seq1, seq2, eff1, eff2, icyc, jcyc, alloclen, constraint, impmatch, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
 	}
 	else
 	{
-		val = D__align( n_dynamicmtx, seq2, seq1, eff2, eff1, jcyc, icyc, alloclen, localhom, impmatch, sgap2, sgap1, egap2, egap1, chudanpt, chudanref, chudanres, headgp, tailgp );
+		val = D__align( n_dynamicmtx, seq2, seq1, eff2, eff1, jcyc, icyc, alloclen, constraint, impmatch, sgap2, sgap1, egap2, egap1, chudanpt, chudanref, chudanres, headgp, tailgp );
 	}
 	return val;
 }
 
 
 
-double D__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, double *impmatch, int *gapmap1, int *gapmap2 )
+double D__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, int constraint, double *impmatch, int *gapmap1, int *gapmap2 )
 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 {
-	fprintf( stderr, "Unexpected error.  Please contact kazutaka.katoh@aist.go.jp\n" );
+	fprintf( stderr, "Unexpected error.  Please contact katoh@ifrec.osaka-u.ac.jp\n" );
 	exit( 1 );
 }
 
 
-double D__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, LocalHom ***localhom, double *impmatch, char *sgap1, char *sgap2, char *egap1, char *egap2, int *chudanpt, int chudanref, int *chudanres, int headgp, int tailgp )
+double D__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 )
 /* score no keisan no sai motokaraaru gap no atukai ni mondai ga aru */
 {
 
@@ -4448,7 +4451,7 @@ double D__align_variousdist( int **which, double ***matrices, double **n_dynamic
 			orlgth1 = 0;
 			orlgth2 = 0;
 
-			imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL );
+			imp_match_init_strictD( NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, 0, 0 );
 
 			free( mseq1 );
 			free( mseq2 );
@@ -5134,7 +5137,7 @@ double D__align_variousdist( int **which, double ***matrices, double **n_dynamic
 //	for( i=0; i<lgth1; i++ ) fprintf( stderr, "%d - %f\n", i, initverticalw[i] );
 
 
-	if( localhom )
+	if( constraint )
 		imp_match_out_vead_tate( initverticalw, 0, lgth1 ); // 060306
 
 //	match_calc( n_dynamicmtx, currentw, cpmx1, cpmx2, 0, lgth2, doublework, intwork, 1 );
@@ -5160,9 +5163,9 @@ double D__align_variousdist( int **which, double ***matrices, double **n_dynamic
 //	exit( 1 );
 
 
-	if( localhom )
+	if( constraint )
 		imp_match_out_vead( currentw, 0, lgth2 ); // 060306
-#if 0 // -> tbfast.c
+#if 0 // -> tbfast.c // impossible
 	if( localhom )
 		imp_match_calc( n_dynamicmtx, currentw, icyc, jcyc, lgth1, lgth2, seq1, seq2, eff1, eff2, localhom, 1, 0 );
 
@@ -5333,7 +5336,7 @@ for( j=0; j<lgth2; j++ )
 }
 fprintf( stderr, "\n" );
 #endif
-		if( localhom )
+		if( constraint )
 		{
 //			fprintf( stderr, "Calling imp_match_calc (o) lgth = %d, i = %d\n", lgth1, i );
 #if  0
@@ -6084,7 +6087,7 @@ fprintf( stderr, "\n" );
 	for( i=0; i<icyc; i++ ) strcpy( mseq1[i], seq1[i] );
 	for( j=0; j<jcyc; j++ ) strcpy( mseq2[j], seq2[j] );
 	*/
-	if( localhom )
+	if( constraint )
 	{
 		Atracking_localhom( impmatch, currentw, lastverticalw, seq1, seq2, mseq1, mseq2, ijp, icyc, jcyc, warpis, warpjs, warpbase );
 	}

