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source: tags/ms_r16q2/ARB_GDE/GDE_ParseMenu.cxx

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Last change on this file was 14435, checked in by westram, 8 years ago
fix macro ids for GDE items (broken by [14433])
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 23.5 KB

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1	#include "GDE_proto.h"
2
3	#include <aw_window.hxx>
4	#include <MultiFileReader.h>
5	#include <arb_file.h>
6
7	#include <cctype>
8
9	/*
10	Copyright (c) 1989, University of Illinois board of trustees. All rights
11	reserved. Written by Steven Smith at the Center for Prokaryote Genome
12	Analysis. Design and implementation guidance by Dr. Gary Olsen and Dr.
13	Carl Woese.
14
15	Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
16	All rights reserved.
17
18	Changed to fit into ARB by ARB development team.
19	*/
20
21
22	inline bool only_whitespace(const char *line) {
23	size_t white = strspn(line, " \t");
24	return line[white] == 0; // only 0 after leading whitespace
25	}
26
27	static char *readableItemname(const GmenuItem& i) {
28	return GBS_global_string_copy("%s/%s", i.parent_menu->label, i.label);
29	}
30
31	inline __ATTR__NORETURN void throwError(const char *msg) {
32	throw string(msg);
33	}
34
35	static __ATTR__NORETURN void throwParseError(const char *msg, const LineReader& file) {
36	fprintf(stderr, "\n%s:%zu: %s\n", file.getFilename().c_str(), file.getLineNumber(), msg);
37	fflush(stderr);
38	throwError(msg);
39	}
40
41	static __ATTR__NORETURN void throwItemError(const GmenuItem& i, const char *error, const LineReader& file) {
42	char *itemName = readableItemname(i);
43	const char *msg = GBS_global_string("[Above this line] Invalid item '%s' defined: %s", itemName, error);
44	free(itemName);
45	throwParseError(msg, file);
46	}
47
48	static void CheckItemConsistency(const GmenuItem *item, const LineReader& file) {
49	// (incomplete) consistency check.
50	// bailing out with ItemError() here, will make unit-test and arb-startup fail!
51
52	if (item) {
53	const GmenuItem& I = *item;
54	if (I.seqtype != '-' && I.numinputs<1) {
55	// Such an item would create a window where alignment/species selection is present,
56	// but no sequence export will take place.
57	//
58	// Pressing 'GO' would result in failure or deadlock.
59	throwItemError(I, "item defines seqtype ('seqtype:' <> '-'), but is lacking input-specification ('in:')", file);
60	}
61	if (I.seqtype == '-' && I.numinputs>0) {
62	// Such an item would create a window where alignment/species selection has no GUI-elements,
63	// but sequences are exported (generating a corrupt sequence file)
64	//
65	// Pressing 'GO' would result in failure.
66	throwItemError(I, "item defines no seqtype ('seqtype:' = '-'), but defines input-specification ('in:')", file);
67	}
68	}
69	}
70
71	#define THROW_IF_NO(ptr,name) do { if (ptr == NULL) throwParseError(GBS_global_string("'%s' used w/o '" name "'", head), in); } while(0)
72
73	#define THROW_IF_NO_MENU() THROW_IF_NO(thismenu, "menu")
74	#define THROW_IF_NO_ITEM() THROW_IF_NO(thisitem, "item")
75	#define THROW_IF_NO_ARG() THROW_IF_NO(thisarg, "arg")
76	#define THROW_IF_NO_INPUT() THROW_IF_NO(thisinput, "in")
77	#define THROW_IF_NO_OUTPUT() THROW_IF_NO(thisoutput, "out")
78
79	static void ParseMenus(LineReader& in) {
80	/* parses menus via LineReader (contains ALL found menu-files) and
81	* assemble an internal representation of the menu/menu-item hierarchy.
