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makedirectionlist.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: 17.4 KB

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1	#include "mltaln.h"
2
3	#define DEBUG 0
4	#define IODEBUG 0
5	#define SCOREOUT 0
6
7	#define END_OF_VEC -1
8
9	int nadd;
10	float thresholdtorev;
11	int dodp;
12	int addfragment;
13
14	typedef struct _thread_arg
15	{
16	int iend;
17	char **seq;
18	char *tmpseq;
19	int *res;
20	int **spointt;
21	short *table1;
22	int iq;
23	#ifdef enablemultithread
24	int *jshare;
25	int thread_no;
26	pthread_mutex_t *mutex_counter;
27	#endif
28	} thread_arg_t;
29
30
31
32	void arguments( int argc, char *argv[] )
33	{
34	int c;
35
36	nthread = 1;
37	inputfile = NULL;
38	nadd = 0;
39	dodp = 0;
40	alg = 'a';
41	alg = 'm';
42	dorp = NOTSPECIFIED;
43	fmodel = 0;
44	// ppenalty = (int)( -2.0 * 1000 - 0.5 );
45	// ppenalty_ex = (int)( -0.1 * 1000 - 0.5 );
46	// poffset = (int)( 0.1 * 1000 - 0.5 );
47	ppenalty = NOTSPECIFIED;
48	ppenalty_ex = NOTSPECIFIED;
49	poffset = NOTSPECIFIED;
50	kimuraR = 2;
51	pamN = 200;
52	thresholdtorev = 0.1;
53	addfragment = 0;
54
55
56	while( --argc > 0 && (*++argv)[0] == '-' )
57	{
58	while ( (c = *++argv[0]) )
59	{
60	switch( c )
61	{
62	case 'i':
63	inputfile = *++argv;
64	fprintf( stderr, "inputfile = %s\n", inputfile );
65	--argc;
66	goto nextoption;
67	case 'I':
68	nadd = atoi( *++argv );
69	fprintf( stderr, "nadd = %d\n", nadd );
70	--argc;
71	goto nextoption;
72	case 'C':
73	nthread = atoi( *++argv );
74	fprintf( stderr, "nthread = %d\n", nthread );
75	--argc;
76	goto nextoption;
77	case 'f':
78	ppenalty = (int)( atof( ++argv ) 1000 - 0.5 );
79	// fprintf( stderr, "ppenalty = %d\n", ppenalty );
80	--argc;
81	goto nextoption;
82	case 'g':
83	ppenalty_ex = (int)( atof( ++argv ) 1000 - 0.5 );
84	fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
85	--argc;
86	goto nextoption;
87	case 'h':
88	poffset = (int)( atof( ++argv ) 1000 - 0.5 );
89	// fprintf( stderr, "poffset = %d\n", poffset );
90	--argc;
91	goto nextoption;
92	case 'k':
93	kimuraR = atoi( *++argv );
94	fprintf( stderr, "kappa = %d\n", kimuraR );
95	--argc;
96	goto nextoption;
97	case 'j':
98	pamN = atoi( *++argv );
99	scoremtx = 0;
100	TMorJTT = JTT;
101	fprintf( stderr, "jtt/kimura %d\n", pamN );
102	--argc;
103	goto nextoption;
104	case 't':
105	thresholdtorev = atof( *++argv );
106	fprintf( stderr, "thresholdtorev = %f\n", thresholdtorev );
107	--argc;
108	goto nextoption;
109	case 'd':
110	dodp = 1;
111	break;
112	case 'F':
113	addfragment = 1;
114	break;
115	#if 1
116	case 'a':
117	fmodel = 1;
118	break;
119	#endif
120	case 'S':
121	alg = 'S';
122	break;
123	case 'M':
124	alg = 'M';
125	break;
126	case 'm':
127	alg = 'm';
128	break;
129	case 'G':
130	alg = 'G';
131	break;
132	case 'D':
133	dorp = 'd';
134	break;
135	case 'P':
136	dorp = 'p';
137	break;
138	default:
139	fprintf( stderr, "illegal option %c\n", c );
140	argc = 0;
141	break;
142	}
143	}
144	nextoption:
145	;
146	}
147	if( argc == 1 )
148	{
149	cut = atof( (*argv) );
150	argc--;
151	}
152	if( argc != 0 )
153	{
154	fprintf( stderr, "options: Check source file !\n" );
155	exit( 1 );
156	}
157	if( tbitr == 1 && outgap == 0 )
158	{
159	fprintf( stderr, "conflicting options : o, m or u\n" );
160	exit( 1 );
161	}
162	}
163
164
165
166
167	static int maxl;
168	static int tsize;
169
170	void seq_grp_nuc( int grp, char seq )
171	{
172	int tmp;
173	int *grpbk = grp;
174	while( *seq )
175	{
176	tmp = amino_grp[(int)*seq++];
177	if( tmp < 4 )
178	*grp++ = tmp;
179	else
180	// fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
181	;
182	}
183	*grp = END_OF_VEC;
184	if( grp - grpbk < 6 )
185	{
186	// fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
187	// exit( 1 );
188	*grpbk = -1;
189	}
190	}
191
192	void seq_grp( int grp, char seq )
193	{
194	int tmp;
195	int *grpbk = grp;
196	while( *seq )
197	{
198	tmp = amino_grp[(int)*seq++];
199	if( tmp < 6 )
200	*grp++ = tmp;
201	else
202	// fprintf( stderr, "WARNING : Unknown character %c\r", *(seq-1) );
203	;
204	}
205	*grp = END_OF_VEC;
206	if( grp - grpbk < 6 )
207	{
208	// fprintf( stderr, "\n\nWARNING: Too short.\nPlease also consider use mafft-ginsi, mafft-linsi or mafft-ginsi.\n\n\n" );
209	// exit( 1 );
210	*grpbk = -1;
211	}
212	}
213
214	void makecompositiontable_p( short table, int pointt )
215	{
216	int point;
217
218	while( ( point = *pointt++ ) != END_OF_VEC )
219	table[point]++;
220	}
221
222
223	void makepointtable_nuc( int pointt, int n )
224	{
225	int point;
226	register int *p;
227
228	if( *n == -1 )
229	{
230	*pointt = -1;
231	return;
232	}
233
234	p = n;
235	point = n++ 1024;
236	point += n++ 256;
237	point += n++ 64;
238	point += n++ 16;
239	point += n++ 4;
240	point += *n++;
241	*pointt++ = point;
242
243	while( *n != END_OF_VEC )
244	{
245	point -= p++ 1024;
246	point *= 4;
247	point += *n++;
248	*pointt++ = point;
249	}
250	*pointt = END_OF_VEC;
251	}
252
253	void makepointtable( int pointt, int n )
254	{
255	int point;
256	register int *p;
257
258	if( *n == -1 )
259	{
260	*pointt = -1;
261	return;
262	}
263
264	p = n;
265	point = n++ 7776;
266	point += n++ 1296;
267	point += n++ 216;
268	point += n++ 36;
269	point += n++ 6;
270	point += *n++;
271	*pointt++ = point;
272
273	while( *n != END_OF_VEC )
274	{
275	point -= p++ 7776;
276	point *= 6;
277	point += *n++;
278	*pointt++ = point;
279	}
280	*pointt = END_OF_VEC;
281	}
282
283	static int commonsextet_p2( short table, int pointt )
284	{
285	int value = 0;
286	short tmp;
287	int point;
288	short *memo;
289	int *ct;
290	int *cp;
291
292	if( *pointt == -1 )
293	return( 0 );
294
295	memo = (short *)calloc( tsize, sizeof( short ) );
296	if( !memo ) ErrorExit( "Cannot allocate memo\n" );
297	ct = (int *)calloc( MIN( maxl, tsize )+1, sizeof( int ) ); // chuui!!