core/Falign.c

@@ -708,13 +708,13 @@ system( "/usr/bin/gnuplot list.plot" );
 				Aalign( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen );
 				break;
 			case( 'M' ):
-					MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp );
+					MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp, NULL, NULL, NULL, 0.0, 0.0 );
 				break;
 			case( 'A' ):
 				if( clus1 == 1 && clus2 == 1 )
 					G__align11( n_dynamicmtx, tmpres1, tmpres2, alloclen, headgp, tailgp );
 				else
-					A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp, -1, -1 );
+					A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, headgp, tailgp, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 				break;
 			default:
 				fprintf( stderr, "alg = %c\n", alg );
@@ -825,10 +825,10 @@ double Falign( int **whichmtx, double ***scoringmatrices, double **n_dynamicmtx,
 			mymergesort( 0, 0, NULL );
 			alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
 			fft( 0, NULL, 1 );
-			A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1 );
-			D__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
-			A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
-			D__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+			A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+			D__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+			A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+			D__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
 			G__align11( NULL, NULL, NULL, 0, 0, 0 );
 			blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
 			if( crossscore ) FreeDoubleMtx( crossscore );
@@ -1514,7 +1514,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 					if( scoringmatrices ) // called by tditeration.c
 						totalscore += MSalignmm_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
 					else
-						totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+						totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp, NULL, NULL, NULL, 0.0, 0.0 );
 //						totalscore += MSalignmm( n_dis_consweight_multi, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
 				break;
 			case( 'd' ):
@@ -1526,10 +1526,10 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 				{
 					if( scoringmatrices ) // called by tditeration.c
 					{
-						totalscore += D__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+						totalscore += D__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, 0, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
 					}
 					else
-					totalscore += D__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+					totalscore += D__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, 0, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
 				}
 				break;
 			case( 'A' ):
@@ -1541,10 +1541,10 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 				{
 					if( scoringmatrices ) // called by tditeration.c
 					{
-						totalscore += A__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
+						totalscore += A__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, 0, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp );
 					}
 					else
-						totalscore += A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, NULL, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp, -1, -1 );
+						totalscore += A__align( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, 0, &dumdb, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres, headgp, tailgp, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 				}
 				break;
 			default:
@@ -1678,9 +1678,9 @@ double Falign_udpari_long(
 			mymergesort( 0, 0, NULL );
 			alignableReagion( 0, 0, NULL, NULL, NULL, NULL, NULL );
 			fft( 0, NULL, 1 );
-			A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1 );
-			A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
-			D__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+			A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
+			A__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
+			D__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0 );
 			G__align11( NULL, NULL, NULL, 0, 0, 0 );
 			blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
 			if( crossscore ) FreeDoubleMtx( crossscore );
@@ -1843,7 +1843,7 @@ system( "less input_of_Falign < /dev/tty > /dev/tty" );
 #endif
 	if( !kobetsubunkatsu )
 	{
-		fprintf( stderr,  " FFT ... " );
+		if( fftkeika ) fprintf( stderr,  " FFT ... " );
 
 		for( j=0; j<n20or4or2; j++ ) vec_init( seqVector1[j], nlen );
 		if( scoremtx == -1 )
@@ -2112,7 +2112,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 	}
 #if 1
 	if( !kobetsubunkatsu )
-		fprintf( stderr, "done. (%d anchors) ", count );
+		if( fftkeika ) fprintf( stderr, "done. (%d anchors) ", count );
 #endif
 	if( !count && fftNoAnchStop )
 		ErrorExit( "Cannot detect anchor!" );
@@ -2334,7 +2334,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 		fprintf( stderr, "DP %03d / %03d %4d to ", i+1, count-1, totallen );
 #else
 #if 1
-		fprintf( stderr, "DP %05d / %05d \b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", i+1, count-1 );
+		if( 1 || fftkeika ) fprintf( stderr, "DP %05d / %05d \b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b", i+1, count-1 );
 #endif
 #endif
 		for( j=0; j<clus1; j++ )
@@ -2395,7 +2395,7 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 					if( scoringmatrices ) // called by tditeration.c
 						totalscore += MSalignmm_variousdist( NULL, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
 					else
-						totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp );
+						totalscore += MSalignmm( n_dynamicmtx, tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, sgap1, sgap2, egap1, egap2, NULL, 0, NULL, headgp, tailgp, NULL, NULL, NULL, 0.0, 0.0 );
 				break;
 			default:
 				fprintf( stderr, "alg = %c\n", alg );

