diff mafft/core/dvtditr.c @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/dvtditr.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,1076 @@
+ /* Tree-dependent-iteration */
+ /* Devide to segments       */ 
+
+#include "mltaln.h"
+
+extern char **seq_g;
+extern char **res_g;
+static int subalignment;
+static int subalignmentoffset;
+
+static int intop;
+static int intree;
+static double autosubalignment;
+
+
+static void calcmaxdistclass( void )
+{
+	int c;
+	float rep;
+	for( c=0; c<ndistclass; c++ )
+	{
+		rep = (double) 2 * c / ndistclass; // dist:0-2 for dist2offset 
+//		fprintf( stderr, "c=%d, rep=%f, offset=%f\n", c, rep, dist2offset( rep )  );
+		if( dist2offset( rep ) == 0.0 )
+			break;
+	}
+	fprintf( stderr, "ndistclass = %d, maxdistclass = %d\n", ndistclass, c+1 );
+	maxdistclass = c + 1;
+//	maxdistclass = ndistclass; // CHUUI!!!!
+	return;
+}
+
+void arguments( int argc, char *argv[] )
+{
+	int c;
+	char *argkey;
+
+	outnumber = 0;
+	nthread = 1;
+	randomseed = 0;
+	scoreout = 0;
+	spscoreout = 0;
+	parallelizationstrategy = BAATARI1;
+	intop = 0;
+	intree = 0;
+	inputfile = NULL;
+	rnakozo = 0;
+	rnaprediction = 'm';
+	nevermemsave = 0;
+	score_check = 1;
+	fftkeika = 1;
+	constraint = 0;
+	fmodel = 0;
+	kobetsubunkatsu = 1;
+	bunkatsu = 1;
+	nblosum = 62;
+	niter = 100;
+	calledByXced = 0;
+	devide = 1;
+	divWinSize = 20; /* 70 */
+	divThreshold = 65;
+	fftscore = 1;
+	fftRepeatStop = 0;
+	fftNoAnchStop = 0;
+    scmtd = 5;
+	cooling = 1;
+    weight = 4;
+    utree = 1;
+    refine = 1;
+    check = 1;
+    cut = 0.0;
+	disp = 0;
+	outgap = 1;
+	use_fft = 0; // CHUUI dochira demo mafft.tmpl deha F
+	force_fft = 0;
+	alg = 'A';  /* chuui */
+	mix = 0;
+	checkC = 0;
+	tbitr = 0;
+	treemethod = 'X';
+	sueff_global = 0.1;
+	scoremtx = 1;
+	dorp = NOTSPECIFIED;
+	ppenalty = NOTSPECIFIED;
+	penalty_shift_factor = 1000.0;
+	ppenalty_ex = NOTSPECIFIED;
+	poffset = NOTSPECIFIED;
+	kimuraR = NOTSPECIFIED;
+	pamN = NOTSPECIFIED;
+	geta2 = GETA2;
+	fftWinSize = NOTSPECIFIED;
+	fftThreshold = NOTSPECIFIED;
+	RNAppenalty = NOTSPECIFIED;
+	RNAppenalty_ex = NOTSPECIFIED;
+	RNApthr = NOTSPECIFIED;
+	TMorJTT = JTT;
+	consweight_multi = 1.0;
+	consweight_rna = 0.0;
+	subalignment = 0;
+	subalignmentoffset = 0;
+	legacygapcost = 0;
+	specificityconsideration = 0.0;
+	autosubalignment = 0.0;
+
+	while( --argc > 0 && (*++argv)[0] == '-' )
+	{
+		while ( (c = *++argv[0]) )
+		{
+			switch( c )
+			{
+				case 'i':
+					inputfile = *++argv;
+					fprintf( stderr, "inputfile = %s\n", inputfile );
+					--argc;
+					goto nextoption;
+				case 'I':
+					niter = myatoi( *++argv );
+					fprintf( stderr, "niter = %d\n", niter );
+					--argc;
+					goto nextoption;
+				case 'e':
+					RNApthr = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'o':
+					RNAppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+					--argc;
+					goto nextoption;
+				case 'f':
+					ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
+//					fprintf( stderr, "ppenalty = %d\n", ppenalty );
+					--argc;
+					goto nextoption;
+				case 'Q':
+					penalty_shift_factor = atof( *++argv );
+					if( penalty_shift_factor < 100.0 && penalty_shift_factor != 2.0 )
+					{
+						fprintf( stderr, "%f, penalty_shift is fixed to penalty x 2 in the iterative refinement phase.\n", penalty_shift_factor );
+						penalty_shift_factor = 2.0;
+					}
+					--argc;
+					goto nextoption;
+				case 'g':
+					ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
