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source: tags/ms_r17q3/ARBDB/adlang1.cxx

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Last change on this file was 16434, checked in by westram, 7 years ago
reintegrates 'aci' into 'trunk' fix/tweak parameter-handling of ACI commands adds: log:branches/aci@16427:16433
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 90.0 KB

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1	// =============================================================== //
2	// //
3	// File : adlang1.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "gb_aci_impl.h"
12	#include "gb_key.h"
13
14	#include "TreeNode.h"
15
16	#include <aw_awar_defs.hxx>
17
18	#include <adGene.h>
19	#include <ad_cb.h>
20
21	#include <arb_defs.h>
22	#include <arb_strbuf.h>
23	#include <arb_file.h>
24	#include <arb_strarray.h>
25	#include <arb_sort.h>
26
27	#include <cctype>
28	#include <cmath>
29	#include <algorithm>
30
31	// hook for 'export_sequence'
32
33	static gb_export_sequence_cb get_export_sequence = 0;
34
35	NOT4PERL void GB_set_export_sequence_hook(gb_export_sequence_cb escb) {
36	gb_assert(!get_export_sequence \|\| !escb); // avoid unwanted overwrite
37	get_export_sequence = escb;
38	}
39
40	using namespace GBL_IMPL;
41
42	namespace GBL_IMPL {
43	// global ACI/SRT debug switch
44	int traceACI = 0;
45	int traceIndent = 0;
46
47	void print_trace(const char *text) {
48	FILE *DUMPOUT = stdout;
49
50	gb_assert(traceACI>0);
51	if (traceIndent>0) {
52	ConstStrArray line;
53	GBT_split_string(line, text, "\n", true);
54	for (unsigned L = 0; L<line.size(); ++L) {
55	for (int i = 0; i<traceIndent; ++i) {
56	fputc(' ', DUMPOUT);
57	}
58	fputs(line[L], DUMPOUT);
59	fputc('\n', DUMPOUT);
60	}
61	}
62	else {
63	fputs(text, DUMPOUT);
64	}
65	fflush(DUMPOUT);
66	}
67
68	GB_ERROR trace_params(const GBL_streams& param, gbl_param ppara, const char com) {
69	GB_ERROR error = 0;
70	int i;
71
72	int argc = param.size();
73	for (i=0; i<argc; i++) {
74	gbl_param *para;
75	const char *argument = param.get(i);
76
77	for (para = ppara; para && !error; para = para->next) {
78	if (para->param_name) { // NULL means param is inactive (see PARAM_IF)
79	int len = strlen(para->param_name);
80
81	if (strncmp(argument, para->param_name, len) == 0) {
82	const char *value = argument+len; // set to start of value
83
84	if (para->type == GB_BIT) {
85	// GB_BIT is special cause param_name does NOT contain trailing '='
86
87	if (!value[0]) { // only 'name' -> handle like 'name=1'
88	;
89	}
90	else if (value[0] == '=') {
91	value++;
92	}
93	}
94
95	switch (para->type) {
96	case GB_STRING:
97	(const char *)para->varaddr = value;
98	break;
99
100	case GB_INT:
101	STATIC_ASSERT(sizeof(int) == sizeof(nat)); // assumed by GBL_PARAM_UINT
102	(int )para->varaddr = atoi(value);
103	break;
104
105	case GB_BIT:
106	// 'param=' is same as 'param' or 'param=1' (historical reason, don't change)
107	(int )para->varaddr = (value[0] ? atoi(value) : 1);
108	break;
109
110	case GB_BYTE:
111	(char )para->varaddr = *value; // this may use the terminal zero-byte (e.g. for p1 in 'p0=0,p1=,p2=2' )
112	if (value[0] && value[1]) { // found at least 2 chars
113	GB_warningf("Only one character expected in value '%s' of param '%s' - rest is ignored", value, para->param_name);
114	}
115	break;
116
117	default:
118	gb_assert(0);
119	error = GBS_global_string("Parameter '%s': Unknown type %i (internal error)", para->param_name, para->type);
120	break;
121	}
122	break; // accept parameter
123	}
124	}
125	}
126
127	if (!error && !para) { // no parameter found for argument
128	int pcount = 0;
129	gbl_param **params;
130	int k;
131	char *res;
132	GBS_strstruct *str = GBS_stropen(1000);
133	GB_ERROR err;
134
135
136	for (para = ppara; para; para = para->next) pcount++;
137	ARB_calloc(params, pcount);
138	for (k = 0, para = ppara; para; para = para->next) params[k++] = para;
139
140
141	for (pcount--; pcount>=0; pcount--) {
142	para = params[pcount];
143	if (para->param_name) {
144	GBS_strcat(str, " ");
145	GBS_strcat(str, para->param_name);
146	switch (para->type) {
147	case GB_STRING: GBS_strcat(str, "STRING"); break;
148	case GB_INT: GBS_strcat(str, "INT"); break;
149	case GB_FLOAT: GBS_strcat(str, "FLOAT"); break;