core/Falign_localhom.c

@@ -166,7 +166,7 @@ double Falign_localhom( int **whichmtx, double ***scoringmatrices, double **n_dy
 			  double **eff1s, double **eff2s,
 			  int    clus1, int    clus2,
 			  int alloclen, 
-			   LocalHom ***localhom, double *totalimpmatch,
+			   int constraint, double *totalimpmatch,
 			   int *gapmap1, int *gapmap2,
 				int *chudanpt, int chudanref, int *chudanres )
 {
@@ -227,8 +227,8 @@ double Falign_localhom( int **whichmtx, double ***scoringmatrices, double **n_dy
 			fft( 0, NULL, 1 );
 //			A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1 ); // iru?
 			G__align11( NULL, NULL, NULL, 0, 0, 0 );
-			partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
-			partA__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
+			partA__align( NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
+			partA__align_variousdist( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL );
 			blockAlign2( NULL, NULL, NULL, NULL, NULL, NULL );
 			if( crossscore ) FreeDoubleMtx( crossscore );
 			FreeCharMtx( result1 );
@@ -809,10 +809,10 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );
 			case( 'A' ):
 				if( scoringmatrices ) // called by tditeration.c 
 				{
-					totalscore += partA__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
+					totalscore += partA__align_variousdist( whichmtx, scoringmatrices, NULL, tmpres1, tmpres2, eff1, eff2, eff1s, eff2s, clus1, clus2, alloclen, constraint, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
 				}
 				else
-					totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, localhom, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
+					totalscore += partA__align( tmpres1, tmpres2, eff1, eff2, clus1, clus2, alloclen, constraint, &impmatch, cut1[i], cut1[i+1]-1, cut2[i], cut2[i+1]-1, gapmap1, gapmap2, sgap1, sgap2, egap1, egap2, chudanpt, chudanref, chudanres );
 				*totalimpmatch += impmatch;
 //				fprintf( stderr, "*totalimpmatch in Falign_localhom = %f\n", *totalimpmatch );
 

core/Galign11.c

@@ -797,7 +797,8 @@ double G__align11_noalign( double **n_dynamicmtx, int penal, int penal_ex, char
 		intwork = AllocateIntMtx( nalphabets, MAX( ll1, ll2 )+2 ); 
 
 
-		amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
+//		amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 ); 
+		amino_dynamicmtx = AllocateDoubleMtx( 0x100, 0x100 );  // 2017/Nov.  constants.c no 'charsize' wo global hensuu nishita houga yoi?
 #if DEBUG
 		fprintf( stderr, "succeeded\n" );
 #endif
@@ -811,8 +812,6 @@ double G__align11_noalign( double **n_dynamicmtx, int penal, int penal_ex, char
 		amino_dynamicmtx[(int)amino[i]][(int)amino[j]] = (double)n_dynamicmtx[i][j];
 
 
-
-
 #if 0
 	for( i=0; i<lgth1; i++ ) 
 		fprintf( stderr, "ogcp1[%d]=%f\n", i, ogcp1[i] );

core/Lalign11.c

@@ -871,7 +871,8 @@ double L__align11_noalign( double **n_dynamicmtx, char **seq1, char **seq2 )
 #if DEBUG
 		fprintf( stderr, "succeeded\n" );
 #endif
-		amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 );
+//		amino_dynamicmtx = AllocateDoubleMtx( 0x80, 0x80 ); 
+		amino_dynamicmtx = AllocateDoubleMtx( 0x100, 0x100 );  // 2017/Nov.  constants.c no 'charsize' wo global hensuu nishita houga yoi?
 		orlgth1 = ll1 - 100;
 		orlgth2 = ll2 - 100;
 	}

core/Makefile

@@ -10,8 +10,13 @@ ENABLE_MULTITHREAD = -Denablemultithread
 # Comment out the above line if your compiler 
 # does not support TLS (thread-local strage).
 
+#ENABLE_ATOMIC = -Denableatomic
+# Comment out the above line if your compiler 
+# does not support "atomic_int".
+
 CC = gcc
-CFLAGS = -O3 -std=c99
+#CC = icc
+CFLAGS = -O3
 #CFLAGS = -O3 -fPIC
 # add -fPIC when building .so files
 
@@ -25,7 +30,6 @@ CFLAGS = -O3 -std=c99
 #CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 -lprofiler  # ?
 