82	*
83	* please document changes in ../HELP_SOURCE/oldhelp/gde_menus.hlp
84	*/
85
86	memset((char)&menu[0], 0, sizeof(Gmenu)GDEMAXMENU);
87
88	int curarg = 0;
89	int curinput = 0;
90	int curoutput = 0;
91
92	Gmenu *thismenu = NULL;
93	GmenuItem *thisitem = NULL;
94	GmenuItemArg *thisarg = NULL;
95	GfileFormat *thisinput = NULL;
96	GfileFormat *thisoutput = NULL;
97
98	bool thismenu_firstOccurance = true;
99
100	int j;
101	char temp[GBUFSIZ];
102	char head[GBUFSIZ];
103	char tail[GBUFSIZ];
104
105	char *resize;
106
107	string lineStr;
108
109	while (in.getLine(lineStr)) {
110	gde_assert(lineStr.length()<GBUFSIZ); // otherwise buffer usage may fail
111
112	const char *in_line = lineStr.c_str();
113	if (in_line[0] == '#' \|\| (in_line[0] && in_line[1] == '#')) {
114	; // skip line
115	}
116	else if (only_whitespace(in_line)) {
117	; // skip line
118	}
119	else {
120	splitEntry(in_line, head, temp);
121
122	// menu: chooses menu to use (may occur multiple times with same label!)
123	if (strcmp(head, "menu") == 0) {
124	int curmenu = -1;
125	for (j=0; j<num_menus && curmenu == -1; j++) {
126	if (strcmp(temp, menu[j].label) == 0) curmenu=j;
127	}
128
129	thismenu_firstOccurance = curmenu == -1;
130
131	// If menu not found, make a new one
132	if (thismenu_firstOccurance) {
133	curmenu = num_menus++;
134	thismenu = &menu[curmenu];
135	thismenu->label = (char*)calloc(strlen(temp)+1, sizeof(char));
136
137	(void)strcpy(thismenu->label, temp);
138	thismenu->numitems = 0;
139	thismenu->active_mask = AWM_ALL;
140	}
141	else {
142	thismenu = &menu[curmenu];
143	}
144
145	CheckItemConsistency(thisitem, in);
146	thisitem = NULL;
147	thisarg = NULL;
148	thisoutput = NULL;
149	thisinput = NULL;
150	}
151	else if (strcmp(head, "menumask") == 0) {
152	THROW_IF_NO_MENU();
153	AW_active wanted_mask = strcmp("expert", temp) == 0 ? AWM_EXP : AWM_ALL;
154	if (!thismenu_firstOccurance && thismenu->active_mask != wanted_mask) {
155	throwParseError(GBS_global_string("menumask has inconsistent definitions (in different definitions of menu '%s')", thismenu->label), in);
156	}
157	thismenu->active_mask = wanted_mask;
158	}
159	else if (strcmp(head, "menumeta") == 0) {
160	THROW_IF_NO_MENU();
161	char wanted_meta = temp[0];
162	if (!thismenu_firstOccurance && thismenu->meta != wanted_meta) {
163	if (wanted_meta != 0) {
164	if (thismenu->meta != 0) {
165	throwParseError(GBS_global_string("menumeta has inconsistent definitions (in different definitions of menu '%s')", thismenu->label), in);
166	}
167	else {
168	thismenu->meta = wanted_meta;
169	}
170	}
171	}
172	else {
173	thismenu->meta = wanted_meta;
174	}
175	}
176	// item: chooses menu item to use
177	else if (strcmp(head, "item") == 0) {
178	CheckItemConsistency(thisitem, in);
179
180	THROW_IF_NO_MENU();
181
182	curarg = -1;
183	curinput = -1;
184	curoutput = -1;
185
186	int curitem = thismenu->numitems++;
187
188	// Resize the item list for this menu (add one item)
189	if (curitem == 0) {
190	resize = (char*)GB_calloc(1, sizeof(GmenuItem));
191	}
192	else {
193	resize = (char )realloc((char )thismenu->item, thismenu->numitems*sizeof(GmenuItem));
194	}
195
196	thismenu->item = (GmenuItem*)resize;
197
198	thisitem = &(thismenu->item[curitem]);
199
200	thisitem->numargs = 0;
201	thisitem->numoutputs = 0;
202	thisitem->numinputs = 0;
