X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fmafft%2Fcore%2Fdvtditr.c;h=a25890204b2b78736c0d56391da414043f48fb75;hb=711ff37b582bf25ba17d553008c4bf06cbdb8c84;hp=54b44c6c5d9469b3b12015a4b09316498f200648;hpb=7c6018cf87e67d7ac21f5230284ef2162a19320f;p=jabaws.git

diff --git a/binaries/src/mafft/core/dvtditr.c b/binaries/src/mafft/core/dvtditr.c
index 54b44c6..a258902 100644
--- a/binaries/src/mafft/core/dvtditr.c
+++ b/binaries/src/mafft/core/dvtditr.c
@@ -5,9 +5,31 @@
 
 extern char **seq_g;
 extern char **res_g;
+static int subalignment;
+static int subalignmentoffset;
+static int specifictarget;
 
 static int intop;
 static int intree;
+static double autosubalignment;
+
+
+static void calcmaxdistclass( void )
+{
+	int c;
+	double 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[] )
 {
@@ -18,6 +40,7 @@ void arguments( int argc, char *argv[] )
 	nthread = 1;
 	randomseed = 0;
 	scoreout = 0;
+	spscoreout = 0;
 	parallelizationstrategy = BAATARI1;
 	intop = 0;
 	intree = 0;
@@ -56,9 +79,11 @@ void arguments( int argc, char *argv[] )
 	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;
@@ -72,6 +97,13 @@ void arguments( int argc, char *argv[] )
 	TMorJTT = JTT;
 	consweight_multi = 1.0;
 	consweight_rna = 0.0;
+	subalignment = 0;
+	subalignmentoffset = 0;
+	legacygapcost = 0;
+	specificityconsideration = 0.0;
+	autosubalignment = 0.0;
+	specifictarget = 0;
+	nwildcard = 0;
 