 
-MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
 
 ifdef ENABLE_MULTITHREAD
 LIBS = -lm  -lpthread
@@ -33,11 +37,19 @@ else
 LIBS = -lm
 endif
 
+ifdef ENABLE_ATOMIC
+STDF = -std=c11
+else
+STDF = -std=c99
+endif
+
+MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(ENABLE_ATOMIC) $(STDF) $(CFLAGS)
+
 INSTALL = install
 
 PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
-		multi2hat3s pairash addsingle \
-        splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen \
+		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
 SOS = libdisttbfast.so
 DLLS = libdisttbfast.dll
@@ -45,82 +57,80 @@ DYLIBS = libdisttbfast.dylib
 
 PERLPROGS = mafftash_premafft.pl seekquencer_premafft.pl
 SCRIPTS = mafft mafft-homologs.rb mafft-sparsecore.rb
-OBJSETDIRECTION = mtxutl.o io.o setdirection.o defs.o mltaln9.o
-OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o
-OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o
-OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o
+OBJSETDIRECTION = mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o
+OBJREPLACEU = mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o
+OBJRESTOREU = mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o
+OBJREGTABLE2SEQ = mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o
 OBJSEQ2REGTABLE = mtxutl.o io.o seq2regtable.o defs.o
 OBJCOUNTLEN = mtxutl.o io.o countlen.o defs.o
 OBJF2CL = mtxutl.o io.o f2cl.o constants.o defs.o
-OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o
-OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o
+OBJMCCASKILLWRAP = mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o
+OBJCONTRAFOLDWRAP = mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o
 OBJMULTI2HAT3S = mtxutl.o io.o mltaln9.o tddis.o constants.o \
-				 multi2hat3s.o defs.o fft.o fftFunctions.o
+				 multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o
 OBJPAIRASH = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-			 Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o \
+			 Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o \
 			 pairash.o defs.o fft.o fftFunctions.o
 OBJPAIRLOCALALIGN = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		            Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o \
+		            Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o \
 					pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o
 OBJDUMMY = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
 			disttbfast_dummy.o dummy.o defs.o fft.o fftFunctions.o
 OBJSPLITFROMALN = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
-			Lalign11.o splitfromaln.o defs.o fft.o fftFunctions.o
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
+			splitfromaln.o defs.o fft.o fftFunctions.o
 OBJSPLITTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
-			Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o 
-OBJSPLITTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
-			Lalign11.o splittbfast2.o defs.o fft.o fftFunctions.o
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
+			splittbfast.o defs.o fft.o fftFunctions.o 
 OBJSPLITTBFASTP = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
-			Lalign11.o defs.o fft.o fftFunctions.o
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
+			defs.o fft.o fftFunctions.o
 OBJDISTTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
 			disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o
 OBJMAKEDIRECTIONLIST = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
-			Lalign11.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
+			makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o
 OBJTBFAST = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \
 			tbfast.o defs.o fft.o fftFunctions.o addfunctions.o \
-			pairlocalalign.o genalign11.o MSalign11.o Lalign11.o 
+			pairlocalalign.o MSalign11.o 
+OBJNODPAIR = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \
+			nodepair.o defs.o fft.o fftFunctions.o addfunctions.o \
+			pairlocalalign.o MSalign11.o
 OBJADDSINGLE = mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o \
 			addsingle.o defs.o fft.o fftFunctions.o addfunctions.o
-OBJTBFAST2 = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  MSalignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o \
-			tbfast2.o defs.o fft.o fftFunctions.o
 OBJSETCORE = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o \
 			setcore.o defs.o fft.o fftFunctions.o
 OBJTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o  \
-		   Falign.o Falign_localhom.o Galign11.o fftFunctions.o fft.o  \
+		   Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o fftFunctions.o fft.o  \
 		   tditeration.o tditr.o defs.o SAalignmm.o treeOperation.o
 OBJDVTDITR = mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-			Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o  \
+			Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o  \
 			tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o 
 OBJGETLAG = mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  \
-		    Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Dalignmm.o \
+		    Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o \
 			getlag.o defs.o fft.o fftFunctions.o
 OBJGAPFILL = mtxutl.o io.o constants.o gapfill.o defs.o
 OBJDNDFAST5 = dndfast5.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
-OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
-OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
+OBJDNDBLAST = dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o
+OBJDNDFAST7 = dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o
 OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
 OBJDNDFAST4 = dndfast4.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
 OBJDNDFAST6 = dndfast6.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
-OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o
-OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o
+OBJSEXTET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o
+OBJDISTANCE = io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o
 OBJTRIPLET6 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet6.o defs.o
 OBJTRIPLET5 = io.o constants.o mtxutl.o mltaln9.o tddis.o triplet5.o defs.o
 OBJOCTET4 = io.o constants.o mtxutl.o mltaln9.o tddis.o octet4.o defs.o
-OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o
+OBJDNDPRE = dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o
 OBJGALN = io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o \
-          SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o
-OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o
+          SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o
+OBJSCORE = io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o
 