298	if( !ct ) ErrorExit( "Cannot allocate memo\n" );
299
300	cp = ct;
301	while( ( point = *pointt++ ) != END_OF_VEC )
302	{
303	tmp = memo[point]++;
304	if( tmp < table[point] )
305	value++;
306	if( tmp == 0 ) *cp++ = point;
307	}
308	*cp = END_OF_VEC;
309
310	cp = ct;
311	while( *cp != END_OF_VEC )
312	memo[*cp++] = 0;
313
314	free( memo );
315	free( ct );
316	return( value );
317	}
318
319	static void directionthread( void arg )
320	{
321	thread_arg_t targ = (thread_arg_t )arg;
322	int iend = targ->iend;
323	char **seq = targ->seq;
324	char *tmpseq = targ->tmpseq;
325	int *res = targ->res;
326	int **spointt = targ->spointt;
327	short *table1 = targ->table1;
328	int iq = targ->iq;
329	#ifdef enablemultithread
330	int thread_no = targ->thread_no;
331	int *jshare = targ->jshare;
332	#endif
333	int j;
334	char mseq1, mseq2;
335
336
337	if( dodp ) // nakuserukamo
338	{
339	mseq1 = AllocateCharMtx( 1, 0 );
340	mseq2 = AllocateCharMtx( 1, 0 );
341	}
342
343	j = -1;
344	while( 1 )
345	{
346	#ifdef enablemultithread
347	if( nthread )
348	{
349	pthread_mutex_lock( targ->mutex_counter );
350	j = *jshare;
351	if( j == iend )
352	{
353	fprintf( stderr, "\r %d / %d (thread %d) \r", iq, njob, thread_no );
354	pthread_mutex_unlock( targ->mutex_counter );
355	break;
356	}
357	++(*jshare);
358	pthread_mutex_unlock( targ->mutex_counter );
359	}
360	else
361	#endif
362	{
363	j++;
364	if( j == iend )
365	{
366	fprintf( stderr, "\r %d / %d \r", iq, njob );
367	break;
368	}
369	}
370
371
372	if( dodp )
373	{
374	// strcpy( mseq1[0], tmpseq );
375	// strcpy( mseq2[0], seq[j] );
376	mseq1[0] = tmpseq;
377	mseq2[0] = seq[j];
378	// res[j] = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1, mseq2, 0 );
379	res[j] = L__align11_noalign( mseq1, mseq2 );
380	}
381	else
382	res[j] = commonsextet_p2( table1, spointt[j] );
383	}
384	if( dodp ) // nakuserukamo
385	{
386	free( mseq1 );
387	free( mseq2 );
388	// G__align11_noalign( NULL, 0, 0, NULL, NULL, 0 );
389	L__align11_noalign( NULL, NULL );
390	}
391	// else
392	// if( nthread ) // inthread == 0 no toki free suru to, error. nazeda
393	// commonsextet_p( NULL, NULL );
394	return( NULL );
395	}
396
397	int main( int argc, char *argv[] )
398	{
399	static int *nlen;
400	static int *nogaplen;
401	static char name, seq;
402	int i, j, istart, iend;
403	FILE *infp;
404	// FILE *adfp;
405	char c;
406
407	int *grpseq;
408	char tmpseq, revseq;
409	int pointt, pointt_rev, **spointt;
410	float res_forward, res_reverse, res_max;
411	int ires, mres, mres2;
412	int *res;
413	static short table1, table1_rev;
414	static char mseq1f, mseq1r, **mseq2;
415
416	arguments( argc, argv );
417	#ifndef enablemultithread
418	nthread = 0;
419	#endif
420
421	if( inputfile )
422	{
423	infp = fopen( inputfile, "r" );
424	if( !infp )
425	{
426	fprintf( stderr, "Cannot open %s\n", inputfile );
427	exit( 1 );
428	}
429	}
430	else
431	infp = stdin;
432
433	getnumlen( infp );
434	rewind( infp );
435
436	if( alg == 'a' )
437	{
438	if( nlenmax < 10000 )
439	alg = 'G';
440	else
441	alg = 'S';
442	}
443
444	seq = AllocateCharMtx( njob, nlenmax*1+1 );
445
446	#if 0
447	Read( name, nlen, seq );
448	readData( infp, name, nlen, seq );
449	#else
450	name = AllocateCharMtx( njob, B+1 );
451	nlen = AllocateIntVec( njob );
452	nogaplen = AllocateIntVec( njob );
453	readData_pointer( infp, name, nlen, seq );
454	fclose( infp );
455
456	if( dorp != 'd' )
457	{
458	fprintf( stderr, "Not necessary!\n" );
459	for( i=0; i<njob; i++ )
460	fprintf( stdout, "_F_%-10.10s\n", name[i]+1 );
461	exit( 1 );
462	}
463	#endif
464
465	constants( njob, seq );
466
467
468	#if 0
469	fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