+//					fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
+					--argc;
+					goto nextoption;
+				case 'h':
+					poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
+					fprintf( stderr, "poffset = %d\n", poffset );
+					--argc;
+					goto nextoption;
+				case 'k':
+					kimuraR = myatoi( *++argv );
+					fprintf( stderr, "kappa = %d\n", kimuraR );
+					--argc; 
+					goto nextoption;
+				case 'b':
+					nblosum = myatoi( *++argv );
+					scoremtx = 1;
+					fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
+					--argc; 
+					goto nextoption;
+				case 'j':
+					pamN = myatoi( *++argv );
+					scoremtx = 0;
+					TMorJTT = JTT;
+					fprintf( stderr, "jtt/kimura %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;
+				case 'r':
+					consweight_rna = atof( *++argv );
+					rnakozo = 1;
+					--argc;
+					goto nextoption;
+				case 'c':
+					consweight_multi = atof( *++argv );
+					--argc;
+					goto nextoption;
+				case 'C':
+					nthread = myatoi( *++argv );
+					fprintf( stderr, "nthread = %d\n", nthread );
+					--argc; 
+					goto nextoption;
+				case 'H':
+					subalignment = 1;
+					subalignmentoffset = myatoi( *++argv );
+					--argc;
+					goto nextoption;
+				case 't':
+					randomseed = myatoi( *++argv );
+					fprintf( stderr, "randomseed = %d\n", randomseed );
+					--argc; 
+					goto nextoption;
+				case 'p':
+					argkey = *++argv;
+					if( !strcmp( argkey, "BESTFIRST" ) ) parallelizationstrategy = BESTFIRST;
+					else if( !strcmp( argkey, "BAATARI0" ) ) parallelizationstrategy = BAATARI0;
+					else if( !strcmp( argkey, "BAATARI1" ) ) parallelizationstrategy = BAATARI1;
+					else if( !strcmp( argkey, "BAATARI2" ) ) parallelizationstrategy = BAATARI2;
+					else
+					{
+						fprintf( stderr, "Unknown parallelization strategy, %s\n", argkey );
+						exit( 1 );
+					}
+//					exit( 1 );
+					--argc; 
+					goto nextoption;
+				case 's':
+					specificityconsideration = (double)myatof( *++argv );
+//					fprintf( stderr, "specificityconsideration = %f\n", specificityconsideration );
+					--argc; 
+					goto nextoption;
+#if 0
+				case 'S' :
+					scoreout = 1; // for checking parallel calculation
+					break;
+#else
+				case 'S' :
+					spscoreout = 1; // 2014/Dec/30, sp score
+					break;
+#endif
+#if 0
+				case 's' :
+					RNAscoremtx = 'r';
+					break;
+#endif
+#if 1
+				case 'a':
+					fmodel = 1;
+					break;
+#endif
+				case 'N':
+					nevermemsave = 1;
+					break;
+				case 'D':
+					dorp = 'd';
+					break;
+				case 'P':
+					dorp = 'p';
+					break;
+#if 0
+				case 'Q':
+					alg = 'Q';
+					break;
+#endif
+				case 'R':
+					rnaprediction = 'r';
+					break;
+				case 'O':
+					fftNoAnchStop = 1;
+					break;
+#if 0
+				case 'e':
+					fftscore = 0;
+					break;
+				case 'r':
+					fmodel = -1;
+					break;
+				case 'R':
+					fftRepeatStop = 1;
+					break;
+#endif
+				case 'T':
+					kobetsubunkatsu = 0;
+					break;
+				case 'B':
+					bunkatsu = 0;
+					break;
+#if 0
+				case 'c':
+					cooling = 1;
+					break;
+				case 'a':
+					alg = 'a';
+					break;
+				case 's' :
+					treemethod = 's';
+					break;
+				case 'H':
+					alg = 'H';
+					break;
+#endif
+				case 'A':
+					alg = 'A';
+					break;
+				case 'M':
+					alg = 'M';
+					break;
+				case 'F':
+					use_fft = 1;
+					break;
+#if 0
+				case 't':
+					weight = 4;
+					break;
+#endif
+				case 'u':
+					weight = 0;
