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interface.c

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Last change on this file was 10307, checked in by aboeckma, 11 years ago
added most recent version of phyml
File size: 48.0 KB

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1	/*
2
3	PhyML: a program that computes maximum likelihood phylogenies from
4	DNA or AA homologous sequences.
5
6	Copyright (C) Stephane Guindon. Oct 2003 onward.
7
8	All parts of the source except where indicated are distributed under
9	the GNU public licence. See http://www.opensource.org for details.
10
11	*/
12
13	#include "interface.h"
14	#include "mg.h"
15
16
17	void Launch_Interface(option *io)
18	{
19	Launch_Interface_Input(io);
20	io->ready_to_go = 0;
21	do
22	{
23	switch(io->curr_interface)
24	{
25	case INTERFACE_DATA_TYPE :
26	{
27	Launch_Interface_Data_Type(io);
28	break;
29	}
30	case INTERFACE_MULTIGENE :
31	{
32	Launch_Interface_Multigene(io);
33	break;
34	}
35	case INTERFACE_MODEL :
36	{
37	Launch_Interface_Model(io);
38	break;
39	}
40	case INTERFACE_TOPO_SEARCH :
41	{
42	Launch_Interface_Topo_Search(io);
43	break;
44	}
45	case INTERFACE_BRANCH_SUPPORT :
46	{
47	Launch_Interface_Branch_Support(io);
48	break;
49	}
50	default :
51	{
52	PhyML_Printf("\n== Err in file %s at line %d\n\n",__FILE__,__LINE__);
53	Exit("");
54	break;
55	}
56	}
57	}while(!io->ready_to_go);
58
59
60	if(io->in_tree == 2)
61	{
62	PhyML_Printf("\n. Enter the name of the input tree file > ");
63	Getstring_Stdin(io->in_tree_file);
64	io->fp_in_tree = Openfile(io->in_tree_file,0);
65	}
66
67	if((io->mod->whichmodel == CUSTOMAA) && (io->datatype == AA))
68	{
69	char *filename;
70
71	filename = (char *)mCalloc(T_MAX_NAME,sizeof(char));
72
73	fflush(NULL);
74	PhyML_Printf("\n");
75	PhyML_Printf("\n. Enter the rate matrix file name > "); fflush(NULL);
76	Getstring_Stdin(filename);
77	io->mod->fp_aa_rate_mat = Openfile(filename,0);
78	strcpy(io->mod->aa_rate_mat_file->s,filename);
79	PhyML_Printf("\n");
80	Free(filename);
81	fflush(NULL);
82	}
83
84	if((io->mod->s_opt->n_rand_starts) &&
85	(io->mod->s_opt->topo_search == NNI_MOVE) &&
86	(io->mod->s_opt->random_input_tree))
87	{
88	Warn_And_Exit("\n. The random starting tree option is only compatible with SPR based search options.\n");
89	}
90
91	if ((io->datatype == NT) && (io->mod->whichmodel > 10))
92	{
93	char choix;
94	PhyML_Printf("\n== Err: model incompatible with the data type. Please use JC69, K80, F81, HKY, F84, TN93 or GTR\n");
95	PhyML_Printf("\n. Type any key to exit.\n");
96	if(!scanf("%c",&choix)) Exit("\n");
97	Warn_And_Exit("\n");
98	}
99	else if ((io->datatype == AA) && (io->mod->whichmodel < 11))
100	{
101	char choix;
102	PhyML_Printf("\n== Err: model incompatible with the data type. Please use LG, Dayhoff, JTT, MtREV, WAG, DCMut, RtREV, CpREV, VT, Blosum62, MtMam, MtArt, HIVw or HIVb.\n");
103	PhyML_Printf("\n. Type any key to exit.\n");
104	if(!scanf("%c",&choix)) Exit("\n");
105	Exit("\n");
106	}
107
108	if(io->m4_model == YES)
109	{
110	#ifdef M4
111	io->mod->ns *= io->mod->m4mod->n_h;
112	io->mod->use_m4mod = 1;
113	M4_Make_Complete(io->mod->m4mod->n_h,
114	io->mod->m4mod->n_o,
115	io->mod->m4mod);
116	#endif
117	}
118	else
119	{
120	io->mod->s_opt->opt_cov_delta = 0;
121	io->mod->s_opt->opt_cov_alpha = 0;
122	io->mod->s_opt->opt_cov_free_rates = 0;
123	}
124
125	if((io->mod->s_opt->opt_cov_free_rates) && (io->mod->s_opt->opt_cov_alpha))
126	{
127	io->mod->s_opt->opt_cov_free_rates = 0;
128	io->mod->m4mod->use_cov_alpha = 0;
129	io->mod->m4mod->use_cov_free = 1;
130	}
131
132
133	if(io->print_site_lnl)
134	{
135	strcpy(io->out_lk_file,io->in_align_file);
136	strcat(io->out_lk_file, "_phyml_lk");
137	if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
138	strcat(io->out_lk_file, ".txt");
139	io->fp_out_lk = Openfile(io->out_lk_file,1);
140	}
141
142	if(io->print_trace)
143	{
144	strcpy(io->out_trace_file,io->in_align_file);
145	strcat(io->out_trace_file,"_phyml_trace");
146	if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
147	strcat(io->out_trace_file,".txt");
148	io->fp_out_trace = Openfile(io->out_trace_file,1);
149	}
150
151	if(io->mod->s_opt->random_input_tree)
152	{
153	strcpy(io->out_trees_file,io->in_align_file);
154	strcat(io->out_trees_file,"_phyml_trees");
155	if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
156	strcat(io->out_trees_file,".txt");
157	io->fp_out_trees = Openfile(io->out_trees_file,1);
158	}
159
160	if((io->print_boot_trees) && (io->mod->bootstrap > 0))
161	{
162	strcpy(io->out_boot_tree_file,io->in_align_file);
163	strcat(io->out_boot_tree_file,"_phyml_boot_trees");
164	if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
165	strcat(io->out_boot_tree_file,".txt");
166	io->fp_out_boot_tree = Openfile(io->out_boot_tree_file,1);
167
168	strcpy(io->out_boot_stats_file,io->in_align_file);
169	strcat(io->out_boot_stats_file,"_phyml_boot_stats");
170	if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
171	strcat(io->out_boot_stats_file,".txt");
172	io->fp_out_boot_stats = Openfile(io->out_boot_stats_file,1);
173	}
174
175	if(io->append_run_ID)
176	{
177	strcat(io->out_tree_file,"_");
178	strcat(io->out_stats_file,"_");
179	strcat(io->out_tree_file,io->run_id_string);
180	strcat(io->out_stats_file,io->run_id_string);
181	strcat(io->out_tree_file,".txt");
182	strcat(io->out_stats_file,".txt");
183	}
184
185	if(io->mod->ras->n_catg == 1) io->mod->s_opt->opt_alpha = 0;
186
187	if(io->mod->whichmodel != K80 &&
188	io->mod->whichmodel != HKY85 &&
189	io->mod->whichmodel != F84 &&
190	io->mod->whichmodel != TN93)
191	{
192	io->mod->s_opt->opt_kappa = 0;
193	}
194
195	io->fp_out_tree = Openfile(io->out_tree_file,1);
196	io->fp_out_stats = Openfile(io->out_stats_file,1);
197
198	if(io->mod->whichmodel == GTR)
199	{
200	/* Make_Custom_Model(io->mod); */
201	io->mod->s_opt->opt_rr = 1;
202	}
203	}
204
205	//////////////////////////////////////////////////////////////
206	//////////////////////////////////////////////////////////////
207
208
209	void Clear()
210	{
211	#ifdef WIN32
212	system("cls");
213	#elif UNIX
214	PhyML_Printf("\033[2J\033[H");
