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dvtditr.c

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Last change on this file was 10371, checked in by aboeckma, 11 years ago
updated mafft version. Added extensions (no svn ignore, yet)
File size: 22.0 KB

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1	/* Tree-dependent-iteration */
2	/* Devide to segments */
3
4	#include "mltaln.h"
5
6	extern char **seq_g;
7	extern char **res_g;
8	static int subalignment;
9	static int subalignmentoffset;
10
11	static int intop;
12	static int intree;
13
14	void arguments( int argc, char *argv[] )
15	{
16	int c;
17	char *argkey;
18
19	outnumber = 0;
20	nthread = 1;
21	randomseed = 0;
22	scoreout = 0;
23	parallelizationstrategy = BAATARI1;
24	intop = 0;
25	intree = 0;
26	inputfile = NULL;
27	rnakozo = 0;
28	rnaprediction = 'm';
29	nevermemsave = 0;
30	score_check = 1;
31	fftkeika = 1;
32	constraint = 0;
33	fmodel = 0;
34	kobetsubunkatsu = 1;
35	bunkatsu = 1;
36	nblosum = 62;
37	niter = 100;
38	calledByXced = 0;
39	devide = 1;
40	divWinSize = 20; /* 70 */
41	divThreshold = 65;
42	fftscore = 1;
43	fftRepeatStop = 0;
44	fftNoAnchStop = 0;
45	scmtd = 5;
46	cooling = 1;
47	weight = 4;
48	utree = 1;
49	refine = 1;
50	check = 1;
51	cut = 0.0;
52	disp = 0;
53	outgap = 1;
54	use_fft = 0; // CHUUI dochira demo mafft.tmpl deha F
55	force_fft = 0;
56	alg = 'A'; /* chuui */
57	mix = 0;
58	checkC = 0;
59	tbitr = 0;
60	treemethod = 'X';
61	scoremtx = 1;
62	dorp = NOTSPECIFIED;
63	ppenalty = NOTSPECIFIED;
64	ppenalty_ex = NOTSPECIFIED;
65	poffset = NOTSPECIFIED;
66	kimuraR = NOTSPECIFIED;
67	pamN = NOTSPECIFIED;
68	geta2 = GETA2;
69	fftWinSize = NOTSPECIFIED;
70	fftThreshold = NOTSPECIFIED;
71	RNAppenalty = NOTSPECIFIED;
72	RNAppenalty_ex = NOTSPECIFIED;
73	RNApthr = NOTSPECIFIED;
74	TMorJTT = JTT;
75	consweight_multi = 1.0;
76	consweight_rna = 0.0;
77	subalignment = 0;
78	subalignmentoffset = 0;
79
80	while( --argc > 0 && (*++argv)[0] == '-' )
81	{
82	while ( (c = *++argv[0]) )
83	{
84	switch( c )
85	{
86	case 'i':
87	inputfile = *++argv;
88	fprintf( stderr, "inputfile = %s\n", inputfile );
89	--argc;
90	goto nextoption;
91	case 'I':
92	niter = atoi( *++argv );
93	fprintf( stderr, "niter = %d\n", niter );
94	--argc;
95	goto nextoption;
96	case 'e':
97	RNApthr = (int)( atof( ++argv ) 1000 - 0.5 );
98	--argc;
99	goto nextoption;
100	case 'o':
101	RNAppenalty = (int)( atof( ++argv ) 1000 - 0.5 );
102	--argc;
103	goto nextoption;
104	case 'f':
105	ppenalty = (int)( atof( ++argv ) 1000 - 0.5 );
106	// fprintf( stderr, "ppenalty = %d\n", ppenalty );
107	--argc;
108	goto nextoption;
109	case 'g':
110	ppenalty_ex = (int)( atof( ++argv ) 1000 - 0.5 );
111	// fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
112	--argc;
113	goto nextoption;
114	case 'h':
115	poffset = (int)( atof( ++argv ) 1000 - 0.5 );