+					break;
+				case 'U':
+					intree = 1;
+					break;
+				case 'V':
+					intop = 1;
+					break;
+				case 'J':
+					utree = 0;
+					break;
+				case 'd':
+					disp = 1;
+					break;
+				case 'Z':
+					score_check = 0;
+					break;
+				case 'Y':
+					score_check = 2;
+					break;
+				case 'L':
+					legacygapcost = 1;
+					break;
+#if 0
+				case 'n' :
+					treemethod = 'n';
+					break;
+#endif
+				case 'n' :
+					outnumber = 1;
+					break;
+				case 'X':
+					treemethod = 'X';
+					sueff_global = atof( *++argv );
+					fprintf( stderr, "sueff_global = %f\n", sueff_global );
+					--argc;
+					goto nextoption;
+#if 0
+				case 'E' :
+					treemethod = 'E';
+					break;
+				case 'q' :
+					treemethod = 'q';
+					break;
+#endif
+				case 'E':
+					autosubalignment = atof( *++argv );
+					fprintf( stderr, "autosubalignment = %f\n", autosubalignment );
+					--argc;
+					goto nextoption;
+				case 'z':
+					fftThreshold = myatoi( *++argv );
+					--argc;
+					goto nextoption;
+				case 'w':
+					fftWinSize = myatoi( *++argv );
+					--argc;
+					goto nextoption;
+				default:
+					fprintf( stderr, "illegal option %c\n", c );
+					argc = 0;
+					break;
+			}
+		}
+		nextoption:
+			;
+	}
+	if( argc == 1 )
+	{
+		cut = atof( (*argv) );
+		argc--;
+	}
+	if( argc != 0 ) 
+	{
+		fprintf( stderr, "options : Check source file!\n" );
+		exit( 1 );
+	}
+#if 0
+	if( alg == 'A' && weight == 0 ) 
+		ErrorExit( "ERROR : Algorithm A+ and un-weighted\n" ); 
+#endif
+}
+
+
+int main( int argc, char *argv[] )
+{
+    int identity;
+	static int nlen[M];
+	static char **name, **seq, **aseq, **bseq;
+	static Segment *segment = NULL;
+	static int anchors[MAXSEG];
+	int i, j;
+	int iseg, nseg;
+	int ***topol;
+	double **len;
+	double **eff;
+	FILE *prep;
+	FILE *infp;
+	FILE *orderfp;
+	int alloclen;
+	int returnvalue;
+	char c;
+	int ocut;
+	char **seq_g_bk;
+	LocalHom **localhomtable = NULL; // by D.Mathog
+	RNApair ***singlerna;
+	int nogaplen;
+	static char **nogap1seq;
+	static char *kozoarivec;
+	int nkozo;
+	int alignmentlength;
+	int **skipthisbranch;
+	int foundthebranch;
+	int nsubalignments, maxmem;
+	int **subtable;
+	int *insubtable;
+	int *preservegaps;
+	char ***subalnpt;
+
+	arguments( argc, argv );
+#ifndef enablemultithread
+	nthread = 0;
+#endif
+	if( fastathreshold < 0.0001 ) constraint = 0;
+
+	if( inputfile )
+	{
+		infp = fopen( inputfile, "r" );
+		if( !infp ) 
+		{
+			fprintf( stderr, "Cannot open %s\n", inputfile );
+			exit( 1 );
+		}
+	}
+	else    
+		infp = stdin;
+
+#if 0
+	PreRead( stdin, &njob, &nlenmax );
+#else
+	getnumlen( infp );
+#endif
+	rewind( infp );
+
+	nkozo = 0;
+
+	if( njob < 2 ) 
+	{
+		fprintf( stderr, "At least 2 sequences should be input!\n"
+						 "Only %d sequence found.\n", njob ); 
+		exit( 1 );
+	}
+
+
+	if( subalignment )
+	{
+		readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );
+		fprintf( stderr, "nsubalignments = %d\n", nsubalignments );
+		fprintf( stderr, "maxmem = %d\n", maxmem );
+		subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
+		insubtable = AllocateIntVec( njob );
+		preservegaps = AllocateIntVec( njob );
+		for( i=0; i<njob; i++ ) insubtable[i] = 0;
+		for( i=0; i<njob; i++ ) preservegaps[i] = 0;
+		subalnpt = AllocateCharCub( nsubalignments, maxmem, 0 );
+		readsubalignmentstable( njob, subtable, preservegaps, NULL, NULL );
+		for( i=0; i<nsubalignments; i++ ) for( j=0; j<insubtable[i]; j++ )
+		{