215	#endif
216	}
217
218	//////////////////////////////////////////////////////////////
219	//////////////////////////////////////////////////////////////
220
221
222	void Launch_Interface_Input(option *io)
223	{
224	char choix;
225	int n_trial;
226
227	Clear();
228	Print_Banner(stdout);
229
230
231	#ifdef EVOLVE
232
233	char *n_data_sets;
234
235	PhyML_Printf("\n\n");
236	PhyML_Printf("\n. Enter the tree file name > "); fflush(NULL);
237	Getstring_Stdin(io->in_tree_file);
238	io->fp_in_tree = Openfile(io->in_tree_file,0);
239	PhyML_Printf("\n");
240
241	PhyML_Printf("\n. Enter the reference sequence file name > "); fflush(NULL);
242	Getstring_Stdin(io->in_align_file);
243	io->fp_in_align = Openfile(io->in_align_file,0);
244	PhyML_Printf("\n");
245
246	PhyML_Printf("\n. Number of data sets > ");
247	n_data_sets = (char *)mCalloc(10000,sizeof(char));
248	Getstring_Stdin(n_data_sets);
249	n_trial = 0;
250	while((!atoi(n_data_sets)) \|\| (atoi(n_data_sets) < 0))
251	{
252	if(++n_trial > 10) Exit("\n== Err : the number of sets must be a positive integer");
253	PhyML_Printf("\n. The number of sets must be a positive integer");
254	PhyML_Printf("\n. Enter a new value > ");
255	Getstring_Stdin(n_data_sets);
256	}
257	io->n_data_set_asked = atoi(n_data_sets);
258	Free(n_data_sets);
259
260	#elif OPTIMIZ
261
262	PhyML_Printf("\n. Enter the tree file name > "); fflush(NULL);
263	Getstring_Stdin(io->in_tree_file);
264	io->fp_in_tree = Openfile(io->in_tree_file,0);
265	PhyML_Printf("\n");
266
267	PhyML_Printf("\n. Enter the reference sequence file name > "); fflush(NULL);
268	Getstring_Stdin(io->in_align_file);
269	io->fp_in_align = Openfile(io->in_align_file,0);
270	PhyML_Printf("\n");
271
272	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
273
274	PhyML_Printf("\n. Enter the sequence file name > "); fflush(NULL);
275	Getstring_Stdin(io->in_align_file);
276	io->fp_in_align = Openfile(io->in_align_file,0);
277
278	#endif
279
280
281	#if defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
282
283	strcpy(io->out_stats_file,io->in_align_file);
284	strcat(io->out_stats_file,"_phyml_stats.txt");
285
286	strcpy(io->out_tree_file,io->in_align_file);
287	strcat(io->out_tree_file,"_phyml_tree.txt");
288
289	strcpy(io->out_lk_file,io->in_align_file);
290	strcat(io->out_lk_file,"_phyml_lk.txt");
291
292
293	#endif
294
295
296	#ifdef WIN32
297	#ifdef EVOLVE
298	if(Filexists("evolve_out.txt"));
299	#elif OPTIMIZ
300	if(Filexists("optimiz_out.txt"))
301	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
302	if(Filexists(io->out_stats_file))
303	#endif
304	#elif UNIX
305	#ifdef EVOLVE
306	if(Filexists("evolve_out"));
307	#elif OPTIMIZ
308	if(Filexists("optimiz_out"))
309	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
310	if(Filexists(io->out_stats_file))
311	#endif
312	#endif
313	{
314	PhyML_Printf("\n");
315	#ifdef EVOLVE
316	PhyML_Printf("\n. A file 'evolve_out' already exists");
317	#elif OPTIMIZ
318	PhyML_Printf("\n. A file 'optimiz_out' already exists");
319	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
320	PhyML_Printf("\n. A file '%s' already exists",io->out_stats_file);
321	#endif
322	PhyML_Printf("\n. Do you want to Replace it or Append to it ? ");
323	n_trial = 0;
324	do
325	{
326	PhyML_Printf("\n. Please type R or A > ");
327	if(!scanf("%c",&choix)) Exit("\n");
328	if(choix == '\n') choix = 'r';
329	else getchar();
330	if(++n_trial>10) Exit("\n");
331	Uppercase(&choix);
332	}
333	while((choix != 'R') && (choix != 'A'));
334	if(choix == 'R') io->out_stats_file_open_mode = 1;
335	else io->out_stats_file_open_mode = 2;
336	}
337
338	/* io->fp_out_stats = Openfile(io->out_stats_file,io->out_stats_file_open_mode); */
339
340	#ifdef WIN32
341	#ifdef EVOLVE
342	if(Filexists("evolve_seq.txt"))
343	#elif OPTIMIZ
344	if(Filexists("optimiz_tree.txt"))
345	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
346	if(Filexists(io->out_tree_file))
347	#endif
348	#elif UNIX
349	#ifdef EVOLVE
350	if(Filexists("evolve_seq"))
351	#elif OPTIMIZ
352	if(Filexists("optimiz_tree"))
353	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
354	if(Filexists(io->out_tree_file))
355	#endif
356	#endif
357	{
358	PhyML_Printf("\n");
359	#ifdef EVOLVE
360	PhyML_Printf("\n. A file 'evolve_seq' already exists");
361	#elif OPTIMIZ
362	PhyML_Printf("\n. A file 'optimiz_tree' already exists");
363	#elif defined(PHYML) \|\| defined(PART) \|\| defined(PHYML_INSERT)
364	PhyML_Printf("\n. A file '%s' already exists",io->out_tree_file);
365	#endif
366	PhyML_Printf("\n. Do you want to Replace it or Append to it ? ");
367	n_trial = 0;
368	do
369	{
370	PhyML_Printf("\n. Please type R or A > ");
371	if(!scanf("%c",&choix)) Exit("\n");
372	if(choix == '\n') choix = 'r';
373	else getchar();
374	Uppercase(&choix);
375	if(++n_trial>10) Exit("\n");
376	}
377	while((choix != 'R') && (choix != 'A'));
378	if(choix == 'R') io->out_tree_file_open_mode = 1;
379	else io->out_tree_file_open_mode = 2;
380	}
381
382	/* io->fp_out_tree = Openfile(io->out_tree_file,io->out_tree_file_open_mode); */
383	}
384
385	//////////////////////////////////////////////////////////////
386	//////////////////////////////////////////////////////////////
387
388
389	void Launch_Interface_Data_Type(option *io)
390	{
391	char choix;
392	char *s;
393	char *buff;
394
395	Clear();
396	Print_Banner(stdout);
397	if(io->config_multigene) Print_Data_Set_Number(io,stdout);
398
399	s = (char *)mCalloc(100,sizeof(char));
400	buff = (char *)mCalloc(100,sizeof(char));
401
402
403	PhyML_Printf("\n\n");
404
405	PhyML_Printf(" ................... \n");
406	PhyML_Printf(" Menu : Input Data \n");
407	PhyML_Printf(" ......................... \n");
408
409	PhyML_Printf("\n\n");
410
411	PhyML_Printf(" [+] "
412	".................................... Next sub-menu\n");
413
414	PhyML_Printf(" [-] "
415	"................................ Previous sub-menu\n");
416
417	PhyML_Printf(" [Y] "
418	".............................. Launch the analysis\n");
419
420	PhyML_Printf("\n");
421
422	if(io->datatype == NT) strcpy(s,"DNA");
423	else if(io->datatype == AA) strcpy(s,"AA");
424	else strcpy(s,"Generic");
425
426	PhyML_Printf(" [D] "