150	case GB_BYTE: GBS_strcat(str, "CHAR"); break;
151	case GB_BIT: GBS_strcat(str, " "); break;
152	default: gb_assert (0); GBS_strcat(str, "????"); break;
153	}
154	GBS_strcat(str, "\t\t;");
155	GBS_strcat(str, para->help_text);
156	GBS_strcat(str, "\n");
157	}
158	}
159	freenull(params);
160	res = GBS_strclose(str);
161	err = GB_export_errorf("Unknown Parameter '%s' in command '%s'\n PARAMETERS:\n%s", argument, com, res);
162	free(res);
163	return err;
164	}
165	}
166
167	return error;
168	}
169	};
170
171
172
173	// -------------------------
174	// String functions
175
176	static int gbl_stricmp(const char s1, const char s2) {
177	// case insensitive strcmp
178	int i;
179	for (i = 0; ; ++i) {
180	char c1 = tolower(s1[i]);
181	char c2 = tolower(s2[i]);
182
183	if (c1 == c2) {
184	if (!c1) break; // equal strings
185	}
186	else {
187	if (c1<c2) return -1;
188	return 1;
189	}
190	}
191	return 0;
192	}
193	static int gbl_strincmp(const char s1, const char s2, int size2) {
194	// case insensitive strcmp
195	int i;
196	for (i = 0; i<size2; ++i) {
197	char c1 = tolower(s1[i]);
198	char c2 = tolower(s2[i]);
199
200	if (c1 == c2) {
201	if (!c1) break; // equal strings
202	}
203	else {
204	if (c1<c2) return -1;
205	return 1;
206	}
207	}
208	return 0;
209	}
210	static const char gbl_stristr(const char haystack, const char *needle) {
211	// case insensitive strstr
212	const char *hp = haystack;
213	char c1 = toupper(needle[0]);
214	char c2 = tolower(c1);
215	int needle_size = strlen(needle);
216
217	if (c1 == c2) {
218	hp = strchr(hp, c1);
219	while (hp) {
220	if (gbl_strincmp(hp, needle, needle_size) == 0) return hp;
221	hp = strchr(hp+1, c1);
222	}
223	}
224	else {
225	while (hp) {
226	const char *h1 = strchr(hp, c1);
227	const char *h2 = strchr(hp, c2);
228
229	if (h1 && h2) {
230	if (h1<h2) {
231	if (gbl_strincmp(h1, needle, needle_size) == 0) return h1;
232	hp = h1+1;
233	}
234	else {
235	gb_assert(h1>h2);
236	if (gbl_strincmp(h2, needle, needle_size) == 0) return h2;
237	hp = h2+1;
238	}
239	}
240	else {
241	if (h1) { hp = h1; }
242	else if (h2) { hp = h2; c1 = c2; }
243	else { hp = 0; }
244
245	while (hp) {
246	if (gbl_strincmp(hp, needle, needle_size) == 0) return hp;
247	hp = strchr(hp+1, c1);
248	}
249	}
250	}
251	}
252	return 0;
253	}
254
255	inline int approve_pos(int pos, int len) { return pos<0 ? (-pos<len ? len+pos : 0) : pos; }
256
257	static GB_ERROR gbl_mid_streams(const GBL_streams& arg_input, GBL_streams& arg_out, int start, int end) {
258	// used as well to copy all streams (e.g. by 'dd')
259	for (int i=0; i<arg_input.size(); i++) {
260	const char *p = arg_input.get(i);
261	int len = strlen(p);
262
263	int s = approve_pos(start, len);
264	int e = approve_pos(end, len);
265
266	char *res;
267	if (s >= len \|\| e<s) {
268	res = ARB_strdup("");
269	}
270	else {
271	gb_assert(s >= 0);
272	res = ARB_strpartdup(p+s, p+e);
273	}
274	arg_out.insert(res);
275	}
276	return 0;
277	}
278
279	static GB_ERROR gbl_trace(GBL_command_arguments *args) {
280	int tmp_trace;
281
282	EXPECT_PARAMS(args, 1, "0\|1");
283
284	tmp_trace = atoi(args->get_param(0));
285	if (tmp_trace<0 \|\| tmp_trace>1) return GBS_global_string("Illegal value %i to trace", tmp_trace);
286
287	if (tmp_trace != traceACI) {
288	traceACI = 1;
289	print_trace(GBS_global_string("%sctivated ACI trace\n", tmp_trace ? "A" : "De-a"));
290	traceACI = tmp_trace;
291	}
292
293	return gbl_mid_streams(args->input, args->output, 0, -1); // copy all streams
294	}
295
296	/* ---------------------------------------------------------------------------------------
297	* Binary operators work on pairs of values.
298	* Three different operational modes are implemented for all binary operators:
299	*
300	* 1. inputstreams\|operator
301	*
302	* The number of inputstreams has to be even and the operator will be
303	* applied to pairs of them.
304	*
305	* Example : a;b;c;d;e;f \| plus
306	* Result : a+b;c+d;e+f
307	*
308	* 2. inputstreams\|operator(x)
309	*
310	* The number of inputstreams has to be at least 1.
311	* The operator is applied to each inputstream.
312	*
313	* Example : a;b;c \| plus(d)
314	* Result : a+d;b+d;c+d
315	*
316	* 3. operator(x, y)
317	*
318	* @@@ this decription does not match behavior!