+			if( subtable[i][j] < 0 )
+			{
+				fprintf( stderr, "Not supported in the iterative refinmenment mode.\n" );
+				fprintf( stderr, "Please use a positive number to represent a sequence.\n" );
+			}
+		}
+	}
+
+	ocut = cut;
+
+	segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
+//	if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' )
+	topol = AllocateIntCub( njob, 2, njob );
+	len = AllocateDoubleMtx( njob, 2 );
+	eff = AllocateDoubleMtx( njob, njob );
+	seq = AllocateCharMtx( njob, nlenmax*9+1 );
+	name = AllocateCharMtx( njob, B+1 );
+	seq_g = AllocateCharMtx( njob, nlenmax*9+1 );
+	res_g = AllocateCharMtx( njob, nlenmax*9+1 );
+	aseq = AllocateCharMtx( njob, nlenmax*9+1 );
+	bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+	nogap1seq = AllocateCharMtx( 1, nlenmax*1+1 );
+	alloclen = nlenmax * 9;
+	seq_g_bk = AllocateCharMtx( njob, 0 );
+	for( i=0; i<njob; i++ ) seq_g_bk[i] = seq_g[i];
+	kozoarivec = AllocateCharVec( njob );
+	skipthisbranch = AllocateIntMtx( njob, 2 );
+	for( i=0; i<njob; i++ ) skipthisbranch[i][0] = skipthisbranch[i][1] = 0;
+
+	if( constraint )
+	{
+		localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+		for( i=0; i<njob; i++)
+		{
+			localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+			for( j=0; j<njob; j++)
+			{
+				localhomtable[i][j].start1 = -1;
+				localhomtable[i][j].end1 = -1;
+				localhomtable[i][j].start2 = -1;
+				localhomtable[i][j].end2 = -1;
+				localhomtable[i][j].overlapaa = -1.0; 
+				localhomtable[i][j].opt = -1.0;
+				localhomtable[i][j].importance = -1.0; 
+				localhomtable[i][j].next = NULL; 
+				localhomtable[i][j].nokori = 0;
+				localhomtable[i][j].extended = -1;
+				localhomtable[i][j].last = localhomtable[i]+j;
+				localhomtable[i][j].korh = 'h';
+			}
+		}
+		fprintf( stderr, "Loading 'hat3' ... " );
+		fflush( stderr );
+		prep = fopen( "hat3", "r" );
+		if( prep == NULL ) ErrorExit( "Make hat3." );
+		readlocalhomtable2( prep, njob, localhomtable, kozoarivec );
+		fclose( prep ); 
+//		for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
+//			fprintf( stdout, "%d %d %d %d %d %d %d\n", i, j, localhomtable[i][j].opt, localhomtable[i][j].start1, localhomtable[i][j].end1, localhomtable[i][j].start2, localhomtable[i][j].end2 );
+		fprintf( stderr, "done.\n" );
+		fflush( stderr );
+#if 0
+		fprintf( stderr, "Extending localhom ... " );
+		extendlocalhom( njob, localhomtable );
+		fprintf( stderr, "done.\n" );
+#endif
+		nkozo = 0;
+		for( i=0; i<njob; i++ ) if( kozoarivec[i] ) nkozo++;
+	}
+
+
+//		if( nlenmax > 30000 )
+		if( nlenmax > 50000 ) // version >= 6.823
+		{
+#if 0
+			if( constraint )
+			{
+				fprintf( stderr, "\nnlenmax=%d, nagasugi!\n", nlenmax ); 
+				exit( 1 );
+			}
+			if( nevermemsave )
+			{
+				fprintf( stderr, "\nnevermemsave=1, nlenmax=%d, nagasugi!\n", nlenmax ); 
+				exit( 1 );
+			}
+#endif
+			if( !constraint && !nevermemsave && alg != 'M' )
+			{
+				fprintf( stderr, "\nnlenmax=%d, Switching to the memsave mode\n", nlenmax ); 
+				alg = 'M';
+			}
+		}
+
+#if 0
+	Read( name, nlen, seq_g );
+#else
+	readData_pointer( infp, name, nlen, seq_g );
+#endif
+	fclose( infp );
+
+	if( specificityconsideration ) calcmaxdistclass();
+
+	for( i=0; i<njob; i++ )
+	{
+		res_g[i][0] = 0;
+	}
+
+	identity = 1;
+	for( i=0; i<njob; i++ ) 
+	{
+		identity *= ( nlen[i] == nlen[0] );
+	}
+	if( !identity ) 
+	{
+		fprintf( stderr, "Input pre-aligned data\n" );
+		exit( 1 );
+	}
+	constants( njob, seq_g );