427	"....................... Data type (DNA/AA/Generic) "
428	" %-15s \n",s);
429
430	PhyML_Printf(" [I] "
431	"...... Input sequences interleaved (or sequential) "
432	" %-15s \n",
433	(io->interleaved)?("interleaved"):("sequential"));
434
435	strcpy(s,"");
436	sprintf(s," (%d sets)",io->n_data_sets);
437	strcpy(buff,(io->n_data_sets > 1)?("yes"):("no"));
438	buff=strcat(buff,(io->n_data_sets > 1)?(s):("\0"));
439	PhyML_Printf(" [M] "
440	"....................... Analyze multiple data sets "
441	" %-15s \n",buff);
442
443	if(!io->append_run_ID) strcpy(s,"none");
444	else strcpy(s,io->run_id_string);
445	PhyML_Printf(" [R] "
446	"........................................... Run ID "
447	" %-15s \n",s);
448
449
450	PhyML_Printf("\n\n. Are these settings correct ? "
451	"(type '+', '-', 'Y' or other letter for one to change) ");
452
453
454	if(!scanf("%c",&choix)) Exit("\n");
455	if(choix != '\n') getchar(); /* \n */
456	fflush(NULL);
457
458	Uppercase(&choix);
459
460	switch(choix)
461	{
462	/* case '\n': */
463	/* { */
464	/* io->curr_interface++; */
465	/* break; */
466	/* } */
467	case 'R' :
468	{
469	io->append_run_ID = (io->append_run_ID)?(0):(1);
470	PhyML_Printf("\n. Enter a run ID (any string of characters) > ");
471	Getstring_Stdin(io->run_id_string);
472	break;
473	}
474
475
476	case 'M' :
477	{
478	char *c;
479	int n_trial;
480
481	PhyML_Printf("\n. How many data sets > ");
482	c = (char *)mCalloc(100,sizeof(char));
483	Getstring_Stdin(c);
484	n_trial = 0;
485	while((!atoi(c)) \|\| (atoi(c) < 0))
486	{
487	if(++n_trial > 10) Exit("\n== Err : The number of data sets must be a positive integer");
488	PhyML_Printf("\n. The number of data sets must be a positive integer");
489	PhyML_Printf("\n. Enter a new value > ");
490	Getstring_Stdin(c);
491	}
492	io->n_data_sets = atoi(c);
493
494	#ifdef PART
495	if(io->n_data_sets > 1)
496	{
497	io->multigene = 1;
498	}
499	#endif
500
501	if((io->mod->bootstrap > 1) && (io->n_data_sets > 1))
502	{
503	PhyML_Printf("\n. Bootstrap option is not allowed with multiple data sets !\n");
504	PhyML_Printf("\n. Type any key to exit.");
505	if(!scanf("%c",&choix)) Exit("\n");
506	Exit("\n");
507	}
508
509	Free(c);
510	break;
511	}
512	case 'I' :
513	{
514	if(io->interleaved)
515	io->interleaved = 0;
516	else io->interleaved = 1;
517	break;
518	}
519	case 'D' :
520	{
521	if(io->datatype == NT)
522	{
523	io->datatype = AA;
524	io->mod->ns = 20;
525	io->mod->s_opt->opt_kappa = 0;
526	io->mod->whichmodel = LG;
527	strcpy(io->mod->modelname->s,"LG");
528	}
529	else if(io->datatype == AA)
530	{
531	io->datatype = GENERIC;
532	io->mod->whichmodel = JC69;
533	strcpy(io->mod->modelname->s,"JC69");
534	strcpy(io->nt_or_cd,"natural numbers");
535	}
536	else if(io->datatype == GENERIC)
537	{
538	io->datatype = NT;
539	io->mod->ns = 4;
540	io->mod->whichmodel = HKY85;
541	strcpy(io->mod->modelname->s,"HKY85");
542	strcpy(io->nt_or_cd,"nucleotides");
543	}
544	break;
545	}
546	case '-' :
547	{
548	io->curr_interface = (io->config_multigene)?(INTERFACE_MODEL):(INTERFACE_BRANCH_SUPPORT);
549	break;
550	}
551	case '+' :
552	{
553	io->curr_interface = (io->multigene)?(INTERFACE_MULTIGENE):(INTERFACE_MODEL);
554	break;
555	}
556	case 'Y' :
557	{
558	io->ready_to_go = 1;
559	break;
560	}
561	default :
562	{
563	break;
564	}
565	}
566
567	Free(s);
568	Free(buff);
569	}
570	//////////////////////////////////////////////////////////////
571	//////////////////////////////////////////////////////////////
572
573
574	void Launch_Interface_Model(option *io)
575	{
576	char choix;
577	char *s;
578
579	s = (char *)mCalloc(100,sizeof(char));
580
581	Clear();
582	Print_Banner(stdout);
583	if(io->config_multigene) Print_Data_Set_Number(io,stdout);
584
585
586	PhyML_Printf("\n\n");
587
588	PhyML_Printf(" ........................... \n");
589	PhyML_Printf(" Menu : Substitution Model \n");
590	PhyML_Printf(" ................................. \n");
591
592	PhyML_Printf("\n\n");
593
594	PhyML_Printf(" [+] "
595	".................................... Next sub-menu\n");
596
597	PhyML_Printf(" [-] "
598	"................................ Previous sub-menu\n");
599
600	PhyML_Printf(" [Y] "
601	".............................. Launch the analysis\n");
602
603	PhyML_Printf("\n");
604
605	if (io->datatype == NT)
606	{
607	if(!strcmp(io->nt_or_cd,"nucleotides"))
608	{
609	PhyML_Printf(" [M] "
610	"................. Model of nucleotide substitution "
611	" %-15s \n", io->mod->modelname->s);
612
613	if((io->mod->whichmodel == F81) \|\|
614	(io->mod->whichmodel == HKY85) \|\|
615	(io->mod->whichmodel == F84) \|\|
616	(io->mod->whichmodel == TN93) \|\|
617	(io->mod->whichmodel == GTR) \|\|
618	(io->mod->whichmodel == CUSTOM))
619	{
620	/* PhyML_Printf(" [F] " */
621	/* ".......... Base frequency estimates (empirical/ML) " */
622	/* " %-15s \n", */
623	/* (io->mod->s_opt->opt_state_freq)?("ML"):("empirical")); */
624	/* } */
625	/* else if(io->mod->whichmodel == CUSTOM) */
626	/* { */
627	PhyML_Printf(" [F] "
628	"................. Optimise equilibrium frequencies "
629	" %-15s \n",
630	(io->mod->s_opt->opt_state_freq)?("yes"):("no"));
631	}
632
633
634	if(io->mod->whichmodel == CUSTOM)
635	{
636	if(!io->mod->s_opt->opt_state_freq)
637	{
638	PhyML_Printf(" [E] "
639	"......... Equilibrium frequencies (empirical/user) "
640	" %-15s \n",
641	(io->mod->s_opt->user_state_freq)?("user defined"):("empirical"));
642	}
643	PhyML_Printf(" [K] "
644	"............................. Current custom model "
645	" %-15s \n", io->mod->custom_mod_string->s);
646
647	PhyML_Printf(" [O] "
648	"................ Optimise relative rate parameters "
649	" %-15s \n",(io->mod->s_opt->opt_rr)?("yes"):("no"));
650	}
651	}
652	}
653	else if(io->datatype == AA)
654	{
655	PhyML_Printf(" [M] "
656	"................ Model of amino-acids substitution "
657	" %-15s \n", io->mod->modelname->s);
658
659	PhyML_Printf(" [F] "
660	". Amino acid frequencies (empirical/model defined) "
661	" %-15s \n",
662	(io->mod->s_opt->opt_state_freq)?("empirical"):("model"));
663	}
664	else if(io->datatype == GENERIC)
665	{
666	PhyML_Printf(" [M] "
667	"................. Model of nucleotide substitution "