116	fprintf( stderr, "poffset = %d\n", poffset );
117	--argc;
118	goto nextoption;
119	case 'k':
120	kimuraR = atoi( *++argv );
121	fprintf( stderr, "kappa = %d\n", kimuraR );
122	--argc;
123	goto nextoption;
124	case 'b':
125	nblosum = atoi( *++argv );
126	scoremtx = 1;
127	fprintf( stderr, "blosum %d / kimura 200\n", nblosum );
128	--argc;
129	goto nextoption;
130	case 'j':
131	pamN = atoi( *++argv );
132	scoremtx = 0;
133	TMorJTT = JTT;
134	fprintf( stderr, "jtt/kimura %d\n", pamN );
135	--argc;
136	goto nextoption;
137	case 'm':
138	pamN = atoi( *++argv );
139	scoremtx = 0;
140	TMorJTT = TM;
141	fprintf( stderr, "tm %d\n", pamN );
142	--argc;
143	goto nextoption;
144	case 'l':
145	fastathreshold = atof( *++argv );
146	constraint = 2;
147	--argc;
148	goto nextoption;
149	case 'r':
150	consweight_rna = atof( *++argv );
151	rnakozo = 1;
152	--argc;
153	goto nextoption;
154	case 'c':
155	consweight_multi = atof( *++argv );
156	--argc;
157	goto nextoption;
158	case 'C':
159	nthread = atoi( *++argv );
160	fprintf( stderr, "nthread = %d\n", nthread );
161	--argc;
162	goto nextoption;
163	case 'H':
164	subalignment = 1;
165	subalignmentoffset = atoi( *++argv );
166	--argc;
167	goto nextoption;
168	case 't':
169	randomseed = atoi( *++argv );
170	fprintf( stderr, "randomseed = %d\n", randomseed );
171	--argc;
172	goto nextoption;
173	case 'p':
174	argkey = *++argv;
175	if( !strcmp( argkey, "BESTFIRST" ) ) parallelizationstrategy = BESTFIRST;
176	else if( !strcmp( argkey, "BAATARI0" ) ) parallelizationstrategy = BAATARI0;
177	else if( !strcmp( argkey, "BAATARI1" ) ) parallelizationstrategy = BAATARI1;
178	else if( !strcmp( argkey, "BAATARI2" ) ) parallelizationstrategy = BAATARI2;
179	else
180	{
181	fprintf( stderr, "Unknown parallelization strategy, %s\n", argkey );
182	exit( 1 );
183	}
184	// exit( 1 );
185	--argc;
186	goto nextoption;
187	case 'S' :
188	scoreout = 1;
189	break;
190	case 's' :
191	RNAscoremtx = 'r';
192	break;
193	#if 1
194	case 'a':
195	fmodel = 1;
196	break;
197	#endif
198	case 'N':
199	nevermemsave = 1;
200	break;
201	case 'D':
202	dorp = 'd';
203	break;
204	case 'P':
205	dorp = 'p';
206	break;
207	case 'Q':
208	alg = 'Q';
209	break;
210	case 'R':
211	rnaprediction = 'r';
212	break;
213	case 'O':
214	fftNoAnchStop = 1;
215	break;
216	#if 0
217	case 'e':
218	fftscore = 0;
219	break;
220	case 'r':
221	fmodel = -1;
222	break;
223	case 'R':
224	fftRepeatStop = 1;
225	break;
226	#endif
227	case 'T':
228	kobetsubunkatsu = 0;
229	break;
230	case 'B':
231	bunkatsu = 0;
232	break;
233	#if 0
234	case 'c':
235	cooling = 1;
236	break;
237	case 'a':
238	alg = 'a';
239	break;
240	case 's' :
241	treemethod = 's';
242	break;
243	case 'H':
244	alg = 'H';
245	break;
246	#endif
247	case 'A':
248	alg = 'A';
249	break;
250	case 'M':
251	alg = 'M';
252	break;
253	case 'F':
254	use_fft = 1;
255	break;
256	#if 0
257	case 't':
258	weight = 4;