319	* @@@ check description in helpfile as well
320	*
321	* Inputstreams will be ignored and the operator is applied
322	* to the arguments
323	*
324	* Example : a;b \| plus(c,d)
325	* Result : c+d
326	*/
327
328	template <typename T>
329	GB_ERROR gbl_apply_binary_operator(GBL_command_arguments args, char (op)(const char , const char *, T), T client_data) {
330	GB_ERROR error = 0;
331	switch (args->param_count()) {
332	case 0:
333	gb_assert(args->set_params_checked());
334	if (args->input.size() == 0) error = "Expect at least two input streams if called with 0 parameters";
335	else if (args->input.size()%2) error = "Expect an even number of input streams if called with 0 parameters";
336	else {
337	int inputpairs = args->input.size()/2;
338	int i;
339	for (i = 0; i<inputpairs; ++i) {
340	PASS_2_OUT(args, op(args->input.get(i2), args->input.get(i2+1), client_data));
341	}
342	}
343	break;
344
345	case 1:
346	gb_assert(args->set_params_checked());
347	if (args->input.size() == 0) error = "Expect at least one input stream if called with 1 parameter";
348	else {
349	int i;
350	const char *argument = args->get_param(0);
351	for (i = 0; i<args->input.size(); ++i) {
352	PASS_2_OUT(args, op(args->input.get(i), argument, client_data));
353	}
354	}
355	break;
356
357	case 2:
358	gb_assert(args->set_params_checked());
359	for (int i = 0; i<args->input.size(); ++i) {
360	char *result1 = args->get_callEnv().interpret_subcommand(args->input.get(i), args->get_param(0)); // @@@ EVALUATED_PARAM (#768)
361	if (!result1) error = GB_await_error();
362	else {
363	char *result2 = args->get_callEnv().interpret_subcommand(args->input.get(i), args->get_param(1)); // @@@ EVALUATED_PARAM (#768)
364	if (!result2) error = GB_await_error();
365	else {
366	PASS_2_OUT(args, op(result1, result2, client_data));
367	free(result2);
368	}
369	free(result1);
370	}
371	}
372	break;
373
374	default:
375	error = check_optional_parameters(args, 0, NULL, 2, "Expr1[,Expr2]", true, false);
376	break;
377	}
378
379	return error;
380	}
381
382	// --------------------------------
383	// escape/unescape strings
384
385	static char unEscapeString(const char escapedString) {
386	// replaces all \x by x
387	char *result = nulldup(escapedString);
388	char *to = result;
389	char *from = result;
390
391	while (1) {
392	char c = *from++;
393	if (!c) break;
394
395	if (c=='\\') {
396	to++ = from++;
397	}
398	else {
399	*to++ = c;
400	}
401	}
402	*to = 0;
403	return result;
404	}
405	static char escapeString(const char unescapedString) {
406	// replaces all '\' and '"' by '\\' and '\"'
407	int len = strlen(unescapedString);
408	char result = ARB_alloc<char>(2len+1);
409	char *to = result;
410	const char *from = unescapedString;
411
412	while (1) {
413	char c = *from++;
414	if (!c) break;
415
416	if (c=='\\' \|\| c == '\"') {
417	*to++ = '\\';
418	*to++ = c;
419	}
420	else {
421	*to++ = c;
422	}
423	}
424	*to = 0;
425	return result;
426	}
427
428	// ---------------------------------
429	// the commands themselves:
430
431	static GB_ERROR gbl_quote(GBL_command_arguments *args) {
432	EXPECT_NO_PARAM(args);
433
434	for (int i=0; i<args->input.size(); i++) {
435	FORMAT_2_OUT(args, "\"%s\"", args->input.get(i));
436	}
437	return NULL;
438	}
439	static GB_ERROR gbl_unquote(GBL_command_arguments *args) {
440	EXPECT_NO_PARAM(args);
441
442	for (int i=0; i<args->input.size(); i++) {
443	const char *str = args->input.get(i);
444	int len = strlen(str);
445
446	if (str[0] == '\"' && str[len-1] == '\"') {
447	PASS_2_OUT(args, ARB_strpartdup(str+1, str+len-2));
448	}
449	else {
450	IN_2_OUT(args, i);
451	}
452	}
453	return NULL;
454	}
455
456	static GB_ERROR gbl_escape(GBL_command_arguments *args) {
457	EXPECT_NO_PARAM(args);
458
459	for (int i=0; i<args->input.size(); i++) {
460	char *escaped = escapeString(args->input.get(i));
461	PASS_2_OUT(args, escaped);
462	}
463	return NULL;
464	}
465	static GB_ERROR gbl_unescape(GBL_command_arguments *args) {
466	EXPECT_NO_PARAM(args);
467
468	for (int i=0; i<args->input.size(); i++) {
469	char *unescaped = unEscapeString(args->input.get(i));
470	PASS_2_OUT(args, unescaped);
471	}
472	return NULL;
473	}
474
475	static GB_ERROR gbl_command(GBL_command_arguments *args) {
476	EXPECT_PARAMS(args, 1, "\"ACI command\"");
477