668	" %-15s \n", io->mod->modelname->s);
669	}
670
671	if ((io->datatype == NT) &&
672	((io->mod->whichmodel == K80) \|\|
673	(io->mod->whichmodel == HKY85)\|\|
674	(io->mod->whichmodel == F84) \|\|
675	(io->mod->whichmodel == TN93)))
676	{
677	strcpy(s,(io->mod->s_opt->opt_kappa)?("estimated"):("fixed"));
678	(io->mod->s_opt->opt_kappa)?((char )strcat(s,"")):((char )strcat(s," (ts/tv = "));
679	/* (io->mod->s_opt->opt_kappa)?((char )strcat(s,"")):((char )sprintf(s+(int)strlen((char )s),"%3.2f)",io->mod->kappa->v)); /
680	if(io->mod->s_opt->opt_kappa)
681	{
682	strcat((char *)s,"");
683	}
684	else
685	{
686	sprintf((char *)(s+(int)strlen(s)),"%3.2f)",io->mod->kappa->v);
687	}
688
689	PhyML_Printf(" [T] "
690	".................... Ts/tv ratio (fixed/estimated) "
691	" %-15s \n",s);
692	}
693
694
695	(io->mod->s_opt->opt_pinvar)?(strcpy(s,"estimated")):(strcpy(s,"fixed"));
696	(io->mod->s_opt->opt_pinvar)?((char )strcat(s,"")):((char )strcat(s," (p-invar = "));
697
698	if(io->mod->s_opt->opt_pinvar)
699	{
700	strcat(s,"");
701	}
702	else
703	{
704	sprintf((char )(s+strlen((char )s)),"%3.2f)",io->mod->ras->pinvar->v);
705	}
706
707	PhyML_Printf(" [V] "
708	". Proportion of invariable sites (fixed/estimated)"
709	" %-15s \n",s);
710
711	PhyML_Printf(" [R] "
712	"....... One category of substitution rate (yes/no) "
713	" %-15s \n",
714	(io->mod->ras->n_catg > 1)?("no"):("yes"));
715
716	if(io->mod->ras->n_catg > 1)
717	{
718	PhyML_Printf(" [C] "
719	"........... Number of substitution rate categories "
720	" %-15d \n",
721	io->mod->ras->n_catg);
722	}
723
724
725	if(io->mod->ras->n_catg > 1)
726	{
727	PhyML_Printf(" [G] "
728	"............. Gamma distributed rates across sites "
729	" %-15s \n",(io->mod->ras->free_mixt_rates)?("no"):("yes"));
730	}
731
732
733	if((io->mod->ras->n_catg > 1) && (io->mod->ras->free_mixt_rates == NO))
734	{
735	strcpy(s,(io->mod->s_opt->opt_alpha)?("estimated"):("fixed"));
736	(io->mod->s_opt->opt_alpha)?(strcat(s, "")):(strcat(s," (alpha = "));
737
738	if(io->mod->s_opt->opt_alpha)
739	{
740	strcat(s, "");
741	}
742	else
743	{
744	sprintf(s+strlen(s),"%3.2f)",io->mod->ras->alpha->v);
745	}
746
747	PhyML_Printf(" [A] "
748	"... Gamma distribution parameter (fixed/estimated) "
749	" %-15s \n",s);
750
751
752	/* strcpy(s,(io->mod->ras->gamma_median)?("median"):("mean")); */
753
754	/* PhyML_Printf(" [G] " */
755	/* ".........'Middle' of each rate class (mean/median) " */
756	/* " %-15s \n",s); */
757
758
759	}
760
761	PhyML_Printf("\n\n. Are these settings correct ? "
762	"(type '+', '-', 'Y' or other letter for one to change) ");
763
764
765	if(!scanf("%c",&choix)) Exit("\n");
766	if(choix != '\n') getchar(); /* \n */
767
768	Uppercase(&choix);
769
770	switch(choix)
771	{
772	/* case '\n': */
773	/* { */
774	/* io->curr_interface++; */
775	/* break; */
776	/* } */
777
778	case 'G' :
779	{
780	io->mod->ras->free_mixt_rates = (io->mod->ras->free_mixt_rates)?(NO):(YES);
781	break;
782	}
783
784	case 'O' :
785	{
786	io->mod->s_opt->opt_rr = (io->mod->s_opt->opt_rr)?(0):(1);
787	break;
788	}
789
790	case 'K' :
791	{
792	int i,j;
793	char *rr_param,rr;
794	t_mod *mod;
795	int n_trial;
796
797	if(io->mod->whichmodel == CUSTOM)
798	{
799	rr_param = (char *)mCalloc(6,sizeof(char ));
800	For(i,6) rr_param[i] = (char *)mCalloc(10,sizeof(char));
801	rr = (char *)mCalloc(50,sizeof(char));
802
803	mod = io->mod;
804	mod->s_opt->opt_rr = 1;
805
806	n_trial = 0;
807	do
808	{
809	PhyML_Printf("\n. Enter a new custom model > ");
810	Getstring_Stdin(io->mod->custom_mod_string->s);
811	if(strlen(io->mod->custom_mod_string->s) == 6)
812	{
813	For(i,6)
814	{
815	while(!isdigit((int)io->mod->custom_mod_string->s[i]))
816	{
817	if(++n_trial > 10) Exit("\n== Err : this string is not valid !\n");
818	PhyML_Printf("\n. This string is not valid\n");
819	PhyML_Printf("\n. Enter a new model > ");
820	Getstring_Stdin(io->mod->custom_mod_string->s);
821	}
822	}
823	if(i == 6) break;
824	}
825	else
826	{
827	PhyML_Printf("\n. The string should be of length 6\n");
828	n_trial++;
829	}
830	}while(n_trial < 10);
831	if(n_trial == 10) Exit("");
832
833	if(!mod->r_mat)
834	{
835	mod->r_mat = (t_rmat *)Make_Rmat(mod->ns);
836	Init_Rmat(mod->r_mat);
837	Make_Custom_Model(mod);
838	Translate_Custom_Mod_String(io->mod);
839	}
840
841	strcpy(rr_param[0],"A<->C");
842	strcpy(rr_param[1],"A<->G");
843	strcpy(rr_param[2],"A<->T");
844	strcpy(rr_param[3],"C<->G");
845	strcpy(rr_param[4],"C<->T");
846	strcpy(rr_param[5],"G<->T");
847
848	PhyML_Printf("\n. Set the relative rate values\n");
849	For(i,mod->r_mat->n_diff_rr)
850	{
851	sprintf(rr,"\n. [");
852	For(j,6)
853	{
854	if(mod->r_mat->rr_num->v[j] == i)
855	{
856	sprintf(rr+strlen(rr),"%s = ",rr_param[j]);
857	}
858	}
859	sprintf(rr+strlen(rr)-3,"]");
860	PhyML_Printf("%s",rr);
861
862	PhyML_Printf(" (current=%.2f) > ",mod->r_mat->rr_val->v[i]);
863
864	Getstring_Stdin(rr);
865
866	if(rr[0] != '\0')
867	{
868	n_trial = 0;
869	while((atof(rr) < .0))
870	{
871	if(++n_trial > 10)
872	Exit("\n== Err : the value of this parameter must be a positive number\n");
873	PhyML_Printf("\n. The value of this parameter must be a positive number\n");
874	PhyML_Printf("\n. Enter a new value > ");
875	Getstring_Stdin(rr);
876	}
877	io->mod->r_mat->rr_val->v[i] = (phydbl)atof(rr);
878	}
879	}
880
881	For(i,6) Free(rr_param[i]);
882	Free(rr_param);
883	Free(rr);
884	}
885	break;
886	}
887	case 'E' :
888	{
889	int i;
890
891	if(io->mod->whichmodel == CUSTOM)
892	{
893	io->mod->s_opt->user_state_freq = (io->mod->s_opt->user_state_freq)?(0):(1);
894
895	if(io->mod->s_opt->user_state_freq)
896	{
897	if(!io->mod->s_opt->opt_state_freq)
898	{
899	char **bases;
900	char *bs;
901	phydbl sum;
902	int n_trial;
903
904	bases = (char *)mCalloc(4,sizeof(char ));
905	For(i,4) bases[i] = (char *)mCalloc(50,sizeof(char));
906	bs = (char *)mCalloc(100,sizeof(char));
907
908	strcpy(bases[0],". f(A)> ");
909	strcpy(bases[1],". f(C)> ");
910	strcpy(bases[2],". f(G)> ");
911	strcpy(bases[3],". f(T)> ");
912
913	PhyML_Printf("\n. Set nucleotide frequencies \n");
914	sum = .0;
915	For(i,4)
916	{
917	PhyML_Printf("%s",bases[i]);