259	break;
260	#endif
261	case 'u':
262	weight = 0;
263	break;
264	case 'U':
265	intree = 1;
266	break;
267	case 'V':
268	intop = 1;
269	break;
270	case 'J':
271	utree = 0;
272	break;
273	case 'd':
274	disp = 1;
275	break;
276	case 'Z':
277	score_check = 0;
278	break;
279	case 'Y':
280	score_check = 2;
281	break;
282	#if 0
283	case 'n' :
284	treemethod = 'n';
285	break;
286	#endif
287	case 'n' :
288	outnumber = 1;
289	break;
290	case 'X' :
291	treemethod = 'X';
292	break;
293	case 'E' :
294	treemethod = 'E';
295	break;
296	case 'q' :
297	treemethod = 'q';
298	break;
299	case 'z':
300	fftThreshold = atoi( *++argv );
301	--argc;
302	goto nextoption;
303	case 'w':
304	fftWinSize = atoi( *++argv );
305	--argc;
306	goto nextoption;
307	default:
308	fprintf( stderr, "illegal option %c\n", c );
309	argc = 0;
310	break;
311	}
312	}
313	nextoption:
314	;
315	}
316	if( argc == 1 )
317	{
318	cut = atof( (*argv) );
319	argc--;
320	}
321	if( argc != 0 )
322	{
323	fprintf( stderr, "options : Check source file!\n" );
324	exit( 1 );
325	}
326	#if 0
327	if( alg == 'A' && weight == 0 )
328	ErrorExit( "ERROR : Algorithm A+ and un-weighted\n" );
329	#endif
330	}
331
332
333	int main( int argc, char *argv[] )
334	{
335	int identity;
336	static int nlen[M];
337	static char name, seq, aseq, bseq;
338	static Segment *segment = NULL;
339	static int anchors[MAXSEG];
340	int i, j;
341	int iseg, nseg;
342	int ***topol;
343	double **len;
344	double **eff;
345	FILE *prep;
346	FILE *infp;
347	FILE *orderfp;
348	int alloclen;
349	int returnvalue;
350	char c;
351	int ocut;
352	char **seq_g_bk;
353	LocalHom **localhomtable = NULL; // by D.Mathog
354	RNApair ***singlerna;
355	int nogaplen;
356	static char **nogap1seq;
357	static char *kozoarivec;
358	int nkozo;
359	int alignmentlength;
360	int **skipthisbranch;
361	int foundthebranch;
362	int nsubalignments, maxmem;
363	int **subtable;
364	int *insubtable;
365	int *preservegaps;
366	char ***subalnpt;
367
368	arguments( argc, argv );
369	#ifndef enablemultithread
370	nthread = 0;
371	#endif
372
373	if( inputfile )
374	{
375	infp = fopen( inputfile, "r" );
376	if( !infp )
377	{
378	fprintf( stderr, "Cannot open %s\n", inputfile );
379	exit( 1 );
380	}
381	}
382	else
383	infp = stdin;
384
385	#if 0
386	PreRead( stdin, &njob, &nlenmax );
387	#else
388	getnumlen( infp );
389	#endif
390	rewind( infp );
391
392	nkozo = 0;
393
394	if( njob < 2 )
395	{
396	fprintf( stderr, "At least 2 sequences should be input!\n"
397	"Only %d sequence found.\n", njob );
398	exit( 1 );
399	}
400
401
402	if( subalignment )
403	{
404	readsubalignmentstable( njob, NULL, NULL, &nsubalignments, &maxmem );
405	fprintf( stderr, "nsubalignments = %d\n", nsubalignments );
406	fprintf( stderr, "maxmem = %d\n", maxmem );
407	subtable = AllocateIntMtx( nsubalignments, maxmem+1 );
408	insubtable = AllocateIntVec( njob );