478	GB_ERROR error = NULL;
479	char *command = unEscapeString(args->get_param(0));
480
481	if (traceACI) {
482	print_trace(GBS_global_string("executing command '%s'\n", command));
483	}
484
485	for (int i=0; i<args->input.size() && !error; i++) {
486	char *result = args->get_callEnv().interpret_subcommand(args->input.get(i), command);
487	if (!result) error = GB_await_error();
488	else PASS_2_OUT(args, result);
489	}
490	free(command);
491	return error;
492	}
493
494	static GB_ERROR gbl_eval(GBL_command_arguments *args) {
495	EXPECT_PARAMS(args, 1, "\"expression evaluating to ACI command\"");
496
497	GB_ERROR error = NULL;
498	char *to_eval = unEscapeString(args->get_param(0));
499	TRACE_ACI(GBS_global_string("evaluating '%s'\n", to_eval));
500
501	char *command = args->get_callEnv().interpret_subcommand("", to_eval); // evaluate independent
502	if (!command) error = GB_await_error();
503	else {
504	TRACE_ACI(GBS_global_string("executing '%s'\n", command));
505
506	for (int i=0; i<args->input.size() && !error; i++) {
507	char *result = args->get_callEnv().interpret_subcommand(args->input.get(i), command);
508	if (!result) error = GB_await_error();
509	else PASS_2_OUT(args, result);
510	}
511	free(command);
512	}
513	free(to_eval);
514	return error;
515	}
516
517	class DefinedCommands : virtual Noncopyable {
518	GB_HASH *cmds;
519	public:
520	DefinedCommands() { cmds = GBS_create_dynaval_hash(100, GB_MIND_CASE, GBS_dynaval_free); }
521	~DefinedCommands() { GBS_free_hash(cmds); }
522
523	void set(const char name, char cmd) { GBS_dynaval_free(GBS_write_hash(cmds, name, (long)cmd)); } // takes ownership of 'cmd'!
524	const char get(const char name) const { return (const char *)GBS_read_hash(cmds, name); }
525	};
526
527	static DefinedCommands defined_commands;
528
529	static GB_ERROR gbl_define(GBL_command_arguments *args) {
530	COMMAND_DROPS_INPUT_STREAMS(args);
531	EXPECT_PARAMS(args, 2, "name, \"ACI command\"");
532
533	const char *name = args->get_param(0);
534	char *cmd = unEscapeString(args->get_param(1));
535
536	defined_commands.set(name, cmd);
537	TRACE_ACI(GBS_global_string("defining command '%s'='%s'\n", name, cmd));
538	return NULL;
539	}
540
541	static GB_ERROR gbl_do(GBL_command_arguments *args) {
542	EXPECT_PARAMS(args, 1, "definedCommandName");
543
544	GB_ERROR error = 0;
545	const char *name = args->get_param(0);
546	const char *cmd = defined_commands.get(name);
547
548	if (!cmd) {
549	error = GBS_global_string("Can't do undefined command '%s' - use define(%s, ...) first", name, name);
550	}
551	else {
552	TRACE_ACI(GBS_global_string("executing defined command '%s'='%s' on %i streams\n", name, cmd, args->input.size()));
553
554	for (int i=0; i<args->input.size() && !error; i++) {
555	char *result = args->get_callEnv().interpret_subcommand(args->input.get(i), cmd);
556	if (!result) error = GB_await_error();
557	else PASS_2_OUT(args, result);
558	}
559	}
560	return error;
561	}
562
563	static GB_ERROR gbl_streams(GBL_command_arguments *args) {
564	EXPECT_NO_PARAM(args);
565
566	FORMAT_2_OUT(args, "%i", args->input.size());
567	return 0;
568	}
569
570	static GB_ERROR apply_to_origin(GBL_command_arguments *args, bool organism) {
571	EXPECT_PARAMS(args, 1, "\"ACI command\"");
572
573	GB_ERROR error = NULL;
574	if (!GEN_is_pseudo_gene_species(args->get_ref())) {
575	error = GBS_global_string("'%s' applies to gene-species only", args->get_cmdName());
576	}
577	else {
578	GBDATA *gb_origin = NULL;
579	if (organism) {
580	gb_origin = GEN_find_origin_organism(args->get_ref(), 0);
581	}
582	else {
583	gb_origin = GEN_find_origin_gene(args->get_ref(), 0);
584	}
585
586	if (!error && !gb_origin) error = GB_await_error();
587
588	if (!error) {
589	char *command = unEscapeString(args->get_param(0));
590	GBL_call_env callEnv(gb_origin, args->get_env()); // refer to gb_origin for subcommands
591
592	for (int i=0; i<args->input.size() && !error; i++) {
593	char *result = callEnv.interpret_subcommand(args->input.get(i), command);
594	if (!result) error = GB_await_error();
595	else PASS_2_OUT(args, result);
596	}
597
598	free(command);
599	}
600	}
601
602	return error;
603	}
604
605	static GB_ERROR gbl_origin_gene(GBL_command_arguments *args) { return apply_to_origin(args, false); }