918	Getstring_Stdin(bs);
919	n_trial = 0;
920
921	while((atof(bs) < .0001) \|\| (bs[0] == '\0'))
922	{
923	if(++n_trial > 10)
924	Exit("\n== Err : the value of this parameter must be a positive number\n");
925	PhyML_Printf("\n. The value of this parameter must be a positive number\n");
926	PhyML_Printf("\n. Enter a new value > ");
927	Getstring_Stdin(bs);
928	}
929	io->mod->user_b_freq->v[i] = (phydbl)atof(bs);
930	sum += io->mod->user_b_freq->v[i];
931	}
932
933	For(i,4) io->mod->user_b_freq->v[i] /= sum;
934
935	if(sum > 1.0 \|\| sum < 1.0)
936	{
937	PhyML_Printf("\n. The nucleotide frequencies have to be normalised in order to sum to 1.0.\n");
938	PhyML_Printf("\n. The frequencies are now : f(A)=%f, f(C)=%f, f(G)=%f, f(T)=%f.\n",
939	io->mod->user_b_freq->v[0],
940	io->mod->user_b_freq->v[1],
941	io->mod->user_b_freq->v[2],
942	io->mod->user_b_freq->v[3]);
943	PhyML_Printf("\n. Enter any key to continue.\n");
944	if(!scanf("%c",bs)) Exit("\n");
945	}
946
947	For(i,4) Free(bases[i]);
948	Free(bases);
949	Free(bs);
950	}
951	else
952	{
953	Warn_And_Exit("\n. 'E' is not a valid option with these model settings.\n");
954	}
955	}
956	}
957	break;
958	}
959	case 'A' :
960	{
961	char answer;
962	int n_trial;
963
964	switch(io->mod->s_opt->opt_alpha)
965	{
966	case 0 :
967	{
968	PhyML_Printf("\n. Optimise alpha ? [Y/n] ");
969	if(!scanf("%c",&answer)) Exit("\n");
970	if(answer == '\n') answer = 'Y';
971	else getchar();
972	break;
973	}
974	case 1 :
975	{
976	PhyML_Printf("\n. Optimise alpha ? [N/y] ");
977	if(!scanf("%c",&answer)) Exit("\n");
978	if(answer == '\n') answer = 'N';
979	else getchar();
980	break;
981	}
982	default : Exit("\n");
983	}
984
985	n_trial = 0;
986	while((answer != 'Y') && (answer != 'y') &&
987	(answer != 'N') && (answer != 'n'))
988	{
989	if(++n_trial > 10) Exit("\n== Err : wrong answers !");
990	PhyML_Printf("\n. Optimise alpha ? [N/y] ");
991	if(!scanf("%c",&answer)) Exit("\n");
992	if(answer == '\n') answer = 'N';
993	else getchar();
994	}
995
996	switch(answer)
997	{
998	case 'Y' : case 'y' :
999	{
1000	io->mod->s_opt->opt_alpha = 1;
1001	io->mod->s_opt->opt_subst_param = 1;
1002	break;
1003	}
1004	case 'N' : case 'n' :
1005	{
1006	char *a;
1007	a = (char *)mCalloc(100,sizeof(char));
1008	io->mod->ras->alpha->v = 10.0;
1009	io->mod->s_opt->opt_alpha = 0;
1010	PhyML_Printf("\n. Enter your value of alpha > ");
1011	Getstring_Stdin(a);
1012	n_trial = 0;
1013	while(atof(a) < 1.E-10)
1014	{
1015	if(++n_trial > 10) Exit("\n== Err : alpha must be > 1.E-10\n");
1016	PhyML_Printf("\n. Alpha must be 1.E-10\n");
1017	PhyML_Printf("\n. Enter a new value > ");
1018	Getstring_Stdin(a);
1019	}
1020	io->mod->ras->alpha->v = (phydbl)atof(a);
1021	Free(a);
1022	io->mod->s_opt->opt_alpha = 0;
1023	break;
1024	}
1025	}
1026	break;
1027	}
1028
1029	case 'C' :
1030	{
1031	char *c;
1032	int n_trial;
1033
1034	PhyML_Printf("\n. Enter your number of categories > ");
1035	c = (char *)mCalloc(100,sizeof(char));
1036	Getstring_Stdin(c);
1037	n_trial = 0;
1038	while((!atoi(c)) \|\| (atoi(c) < 0))
1039	{
1040	if(++n_trial > 10) Exit("\n== Err : the number of categories must be a positive integer\n");
1041	PhyML_Printf("\n. The number of categories must be a positive integer\n");
1042	PhyML_Printf("\n. Enter a new value > ");
1043	Getstring_Stdin(c);
1044	}
1045	io->mod->ras->n_catg = atoi(c);
1046	Free(c);
1047	break;
1048	}
1049
1050	case 'R' :
1051	{
1052	(io->mod->ras->n_catg == 1)?(io->mod->ras->n_catg = 4):(io->mod->ras->n_catg = 1);
1053	break;
1054	}
1055
1056	case 'V' :
1057	{
1058	char answer;
1059	int n_trial;
1060
1061	switch(io->mod->s_opt->opt_pinvar)
1062	{
1063	case 0 :
1064	{
1065	PhyML_Printf("\n. Optimise p-invar ? [Y/n] ");
1066	if(!scanf("%c", &answer)) Exit("\n");
1067	if(answer == '\n') answer = 'Y';
1068	else getchar();
1069	break;
1070	}
1071	case 1 :
1072	{
1073	PhyML_Printf("\n. Optimise p-invar ? [N/y] ");
1074	if(!scanf("%c", &answer)) Exit("\n");
1075	if(answer == '\n') answer = 'N';
1076	else getchar();
1077	break;
1078	}
1079	default : Exit("\n");
1080	}
1081
1082	n_trial = 0;
1083	while((answer != 'Y') && (answer != 'y') &&
1084	(answer != 'N') && (answer != 'n'))
1085	{
1086	if(++n_trial > 10) Exit("\n== Err : wrong answers !");
1087	PhyML_Printf("\n. Optimise p-invar ? [N/y] ");
1088	if(!scanf("%c", &answer)) Exit("\n");
1089	if(answer == '\n') answer = 'N';
1090	else getchar();
1091	}
1092
1093	switch(answer)
1094	{
1095	case 'Y' : case 'y' :
1096	{
1097	io->mod->s_opt->opt_subst_param = 1;
1098	io->mod->s_opt->opt_pinvar = 1;
1099	io->mod->ras->pinvar->v = 0.2;
1100	io->mod->ras->invar = 1;
1101	break;
1102	}
1103	case 'N' : case 'n' :
1104	{
1105	char *p;
1106	p = (char *)mCalloc(100,sizeof(char));
1107	PhyML_Printf("\n. Enter your value of p-invar > ");
1108	Getstring_Stdin(p);
1109	n_trial = 0;
1110	while((atof(p) < 0.0) \|\| (atof(p) > 1.0))
1111	{
1112	if(++n_trial > 10)
1113	Exit("\n== Err : the proportion of invariable sites must be a positive number between 0.0 and 1.0");
1114	PhyML_Printf("\n. The proportion must be a positive number between 0.0 and 1.0\n");
1115	PhyML_Printf("\n. Enter a new value > ");
1116	Getstring_Stdin(p);
1117	}
1118	io->mod->ras->pinvar->v = (phydbl)atof(p);
1119
1120	if(io->mod->ras->pinvar->v > 0.0+SMALL) io->mod->ras->invar = 1;
1121	else io->mod->ras->invar = 0;
1122
1123	Free(p);
1124
1125	io->mod->s_opt->opt_pinvar = 0;
1126	break;
1127	}
1128	}
1129	break;
1130	}
1131
1132	case 'T' :
1133	{
1134	char answer;
1135	int n_trial;
1136
1137	if((io->datatype == AA) \|\|
1138	(io->mod->whichmodel == JC69)\|\|
1139	(io->mod->whichmodel == F81) \|\|
1140	(io->mod->whichmodel == GTR) \|\|
1141	(io->mod->whichmodel == CUSTOM))
1142	{
1143	PhyML_Printf("\n. 'K' is not a valid choice for this model\n");
1144	PhyML_Printf("\n. Type any key to exit.\n");
1145	if(!scanf("%c",&choix)) Exit("\n");
1146	Exit("\n");
1147	}
1148
1149	switch(io->mod->s_opt->opt_kappa)
1150	{
1151	case 0 :
1152	{
1153	PhyML_Printf("\n. Optimise ts/tv ratio ? [Y/n] ");
1154	if(!scanf("%c", &answer)) Exit("\n");
1155	if(answer == '\n') answer = 'Y';
1156	else getchar();
1157	break;