409	preservegaps = AllocateIntVec( njob );
410	for( i=0; i<njob; i++ ) insubtable[i] = 0;
411	for( i=0; i<njob; i++ ) preservegaps[i] = 0;
412	subalnpt = AllocateCharCub( nsubalignments, maxmem, 0 );
413	readsubalignmentstable( njob, subtable, preservegaps, NULL, NULL );
414	for( i=0; i<nsubalignments; i++ ) for( j=0; j<insubtable[i]; j++ )
415	{
416	if( subtable[i][j] < 0 )
417	{
418	fprintf( stderr, "Not supported in the iterative refinmenment mode.\n" );
419	fprintf( stderr, "Please use a positive number to represent a sequence.\n" );
420	}
421	}
422	}
423
424	ocut = cut;
425
426	segment = (Segment *)calloc( MAXSEG, sizeof( Segment ) );
427	// if( treemethod == 'X' \|\| treemethod == 'E' \|\| treemethod == 'q' )
428	topol = AllocateIntCub( njob, 2, njob );
429	len = AllocateDoubleMtx( njob, 2 );
430	eff = AllocateDoubleMtx( njob, njob );
431	seq = AllocateCharMtx( njob, nlenmax*9+1 );
432	name = AllocateCharMtx( njob, B+1 );
433	seq_g = AllocateCharMtx( njob, nlenmax*9+1 );
434	res_g = AllocateCharMtx( njob, nlenmax*9+1 );
435	aseq = AllocateCharMtx( njob, nlenmax*9+1 );
436	bseq = AllocateCharMtx( njob, nlenmax*9+1 );
437	nogap1seq = AllocateCharMtx( 1, nlenmax*1+1 );
438	alloclen = nlenmax * 9;
439	seq_g_bk = AllocateCharMtx( njob, 0 );
440	for( i=0; i<njob; i++ ) seq_g_bk[i] = seq_g[i];
441	kozoarivec = AllocateCharVec( njob );
442	skipthisbranch = AllocateIntMtx( njob, 2 );
443	for( i=0; i<njob; i++ ) skipthisbranch[i][0] = skipthisbranch[i][1] = 0;
444
445	if( constraint )
446	{
447	localhomtable = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
448	for( i=0; i<njob; i++)
449	{
450	localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
451	for( j=0; j<njob; j++)
452	{
453	localhomtable[i][j].start1 = -1;
454	localhomtable[i][j].end1 = -1;
455	localhomtable[i][j].start2 = -1;
456	localhomtable[i][j].end2 = -1;
457	localhomtable[i][j].overlapaa = -1.0;
458	localhomtable[i][j].opt = -1.0;
459	localhomtable[i][j].importance = -1.0;
460	localhomtable[i][j].next = NULL;
461	localhomtable[i][j].nokori = 0;
462	localhomtable[i][j].extended = -1;
463	localhomtable[i][j].last = localhomtable[i]+j;
464	localhomtable[i][j].korh = 'h';
465	}
466	}
467	fprintf( stderr, "Loading 'hat3' ... " );
468	fflush( stderr );
469	prep = fopen( "hat3", "r" );
470	if( prep == NULL ) ErrorExit( "Make hat3." );
471	readlocalhomtable2( prep, njob, localhomtable, kozoarivec );
472	fclose( prep );
473	// for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
474	// 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 );
475	fprintf( stderr, "done.\n" );
476	fflush( stderr );
477	#if 0
478	fprintf( stderr, "Extending localhom ... " );
479	extendlocalhom( njob, localhomtable );
480	fprintf( stderr, "done.\n" );
481	#endif
482	nkozo = 0;
483	for( i=0; i<njob; i++ ) if( kozoarivec[i] ) nkozo++;
484	}
485
486
487	// if( nlenmax > 30000 )