606	static GB_ERROR gbl_origin_organism(GBL_command_arguments *args) { return apply_to_origin(args, true); }
607
608	class Tab {
609	bool tab[256];
610	public:
611	Tab(bool take, const char *invert) {
612	bool init = !take;
613	for (int i = 0; i<256; ++i) tab[i] = init;
614	for (int i = 0; invert[i]; ++i) tab[safeCharIndex(invert[i])] = take;
615	}
616	bool operator[](int i) const { return tab[i]; }
617	};
618
619	inline GB_ERROR count_by_tab(GBL_command_arguments *args, const Tab& tab) {
620	for (int i=0; i<args->input.size(); ++i) {
621	long sum = 0; // count frequencies
622	const char *p = args->input.get(i);
623
624	while (p) sum += tab[safeCharIndex((p++))];
625	FORMAT_2_OUT(args, "%li", sum);
626	}
627	return NULL;
628	}
629	inline GB_ERROR remove_by_tab(GBL_command_arguments *args, const Tab& tab) {
630	for (int i=0; i<args->input.size(); ++i) {
631	GBS_strstruct *strstruct = GBS_stropen(1000);
632	for (const char p = args->input.get(i); p; p++) {
633	if (!tab[(unsigned int)*p]) {
634	GBS_chrcat(strstruct, *p);
635	}
636	}
637	PASS_2_OUT(args, GBS_strclose(strstruct));
638	}
639	return NULL;
640	}
641
642	static GB_ERROR gbl_count(GBL_command_arguments *args) {
643	EXPECT_PARAMS(args, 1, "\"characters to count\"");
644	return count_by_tab(args, Tab(true, args->get_param(0)));
645	}
646	static GB_ERROR gbl_len(GBL_command_arguments *args) {
647	EXPECT_OPTIONAL_PARAMS(args, 0, NULL, 1, "\"characters not to count\"");
648	const char *exclude = args->get_optional_param(0, "");
649	return count_by_tab(args, Tab(false, exclude));
650	}
651	static GB_ERROR gbl_remove(GBL_command_arguments *args) {
652	EXPECT_PARAMS(args, 1, "\"characters to remove\"");
653	return remove_by_tab(args, Tab(true, args->get_param(0)));
654	}
655	static GB_ERROR gbl_keep(GBL_command_arguments *args) {
656	EXPECT_PARAMS(args, 1, "\"characters to keep\"");
657	return remove_by_tab(args, Tab(false, args->get_param(0)));
658	}
659
660
661	static char binop_compare(const char arg1, const char *arg2, bool case_sensitive) {
662	int result;
663
664	if (case_sensitive) result = strcmp(arg1, arg2);
665	else result = gbl_stricmp(arg1, arg2);
666
667	return GBS_global_string_copy("%i", result<0 ? -1 : (result>0 ? 1 : 0));
668	}
669	static char binop_equals(const char arg1, const char *arg2, bool case_sensitive) {
670	int result;
671
672	if (case_sensitive) result = strcmp(arg1, arg2);
673	else result = gbl_stricmp(arg1, arg2);
674
675	return GBS_global_string_copy("%i", result == 0 ? 1 : 0);
676	}
677	static char binop_contains(const char arg1, const char *arg2, bool case_sensitive) {
678	const char *found = 0;
679
680	if (!arg2[0]) return strdup("0"); // do not report matches of empty string
681
682	if (case_sensitive) found = strstr(arg1, arg2);
683	else found = gbl_stristr(arg1, arg2);
684
685	return GBS_global_string_copy("%ti", found == 0 ? 0 : (found-arg1)+1);
686	}
687	static char binop_partof(const char arg1, const char *arg2, bool case_sensitive) {
688	return binop_contains(arg2, arg1, case_sensitive);
689	}
690
691	static GB_ERROR gbl_compare (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_compare, true); }
692	static GB_ERROR gbl_icompare (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_compare, false); }
693	static GB_ERROR gbl_equals (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_equals, true); }
694	static GB_ERROR gbl_iequals (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_equals, false); }
695	static GB_ERROR gbl_contains (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_contains, true); }
696	static GB_ERROR gbl_icontains(GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_contains, false); }
697	static GB_ERROR gbl_partof (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_partof, true); }
698	static GB_ERROR gbl_ipartof (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, binop_partof, false); }
699
700	static GB_ERROR gbl_isEmpty(GBL_command_arguments *args) {
701	EXPECT_NO_PARAM(args);
702	for (int i=0; i<args->input.size(); i++) {
703	const char *str = args->input.get(i);
704	FORMAT_2_OUT(args, "%i", str[0] == 0);
705	}
706	return NULL;
707	}
708	static GB_ERROR gbl_inRange(GBL_command_arguments *args) {
709	EXPECT_PARAMS(args, 2, "low,high");
710
711	double low = strtod(args->get_param(0), NULL);