 	while( --argc > 0 && (*++argv)[0] == '-' )
 	{
@@ -85,7 +117,7 @@ void arguments( int argc, char *argv[] )
 					--argc;
 					goto nextoption;
 				case 'I':
-					niter = atoi( *++argv );
+					niter = myatoi( *++argv );
 					fprintf( stderr, "niter = %d\n", niter );
 					--argc;
 					goto nextoption;
@@ -102,6 +134,15 @@ void arguments( int argc, char *argv[] )
 //					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 );
@@ -113,25 +154,25 @@ void arguments( int argc, char *argv[] )
 					--argc;
 					goto nextoption;
 				case 'k':
-					kimuraR = atoi( *++argv );
+					kimuraR = myatoi( *++argv );
 					fprintf( stderr, "kappa = %d\n", kimuraR );
 					--argc; 
 					goto nextoption;
 				case 'b':
-					nblosum = atoi( *++argv );
+					nblosum = myatoi( *++argv );
 					scoremtx = 1;
 					fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
 					--argc; 
 					goto nextoption;
 				case 'j':
-					pamN = atoi( *++argv );
+					pamN = myatoi( *++argv );
 					scoremtx = 0;
 					TMorJTT = JTT;
 					fprintf( stderr, "jtt/kimura %d\n", pamN );
 					--argc; 
 					goto nextoption;
 				case 'm':
-					pamN = atoi( *++argv );
+					pamN = myatoi( *++argv );
 					scoremtx = 0;
 					TMorJTT = TM;
 					fprintf( stderr, "tm %d\n", pamN );
@@ -152,12 +193,17 @@ void arguments( int argc, char *argv[] )
 					--argc;
 					goto nextoption;
 				case 'C':
-					nthread = atoi( *++argv );
+					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 = atoi( *++argv );
+					randomseed = myatoi( *++argv );
 					fprintf( stderr, "randomseed = %d\n", randomseed );
 					--argc; 
 					goto nextoption;
@@ -175,12 +221,25 @@ void arguments( int argc, char *argv[] )
 //					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' :
-					scoreout = 1;
+					spscoreout = 1; // 2014/Dec/30, sp score
 					break;
+#endif
+#if 0
 				case 's' :
 					RNAscoremtx = 'r';
 					break;
+#endif
 #if 1
 				case 'a':
 					fmodel = 1;
@@ -195,9 +254,11 @@ void arguments( int argc, char *argv[] )
 				case 'P':
 					dorp = 'p';
 					break;
+#if 0
 				case 'Q':
 					alg = 'Q';
 					break;
+#endif
 				case 'R':
 					rnaprediction = 'r';
 					break;
@@ -231,16 +292,19 @@ void arguments( int argc, char *argv[] )
 				case 's' :
 					treemethod = 's';
 					break;
-#endif
 				case 'H':
 					alg = 'H';
 					break;
+#endif
 				case 'A':
 					alg = 'A';
 					break;
 				case 'M':
 					alg = 'M';
 					break;
+				case '@':
+					alg = 'd';
+					break;
 				case 'F':
 					use_fft = 1;
 					break;
@@ -261,15 +325,20 @@ void arguments( int argc, char *argv[] )
 				case 'J':
 					utree = 0;
 					break;
+#if 0
 				case 'd':
 					disp = 1;
 					break;
+#endif
 				case 'Z':
 					score_check = 0;
 					break;
 				case 'Y':
 					score_check = 2;
 					break;
+				case 'L':
+					legacygapcost = 1;
+					break;
 #if 0
 				case 'n' :
 					treemethod = 'n';
@@ -278,23 +347,44 @@ void arguments( int argc, char *argv[] )
 				case 'n' :
 					outnumber = 1;
 					break;
-				case 'X' :
+				case 'X':
 					treemethod = 'X';
-					break;
+					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 'W':
+					minimumweight = atof( *++argv );
+					fprintf( stderr, "minimumweight = %f\n", minimumweight );
+					--argc;
+					goto nextoption;
 				case 'z':
-					fftThreshold = atoi( *++argv );
+					fftThreshold = myatoi( *++argv );
 					--argc;
 					goto nextoption;
 				case 'w':
-					fftWinSize = atoi( *++argv );
+					fftWinSize = myatoi( *++argv );
 					--argc;
 					goto nextoption;
+				case '=':
+					specifictarget = 1;
+					break;
+				case ':':
+					nwildcard = 1;
+					break;
 				default:
 					fprintf( stderr, "illegal option %c\n", c );
 					argc = 0;
@@ -335,6 +425,7 @@ int main( int argc, char *argv[] )
 	double **eff;
 	FILE *prep;
 	FILE *infp;
+	FILE *orderfp;
 	int alloclen;
 	int returnvalue;
 	char c;
@@ -346,11 +437,22 @@ int main( int argc, char *argv[] )
 	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;
+	int ntarget, *targetmap, *targetmapr;
+	int ilim;
 
 	arguments( argc, argv );
 #ifndef enablemultithread
 	nthread = 0;
 #endif
+	if( fastathreshold < 0.0001 ) constraint = 0;
 
 	if( inputfile )
 	{
@@ -380,6 +482,29 @@ int main( int argc, char *argv[] )
 		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 ) );
@@ -398,14 +523,48 @@ int main( int argc, char *argv[] )
 	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 0
+	Read( name, nlen, seq_g );
+#else
+	readData_pointer( infp, name, nlen, seq_g );
+#endif
+	fclose( infp );
+
+	if( specifictarget )
+	{
+		targetmap = calloc( njob, sizeof( int ) );
+		ntarget = 0;
+		for( i=0; i<njob; i++ )
+		{
+			targetmap[i] = -1;
+			if( !strncmp( name[i]+1, "_focus_", 7 ) )
+				targetmap[i] = ntarget++;
+		}
+		targetmapr = calloc( ntarget, sizeof( int ) );
+		for( i=0; i<njob; i++ )
+			if( targetmap[i] != -1 ) targetmapr[targetmap[i]] = i;
+	}
+	else
+	{
+		ntarget = njob;
+		targetmap = calloc( njob, sizeof( int ) );
+		targetmapr = calloc( njob, sizeof( int ) );
+		for( i=0; i<njob; i++ )
+			targetmap[i] = targetmapr[i] = i;
+	}
 