+
+#if 0
+	fprintf( stderr, "penalty = %d\n", penalty ); 
+	fprintf( stderr, "penalty_ex = %d\n", penalty_ex ); 
+	fprintf( stderr, "offset = %d\n", offset ); 
+#endif
+
+	initSignalSM();
+
+	initFiles();
+
+#if 0
+	if( njob == 2 )
+	{
+		writePre( njob, name, nlen, seq_g, 1 );
+		SHOWVERSION;
+		return( 0 );
+	}
+#else
+	if( njob == 2 )
+	{
+		weight = 0;
+		niter = 1;
+	}
+#endif
+
+	c = seqcheck( seq_g );
+	if( c )
+	{
+		fprintf( stderr, "Illegal character %c\n", c );
+		exit( 1 );
+	}
+	commongappick( njob, seq_g );
+
+	if( rnakozo && rnaprediction == 'm' )
+	{
+		singlerna = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
+		prep = fopen( "hat4", "r" );
+		if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
+		fprintf( stderr, "Loading 'hat4' ... " );
+		fflush( stderr );
+		for( i=0; i<njob; i++ )
+		{
+			gappick0( nogap1seq[0], seq_g[i] );
+			nogaplen = strlen( nogap1seq[0] );
+			singlerna[i] = (RNApair **)calloc( nogaplen+1, sizeof( RNApair * ) );
+			for( j=0; j<nogaplen; j++ )
+			{
+				singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
+				singlerna[i][j][0].bestpos = -1;
+				singlerna[i][j][0].bestscore = -1.0;
+			}
+			singlerna[i][nogaplen] = NULL;
+			readmccaskill( prep, singlerna[i], nogaplen );
+		}
+		fclose( prep );
+		fprintf( stderr, "\ndone.\n" );
+		fflush( stderr );
+	}
+	else
+		singlerna = NULL;
+
+
+
+	if( utree )
+	{
+		prep = fopen( "hat2", "r" );
+		if( !prep ) ErrorExit( "Make hat2." );
+		readhat2_pointer( prep, njob, name, eff );
+		fclose( prep );
+#if 0
+		fprintf( stderr, "eff = \n" );
+		for( i=0; i<njob-1; i++ ) 
+		{
+			for( j=i+1; j<njob; j++ ) 
+			{
+				fprintf( stderr, "%d-%d,  %f\n", i, j, eff[i][j] );
+			}
+			fprintf( stderr, "\n" );
+		}
+#endif
+		if( intree )
+		{
+			veryfastsupg_double_loadtree( njob, eff, topol, len, name );
+#if 0
+			fprintf( stderr, "eff = \n" );
+			for( i=0; i<njob-1; i++ ) 
+			{
+				for( j=i+1; j<njob; j++ ) 
+				{
+					fprintf( stderr, "%d-%d,  %f\n", i, j, eff[i][j] );
+				}
+				fprintf( stderr, "\n" );
+			}
+exit( 1 );
+#endif
+		}
+		else if( intop ) // v6.528 deha if( intop ) dattanode intree ga mukou datta.
+		{
+			fprintf( stderr, "--topin has been disabled\n" );
+			exit( 1 );
+//			veryfastsupg_double_loadtop( njob, eff, topol, len );
+		}
+		else if( subalignment )
+			fixed_supg_double_treeout_constrained( njob, eff, topol, len, name, nsubalignments, subtable );
+		else if( treemethod == 'X' || treemethod == 'E' || treemethod == 'q' ) 
+//			veryfastsupg_double_outtree( njob, eff, topol, len, name );
+			fixed_musclesupg_double_treeout( njob, eff, topol, len, name );
+		else if( treemethod == 'n' ) 
+			nj( njob, eff, topol, len );
+		else if( treemethod == 's' )
+			spg( njob, eff, topol, len );
+		else if( treemethod == 'p' )
+			upg2( njob, eff, topol, len );
+		else ErrorExit( "Incorrect treemethod.\n" );
+	}
+#if DEBUG
+	printf( "utree = %d\n", utree );
+#endif
+
+	if( autosubalignment > 0.0 && subalignment == 0 )
+	{
+//		reporterr( "Computing skipthisbranch..\n" );
+		insubtable = AllocateIntVec( njob );
+		preservegaps = AllocateIntVec( njob );
+		subtable = calloc( 1, sizeof( char * ) );
+		subtable[0] = NULL; // for FreeIntMtx
+		for( i=0; i<njob; i++ ) insubtable[i] = 0;
+		for( i=0; i<njob; i++ ) preservegaps[i] = 0; // tsukawanaikamo
+		if( generatesubalignmentstable( njob, &subtable, &nsubalignments, &maxmem, topol, len, autosubalignment ) ) // subtable ha allocate sareru.