712	double high = strtod(args->get_param(1), NULL);
713
714	for (int i=0; i<args->input.size(); i++) {
715	double val = strtod(args->input.get(i), NULL);
716	bool inRange = low<=val && val<=high;
717	FORMAT_2_OUT(args, "%i", inRange);
718	}
719	return NULL;
720	}
721
722
723	static GB_ERROR gbl_translate(GBL_command_arguments *args) {
724	EXPECT_OPTIONAL_PARAMS(args, 2, "old,new", 1, "other");
725
726	const char *other = args->get_optional_param(2, NULL);
727	if (other && (other[0] == 0 \|\| other[1] != 0)) {
728	return "third parameter of translate has to be one character (i.e. \"-\")";
729	}
730	const char replace_other = other ? other[0] : 0;
731
732	// build translation table :
733	unsigned char tab[256];
734	{
735	const unsigned char o = (const unsigned char )args->get_param(0);
736	const unsigned char n = (const unsigned char )args->get_param(1);
737	char used[256];
738
739	if (strlen((const char )o) != strlen((const char )n)) {
740	return "arguments 1 and 2 of translate should be strings with identical length";
741	}
742
743	for (int i = 0; i<256; ++i) {
744	tab[i] = replace_other ? replace_other : i; // replace unused or identity translation
745	used[i] = 0;
746	}
747
748	for (int i = 0; o[i]; ++i) {
749	if (used[o[i]]) return GBS_global_string("character '%c' used twice in argument 1 of translate", o[i]);
750	used[o[i]] = 1;
751	tab[o[i]] = n[i]; // real translation
752	}
753	}
754
755	for (int i=0; i<args->input.size(); i++) {
756	GBS_strstruct *strstruct = GBS_stropen(1000);
757	for (const char p = args->input.get(i); p; p++) {
758	GBS_chrcat(strstruct, tab[(unsigned char)*p]);
759	}
760	PASS_2_OUT(args, GBS_strclose(strstruct));
761	}
762	return 0;
763	}
764
765
766	static GB_ERROR gbl_echo(GBL_command_arguments *args) {
767	ACCEPT_ANY_PARAMS(args);
768	COMMAND_DROPS_INPUT_STREAMS(args);
769	for (int i=0; i<args->param_count(); i++) PARAM_2_OUT(args, i);
770	return 0;
771	}
772
773	static GB_ERROR gbl_dd(GBL_command_arguments *args) {
774	EXPECT_NO_PARAM(args);
775	return gbl_mid_streams(args->input, args->output, 0, -1); // copy all streams
776	}
777
778	enum Case { UPPER, LOWER, CAPS };
779
780	static GB_ERROR convert_case(GBL_command_arguments *args, Case convTo) {
781	EXPECT_NO_PARAM(args);
782
783	for (int i=0; i<args->input.size(); i++) {
784	char *p = ARB_strdup(args->input.get(i));
785	bool last_was_alnum = false;
786
787	for (char *pp = p; pp[0]; ++pp) {
788	switch (convTo) {
789	case LOWER: pp[0] = tolower(pp[0]); break;
790	case UPPER: pp[0] = toupper(pp[0]); break;
791	case CAPS: {
792	bool alnum = isalnum(pp[0]);
793	if (alnum) pp[0] = (last_was_alnum ? tolower : toupper)(pp[0]);
794	last_was_alnum = alnum;
795	break;
796	}
797	default: gb_assert(0); break;
798	}
799	}
800
801	PASS_2_OUT(args, p);
802	}
803
804	return 0;
805	}
806
807	static GB_ERROR gbl_caps (GBL_command_arguments *args) { return convert_case(args, CAPS); }
808	static GB_ERROR gbl_upper(GBL_command_arguments *args) { return convert_case(args, UPPER); }
809	static GB_ERROR gbl_lower(GBL_command_arguments *args) { return convert_case(args, LOWER); }
810
811	static GB_ERROR gbl_head(GBL_command_arguments *args) {
812	EXPECT_PARAMS(args, 1, "length_of_head");
813	int start = atoi(args->get_param(0));
814	if (start <= 0) return gbl_mid_streams(args->input, args->output, 1, 0); // empty all streams
815	return gbl_mid_streams(args->input, args->output, 0, start-1);
816	}
817	static GB_ERROR gbl_tail(GBL_command_arguments *args) {
818	EXPECT_PARAMS(args, 1, "length_of_tail");
819	int end = atoi(args->get_param(0));
820	if (end <= 0) return gbl_mid_streams(args->input, args->output, 1, 0); // empty all streams
821	return gbl_mid_streams(args->input, args->output, -end, -1);
822	}
823
824	inline GB_ERROR mid(GBL_command_arguments *args, int start_index) {
825	EXPECT_PARAMS(args, 2, "start,end");
826	return gbl_mid_streams(args->input, args->output, atoi(args->get_param(0))-start_index, atoi(args->get_param(1))-start_index);
827	}
828	static GB_ERROR gbl_mid0(GBL_command_arguments *args) { return mid(args, 0); }
829	static GB_ERROR gbl_mid (GBL_command_arguments *args) { return mid(args, 1); }
830
831	static GB_ERROR tab(GBL_command_arguments *args, bool pretab) {
832	EXPECT_PARAMS(args, 1, "tabstop");