488	if( nlenmax > 50000 ) // version >= 6.823
489	{
490	#if 0
491	if( constraint )
492	{
493	fprintf( stderr, "\nnlenmax=%d, nagasugi!\n", nlenmax );
494	exit( 1 );
495	}
496	if( nevermemsave )
497	{
498	fprintf( stderr, "\nnevermemsave=1, nlenmax=%d, nagasugi!\n", nlenmax );
499	exit( 1 );
500	}
501	#endif
502	if( !constraint && !nevermemsave && alg != 'M' )
503	{
504	fprintf( stderr, "\nnlenmax=%d, Switching to the memsave mode\n", nlenmax );
505	alg = 'M';
506	}
507	}
508
509	#if 0
510	Read( name, nlen, seq_g );
511	#else
512	readData_pointer( infp, name, nlen, seq_g );
513	#endif
514	fclose( infp );
515
516
517	for( i=0; i<njob; i++ )
518	{
519	res_g[i][0] = 0;
520	}
521
522	identity = 1;
523	for( i=0; i<njob; i++ )
524	{
525	identity *= ( nlen[i] == nlen[0] );
526	}
527	if( !identity )
528	{
529	fprintf( stderr, "Input pre-aligned data\n" );
530	exit( 1 );
531	}
532	constants( njob, seq_g );
533
534	#if 0
535	fprintf( stderr, "penalty = %d\n", penalty );
536	fprintf( stderr, "penalty_ex = %d\n", penalty_ex );
537	fprintf( stderr, "offset = %d\n", offset );
538	#endif
539
540	initSignalSM();
541
542	initFiles();
543
544	#if 0
545	if( njob == 2 )
546	{
547	writePre( njob, name, nlen, seq_g, 1 );
548	SHOWVERSION;
549	return( 0 );
550	}
551	#else
552	if( njob == 2 )
553	{
554	weight = 0;
555	niter = 1;
556	}
557	#endif
558
559	c = seqcheck( seq_g );
560	if( c )
561	{
562	fprintf( stderr, "Illegal character %c\n", c );
563	exit( 1 );
564	}
565	commongappick( njob, seq_g );
566
567	if( rnakozo && rnaprediction == 'm' )
568	{
569	singlerna = (RNApair *)calloc( njob, sizeof( RNApair ) );
570	prep = fopen( "hat4", "r" );
571	if( prep == NULL ) ErrorExit( "Make hat4 using mccaskill." );
572	fprintf( stderr, "Loading 'hat4' ... " );
573	fflush( stderr );
574	for( i=0; i<njob; i++ )
575	{
576	gappick0( nogap1seq[0], seq_g[i] );
577	nogaplen = strlen( nogap1seq[0] );
578	singlerna[i] = (RNApair *)calloc( nogaplen+1, sizeof( RNApair ) );
579	for( j=0; j<nogaplen; j++ )
580	{
581	singlerna[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
582	singlerna[i][j][0].bestpos = -1;
583	singlerna[i][j][0].bestscore = -1.0;
584	}
585	singlerna[i][nogaplen] = NULL;
586	readmccaskill( prep, singlerna[i], nogaplen );
587	}
588	fclose( prep );
589	fprintf( stderr, "\ndone.\n" );
590	fflush( stderr );
591	}
592	else
593	singlerna = NULL;
594
595
596
597	if( utree )
598	{
599	prep = fopen( "hat2", "r" );
600	if( !prep ) ErrorExit( "Make hat2." );
601	readhat2_pointer( prep, njob, name, eff );
602	fclose( prep );
603	#if DEBUG
604	for( i=0; i<njob-1; i++ )
605	{
606	for( j=i+1; j<njob; j++ )
607	{
608	printf( " %f", eff[i][j] );
609	}
610	printf( "\n" );
611	}
612	#endif
613	if( intree )
614	veryfastsupg_double_loadtree( njob, eff, topol, len, name );
615	else if( intop ) // v6.528 deha if( intop ) dattanode intree ga mukou datta.