 HEADER = mltaln.h mtxutl.h mafft.h
 FFTHEADER = fft.h
@@ -160,17 +170,23 @@ mltaln.h : functions.h
 	touch mltaln.h
 
 version : version.c mltaln.h
-	$(CC) -o $@ version.c $(MYCFLAGS) $(LDFLAGS)
+	$(CC) -o $@ version.c $(MYCFLAGS) $(LDFLAGS) $(LIBS) 
+
+maffttext2hex : maffttext2hex.c
+	$(CC) -o $@ maffttext2hex.c $(MYCFLAGS) $(LDFLAGS) $(LIBS)
+
+hex2maffttext : hex2maffttext.c
+	$(CC) -o $@ hex2maffttext.c $(MYCFLAGS) $(LDFLAGS) $(LIBS)
 
 tbfast : $(OBJTBFAST)
 	$(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
 
+nodepair : $(OBJNODPAIR)
+	$(CC) -o $@ $(OBJNODPAIR) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
+
 addsingle : $(OBJADDSINGLE)
 	$(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
 
-tbfast2 : $(OBJTBFAST2)
-	$(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
-
 disttbfast : $(OBJDISTTBFAST)
 	$(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
 
@@ -192,9 +208,6 @@ splittbfast : $(OBJSPLITTBFAST)
 splitfromaln : $(OBJSPLITFROMALN)
 	$(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
 
-splittbfast2 : $(OBJSPLITTBFAST2)
-	$(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
-
 dummy : $(OBJDUMMY)
 	$(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LDFLAGS) $(LIBS)
 
@@ -390,6 +403,10 @@ dummy.o : dummy.c $(HEADER) $(FFTHEADER)
 tbfast.o : tbfast.c $(HEADER) $(FFTHEADER)
 	$(CC) $(MYCFLAGS) -c tbfast.c
 
+nodepair.o : nodepair.c $(HEADER) $(FFTHEADER)
+	$(CC) $(MYCFLAGS) -c nodepair.c
+
+addsingle.o : addsingle.c $(HEADER) $(FFTHEADER)
 addsingle.o : addsingle.c $(HEADER) $(FFTHEADER)
 	$(CC) $(MYCFLAGS) -c addsingle.c
 
@@ -489,8 +506,11 @@ sextet5.o : sextet5.c $(HEADER) $(MTXHEADER)
 mafft-distance.o : mafft-distance.c $(HEADER) $(MTXHEADER)
 	$(CC) $(MYCFLAGS) -c mafft-distance.c
 
-triplet5.o : triplet5.c $(HEADER) $(MTXHEADER)
-	$(CC) $(MYCFLAGS) -c triplet5.c
+maffttext2hex.o : maffttext2hex.c
+	$(CC) $(MYCFLAGS) -c maffttext2hex.c
+
+hex2maffttext.o : hex2maffttext.c
+	$(CC) $(MYCFLAGS) -c hex2maffttext.c
 
 triplet6.o : triplet6.c $(HEADER) $(MTXHEADER)
 	$(CC) $(MYCFLAGS) -c triplet6.c

core/addfunctions.c

@@ -84,9 +84,9 @@ void profilealignment2( int n0, int n2, char **aln0, char **aln2, int alloclen,
 
 	newgapstr = "-";
 	if( alg == 'M' )
-		MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap=1, 2014/Dec/1
+		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, NULL, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1 ); //outgap=1, 2014/Dec/1
+		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
 
 	newlen = strlen( aln0[0] );
 