833
834	int tab = atoi(args->get_param(0));
835	for (int i=0; i<args->input.size(); i++) {
836	int len = strlen(args->input.get(i));
837	if (len >= tab) IN_2_OUT(args, i);
838	else {
839	char *p = ARB_alloc<char>(tab+1);
840	if (pretab) {
841	int spaces = tab-len;
842	for (int j = 0; j<spaces; ++j) p[j] = ' ';
843	strcpy(p+spaces, args->input.get(i));
844	}
845	else {
846	strcpy(p, args->input.get(i));
847	for (int j=len; j<tab; j++) p[j] = ' ';
848	p[tab] = 0;
849	}
850	PASS_2_OUT(args, p);
851	}
852	}
853	return 0;
854	}
855	static GB_ERROR gbl_tab (GBL_command_arguments *args) { return tab(args, false); }
856	static GB_ERROR gbl_pretab(GBL_command_arguments *args) { return tab(args, true); }
857
858	static GB_ERROR gbl_crop(GBL_command_arguments *args) {
859	EXPECT_PARAMS(args, 1, "\"chars_to_crop\"");
860
861	const char *chars_to_crop = args->get_param(0);
862	for (int i=0; i<args->input.size(); i++) {
863	const char *s = args->input.get(i);
864	while (s[0] && strchr(chars_to_crop, s[0]) != 0) s++; // crop at beg of line
865
866	int len = strlen(s);
867	char *p = ARB_alloc<char>(len+1);
868	strcpy(p, s);
869
870	{
871	char *pe = p+len-1;
872
873	while (pe >= p && strchr(chars_to_crop, pe[0]) != 0) { // crop at end of line
874	--pe;
875	}
876	gb_assert(pe >= (p-1));
877	pe[1] = 0;
878	}
879	PASS_2_OUT(args, p);
880	}
881	return 0;
882	}
883
884
885
886	static GB_ERROR gbl_cut(GBL_command_arguments *args) {
887	EXPECT_PARAMS_PASSED(args, "streamnumber[,streamnumber]+");
888
889	for (int i=0; i<args->param_count(); i++) {
890	int stream = atoi(args->get_param(i));
891	EXPECT_LEGAL_STREAM_INDEX(args, stream);
892	IN_2_OUT(args, bio2info(stream));
893	}
894	return 0;
895	}
896	static GB_ERROR gbl_drop(GBL_command_arguments *args) {
897	EXPECT_PARAMS_PASSED(args, "streamnumber[,streamnumber]+");
898
899	GB_ERROR error = 0;
900	bool *dropped = ARB_alloc<bool>(args->input.size());
901
902	for (int i=0; i<args->input.size(); ++i) dropped[i] = false;
903
904	for (int i=0; i<args->param_count() && !error; ++i) {
905	int stream = atoi(args->get_param(i));
906	error = check_valid_stream_index(args, stream);
907	if (!error) dropped[bio2info(stream)] = true;
908	}
909
910	if (!error) {
911	for (int i=0; i<args->input.size(); ++i) {
912	if (!dropped[i]) IN_2_OUT(args, i);
913	}
914	}
915	free(dropped);
916
917	return error;
918	}
919
920	static GB_ERROR gbl_dropempty(GBL_command_arguments *args) {
921	EXPECT_NO_PARAM(args);
922
923	for (int i=0; i<args->input.size(); ++i) {
924	if (args->input.get(i)[0]) { // if non-empty
925	IN_2_OUT(args, i);
926	}
927	}
928	return 0;
929	}
930
931	static GB_ERROR gbl_dropzero(GBL_command_arguments *args) {
932	EXPECT_NO_PARAM(args);
933
934	for (int i=0; i<args->input.size(); ++i) {
935	if (atoi(args->input.get(i))) { // if non-zero
936	IN_2_OUT(args, i);
937	}
938	}
939	return 0;
940	}
941
942	static GB_ERROR gbl_swap(GBL_command_arguments *args) {
943	EXPECT_OPTIONAL_PARAMS(args, 0, NULL, 2, "streamnumber,streamnumber");
944
945	if (args->input.size()<2) return "need at least two input streams";
946
947	int swap1;
948	int swap2;
949	if (args->param_count() == 0) {
950	swap1 = args->input.size()-1;
951	swap2 = args->input.size()-2;
952	}
953	else {
954	gb_assert(args->param_count() == 2);
955
956	swap1 = atoi(args->get_param(0));
957	swap2 = atoi(args->get_param(1));
958
959	EXPECT_LEGAL_STREAM_INDEX(args, swap1);
960	EXPECT_LEGAL_STREAM_INDEX(args, swap2);
961
962	swap1 = bio2info(swap1);
963	swap2 = bio2info(swap2);
964	}
965
966	for (int i = 0; i<args->input.size(); ++i) {
967	int j = i == swap1 ? swap2 : (i == swap2 ? swap1 : i);
968	IN_2_OUT(args, j);
969	}
970
971	return 0;
972	}
973
974	static GB_ERROR backfront_stream(GBL_command_arguments *args, int toback) {
975	EXPECT_PARAMS(args, 1, "streamnumber");
976	if (args->input.size()<1) return "need at least one input stream";
977
978	int stream_to_move = atoi(args->get_param(0));
979	EXPECT_LEGAL_STREAM_INDEX(args, stream_to_move);
980	stream_to_move = bio2info(stream_to_move);
981
982	if (!toback) IN_2_OUT(args, stream_to_move);
983	for (int i = 0; i<args->input.size(); ++i) {
984	if (i != stream_to_move) IN_2_OUT(args, i);
985	}
986	if (toback) IN_2_OUT(args, stream_to_move);
987
988	return 0;
989	}