616	{
617	fprintf( stderr, "--topin has been disabled\n" );
618	exit( 1 );
619	// veryfastsupg_double_loadtop( njob, eff, topol, len );
620	}
621	else if( subalignment )
622	fixed_supg_double_treeout_constrained( njob, eff, topol, len, name, nsubalignments, subtable );
623	else if( treemethod == 'X' \|\| treemethod == 'E' \|\| treemethod == 'q' )
624	// veryfastsupg_double_outtree( njob, eff, topol, len, name );
625	fixed_musclesupg_double_treeout( njob, eff, topol, len, name );
626	else if( treemethod == 'n' )
627	nj( njob, eff, topol, len );
628	else if( treemethod == 's' )
629	spg( njob, eff, topol, len );
630	else if( treemethod == 'p' )
631	upg2( njob, eff, topol, len );
632	else ErrorExit( "Incorrect treemethod.\n" );
633	}
634	#if DEBUG
635	printf( "utree = %d\n", utree );
636	#endif
637
638	orderfp = fopen( "order", "w" );
639	if( !orderfp )
640	{
641	fprintf( stderr, "Cannot open 'order'\n" );
642	exit( 1 );
643	}
644	for( i=0; (j=topol[njob-2][0][i])!=-1; i++ )
645	{
646	fprintf( orderfp, "%d\n", j );
647	}
648	for( i=0; (j=topol[njob-2][1][i])!=-1; i++ )
649	{
650	fprintf( orderfp, "%d\n", j );
651	}
652	fclose( orderfp );
653
654
655	fprintf( stderr, "\n" );
656	if( ( !utree && kobetsubunkatsu ) \|\| constraint \|\| !bunkatsu )
657	{
658	nseg = 0;
659	anchors[0] =0;
660	anchors[1] =strlen( seq_g[0] );
661	nseg += 2;
662	}
663	else
664	{
665	nseg = searchAnchors( njob, seq_g, segment );
666	#if 0
667	fprintf( stderr, "### nseg = %d\n", nseg );
668	fprintf( stderr, "### seq_g[0] = %s\n", seq_g[0] );
669	fprintf( stderr, "### nlenmax = %d\n", nlenmax );
670	fprintf( stderr, "### len = %d\n", strlen( seq_g[0] ) );
671
672	#endif
673
674	anchors[0] = 0;
675	for( i=0; i<nseg; i++ ) anchors[i+1] = segment[i].center;
676	anchors[nseg+1] = strlen( seq_g[0] );
677	nseg +=2;
678
679	#if 0
680	for( i=0; i<nseg; i++ )
681	fprintf( stderr, "anchor[%d] = %d\n", i, anchors[i] );
682	#endif
683	}
684
685
686	//--------------- kokokara ----
687	if( subalignment )
688	{
689	for( i=0; i<nsubalignments; i++ )
690	{
691	fprintf( stderr, "Checking subalignment %d:\n", i+1 );
692	alignmentlength = strlen( seq[subtable[i][0]] );
693	// for( j=0; subtable[i][j]!=-1; j++ )
694	// fprintf( stderr, " %d. %-30.30s\n", subtable[i][j]+1, name[subtable[i][j]]+1 );
695	for( j=0; subtable[i][j]!=-1; j++ )
696	{
697	if( subtable[i][j] >= njob )
698	{
699	fprintf( stderr, "No such sequence, %d.\n", subtable[i][j]+1 );
700	exit( 1 );
701	}
702	if( alignmentlength != strlen( seq[subtable[i][j]] ) )
703	{
704	fprintf( stderr, "\n" );
705	fprintf( stderr, "###############################################################################\n" );
706	fprintf( stderr, "# ERROR!\n" );
707	fprintf( stderr, "# Subalignment %d must be aligned.\n", i+1 );
708	fprintf( stderr, "# Please check the alignment lengths of following sequences.\n" );
709	fprintf( stderr, "#\n" );
710	fprintf( stderr, "# %d. %-10.10s -> %d letters (including gaps)\n", subtable[i][0]+1, name[subtable[i][0]]+1, alignmentlength );
711	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]] ) );
712	fprintf( stderr, "#\n" );
713	fprintf( stderr, "# See http://mafft.cbrc.jp/alignment/software/merge.html for details.\n" );