470	#endif
471
472	initSignalSM();
473
474	initFiles();
475
476	c = seqcheck( seq );
477	if( c )
478	{
479	fprintf( stderr, "Illegal character %c\n", c );
480	exit( 1 );
481	}
482
483	fprintf( stderr, "\n" );
484	if( alg == 'G' ) // do to the first sequence
485	{
486	mseq1f = AllocateCharMtx( 1, nlenmax+nlenmax );
487	mseq1r = AllocateCharMtx( 1, nlenmax+nlenmax );
488	mseq2 = AllocateCharMtx( 1, nlenmax+nlenmax );
489	tmpseq = AllocateCharVec( MAX( nlenmax, B ) +1 );
490
491	gappick0( mseq1f[0], seq[0] );
492	sreverse( mseq1r[0], mseq1f[0] );
493	strcpy( seq[0], mseq1f[0] );
494
495	if( nadd )
496	istart = njob - nadd;
497	else
498	istart = 1;
499
500	fprintf( stderr, "\n" );
501
502	for( i=0; i<istart; i++ )
503	{
504	gappick0( tmpseq, seq[i] );
505	strcpy( seq[i], tmpseq );
506	strcpy( tmpseq, name[i] );
507	strcpy( name[i], "_F_" );
508	strncpy( name[i]+3, tmpseq+1, 10 );
509	name[i][13] = 0;
510	}
511	for( i=istart; i<njob; i++ )
512	{
513	gappick0( mseq2[0], seq[i] );
514
515	// res_forward = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1f, mseq2, 0 );
516	// res_reverse = G__align11_noalign( amino_dis, penalty, penalty_ex, mseq1r, mseq2, 0 );
517
518	res_forward = L__align11_noalign( mseq1f, mseq2 );
519	res_reverse = L__align11_noalign( mseq1r, mseq2 );
520	#if 0
521
522	strcpy( mseq2[0], seq[i] );
523	strcpy( mseq1f[0], seq[0] );
524	res_forward = G__align11( mseq1f, mseq2, nlenmax*2, 0, 0 );
525	fprintf( stdout, "%s\n", mseq1f[0] );
526	fprintf( stdout, "%s\n", mseq2[0] );
527
528	strcpy( mseq2[0], seq[i] );
529	sreverse( mseq1r[0], seq[0] );
530	res_reverse = G__align11( mseq1r, mseq2, nlenmax*2, 0, 0 );
531	fprintf( stdout, "%s\n", mseq1r[0] );
532	fprintf( stdout, "%s\n", mseq2[0] );
533	#endif
534
535	// fprintf( stdout, "\nscore_for(%d,%d) = %f\n", 0, i, res_forward );
536	// fprintf( stdout, "score_rev(%d,%d) = %f\n", 0, i, res_reverse );
537	res_max = MAX(res_reverse,res_forward);
538	if( (res_reverse-res_forward)/res_max > thresholdtorev ) // tekitou
539	{
540	// fprintf( stderr, "REVERSE!!!\n" );
541	sreverse( seq[i], mseq2[0] );
542
543	strcpy( tmpseq, name[i] );
544	strcpy( name[i], "_R_" );
545	strncpy( name[i]+3, tmpseq+1, 10 );
546	name[i][13] = 0;
547	}
548	else
549	{
550	strcpy( seq[i], mseq2[0] );
551
552	strcpy( tmpseq, name[i] );
553	strcpy( name[i], "_F_" );
554	strncpy( name[i]+3, tmpseq+1, 10 );
555	name[i][13] = 0;
556	}
557	}
558	FreeCharMtx( mseq1f );
559	FreeCharMtx( mseq1r );
560	FreeCharMtx( mseq2 );
561	free( tmpseq );
562	}
563	else if( alg == 'm' )
564	{
565	if( dodp ) // nakuserukamo
566	{
567	mseq1f = AllocateCharMtx( 1, nlenmax+1);
568	mseq1r = AllocateCharMtx( 1, nlenmax+1 );
569	mseq2 = AllocateCharMtx( 1, nlenmax+1 );
570	}
571	else
572	{
573	spointt = AllocateIntMtx( njob, 0 );
574	pointt = AllocateIntMtx( njob, nlenmax+1 );
575	pointt_rev = AllocateIntMtx( njob, nlenmax+1 );
576	}
577	tmpseq = AllocateCharVec( MAX( nlenmax, B ) +1 );
578	revseq = AllocateCharVec( nlenmax+1 );
579	grpseq = AllocateIntVec( nlenmax+1 );
580	res = AllocateIntVec( njob );
581	if( dorp == 'd' ) tsize = (int)pow( 4, 6 );
582	else tsize = (int)pow( 6, 6 ); // iranai
583
584	maxl = 0;
585	for( i=0; i<njob; i++ )
586	{
587	gappick0( tmpseq, seq[i] );
588	nogaplen[i] = strlen( tmpseq );
589	if( nogaplen[i] > maxl ) maxl = nogaplen[i];
590	}
591
592	if( nadd )
593	iend = njob - nadd;
594	else
595	iend = 1;
596
597	for( i=0; i<iend; i++ )
598	{
599	// fprintf( stdout, "%d, SKIP\n", i );
600	gappick0( tmpseq, seq[i] );
601	strcpy( seq[i], tmpseq );
602	// if( !nadd ) strcpy( seq[i], tmpseq ); // seq ha tsukawanaikara ii.