+		{
+			reporterr( "################################################################################################ \n" );
+			reporterr( "#\n" );
+			reporterr( "# WARNING: Iterative refinment was not done because you gave a large --fix value (%6.3f).\n", autosubalignment );
+			reporterr( "#\n" );
+			reporterr( "################################################################################################ \n" );
+			writePre( njob, name, nlen, seq_g, 1 );
+
+			FreeCharMtx( seq_g_bk );
+			FreeIntCub( topol );
+			FreeDoubleMtx( len );
+			FreeDoubleMtx( eff );
+			FreeIntMtx( skipthisbranch );
+			FreeIntMtx( subtable );
+			free( preservegaps );
+			free( insubtable );
+			SHOWVERSION;
+			return( 0 );
+		}
+//		subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
+		fprintf( stderr, "nsubalignments = %d, maxmem = %d\n", nsubalignments, maxmem );
+		subalnpt = AllocateCharCub( nsubalignments, maxmem, 0 );
+#if 0
+		for( i=0; i<nsubalignments; i++ )
+		{
+			reporterr( "subalignment %d\n", i );
+			for( j=0; subtable[i][j]!=-1; j++ )
+			{
+				reporterr( "%5d", subtable[i][j] );
+			}
+			reporterr( "\n" );
+		}
+#endif
+#if 0 // wakaran
+		for( i=0; i<nsubalignments; i++ ) for( j=0; j<insubtable[i]; j++ )
+		{
+			if( subtable[i][j] < 0 )
+			{
+				fprintf( stderr, "Not supported in the iterative refinmenment mode.\n" );
+				fprintf( stderr, "Please use a positive number to represent a sequence.\n" );
+			}
+		}
+#endif
+//		reporterr( "done.\n" );
+	}
+
+
+	orderfp = fopen( "order", "w" );
+	if( !orderfp )
+	{
+		fprintf( stderr, "Cannot open 'order'\n" );
+		exit( 1 );
+	}
+	for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
+	{
+		fprintf( orderfp, "%d\n", j );
+	}
+	for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
+	{
+		fprintf( orderfp, "%d\n", j );
+	}
+	fclose( orderfp );
+
+
+
+	fprintf( stderr, "\n" );
+	if( ( !utree && kobetsubunkatsu ) || constraint || !bunkatsu )
+	{
+		nseg = 0;
+		anchors[0] =0;
+		anchors[1] =strlen( seq_g[0] );
+		nseg += 2;
+	}
+	else
+	{
+		nseg = searchAnchors( njob, seq_g, segment );
+#if 0
+		fprintf( stderr, "### nseg = %d\n", nseg );
+		fprintf( stderr, "### seq_g[0] = %s\n", seq_g[0] );
+		fprintf( stderr, "### nlenmax = %d\n", nlenmax );
+		fprintf( stderr, "### len = %d\n", strlen( seq_g[0] ) );
+
+#endif
+
+		anchors[0] = 0;
+		for( i=0; i<nseg; i++ ) anchors[i+1] = segment[i].center;
+		anchors[nseg+1] = strlen( seq_g[0] );
+		nseg +=2;
+
+#if 0
+		for( i=0; i<nseg; i++ )
+			fprintf( stderr, "anchor[%d] = %d\n", i, anchors[i] );
+#endif
+	}
+
+
+//--------------- kokokara ----
+	if( subalignment || autosubalignment )
+	{
+		for( i=0; i<nsubalignments; i++ )
+		{
+			fprintf( stderr, "\nChecking subalignment %d:\n", i+1 );
+			alignmentlength = strlen( seq[subtable[i][0]] );
+			for( j=0; subtable[i][j]!=-1; j++ )
+				fprintf( stderr, " %d ", subtable[i][j]+1 );
+//				fprintf( stderr, " ##### %d-%d. %-30.30s\n", i, subtable[i][j]+1, name[subtable[i][j]]+1 );
+			fprintf( stderr, "\n" );
+			for( j=0; subtable[i][j]!=-1; j++ )
+			{
+				if( subtable[i][j] >= njob )
+				{
+					fprintf( stderr, "No such sequence, %d.\n", subtable[i][j]+1 );
+					exit( 1 );
+				}
+				if( alignmentlength != strlen( seq[subtable[i][j]] ) )
+				{
+					fprintf( stderr, "\n" );
+					fprintf( stderr, "###############################################################################\n" );
+					fprintf( stderr, "# ERROR!\n" );
+					fprintf( stderr, "# Subalignment %d must be aligned.\n", i+1 );