714	if( subalignmentoffset )
715	{
716	fprintf( stderr, "#\n" );
717	fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
718	fprintf( stderr, "# In this case, the rule of numbering is:\n" );
719	fprintf( stderr, "# The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
720	fprintf( stderr, "# The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
721	}
722	fprintf( stderr, "###############################################################################\n" );
723	fprintf( stderr, "\n" );
724	exit( 1 );
725	}
726	insubtable[subtable[i][j]] = 1;
727	}
728	for( j=0; j<njob-1; j++ )
729	{
730	if( includemember( topol[j][0], subtable[i] ) && !samemember( topol[j][0], subtable[i] ) )
731	skipthisbranch[j][0] = 1;
732	if( includemember( topol[j][1], subtable[i] ) && !samemember( topol[j][1], subtable[i] ) )
733	skipthisbranch[j][1] = 1;
734	}
735	foundthebranch = 0;
736	for( j=0; j<njob-1; j++ )
737	{
738	if( samemember( topol[j][0], subtable[i] ) \|\| samemember( topol[j][1], subtable[i] ) )
739	{
740	foundthebranch = 1;
741	fprintf( stderr, " -> OK\n" );
742	break;
743	}
744	}
745	if( !foundthebranch )
746	{
747	system( "cp infile.tree GuideTree" ); // tekitou
748	fprintf( stderr, "\n" );
749	fprintf( stderr, "###############################################################################\n" );
750	fprintf( stderr, "# ERROR!\n" );
751	fprintf( stderr, "# Subalignment %d does not seem to form a monophyletic cluster\n", i+1 );
752	fprintf( stderr, "# in the guide tree ('GuideTree' in this directory) internally computed.\n" );
753	fprintf( stderr, "# If you really want to use this subalignment, pelase give a tree with --treein \n" );
754	fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/treein.html\n" );
755	fprintf( stderr, "# http://mafft.cbrc.jp/alignment/software/merge.html\n" );
756	if( subalignmentoffset )
757	{
758	fprintf( stderr, "#\n" );
759	fprintf( stderr, "# You specified seed alignment(s) consisting of %d sequences.\n", subalignmentoffset );
760	fprintf( stderr, "# In this case, the rule of numbering is:\n" );
761	fprintf( stderr, "# The aligned seed sequences are numbered as 1 .. %d\n", subalignmentoffset );
762	fprintf( stderr, "# The input sequences to be aligned are numbered as %d .. %d\n", subalignmentoffset+1, subalignmentoffset+njob );
763	}
764	fprintf( stderr, "############################################################################### \n" );
765	fprintf( stderr, "\n" );
766	exit( 1 );
767	}
768	// commongappick( seq[subtable[i]], subalignment[i] ); // irukamo
769	}
770	#if 0
771	for( i=0; i<njob-1; i++ )
772	{
773	fprintf( stderr, "STEP %d\n", i+1 );
774	fprintf( stderr, "group1 = " );
775	for( j=0; topol[i][0][j] != -1; j++ )
776	fprintf( stderr, "%d ", topol[i][0][j]+1 );
777	fprintf( stderr, "\n" );
778	fprintf( stderr, "SKIP -> %d\n\n", skipthisbranch[i][0] );
779	fprintf( stderr, "group2 = " );
780	for( j=0; topol[i][1][j] != -1; j++ )
781	fprintf( stderr, "%d ", topol[i][1][j]+1 );
782	fprintf( stderr, "\n" );
783	fprintf( stderr, "SKIP -> %d\n\n", skipthisbranch[i][1] );
784	}
785	#endif
786
787	for( i=0; i<njob; i++ )
788	{
789	if( insubtable[i] ) strcpy( bseq[i], seq[i] );