203	thisitem->label = strdup(temp);
204	thisitem->method = NULL;
205	thisitem->input = NULL;
206	thisitem->output = NULL;
207	thisitem->arg = NULL;
208	thisitem->meta = '\0';
209	thisitem->seqtype = '-'; // no default sequence export
210	thisitem->aligned = false;
211	thisitem->help = NULL;
212
213	thisitem->parent_menu = thismenu;
214	thisitem->aws = NULL; // no window opened yet
215	thisitem->active_mask = AWM_ALL;
216	thisitem->popup = NULL;
217
218	for (int i = 0; i<curitem; ++i) {
219	if (strcmp(thismenu->item[i].label, thisitem->label) == 0) {
220	throwParseError(GBS_global_string("Duplicated item label '%s'", thisitem->label), in);
221	}
222	}
223
224	thisarg = NULL;
225	}
226
227	// itemmethod: generic command line generated by this item
228	else if (strcmp(head, "itemmethod") == 0) {
229	THROW_IF_NO_ITEM();
230	thisitem->method = (char*)calloc(strlen(temp)+1, sizeof(char));
231
232	{
233	char *to = thisitem->method;
234	char *from = temp;
235	char last = 0;
236	char c;
237
238	do {
239	c = *from++;
240	if (c == '@' && last == '@') {
241	// replace "@@" with "'"
242	// [WHY_USE_DOUBLE_AT]
243	// - cant use 1 single quote ("'"). Things inside will not be preprocessed correctly.
244	// - cant use 2 single quotes ("''") any longer. clang fails on OSX.
245	to[-1] = '\'';
246	}
247	else {
248	*to++ = c;
249	}
250	last = c;
251	}
252	while (c!=0);
253	}
254
255	}
256	// Help file
257	else if (strcmp(head, "itemhelp") == 0) {
258	THROW_IF_NO_ITEM();
259	thisitem->help = GBS_string_eval(temp, ".help=agde_1.hlp", 0);
260	}
261	// Meta key equiv
262	else if (strcmp(head, "itemmeta") == 0) {
263	THROW_IF_NO_ITEM();
264	thisitem->meta = temp[0];
265	}
266	else if (strcmp(head, "itemmask") == 0) {
267	THROW_IF_NO_ITEM();
268	if (strcmp("expert", temp) == 0) thisitem->active_mask = AWM_EXP;
269	}
270	// Sequence type restriction
271	else if (strcmp(head, "seqtype") == 0) {
272	THROW_IF_NO_ITEM();
273	thisitem->seqtype = toupper(temp[0]);
274	/* 'A' -> amino acids,
275	* 'N' -> nucleotides,
276	* '-' -> don't select sequences,
277	* otherwise any alignment
278	*/
279	}
280	/* arg: defines the symbol for a command line argument.
281	* this is used for substitution into the itemmethod
282	* definition.
283	*/
284
285	else if (strcmp(head, "arg") == 0) {
286	THROW_IF_NO_ITEM();
287	curarg=thisitem->numargs++;
288	if (curarg == 0) resize = (char*)calloc(1, sizeof(GmenuItemArg));
289	else resize = (char )realloc((char )thisitem->arg, thisitem->numargs*sizeof(GmenuItemArg));
290
291	memset((char )resize + (thisitem->numargs-1)sizeof(GmenuItemArg), 0, sizeof(GmenuItemArg));
292
293	(thisitem->arg) = (GmenuItemArg*)resize;
294	thisarg = &(thisitem->arg[curarg]);
295	thisarg->symbol = (char*)calloc(strlen(temp)+1, sizeof(char));
296	(void)strcpy(thisarg->symbol, temp);
297
298	thisarg->type = 0;
299	thisarg->min = 0.0;
300	thisarg->max = 0.0;
301	thisarg->numchoices = 0;
302	thisarg->choice = NULL;
303	thisarg->textvalue = NULL;
304	thisarg->ivalue = 0;
305	thisarg->fvalue = 0.0;
306	thisarg->label = 0;
307	thisarg->active_mask= AWM_ALL;
308	}
309	// argtype: Defines the type of argument (menu,chooser, text, slider)
310	else if (strcmp(head, "argtype") == 0) {
311	THROW_IF_NO_ARG();
312	int arglen = -1;
313	if (strncmp(temp, "text", (arglen = 4)) == 0) {