603
604	if( !dodp )
605	{
606	seq_grp_nuc( grpseq, tmpseq );
607	makepointtable_nuc( pointt[i], grpseq );
608	spointt[i] = pointt[i];
609	}
610
611	strcpy( tmpseq, name[i] );
612	strcpy( name[i], "_F_" );
613	strncpy( name[i]+3, tmpseq+1, 10 );
614	name[i][13] = 0;
615	}
616
617	if( nadd )
618	istart = njob - nadd;
619	else
620	istart = 1;
621
622	fprintf( stderr, "\n" );
623	for( i=istart; i<njob; i++ )
624	{
625	// fprintf( stderr, "\r %d / %d ", i, njob );
626	gappick0( tmpseq, seq[i] );
627	strcpy( seq[i], tmpseq );
628	sreverse( revseq, tmpseq );
629
630	if( !dodp )
631	{
632	table1 = (short *)calloc( tsize, sizeof( short ) );
633	if( !table1 ) ErrorExit( "Cannot allocate table1\n" );
634	table1_rev = (short *)calloc( tsize, sizeof( short ) );
635	if( !table1_rev ) ErrorExit( "Cannot allocate table1_rev\n" );
636	seq_grp_nuc( grpseq, tmpseq );
637	makepointtable_nuc( pointt[i], grpseq );
638	makecompositiontable_p( table1, pointt[i] );
639	seq_grp_nuc( grpseq, revseq );
640	makepointtable_nuc( pointt_rev[i], grpseq );
641	makecompositiontable_p( table1_rev, pointt_rev[i] );
642	}
643
644	if( nadd && addfragment )
645	iend = njob-nadd;
646	else
647	iend = i;
648
649
650	#ifdef enablemultithread
651	if( nthread )
652	{
653	pthread_t *handle;
654	pthread_mutex_t mutex_counter;
655	thread_arg_t *targ;
656	int *jsharept;
657
658	targ = calloc( nthread, sizeof( thread_arg_t ) );
659	handle = calloc( nthread, sizeof( pthread_t ) );
660	pthread_mutex_init( &mutex_counter, NULL );
661	jsharept = calloc( 1, sizeof(int) );
662	*jsharept = 0;
663
664	for( j=0; j<nthread; j++ )
665	{
666	targ[j].iend = iend;
667	targ[j].seq = seq;
668	targ[j].tmpseq = tmpseq;
669	targ[j].res = res;
670	targ[j].spointt = spointt;
671	targ[j].table1 = table1;
672	targ[j].jshare = jsharept;
673	targ[j].iq = i;
674	targ[j].mutex_counter = &mutex_counter;
675	targ[j].thread_no = j;
676	pthread_create( handle+j, NULL, directionthread, (void *)(targ+j) );
677	}
678	for( j=0; j<nthread; j++ ) pthread_join( handle[j], NULL );
679	pthread_mutex_destroy( &mutex_counter );
680	free( handle );
681	free( targ );
682	free( jsharept );
683	}
684	else
685	#endif
686	{
687	thread_arg_t *targ;
688	targ = calloc( 1, sizeof( thread_arg_t ) );
689	targ[0].iend = iend;
690	targ[0].seq = seq;
691	targ[0].tmpseq = tmpseq;
692	targ[0].res = res;
693	targ[0].spointt = spointt;
694	targ[0].table1 = table1;
695	targ[0].iq = i;
696	directionthread( targ );
697	free( targ );
698	}
699
700
701	mres = mres2 = 0;
702	for( j=0; j<iend; j++ )
703	{
704	ires = res[j];
705	// fprintf( stdout, "ires (%d,%d) = %d\n", i, j, ires );
706	// fflush( stdout );
707	if( ires>mres2 )
708	{
709	if( ires>mres )
710	{
711	mres2 = mres;
712	mres = ires;
713	}
714	else
715	mres2 = ires;
716	}
717	}
718	res_forward = (float)( mres + mres2 ) / 2;
719
720	#ifdef enablemultithread
721	if( nthread )
722	{
723	pthread_t *handle;
724	pthread_mutex_t mutex_counter;
725	thread_arg_t *targ;
726	int *jsharept;
727
728	targ = calloc( nthread, sizeof( thread_arg_t ) );