@@ -209,9 +209,9 @@ static void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1,
 
 	newgapstr = "-";
 	if( alg == 'M' )
-		MSalignmm( n_dis_consweight_multi, aln0, aln2, effarr0, effarr2, n0, n2, alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1 ); //outgap=1, 2014/Dec/1
+		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, NULL, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, 1, 1, -1, -1 ); //outgap=1, 2014/Dec/1
+		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
 
 	newlen = strlen( aln0[0] );
 
@@ -284,7 +284,7 @@ void eq2dashmatometehayaku( char **s, int n )
 	int *tobechanged;
 	int len = strlen( s[0] );
 
-	tobechanged = calloc( len, sizeof( int ) );
+	tobechanged = calloc( len+1, sizeof( int ) ); // len+1, 2017/Nov/15
 	c = 0;
 	for( j=0; j<len; j++ )
 	{

core/addsingle.c

@@ -6,7 +6,6 @@
 #define IODEBUG 0
 #define SCOREOUT 0
 
-static int nadd;
 static int treein;
 static int topin;
 static int treeout;
@@ -1279,8 +1278,8 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo
 		}
 		else
 		{
-			clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1, 0.0 );
-			clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2, 0.0 );
+			clus1 = fastconjuction_noname( topol[l][0], aseq, mseq1, effarr1, effarr, indication1, 0.0, NULL );
+			clus2 = fastconjuction_noname( topol[l][1], aseq, mseq2, effarr2, effarr, indication2, 0.0, NULL );
 		}
 
 		if( mergeoralign[l] == '1' || mergeoralign[l] == '2' )
@@ -1396,9 +1395,9 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo
 			fprintf( stderr, "c" );
 			if( alg == 'A' )
 			{
-				imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, NULL, 1, topol[l][0], topol[l][1] );
+				imp_match_init_strict( NULL, clus1, clus2, strlen( mseq1[0] ), strlen( mseq2[0] ), mseq1, mseq2, effarr1, effarr2, effarr1_kozo, effarr2_kozo, localhomshrink, NULL, 1, topol[l][0], topol[l][1], NULL, NULL, NULL, -1, 0 );
 				if( rnakozo ) imp_rna( clus1, clus2, mseq1, mseq2, effarr1, effarr2, grouprna1, grouprna2, NULL, NULL, NULL );
-				pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, localhomshrink, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1 );
+				pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, constraint, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxchild0 tsukaeru??
 			}
 			else if( alg == 'Q' )
 			{
@@ -1428,10 +1427,10 @@ static double treebase( int nseq, int *nlen, char **aseq, int nadd, char *mergeo
 					break;
 				case( 'M' ):
 					fprintf( stderr, "m" );
-					pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap );
+					pscore = MSalignmm( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, NULL, NULL, NULL, 0.0, 0.0 );
 					break;
 				case( 'A' ):
-					pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, NULL, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1 );
+					pscore = A__align( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, *alloclen, 0, &dumdb, NULL, NULL, NULL, NULL, NULL, 0, NULL, outgap, outgap, -1, -1, NULL, NULL, NULL, 0.0, 0.0 ); // cpmxchild0 tsukaeru??
 					break;
 				default:
 					ErrorExit( "ERROR IN SOURCE FILE" );
@@ -1975,7 +1974,7 @@ static void	*addsinglethread( void *arg )
 		if( mseq1 ) free( mseq1 ); mseq1 = NULL;
 		if( mseq2 ) free( mseq2 ); mseq2 = NULL;
 		Falign( NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, 0, NULL );
-		A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1 );
+		A__align( NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, NULL, NULL, NULL, NULL, NULL, NULL, 0, NULL, 0, 0, -1, -1, NULL, NULL, NULL, 0.0, 0.0 );
 		if( commonIP ) FreeIntMtx( commonIP );
 		commonIP = NULL;
 		commonAlloc1 = commonAlloc2 = 0;

core/blosum.c

@@ -314,6 +314,62 @@ void BLOSUMmtx( int n, double **matrix, double *freq, unsigned char *amino, char
     for( i=0; i<26; i++ ) amino_grp[(int)amino[i]] = locgrpd[i];
 }
 