314	thisarg->type = TEXTFIELD;
315	freedup(thisarg->textvalue, "");
316
317	if (temp[arglen] == 0) thisarg->textwidth = TEXTFIELDWIDTH; // only 'text'
318	else {
319	if (temp[arglen] != '(' \|\| temp[strlen(temp)-1] != ')') {
320	sprintf(head, "Unknown argtype '%s' -- syntax: text(width) e.g. text(20)", temp);
321	throwParseError(head, in);
322	}
323	thisarg->textwidth = atoi(temp+arglen+1);
324	if (thisarg->textwidth<1) {
325	sprintf(head, "Illegal textwidth specified in '%s'", temp);
326	throwParseError(head, in);
327	}
328	}
329	}
330	else if (strcmp(temp, "choice_list") == 0) thisarg->type = CHOICE_LIST;
331	else if (strcmp(temp, "choice_menu") == 0) thisarg->type = CHOICE_MENU;
332	else if (strcmp(temp, "chooser") == 0) thisarg->type = CHOOSER;
333	else if (strcmp(temp, "filename") == 0) {
334	thisarg->type = FILE_SELECTOR;
335	freedup(thisarg->textvalue, "");
336	}
337	else if (strcmp(temp, "sai") == 0) thisarg->type = CHOICE_SAI;
338	else if (strcmp(temp, "slider") == 0) thisarg->type = SLIDER;
339	else if (strcmp(temp, "tree") == 0) thisarg->type = CHOICE_TREE;
340	else if (strcmp(temp, "weights") == 0) thisarg->type = CHOICE_WEIGHTS;
341	else {
342	sprintf(head, "Unknown argtype '%s'", temp);
343	throwParseError(head, in);
344	}
345	}
346	/* argtext: The default text value of the symbol.
347	* $argument is replaced by this value if it is not
348	* changed in the dialog box by the user.
349	*/
350	else if (strcmp(head, "argtext") == 0) {
351	THROW_IF_NO_ARG();
352	freedup(thisarg->textvalue, temp);
353	}
354	/* arglabel: Text label displayed in the dialog box for
355	* this argument. It should be a descriptive label.
356	*/
357	else if (strcmp(head, "arglabel") == 0) {
358	THROW_IF_NO_ARG();
359	thisarg->label = GBS_string_eval(temp, "\\\\n=\\n", 0);
360	}
361	/* Argument choice values use the following notation:
362	*
363	* argchoice:Displayed value:Method
364	*
365	* Where "Displayed value" is the label displayed in the dialog box
366	* and "Method" is the value passed back on the command line.
367	*/
368	else if (strcmp(head, "argchoice") == 0) {
369	THROW_IF_NO_ARG();
370	splitEntry(temp, head, tail);
371
372	int curchoice = thisarg->numchoices++;
373	if (curchoice == 0) resize = (char*)calloc(1, sizeof(GargChoice));
374	else resize = (char)realloc((char )thisarg->choice, thisarg->numchoices*sizeof(GargChoice));
375
376	thisarg->choice = (GargChoice*)resize;
377
378	(thisarg->choice[curchoice].label) = NULL;
379	(thisarg->choice[curchoice].method) = NULL;
380	(thisarg->choice[curchoice].label) = (char*)calloc(strlen(head)+1, sizeof(char));
381	(thisarg->choice[curchoice].method) = (char*)calloc(strlen(tail)+1, sizeof(char));
382
383	(void)strcpy(thisarg->choice[curchoice].label, head);
384	(void)strcpy(thisarg->choice[curchoice].method, tail);
385	}
386	// argmin: Minimum value for a slider
387	else if (strcmp(head, "argmin") == 0) {
388	THROW_IF_NO_ARG();
389	(void)sscanf(temp, "%lf", &(thisarg->min));
390	}
391	// argmax: Maximum value for a slider
392	else if (strcmp(head, "argmax") == 0) {
393	THROW_IF_NO_ARG();
394	(void)sscanf(temp, "%lf", &(thisarg->max));
395	}
396	// argvalue: default value for a slider
397	else if (strcmp(head, "argvalue") == 0) {
398	THROW_IF_NO_ARG();
399	if (thisarg->type == TEXT) {