+					fprintf( stderr, "# Please check the alignment lengths of following sequences.\n" );
+					fprintf( stderr, "#\n" );
+					fprintf( stderr, "# %d. %-10.10s -> %d letters (including gaps)\n", subtable[i][0]+1, name[subtable[i][0]]+1, alignmentlength );
+					fprintf( stderr, "# %d. %-10.10s -> %d letters (including gaps)\n", subtable[i][j]+1, name[subtable[i][j]]+1, (int)strlen( seq[subtable[i][j]] ) );
+					fprintf( stderr, "#\n" );
+					fprintf( stderr, "# See http://mafft.cbrc.jp/alignment/software/merge.html for details.\n" );
+					if( subalignmentoffset )
+					{
+						fprintf( stderr, "#\n" );
+						fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
+						fprintf( stderr, "# In this case, the rule of numbering is:\n" );
+						fprintf( stderr, "#   The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
+						fprintf( stderr, "#   The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
+					}
+					fprintf( stderr, "###############################################################################\n" );
+					fprintf( stderr, "\n" );
+					exit( 1 );
+				}
+				insubtable[subtable[i][j]] = 1;
+			}
+			for( j=0; j<njob-1; j++ )
+			{
+#if 0
+				int k;
+				reporterr( "####  STEP%d\n", j );
+				for( k=0; topol[j][0][k]!=-1; k++ ) reporterr( "%3d ", topol[j][0][k] );
+				reporterr( "len=%f\n", len[j][0] );
+				for( k=0; topol[j][1][k]!=-1; k++ ) reporterr( "%3d ", topol[j][1][k] );
+				reporterr( "len=%f\n", len[j][1] );
+				reporterr( "\n" );
+#endif
+				if( includemember( topol[j][0], subtable[i] ) && !samemember( topol[j][0], subtable[i] ) )
+				{
+					skipthisbranch[j][0] = 1;
+//					reporterr( "SKIP 0 !!!!!!\n" );
+				}
+				if( includemember( topol[j][1], subtable[i] ) && !samemember( topol[j][1], subtable[i] ) )
+				{
+					skipthisbranch[j][1] = 1;
+//					reporterr( "SKIP 1 !!!!!!\n" );
+				}
+			}
+			foundthebranch = 0;
+			for( j=0; j<njob-1; j++ )
+			{
+				if( samemember( topol[j][0], subtable[i] ) || samemember( topol[j][1], subtable[i] ) )
+				{
+					foundthebranch = 1;
+					fprintf( stderr, " -> OK\n" );
+					break;
+				}
+			}
+			if( !foundthebranch )
+			{
+				system( "cp infile.tree GuideTree" ); // tekitou
+				fprintf( stderr, "\n" );
+				fprintf( stderr, "###############################################################################\n" );
+				fprintf( stderr, "# ERROR!\n" );
+				fprintf( stderr, "# Subalignment %d does not seem to form a monophyletic cluster\n", i+1 );
+				fprintf( stderr, "# in the guide tree ('GuideTree' in this directory) internally computed.\n" );
+				fprintf( stderr, "# If you really want to use this subalignment, pelase give a tree with --treein \n" );
+				fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/treein.html\n" );
+				fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/merge.html\n" );
+				if( subalignmentoffset )
+				{
+					fprintf( stderr, "#\n" );
+					fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
+					fprintf( stderr, "# In this case, the rule of numbering is:\n" );
+					fprintf( stderr, "#   The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
+					fprintf( stderr, "#   The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
+				}
+				fprintf( stderr, "############################################################################### \n" );
+				fprintf( stderr, "\n" );
+				exit( 1 );
+			}
+//			commongappick( seq[subtable[i]], subalignment[i] ); // irukamo
+		}
+#if 0
+		for( i=0; i<njob-1; i++ )