790	else gappick0( bseq[i], seq[i] );
791	}
792
793	for( i=0; i<nsubalignments; i++ )
794	{
795	for( j=0; subtable[i][j]!=-1; j++ ) subalnpt[i][j] = bseq[subtable[i][j]];
796	commongappick( j, subalnpt[i] );
797	}
798
799	FreeIntMtx( subtable );
800	free( insubtable );
801	for( i=0; i<nsubalignments; i++ ) free( subalnpt[i] );
802	free( subalnpt );
803	free( preservegaps );
804	}
805	//--------------- kokomade ----
806
807
808
809
810	for( i=0; i<njob; i++ ) res_g[i][0] = 0;
811
812	for( iseg=0; iseg<nseg-1; iseg++ )
813	{
814	int tmplen = anchors[iseg+1]-anchors[iseg];
815	int pos = strlen( res_g[0] );
816	for( j=0; j<njob; j++ )
817	{
818	strncpy( seq[j], seq_g[j], tmplen );
819	seq[j][tmplen]= 0;
820	seq_g[j] += tmplen;
821
822	}
823	fprintf( stderr, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
824	fflush( stderr );
825	fprintf( trap_g, "Segment %3d/%3d %4d-%4d\n", iseg+1, nseg-1, pos+1, pos+1+tmplen );
826
827	cut = ocut;
828	returnvalue = TreeDependentIteration( njob, name, nlen, seq, bseq, topol, len, skipthisbranch, alloclen, localhomtable, singlerna, nkozo, kozoarivec );
829
830	for( i=0; i<njob; i++ )
831	strcat( res_g[i], bseq[i] );
832	}
833	FreeCharMtx( seq_g_bk );
834	FreeIntCub( topol );
835	FreeDoubleMtx( len );
836	FreeDoubleMtx( eff );
837	FreeIntMtx( skipthisbranch );
838	free( kozoarivec );
839	if( constraint ) FreeLocalHomTable( localhomtable, njob );
840	if( rnakozo && rnaprediction == 'm' )
841	{
842	if( singlerna ) // nen no tame
843	{
844	for( i=0; i<njob; i++ )
845	{
846	for( j=0; singlerna[i][j]!=NULL; j++ )
847	{
848	if( singlerna[i][j] ) free( singlerna[i][j] );
849	}
850	if( singlerna[i] ) free( singlerna[i] );
851	}
852	free( singlerna );
853	singlerna = NULL;
854	}
855	}
856
857	#if 0
858	Write( stdout, njob, name, nlen, bseq );
859	#endif
860
861	fprintf( stderr, "done\n" );
862	fprintf( trap_g, "done\n" );
863	fclose( trap_g );
864
865
866	devide = 0;
867	writePre( njob, name, nlen, res_g, 1 );
868	#if 0
869	writeData( stdout, njob, name, nlen, res_g, 1 );
870	#endif
871
872
873	SHOWVERSION;
874	return( 0 );
875	}
876
877	#if 0
878	signed int main( int argc, char *argv[] )
879	{
880	int i, nlen[M];
881	char b[B];
882	char a[] = "=";
883	int value;
884
885	gets( b ); njob = atoi( b );
886
887	/*
888	scoremtx = 0;
889	if( strstr( b, "ayhoff" ) ) scoremtx = 1;
890	else if( strstr( b, "dna" ) \|\| strstr( b, "DNA" ) ) scoremtx = -1;
891	else if( strstr( b, "M-Y" ) \|\| strstr( b, "iyata" ) ) scoremtx = 2;
892	else scoremtx = 0;
893	*/
894	if( strstr( b, "constraint" ) ) cnst = 1;
895
896	nlenmax = 0;
897	i = 0;
898	while( i<njob )
899	{
900	gets( b );
901	if( !strncmp( b, a, 1 ) )
902	{
903	gets( b ); nlen[i] = atoi( b );
904	if( nlen[i] > nlenmax ) nlenmax = nlen[i];
905	i++;
906	}
907	}
908	if( nlenmax > N \|\| njob > M )
909	{
910	fprintf( stderr, "ERROR in main\n" );
911	exit( 1 );
912	}
913	/*
914	nlenmax = Na;
915	*/
916	rewind( stdin );
917	value = main1( nlen, argc, argv );
918	exit( 0 );
919	}
920	#endif

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source: branches/items/GDE/MAFFT/mafft-7.055-with-extensions/core/dvtditr.c

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