400	freedup(thisarg->textvalue, temp);
401	}
402	else {
403	(void)sscanf(temp, "%lf", &(thisarg->fvalue));
404	thisarg->ivalue = (int) thisarg->fvalue;
405	}
406	}
407	else if (strcmp(head, "argmask") == 0) {
408	THROW_IF_NO_ARG();
409	if (strcmp("expert", temp) == 0) thisarg->active_mask = AWM_EXP;
410	}
411	// in: Input file description
412	else if (strcmp(head, "in") == 0) {
413	THROW_IF_NO_ITEM();
414	curinput = (thisitem->numinputs)++;
415	if (curinput == 0) resize = (char*)calloc(1, sizeof(GfileFormat));
416	else resize = (char )realloc((char )thisitem->input, (thisitem->numinputs)*sizeof(GfileFormat));
417
418	thisitem->input = (GfileFormat*)resize;
419	thisinput = &(thisitem->input)[curinput];
420	thisinput->save = false;
421	thisinput->format = 0;
422	thisinput->symbol = strdup(temp);
423	thisinput->name = NULL;
424	thisinput->typeinfo = BASIC_TYPEINFO;
425	}
426	else if (strcmp(head, "informat") == 0) {
427	THROW_IF_NO_INPUT();
428	if (Find(temp, "genbank")) thisinput->format = GENBANK;
429	else if (Find(temp, "flat")) thisinput->format = NA_FLAT;
430	else throwParseError(GBS_global_string("Unknown informat '%s' (allowed 'genbank' or 'flat')", temp), in);
431	}
432	else if (strcmp(head, "insave") == 0) {
433	THROW_IF_NO_INPUT();
434	thisinput->save = true;
435	}
436	else if (strcmp(head, "intyped") == 0) {
437	THROW_IF_NO_INPUT();
438	if (Find(temp, "detailed")) thisinput->typeinfo = DETAILED_TYPEINFO;
439	else if (Find(temp, "basic")) thisinput->typeinfo = BASIC_TYPEINFO;
440	else throwParseError(GBS_global_string("Unknown value '%s' for 'intyped' (known: 'detailed', 'basic')", temp), in);
441	}
442	// out: Output file description
443	else if (strcmp(head, "out") == 0) {
444	THROW_IF_NO_ITEM();
445	curoutput = (thisitem->numoutputs)++;
446
447	if (curoutput == 0) resize = (char*)calloc(1, sizeof(GfileFormat));
448	else resize = (char )realloc((char )thisitem->output, (thisitem->numoutputs)*sizeof(GfileFormat));
449
450	thisitem->output = (GfileFormat*)resize;
451	thisoutput = &(thisitem->output)[curoutput];
452	thisoutput->save = false;
453	thisoutput->format = 0;
454	thisoutput->symbol = strdup(temp);
455	thisoutput->name = NULL;
456	}
457	else if (strcmp(head, "outformat") == 0) {
458	THROW_IF_NO_OUTPUT();
459	if (Find(temp, "genbank")) thisoutput->format = GENBANK;
460	else if (Find(temp, "gde")) thisoutput->format = GDE;
461	else if (Find(temp, "flat")) thisoutput->format = NA_FLAT;
462	else throwParseError(GBS_global_string("Unknown outformat '%s' (allowed 'genbank', 'gde' or 'flat')", temp), in);
463	}
464	else if (strcmp(head, "outaligned") == 0) {
465	THROW_IF_NO_OUTPUT();
466	if (Find(temp, "yes")) thisitem->aligned = true;
467	else throwParseError(GBS_global_string("Unknown outaligned '%s' (allowed 'yes' or skip entry)", temp), in);
468	}
469	else if (strcmp(head, "outsave") == 0) {
470	THROW_IF_NO_OUTPUT();
471	thisoutput->save = true;
472	}
473	else {
474	throwParseError(GBS_global_string("No known GDE-menu-command found (line='%s')", in_line), in);
475	}
476	}
477	}
478
479	CheckItemConsistency(thisitem, in);
480
481	gde_assert(num_menus>0); // if this fails, the file arb.menu contained no menus (maybe file has zero size)
482	}
483
484	GB_ERROR LoadMenus() {
485	/*! Load menu config files
486	*
487	* loads all '*.menu' from "$ARBHOME/lib/gde" and "$ARB_PROP/gde"