1158	}
1159	case 1 :
1160	{
1161	PhyML_Printf("\n. Optimise ts/tv ratio ? [N/y] ");
1162	if(!scanf("%c", &answer)) Exit("\n");
1163	if(answer == '\n') answer = 'N';
1164	else getchar();
1165	break;
1166	}
1167	default : Exit("\n");
1168	}
1169
1170	n_trial = 0;
1171	while((answer != 'Y') && (answer != 'y') &&
1172	(answer != 'N') && (answer != 'n'))
1173	{
1174	if(++n_trial > 10) Exit("\n== Err : wrong answers !");
1175	PhyML_Printf("\n. Optimise ts/tv ratio ? [N/y] ");
1176	if(!scanf("%c", &answer)) Exit("\n");
1177	if(answer == '\n') answer = 'N';
1178	else getchar();
1179	}
1180
1181	switch(answer)
1182	{
1183	case 'Y' : case 'y' :
1184	{
1185	io->mod->kappa->v = 4.0;
1186	io->mod->s_opt->opt_subst_param = 1;
1187	io->mod->s_opt->opt_kappa = 1;
1188	if(io->mod->whichmodel == TN93)
1189	io->mod->s_opt->opt_lambda = 1;
1190	break;
1191	}
1192	case 'N' : case 'n' :
1193	{
1194	char *t;
1195	t = (char *)mCalloc(100,sizeof(char));
1196	io->mod->s_opt->opt_kappa = 0;
1197	PhyML_Printf("\n. Enter your value of the ts/tv ratio > ");
1198	Getstring_Stdin(t);
1199	n_trial = 0;
1200	while(atof(t) < .0)
1201	{
1202	if(++n_trial > 10) Exit("\n== Err : the ts/tv ratio must be a positive number\n");
1203	PhyML_Printf("\n. The ratio must be a positive number");
1204	PhyML_Printf("\n. Enter a new value > ");
1205	Getstring_Stdin(t);
1206	}
1207	io->mod->kappa->v = (phydbl)atof(t);
1208	io->mod->s_opt->opt_kappa = 0;
1209	io->mod->s_opt->opt_lambda = 0;
1210	Free(t);
1211	break;
1212	}
1213	}
1214	break;
1215	}
1216
1217	case 'F' :
1218	{
1219	if((io->mod->whichmodel == JC69) \|\|
1220	(io->mod->whichmodel == K80))
1221	{
1222	Warn_And_Exit("\n. 'F' is not a valid choice with these model settings.\n");
1223	}
1224	io->mod->s_opt->opt_state_freq = (io->mod->s_opt->opt_state_freq)?(0):(1);
1225	break;
1226	}
1227
1228	case 'M' :
1229	{
1230	if(io->datatype == NT)
1231	{
1232	if(!strcmp(io->nt_or_cd,"nucleotides"))
1233	{
1234	if(io->mod->whichmodel == JC69)
1235	{
1236	io->mod->whichmodel = K80;
1237	}
1238	else if(io->mod->whichmodel == K80)
1239	{
1240	io->mod->whichmodel = F81;
1241	}
1242	else if(io->mod->whichmodel == F81)
1243	{
1244	io->mod->whichmodel = HKY85;
1245	}
1246	else if(io->mod->whichmodel == HKY85)
1247	{
1248	io->mod->whichmodel = F84;
1249	}
1250	else if(io->mod->whichmodel == F84)
1251	{
1252	io->mod->whichmodel = TN93;
1253	}
1254	else if(io->mod->whichmodel == TN93)
1255	{
1256	io->mod->whichmodel = GTR;
1257	}
1258	else if(io->mod->whichmodel == GTR)
1259	{
1260	io->mod->whichmodel = CUSTOM;
1261	}
1262
1263	else if(io->mod->whichmodel == CUSTOM)
1264	{
1265	io->mod->whichmodel = JC69;
1266	}
1267	}
1268	}
1269	else if(io->datatype == AA)
1270	{
1271	if(io->mod->whichmodel == LG)
1272	{
1273	io->mod->whichmodel = WAG;
1274	}
1275	else if(io->mod->whichmodel == WAG)
1276	{
1277	io->mod->whichmodel = DAYHOFF;
1278	}
1279	else if(io->mod->whichmodel == DAYHOFF)
1280	{
1281	io->mod->whichmodel = JTT;
1282	}
1283	else if(io->mod->whichmodel == JTT)
1284	{
1285	io->mod->whichmodel = BLOSUM62;
1286	}
1287	else if(io->mod->whichmodel == BLOSUM62)
1288	{
1289	io->mod->whichmodel = MTREV;
1290	}
1291	else if(io->mod->whichmodel == MTREV)
1292	{
1293	io->mod->whichmodel = RTREV;
1294	}
1295	else if(io->mod->whichmodel == RTREV)
1296	{
1297	io->mod->whichmodel = CPREV;
1298	}
1299	else if(io->mod->whichmodel == CPREV)
1300	{
1301	io->mod->whichmodel = DCMUT;
1302	}
1303	else if(io->mod->whichmodel == DCMUT)
1304	{
1305	io->mod->whichmodel = VT;
1306	}
1307	else if(io->mod->whichmodel == VT)
1308	{
1309	io->mod->whichmodel = MTMAM;
1310	}
1311	else if(io->mod->whichmodel == MTMAM)
1312	{
1313	io->mod->whichmodel = MTART;
1314	}
1315	else if(io->mod->whichmodel == MTART)
1316	{
1317	io->mod->whichmodel = HIVW;
1318	}
1319	else if(io->mod->whichmodel == HIVW)
1320	{
1321	io->mod->whichmodel = HIVB;
1322	}
1323	else if(io->mod->whichmodel == HIVB)
1324	{
1325	io->mod->whichmodel = CUSTOMAA;
1326	}
1327	else if(io->mod->whichmodel == CUSTOMAA)
1328	{
1329	io->mod->whichmodel = LG;
1330	}
1331	}
1332	else if(io->datatype == GENERIC)
1333	{
1334	io->mod->whichmodel = JC69;
1335	}
1336	Set_Model_Name(io->mod);
1337	break;
1338	}
1339	case '-' :
1340	{
1341	io->curr_interface = INTERFACE_DATA_TYPE;
1342	break;
1343	}
1344	case '+' :
1345	{
1346	io->curr_interface = (io->config_multigene)?(INTERFACE_DATA_TYPE):(INTERFACE_TOPO_SEARCH);
1347	break;
1348	}
1349	case 'Y' :
1350	{
1351	io->ready_to_go = 1;
1352	break;
1353	}
1354	default :
1355	{
1356	break;
1357	}
1358	}
1359
1360	if(io->mod->s_opt->opt_alpha \|\|
1361	io->mod->s_opt->opt_kappa \|\|
1362	io->mod->s_opt->opt_lambda \|\|
1363	io->mod->s_opt->opt_pinvar \|\|
1364	io->mod->s_opt->opt_rr) io->mod->s_opt->opt_subst_param = 1;
1365	else io->mod->s_opt->opt_subst_param = 0;
1366
1367	Free(s);
1368	}
1369
1370	//////////////////////////////////////////////////////////////
1371	//////////////////////////////////////////////////////////////
1372
1373
1374	void Launch_Interface_Topo_Search(option *io)
1375	{
1376	char choix;
1377	char *s;
1378
1379	s = (char *)mCalloc(100,sizeof(char));
1380
1381	Clear();
1382	Print_Banner(stdout);
1383
1384	PhyML_Printf("\n\n");
1385
1386
1387	PhyML_Printf(" ....................... \n");
1388	PhyML_Printf(" Menu : Tree Searching \n");
1389	PhyML_Printf(" ............................. \n");
1390
1391
1392	PhyML_Printf("\n\n");
1393
1394	PhyML_Printf(" [+] "
1395	".................................... Next sub-menu\n");
1396
1397	PhyML_Printf(" [-] "
1398	"................................ Previous sub-menu\n");
1399
1400	PhyML_Printf(" [Y] "
1401	".............................. Launch the analysis\n");
1402
1403	PhyML_Printf("\n");
1404
1405	PhyML_Printf(" [O] "
1406	"........................... Optimise tree topology "
1407	" %-15s \n",
1408	(io->mod->s_opt->opt_topo)?("yes"):("no"));
1409
1410
1411	if(io->mod->s_opt->opt_topo)
1412	{
1413	switch(io->in_tree)
1414	{
1415	case 0: { strcpy(s,"BioNJ"); break; }
1416	case 1: { strcpy(s,"parsimony"); break; }
1417	case 2: { strcpy(s,"user tree"); break; }
1418	}
1419
1420	PhyML_Printf(" [U] "