+		{
+			fprintf( stderr, "STEP %d\n", i+1 );
+			fprintf( stderr, "group1 = " );
+			for( j=0; topol[i][0][j] != -1; j++ )
+				fprintf( stderr, "%d ", topol[i][0][j]+1 );
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "SKIP -> %d\n\n", skipthisbranch[i][0] );
+			fprintf( stderr, "group2 = " );
+			for( j=0; topol[i][1][j] != -1; j++ )
+				fprintf( stderr, "%d ", topol[i][1][j]+1 );
+			fprintf( stderr, "\n" );
+			fprintf( stderr, "SKIP -> %d\n\n", skipthisbranch[i][1] );
+		}
+#endif
+
+		for( i=0; i<njob; i++ ) 
+		{
+			if( insubtable[i] ) strcpy( bseq[i], seq[i] );
+			else gappick0( bseq[i], seq[i] );
+		}
+
+		for( i=0; i<nsubalignments; i++ ) 
+		{
+			for( j=0; subtable[i][j]!=-1; j++ ) subalnpt[i][j] = bseq[subtable[i][j]];
+			commongappick( j, subalnpt[i] );
+		}
+
+		FreeIntMtx( subtable );
+		free( insubtable );
+		for( i=0; i<nsubalignments; i++ ) free( subalnpt[i] );
+		free( subalnpt );
+		free( preservegaps );
+	}
+//--------------- kokomade ----
+
+
+
+
+	for( i=0; i<njob; i++ ) res_g[i][0] = 0;
+
+	for( iseg=0; iseg<nseg-1; iseg++ )
+	{
+		int tmplen = anchors[iseg+1]-anchors[iseg];
+		int pos = strlen( res_g[0] );
+		for( j=0; j<njob; j++ )
+		{
+			strncpy( seq[j], seq_g[j], tmplen );
+			seq[j][tmplen]= 0;
+			seq_g[j] += tmplen;	
+
+		}
+		fprintf( stderr, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
+		fflush( stderr );
+		fprintf( trap_g, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
+	
+		cut = ocut;
+		returnvalue = TreeDependentIteration( njob, name, nlen, seq, bseq, topol, len, eff, skipthisbranch, alloclen, localhomtable, singlerna, nkozo, kozoarivec );
+
+		for( i=0; i<njob; i++ )
+			strcat( res_g[i], bseq[i] );
+	}
+	FreeCharMtx( seq_g_bk );
+	FreeIntCub( topol );
+	FreeDoubleMtx( len );
+	FreeDoubleMtx( eff );
+	FreeIntMtx( skipthisbranch );
+	free( kozoarivec );
+	if( constraint ) FreeLocalHomTable( localhomtable, njob );
+	if( rnakozo && rnaprediction == 'm' ) 
+	{
+		if( singlerna ) // nen no tame
+		{
+			for( i=0; i<njob; i++ ) 
+			{
+				for( j=0; singlerna[i][j]!=NULL; j++ )
+				{
+					if( singlerna[i][j] ) free( singlerna[i][j] );
+				}
+				if( singlerna[i] ) free( singlerna[i] );
+			}
+			free( singlerna );
+			singlerna = NULL;
+		}
+	}
+
+#if 0
+	Write( stdout, njob, name, nlen, bseq );
+#endif
+
+	fprintf( stderr, "done\n" );
+	fprintf( trap_g, "done\n" );
+	fclose( trap_g );
+
+
+	devide = 0; 
+	writePre( njob, name, nlen, res_g, 1 );
+#if 0
+	writeData( stdout, njob, name, nlen, res_g, 1 );
+#endif
+
+
+	if( spscoreout ) reporterr( "Unweighted sum-of-pairs score = %10.5f\n", sumofpairsscore( njob, res_g ) );
+
+	SHOWVERSION;
+	return( 0 );
+}
+
+#if 0
+signed int main( int argc, char *argv[] )
+{
+	int i, nlen[M];
+	char b[B];
+	char a[] = "=";
+	int value;
+
+	gets( b ); njob = atoi( b );
+
+/*
+	scoremtx = 0;
+	if( strstr( b, "ayhoff" ) ) scoremtx = 1;
+	else if( strstr( b, "dna" ) || strstr( b, "DNA" ) ) scoremtx = -1;
+	else if( strstr( b, "M-Y" ) || strstr( b, "iyata" ) ) scoremtx = 2;
+	else scoremtx = 0;
+*/
+	if( strstr( b, "constraint" ) ) cnst = 1;
+
+	nlenmax = 0;
+	i = 0;
+	while( i<njob )
+	{
+		gets( b );
+		if( !strncmp( b, a, 1 ) ) 
+		{
+			gets( b ); nlen[i] = atoi( b );
+			if( nlen[i] > nlenmax ) nlenmax = nlen[i];
+			i++;
+		}
+	}
+	if( nlenmax > N || njob > M ) 
+	{
+		fprintf( stderr, "ERROR in main\n" );
+		exit( 1 );
+	}
+	/*
+	nlenmax = Na;
+	*/
+	rewind( stdin );
+	value = main1( nlen, argc, argv );
+	exit( 0 );
+}
+#endif