+static int checkchar( int i )
+{
+	if( i > 0xff || i <= 0x00 || i == 0x3E || i == 0x3D || i == 0x3C || i == 0x2D || i == 0x20 || i == 0x0d || i == 0x0a )
+		return( 1 );
+	return( 0 );
+}
+
+static void overridematrix( double **matrix )
+{
+	char buf[500];
+	FILE *fp;
+	unsigned int i1, i2;
+	double v;
+	char *bpt;
+	int nread;
+
+	fp = fopen( "_aamtx", "r" );
+	if( fp == NULL )
+	{
+		fprintf( stderr, "Cannot open scorematrix\n" );
+		exit( 1 );
+	}
+
+	while( 1 )
+	{
+		fgets( buf, 499, fp );
+		if( feof( fp ) ) break;
+
+		if( ( bpt = strchr( buf, '#' ) ) ) *bpt = 0;
+
+		i1 = i2 = 0;
+		nread = sscanf( buf, "%x %x %lf", &i1, &i2, &v );
+		if( nread == EOF ) continue;
+		if( nread != 3 )
+		{
+			reporterr( "Format error in this line?\n" );
+			reporterr( "%s\n", buf );
+//			reporterr( "To set a score, 100, for a match of 0x41 and 0x42, \n" );
+//			reporterr( "0x41 0x42 100 \n" );
+			exit( 1 );
+		}
+		if( checkchar( i1 ) )
+		{
+			reporterr( "%c=0x%x cannot be used (1)\n", i1, i1 );
+			exit( 1 );
+		}
+		if( checkchar( i2 ) )
+		{
+			reporterr( "%c=0x%x cannot be used (2)\n", i2, i2 );
+			exit( 1 );
+		}
+		reporterr( "Score(%c=0x%x,%c=0x%x)=%f\n", i1, i1, i2, i2, v );
+		matrix[i1][i2] = v;
+	}
+}
+
 void extendedmtx( double **matrix, double *freq, unsigned char *amino, char *amino_grp )
 {
 	int i;
@@ -336,7 +392,9 @@ void extendedmtx( double **matrix, double *freq, unsigned char *amino, char *ami
 	}
 	for( i=0; i<nalphabets; i++ )
 		matrix[i][i] = matrix[i][i] = (double)1.0;
-#if 0 // user-defined matrix no toki fukkatsu saseru.
+
+	overridematrix( matrix );
+#if 0 // user-defined matrix + user-defined freqency ga aru toki fukkatsu saseru.
 	if( tmpmtx[400] != -1.0 ) 
 	{
 		for( i=0; i<20; i++ ) freq[i] = tmpmtx[400+i];

core/defs.c

-#include <stdio.h>
-#include "dp.h"
 #include "mltaln.h"
+#include "dp.h"
 
 int TLS commonAlloc1 = 0;
 int TLS commonAlloc2 = 0;
 int TLS **commonIP = NULL;
 int TLS **commonJP = NULL;
 int nthread = 1;
+int nthreadpair = 1;
 int randomseed = 0;
 int parallelizationstrategy = BAATARI1;
 
@@ -131,6 +131,8 @@ double sueff_global = SUEFF;
 double lenfaca, lenfacb, lenfacc, lenfacd;
 int maxl, tsize;
 
+
+
 void initglobalvariables()
 {
 	commonAlloc1 = 0;
@@ -163,3 +165,11 @@ void initglobalvariables()
 	
 	gmsg = 0;
 }
+
+// for usetmpfile
+int compacttree = 0;
+int lhlimit = INT_MAX;
+int specifictarget = 0;
+int nadd = 0; // <- static in tbfast.c, pairlocalalign.c
+int usenaivescoreinsteadofalignmentscore = 0;
+int nthreadreadlh = 1;

core/dndpre.c

@@ -4,8 +4,6 @@
 
 static int treeout = 0;
 static int maxdist = 1;
-static int nadd = 0;
-static int usenaivescoreinsteadofalignmentscore = 0;
 
 #ifdef enablemultithread
 typedef struct _jobtable
@@ -345,6 +343,14 @@ int main( int argc, char **argv )
 #else
 	getnumlen( infp );
 #endif
+
+	if( njob < 2 )
+	{
+		fprintf( stderr, "At least 2 sequences should be input!\n"
+						 "Only %d sequence found.\n", njob ); 
+		exit( 1 );
+	}
+
 	rewind( infp );
 
 	njob -= nadd; // atarashii hairetsu ha mushi