729	handle = calloc( nthread, sizeof( pthread_t ) );
730	pthread_mutex_init( &mutex_counter, NULL );
731	jsharept = calloc( 1, sizeof(int) );
732	*jsharept = 0;
733
734	for( j=0; j<nthread; j++ )
735	{
736	targ[j].iend = iend;
737	targ[j].seq = seq;
738	targ[j].tmpseq = revseq;
739	targ[j].res = res;
740	targ[j].spointt = spointt;
741	targ[j].table1 = table1_rev;
742	targ[j].jshare = jsharept;
743	targ[j].iq = i;
744	targ[j].mutex_counter = &mutex_counter;
745	targ[j].thread_no = j;
746	pthread_create( handle+j, NULL, directionthread, (void *)(targ+j) );
747	}
748	for( j=0; j<nthread; j++ ) pthread_join( handle[j], NULL );
749	pthread_mutex_destroy( &mutex_counter );
750	free( handle );
751	free( targ );
752	free( jsharept );
753	}
754	else
755	#endif
756	{
757	thread_arg_t *targ;
758	targ = calloc( 1, sizeof( thread_arg_t ) );
759	targ[0].iend = iend;
760	targ[0].seq = seq;
761	targ[0].tmpseq = revseq;
762	targ[0].res = res;
763	targ[0].spointt = spointt;
764	targ[0].table1 = table1_rev;
765	targ[0].iq = i;
766	directionthread( targ );
767	free( targ );
768	}
769
770	mres = mres2 = 0;
771	for( j=0; j<iend; j++ )
772	{
773	ires = res[j];
774	if( ires>mres2 )
775	{
776	if( ires>mres )
777	{
778	mres2 = mres;
779	mres = ires;
780	}
781	else
782	mres2 = ires;
783	}
784	}
785	res_reverse = (float)( mres + mres2 ) / 2;
786
787	// fprintf( stdout, "\n" );
788	// fprintf( stdout, "score_for(%d,%d) = %f\n", 0, i, res_forward );
789	// fprintf( stdout, "score_rev(%d,%d) = %f\n", 0, i, res_reverse );
790	// fflush( stdout );
791	res_max = MAX(res_reverse,res_forward);
792	if( (res_reverse-res_forward)/res_max > thresholdtorev ) // tekitou
793
794	{
795	strcpy( seq[i], revseq );
796
797	strcpy( tmpseq, name[i] );
798	strcpy( name[i], "_R_" );
799	strncpy( name[i]+3, tmpseq+1, 10 );
800	name[i][13] = 0;
801	if( !dodp ) spointt[i] = pointt_rev[i];
802	}
803	else
804	{
805	strcpy( tmpseq, name[i] );
806	strcpy( name[i], "_F_" );
807	strncpy( name[i]+3, tmpseq+1, 10 );
808	name[i][13] = 0;
809	if( !dodp ) spointt[i] = pointt[i];
810	}
811
812	if( !dodp )
813	{
814	free( table1 );
815	free( table1_rev );
816	}
817	}
818
819	free( grpseq );
820	free( tmpseq );
821	free( revseq );
822	free( res );
823	if( dodp )
824	{
825	FreeCharMtx( mseq1f );
826	FreeCharMtx( mseq1r );
827	FreeCharMtx( mseq2 );
828	}
829	else
830	{
831	FreeIntMtx( pointt );
832	FreeIntMtx( pointt_rev );
833	free( spointt );
834	}
835	}
836	else
837	{
838	fprintf( stderr, "Unknown alg %c\n", alg );
839	exit( 1 );
840	}
841	// writeData_pointer( stdout, njob, name, nlen, seq );
842	for( i=0; i<njob; i++ )
843	{
844	// fprintf( stdout, ">%s\n", name[i] );
845	// fprintf( stdout, "%s\n", seq[i] );
846	fprintf( stdout, "%s\n", name[i] );
847	}
848
849	fprintf( stderr, "\n" );
850	SHOWVERSION;
851	return( 0 );
852	}
853

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source: trunk/GDE/MAFFT/mafft-7.055-with-extensions/core/makedirectionlist.c

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