1421	"........ Starting tree (BioNJ/parsimony/user tree) "
1422	" %-15s \n",s);
1423	}
1424	else
1425	{
1426	switch(io->in_tree)
1427	{
1428	case 0: { strcpy(s,"BioNJ"); break; }
1429	case 2: { strcpy(s,"user tree"); break; }
1430	}
1431
1432	PhyML_Printf(" [U] "
1433	"..................... Input tree (BioNJ/user tree) "
1434	" %-15s \n",s);
1435	}
1436
1437	if(io->mod->s_opt->opt_topo)
1438	{
1439	char *s;
1440
1441	s = (char *)mCalloc(T_MAX_OPTION,sizeof(char));
1442	if(io->mod->s_opt->topo_search == NNI_MOVE)
1443	{
1444	strcpy(s,"NNI moves (fast, approximate)\0");
1445	}
1446	else if(io->mod->s_opt->topo_search == SPR_MOVE)
1447	{
1448	strcpy(s,"SPR moves (slow, accurate)\0");
1449	}
1450	else if(io->mod->s_opt->topo_search == BEST_OF_NNI_AND_SPR)
1451	{
1452	strcpy(s,"Best of NNI and SPR \0");
1453	}
1454
1455	PhyML_Printf(" [S] "
1456	".................. Tree topology search operations "
1457	" %-15s \n",s);
1458
1459	Free(s);
1460
1461	if(io->mod->s_opt->topo_search != NNI_MOVE)
1462	{
1463	PhyML_Printf(" [R] "
1464	"........................ Add random starting trees "
1465	" %-15s \n",
1466	(io->mod->s_opt->random_input_tree)?("yes"):("no"));
1467
1468	if(io->mod->s_opt->random_input_tree)
1469	{
1470	PhyML_Printf(" [N] "
1471	".................. Number of random starting trees "
1472	" %-15d \n",io->mod->s_opt->n_rand_starts);
1473	}
1474	}
1475	}
1476	else
1477	{
1478	PhyML_Printf(" [L] "
1479	".......................... Optimise branch lengths "
1480	" %-15s \n",
1481	(io->mod->s_opt->opt_bl)?("yes"):("no"));
1482	}
1483
1484	PhyML_Printf("\n\n. Are these settings correct ? "
1485	"(type '+', '-', 'Y' or other letter for one to change) ");
1486
1487
1488	if(!scanf("%c",&choix)) Exit("\n");
1489	if(choix != '\n') getchar(); /* \n */
1490
1491	Free(s);
1492
1493	Uppercase(&choix);
1494
1495
1496	switch(choix)
1497	{
1498	case '-' :
1499	{
1500	io->curr_interface = INTERFACE_MODEL;
1501	break;
1502	}
1503	case '+' :
1504	{
1505	io->curr_interface = INTERFACE_BRANCH_SUPPORT;
1506	break;
1507	}
1508	case 'Y' :
1509	{
1510	io->ready_to_go = 1;
1511	break;
1512	}
1513	case 'U' :
1514	{
1515	io->in_tree++;
1516	if(!io->mod->s_opt->opt_topo)
1517	{
1518	if(io->in_tree == 1) io->in_tree = 2;
1519	}
1520	if(io->in_tree == 3) io->in_tree = 0;
1521	break;
1522	}
1523	case 'N' :
1524	{
1525	char *n;
1526	int n_trial;
1527
1528	PhyML_Printf("\n. Enter your number of starting trees > ");
1529	n = (char *)mCalloc(100,sizeof(char));
1530	Getstring_Stdin(n);
1531	n_trial = 0;
1532	while(atoi(n) < 1)
1533	{
1534	if(++n_trial > 10) Exit("\n== Err : the number of starting trees must be a positive integer\n");
1535	PhyML_Printf("\n. The number of starting trees must be a positive integer\n");
1536	PhyML_Printf("\n. Enter a new value > ");
1537	Getstring_Stdin(n);
1538	}
1539	io->mod->s_opt->n_rand_starts = atoi(n);
1540	io->n_trees = 1;
1541	Free(n);
1542	break;
1543	}
1544	case 'O' :
1545	{
1546	io->mod->s_opt->opt_topo = (io->mod->s_opt->opt_topo)?(0):(1);
1547	break;
1548	}
1549
1550	case 'L' :
1551	{
1552	if(!io->mod->s_opt->opt_topo)
1553	{
1554	io->mod->s_opt->opt_bl = (io->mod->s_opt->opt_bl)?(0):(1);
1555	}
1556	break;
1557	}
1558
1559	case 'S' :
1560	{
1561	if(io->mod->s_opt->topo_search == NNI_MOVE)
1562	{
1563	io->mod->s_opt->topo_search = SPR_MOVE;
1564	io->mod->s_opt->n_rand_starts = 1;
1565	io->mod->s_opt->random_input_tree = 0;
1566	io->mod->s_opt->greedy = 0;
1567	}
1568	else if(io->mod->s_opt->topo_search == SPR_MOVE)
1569	{
1570	io->mod->s_opt->topo_search = BEST_OF_NNI_AND_SPR;
1571	io->mod->s_opt->n_rand_starts = 1;
1572	io->mod->s_opt->random_input_tree = 0;
1573	io->mod->s_opt->greedy = 0;
1574	}
1575	else if(io->mod->s_opt->topo_search == BEST_OF_NNI_AND_SPR)
1576	{
1577	io->mod->s_opt->topo_search = NNI_MOVE;
1578	io->mod->s_opt->n_rand_starts = 1;
1579	io->mod->s_opt->random_input_tree = 0;
1580	io->mod->s_opt->greedy = 0;
1581	}
1582	break;
1583	}
1584	case 'R' :
1585	{
1586	io->mod->s_opt->random_input_tree = (io->mod->s_opt->random_input_tree)?(0):(1);
1587
1588	if(io->mod->s_opt->random_input_tree)
1589	{
1590	if(io->fp_in_tree) fclose(io->fp_in_tree);
1591	/* io->in_tree = 0; */
1592	io->n_trees = 1;
1593	io->mod->s_opt->n_rand_starts = 5;
1594
1595	strcpy(io->out_trees_file,io->in_align_file);
1596	strcat(io->out_trees_file,"_phyml_trees.txt");
1597	}
1598	break;
1599	}
1600	default :
1601	{
1602	break;
1603	}
1604	}
1605	}
1606
1607	//////////////////////////////////////////////////////////////
1608	//////////////////////////////////////////////////////////////
1609
1610
1611	void Launch_Interface_Branch_Support(option *io)
1612	{
1613	char choix;
1614	char *s;
1615
1616	s = (char *)mCalloc(100,sizeof(char));
1617
1618	Clear();
1619	Print_Banner(stdout);
1620
1621	PhyML_Printf("\n\n");
1622
1623	PhyML_Printf(" ....................... \n");
1624	PhyML_Printf(" Menu : Branch Support \n");
1625	PhyML_Printf(" ............................. \n");
1626
1627	PhyML_Printf("\n\n");
1628
1629	PhyML_Printf(" [+] "
1630	".................................... Next sub-menu\n");
1631
1632	PhyML_Printf(" [-] "
1633	"................................ Previous sub-menu\n");
1634
1635	PhyML_Printf(" [Y] "
1636	".............................. Launch the analysis\n");
1637
1638	PhyML_Printf("\n");
1639
1640
1641	strcpy(s,(io->mod->bootstrap > 0)?("yes"):("no"));
1642	if(io->mod->bootstrap > 0) sprintf(s+strlen(s)," (%d replicate%s)",
1643	io->mod->bootstrap,
1644	(io->mod->bootstrap>1)?("s"):(""));
1645
1646	/* PhyML_Printf(" [+] " */
1647	PhyML_Printf(" [B] "
1648	"................ Non parametric bootstrap analysis "
1649	" %-15s \n",s);
1650
1651	if(io->ratio_test == 0)
1652	{
1653	strcpy(s,"no");
1654	}
1655	else if(io->ratio_test == 1)
1656	{
1657	strcpy(s,"yes / aLRT statistics");
1658	}
1659	else if(io->ratio_test == 2)
1660	{
1661	strcpy(s,"yes / Chi2-based supports");
1662	}
1663	else if(io->ratio_test == 3)
1664	{
1665	strcpy(s,"yes / min of SH-like & Chi2-based supports");
1666	}
1667	else if(io->ratio_test == 4)
1668	{
1669	strcpy(s,"yes / SH-like supports");
1670	}
1671	else if(io->ratio_test == 5)
1672	{
1673	strcpy(s,"yes / aBayes supports");