488	*/
489
490	GB_ERROR error = NULL;
491	StrArray files;
492	{
493	char *user_menu_dir = strdup(GB_path_in_arbprop("gde"));
494
495	if (!GB_is_directory(user_menu_dir)) {
496	error = GB_create_directory(user_menu_dir);
497	}
498	gde_assert(!GB_have_error());
499
500	GBS_read_dir(files, user_menu_dir, "/\\.menu$/");
501	GBS_read_dir(files, GB_path_in_ARBLIB("gde"), "/\\.menu$/");
502
503	if (GB_have_error()) error = GB_await_error();
504
505	free(user_menu_dir);
506	}
507
508	if (!error) {
509	MultiFileReader menus(files);
510	error = menus.get_error();
511	if (!error) {
512	try {
513	ParseMenus(menus);
514	}
515	catch (const string& err) {
516	error = GBS_static_string(err.c_str());
517	}
518	}
519	}
520
521	if (error) error = GBS_global_string("Error while loading menus: %s", error);
522	return error;
523	}
524
525	bool Find(const char target, const char key) {
526	// Search the target string for the given key
527	return strstr(target, key) ? true : false;
528	}
529
530	int Find2(const char target, const char key) {
531	/* Like Find(), but returns the index of the leftmost
532	* occurrence, and -1 if not found.
533	*/
534	const char *found = strstr(target, key);
535	return found ? int(found-target) : -1;
536	}
537
538	// --------------------------------------------------------------------------------
539
540	inline void trim(char *str) {
541	int s = 0;
542	int d = 0;
543
544	while (isspace(str[s])) ++s;
545	while (str[s]) str[d++] = str[s++];
546
547	str[d] = 0;
548	while (d>0 && isspace(str[d-1])) str[--d] = 0;
549	}
550
551	void splitEntry(const char input, char head, char *tail) {
552	/*! Split "this:that[:the_other]" into: "this" and "that[:the_other]"
553	*/
554	const char *colon = strchr(input, ':');
555	if (colon) {
556	int len = colon-input;
557	memcpy(head, input, len);
558	head[len] = 0;
559
560	strcpy(tail, colon+1);
561
562	trim(tail);
563	}
564	else {
565	strcpy(head, input);
566	}
567	trim(head);
568	}
569
570	// --------------------------------------------------------------------------------
571
572	#ifdef UNIT_TESTS
573	#ifndef TEST_UNIT_H
574	#include <test_unit.h>
575	#endif
576
577	void TEST_load_menu() {
578	// very basic test: just detects failing assertions, crashes and errors
579
580	gb_getenv_hook old = GB_install_getenv_hook(arb_test::fakeenv);
581	{
582	// ../UNIT_TESTER/run/homefake/
583
584	TEST_EXPECT_NO_ERROR(LoadMenus());
585
586	// basic check of loaded data (needs to be adapted if menus change):
587	TEST_EXPECT_EQUAL(num_menus, 13);
588
589	string menus;
590	string menuitems;
591	for (int m = 0; m<num_menus; ++m) {
592	menus = menus + menu[m].label + ";";
593	menuitems += GBS_global_string("%i;", menu[m].numitems);
594	}
595
596	TEST_EXPECT_EQUAL(menus,
597	"Import;Export;Print;Align;Network;SAI;Incremental phylogeny;Phylogeny Distance Matrix;"
598	"Phylogeny max. parsimony;Phylogeny max. Likelihood EXP;Phylogeny max. Likelihood;Phylogeny (Other);User;");
599	TEST_EXPECT_EQUAL(menuitems, "3;1;2;10;1;1;1;3;2;1;8;5;0;");
600	}
601	TEST_EXPECT_EQUAL((void)arb_test::fakeenv, (void)GB_install_getenv_hook(old));
602	}
603
604	#endif // UNIT_TESTS
605
606	// --------------------------------------------------------------------------------
607

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