 	if( constraint )
 	{
-		localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
-		for( i=0; i<njob; i++)
+		ilim = njob;
+		localhomtable = (LocalHom **)calloc( ntarget, sizeof( LocalHom *) );
+		for( i=0; i<ntarget; i++)
 		{
-			localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
-			for( j=0; j<njob; j++)
+			localhomtable[i] = (LocalHom *)calloc( ilim, sizeof( LocalHom ) );
+			for( j=0; j<ilim; j++)
 			{
 				localhomtable[i][j].start1 = -1;
 				localhomtable[i][j].end1 = -1;
@@ -420,12 +579,14 @@ int main( int argc, char *argv[] )
 				localhomtable[i][j].last = localhomtable[i]+j;
 				localhomtable[i][j].korh = 'h';
 			}
+			if( !specifictarget ) ilim--;
 		}
 		fprintf( stderr, "Loading 'hat3' ... " );
 		fflush( stderr );
 		prep = fopen( "hat3", "r" );
 		if( prep == NULL ) ErrorExit( "Make hat3." );
-		readlocalhomtable2( prep, njob, localhomtable, kozoarivec );
+		if( specifictarget ) readlocalhomtable2_target( prep, njob, localhomtable, kozoarivec, targetmap );
+		else readlocalhomtable2_half( 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 );
@@ -463,13 +624,8 @@ int main( int argc, char *argv[] )
 			}
 		}
 
-#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++ )
 	{
@@ -532,13 +688,14 @@ int main( int argc, char *argv[] )
 		{
 			gappick0( nogap1seq[0], seq_g[i] );
 			nogaplen = strlen( nogap1seq[0] );
-			singlerna[i] = (RNApair **)calloc( nogaplen, sizeof( RNApair * ) );
+			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 );
@@ -556,20 +713,41 @@ int main( int argc, char *argv[] )
 		if( !prep ) ErrorExit( "Make hat2." );
 		readhat2_pointer( prep, njob, name, eff );
 		fclose( prep );
-#if DEBUG
+#if 0
+		fprintf( stderr, "eff = \n" );
 		for( i=0; i<njob-1; i++ ) 
 		{
 			for( j=i+1; j<njob; j++ ) 
 			{
-				printf( " %f", eff[i][j] );
+				fprintf( stderr, "%d-%d,  %f\n", i, j, eff[i][j] );
 			}
-			printf( "\n" );
+			fprintf( stderr, "\n" );
 		}
 #endif
 		if( intree )
-			veryfastsupg_double_loadtree( njob, eff, topol, len );
+		{
+			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.
-			veryfastsupg_double_loadtop( njob, eff, topol, len );
+		{
+			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 );
@@ -585,6 +763,80 @@ int main( int argc, char *argv[] )
 	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 )
@@ -616,6 +868,148 @@ int main( int argc, char *argv[] )
 #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++ )
@@ -634,7 +1028,7 @@ int main( int argc, char *argv[] )
 		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, alloclen, localhomtable, singlerna, nkozo, kozoarivec );
+		returnvalue = TreeDependentIteration( njob, name, nlen, seq, bseq, topol, len, eff, skipthisbranch, alloclen, localhomtable, singlerna, nkozo, kozoarivec, ntarget, targetmap, targetmapr );
 
 		for( i=0; i<njob; i++ )
 			strcat( res_g[i], bseq[i] );
@@ -643,7 +1037,31 @@ int main( int argc, char *argv[] )
 	FreeIntCub( topol );
 	FreeDoubleMtx( len );
 	FreeDoubleMtx( eff );
-	if( constraint ) FreeLocalHomTable( localhomtable, njob );
+	FreeIntMtx( skipthisbranch );
+	free( kozoarivec );
+	if( constraint ) 
+	{
+		if( specifictarget ) FreeLocalHomTable_part( localhomtable, ntarget, njob );
+		else FreeLocalHomTable_half( localhomtable, njob );
+	}
+	free( targetmap );
+	free( targetmapr );
+	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 );
@@ -652,6 +1070,7 @@ int main( int argc, char *argv[] )
 	fprintf( stderr, "done\n" );
 	fprintf( trap_g, "done\n" );
 	fclose( trap_g );
+	freeconstants();
 
 
 	devide = 0; 
@@ -661,6 +1080,8 @@ int main( int argc, char *argv[] )
 #endif
 
 
+	if( spscoreout ) reporterr( "Unweighted sum-of-pairs score = %10.5f\n", sumofpairsscore( njob, res_g ) );
+
 	SHOWVERSION;
 	return( 0 );
 }