1674	}
1675
1676
1677	/* PhyML_Printf(" [+] " */
1678	PhyML_Printf(" [A] "
1679	"................ Approximate likelihood ratio test "
1680	" %-15s \n",s);
1681
1682	PhyML_Printf("\n. Are these settings correct ? "
1683	"(type '+', '-', 'Y' or other letter for one to change) ");
1684
1685
1686	if(!scanf("%c",&choix)) Exit("\n");
1687	if(choix != '\n') getchar(); /* \n */
1688
1689	Uppercase(&choix);
1690
1691	Free(s);
1692
1693	switch(choix)
1694	{
1695	/* case '\n': */
1696	/* { */
1697	/* io->curr_interface++; */
1698	/* break; */
1699	/* } */
1700
1701	case 'B' :
1702	{
1703	if(io->mod->bootstrap > 0) io->mod->bootstrap = 0;
1704	else
1705	{
1706	char *r;
1707	char answer;
1708	int n_trial;
1709
1710	io->ratio_test = 0;
1711
1712	if(io->n_data_sets > 1)
1713	{
1714	PhyML_Printf("\n. Bootstrap option is not allowed with multiple data sets.\n");
1715	PhyML_Printf("\n. Type any key to exit.\n");
1716	if(!scanf("%c",&choix)) Exit("\n");
1717	Exit("\n");
1718	}
1719
1720
1721	PhyML_Printf("\n. Number of replicates > ");
1722	r = (char *)mCalloc(T_MAX_OPTION,sizeof(char));
1723	Getstring_Stdin(r);
1724	n_trial = 0;
1725	while((!atoi(r)) \|\| (atoi(r) < 0))
1726	{
1727	if(++n_trial > 10) Exit("\n== Err : the number of replicates must be a positive integer\n");
1728	PhyML_Printf("\n. The number of replicates must be a positive integer");
1729	PhyML_Printf("\n. Enter a new value > ");
1730	Getstring_Stdin(r);
1731	}
1732	io->mod->bootstrap = atoi(r);
1733
1734	PhyML_Printf("\n. Print bootstrap trees (and statistics) ? (%s) > ",
1735	(io->print_boot_trees)?("Y/n"):("y/N"));
1736
1737	if(!scanf("%c",&answer)) Exit("\n");
1738	if(answer == '\n') answer = (io->print_boot_trees)?('Y'):('N');
1739	else getchar();
1740
1741	switch(answer)
1742	{
1743	case 'Y' : case 'y' :
1744	{
1745	io->print_boot_trees = 1;
1746
1747	strcpy(io->out_boot_tree_file,io->in_align_file);
1748	strcat(io->out_boot_tree_file,"_phyml_boot_trees.txt");
1749	io->fp_out_boot_tree = Openfile(io->out_boot_tree_file,1);
1750
1751	strcpy(io->out_boot_stats_file,io->in_align_file);
1752	strcat(io->out_boot_stats_file,"_phyml_boot_stats.txt");
1753	io->fp_out_boot_stats = Openfile(io->out_boot_stats_file,1);
1754
1755	break;
1756	}
1757	case 'N' : case 'n' :
1758	{
1759	io->print_boot_trees = 0;
1760	io->fp_out_boot_tree = NULL;
1761	io->fp_out_boot_stats = NULL;
1762	break;
1763	}
1764	}
1765	Free(r);
1766	}
1767	break;
1768	}
1769	case 'A' :
1770	{
1771	io->mod->bootstrap = 0;
1772
1773	switch(io->ratio_test)
1774	{
1775	case 0 :
1776	{
1777	io->ratio_test = 1;
1778	break;
1779	}
1780	case 1 :
1781	{
1782	io->ratio_test = 2;
1783	break;
1784	}
1785	case 2 :
1786	{
1787	/* io->ratio_test = 3; */
1788	io->ratio_test = 4;
1789	break;
1790	}
1791	case 3 :
1792	{
1793	io->ratio_test = 4;
1794	break;
1795	}
1796	case 4 :
1797	{
1798	io->ratio_test = 5;
1799	break;
1800	}
1801	case 5 :
1802	{
1803	io->ratio_test = 0;
1804	break;
1805	}
1806	}
1807	break;
1808	}
1809
1810	case '-' :
1811	{
1812	io->curr_interface = INTERFACE_TOPO_SEARCH;
1813	break;
1814	}
1815	case '+' :
1816	{
1817	io->curr_interface = INTERFACE_DATA_TYPE;
1818	break;
1819	}
1820	case 'Y' :
1821	{
1822	io->ready_to_go = 1;
1823	break;
1824	}
1825	default : break;
1826	}
1827	}
1828
1829	//////////////////////////////////////////////////////////////
1830	//////////////////////////////////////////////////////////////
1831
1832	void Launch_Interface_Multigene(option *io)
1833	{
1834
1835	#ifdef PART
1836
1837	if((io->n_data_sets > 1) && (io->multigene))
1838	{
1839	int set, n_trial;
1840	char choix;
1841
1842	io->n_part = io->n_data_sets;
1843	io->st = (supert_tree *)PART_Make_Supert_tree_Light(io);
1844	io->st->n_part = io->n_data_sets;
1845
1846	For(set,io->n_part)
1847	{
1848	io->st->optionlist[set] = Make_Input();
1849	Set_Defaults_Input(io->st->optionlist[set]);
1850	Set_Defaults_Model(io->st->optionlist[set]->mod);
1851	Set_Defaults_Optimiz(io->st->optionlist[set]->mod->s_opt);
1852	io->st->optionlist[set]->curr_gt = set;
1853	PhyML_Printf("\n. Enter the sequence file name [data set %2d] > ",set+1); fflush(NULL);
1854	Getstring_Stdin(io->st->optionlist[set]->in_align_file);
1855	io->st->optionlist[set]->fp_in_align = Openfile(io->st->optionlist[set]->in_align_file,0);
1856	}
1857
1858
1859	PhyML_Printf("\n. Do you want to use your own initial tree ? [N/y] ");
1860	if(!scanf("%c", &choix)) Exit("\n");
1861	if(choix != '\n') getchar();
1862
1863	n_trial = 0;
1864	while((choix != 'Y') && (choix != 'y') &&
1865	(choix != 'N') && (choix != 'n'))
1866	{
1867	if(++n_trial > 10) Exit("\n== Err : wrong answers !");
1868	PhyML_Printf("\n. Do you want to use your own initial tree ? [N/y] ? ");
1869	if(!scanf("%c", &choix)) Exit("\n");
1870	if(choix == '\n') choix = 'N';
1871	else getchar();
1872	}
1873
1874	switch(choix)
1875	{
1876	case '\n' : break;
1877	case 'Y' : case 'y' :
1878	{
1879	io->in_tree = 2;
1880	PhyML_Printf("\n. Enter the name of the tree file > ");
1881	Getstring_Stdin(io->in_tree_file);
1882	io->fp_in_tree = Openfile(io->in_tree_file,0);
1883	break;
1884	}
1885	case 'N' : case 'n' :
1886	{
1887	io->in_tree = 0;
1888	break;
1889	}
1890	default : break;
1891	}
1892
1893	io->curr_gt = 0;
1894
1895	do
1896	{
1897	io->st->optionlist[io->curr_gt]->config_multigene = 1;
1898	do
1899	{
1900	switch(io->st->optionlist[io->curr_gt]->curr_interface)
1901	{
1902	case INTERFACE_DATA_TYPE :
1903	{
1904	Launch_Interface_Data_Type(io->st->optionlist[io->curr_gt]);
1905	break;
1906	}
1907	case INTERFACE_MODEL :
1908	{
1909	Launch_Interface_Model(io->st->optionlist[io->curr_gt]);
1910	break;
1911	}
1912	default :
1913	{
1914	PhyML_Printf("\n== Err in file %s at line %d\n\n",__FILE__,__LINE__);
1915	Exit("");
1916	break;
1917	}
1918	}
1919	}while(!io->st->optionlist[io->curr_gt]->ready_to_go);
1920	io->curr_gt++;
1921	}while(io->curr_gt < io->n_part);
1922	}
1923	io->ready_to_go = 1;
1924	PART_Fill_Model_Partitions_Table(io->st);
1925	#endif
1926	}

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source: trunk/GDE/PHYML20130708/phyml/src/interface.c

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