990	static GB_ERROR gbl_toback (GBL_command_arguments *args) { return backfront_stream(args, 1); }
991	static GB_ERROR gbl_tofront(GBL_command_arguments *args) { return backfront_stream(args, 0); }
992
993	static GB_ERROR gbl_merge(GBL_command_arguments *args) {
994	EXPECT_OPTIONAL_PARAMS(args, 0, NULL, 1, "\"separator\"");
995	const char *separator = args->get_optional_param(0, NULL);
996
997	if (args->input.size()) {
998	GBS_strstruct *str = GBS_stropen(1000);
999	GBS_strcat(str, args->input.get(0));
1000
1001	for (int i = 1; i<args->input.size(); ++i) {
1002	if (separator) GBS_strcat(str, separator);
1003	GBS_strcat(str, args->input.get(i));
1004	}
1005
1006	PASS_2_OUT(args, GBS_strclose(str));
1007	}
1008	return 0;
1009	}
1010
1011	static GB_ERROR gbl_split(GBL_command_arguments *args) {
1012	EXPECT_OPTIONAL_PARAMS_CUSTOM(args, 0, NULL, 2, "\"separator\"[,mode]", true, false);
1013
1014	const char *separator = args->get_optional_param(0, "\n");
1015	int split_mode = atoi(args->get_optional_param(1, "0")); // 0: remove separator, 1: split before separator, 2: split behind separator
1016
1017	if (split_mode<0 \|\| split_mode>2) return GBS_global_string("Illegal split mode '%i' (valid: 0..2)", split_mode);
1018
1019	{
1020	size_t sepLen = strlen(separator);
1021
1022	for (int i = 0; i<args->input.size(); ++i) {
1023	const char *in = args->input.get(i);
1024	const char *from = in; // search from here
1025
1026	while (in) {
1027	const char *splitAt = strstr(from, separator);
1028	if (splitAt) {
1029	size_t len;
1030	char *copy;
1031
1032	if (split_mode == 2) splitAt += sepLen; // split behind separator
1033
1034	len = splitAt-in;
1035	copy = ARB_strndup(in, len);
1036
1037	PASS_2_OUT(args, copy);
1038
1039	in = splitAt + (split_mode == 0 ? sepLen : 0);
1040	from = in+(split_mode == 1 ? sepLen : 0);
1041	}
1042	else {
1043	COPY_2_OUT(args, in); // last part
1044	in = 0;
1045	}
1046	}
1047	}
1048	}
1049
1050	return 0;
1051	}
1052
1053	// ----------------------------------
1054	// Extended string functions
1055
1056	static char do_extract_words(const char source, const char *chars, float minlen, bool sort_output) {
1057	/* extract all words in a text that:
1058	* if minlen < 1.0 -> contain more than minlen*len_of_text characters that also exists in chars
1059	* if minlen > 1.0 -> contain more than minlen characters that also exists in chars
1060	*/
1061
1062
1063	char *s = ARB_strdup(source);
1064	char *ps = ARB_calloc<char>((strlen(source)>>1) + 1);
1065	GBS_strstruct *strstruct = GBS_stropen(1000);
1066	char *f = s;
1067	int count = 0;
1068	char *p;
1069	char *h;
1070	int cnt;
1071	int len;
1072	int iminlen = (int) (minlen+.5);
1073
1074	while ((p = strtok(f, " \t,;:\|"))) {
1075	f = 0;
1076	cnt = 0;
1077	len = strlen(p);
1078	for (h=p; *h; h++) {
1079	if (strchr(chars, *h)) cnt++;
1080	}
1081
1082	if (minlen == 1.0) {
1083	if (cnt != len) continue;
1084	}
1085	else if (minlen > 1.0) {
1086	if (cnt < iminlen) continue;
1087	}
1088	else {
1089	if (len < 3 \|\| cnt < minlen*len) continue;
1090	}
1091	ps[count] = p;
1092	count ++;
1093	}
1094	if (sort_output) {
1095	GB_sort((void **)ps, 0, count, GB_string_comparator, 0);
1096	}
1097	for (cnt = 0; cnt<count; cnt++) {
1098	if (cnt) {
1099	GBS_chrcat(strstruct, ' ');
1100	}
1101	GBS_strcat(strstruct, ps[cnt]);
1102	}
1103
1104	free(ps);
1105	free(s);
1106	return GBS_strclose(strstruct);
1107	}
1108
1109	static GB_ERROR gbl_extract_words(GBL_command_arguments *args) {
1110	EXPECT_PARAMS(args, 2, "\"chars\", minchars");
1111
1112	float len = atof(args->get_param(1));
1113	for (int i=0; i<args->input.size(); i++) {
1114	char *res = do_extract_words(args->input.get(i), args->get_param(0), len, 1);
1115	gb_assert(res);
1116	PASS_2_OUT(args, res);
1117	}
1118	return 0;
1119	}
1120
1121	static GB_ERROR gbl_extract_sequence(GBL_command_arguments *args) {
1122	EXPECT_PARAMS(args, 2, "\"chars\",minFrequency");
1123
1124	const char *chars = args->get_param(0);
1125	float minFreq = atof(args->get_param(1));
1126
1127	if (minFreq <0.0 \|\| minFreq > 1.0) return GBS_global_string("Illegal minFrequency=%f (allowed: ]0.0 .. 1.0[)", minFreq);
1128
1129	for (int i=0; i<args->input.size(); i++) {
1130	char *res = do_extract_words(args->input.get(i), chars, minFreq, 0);
1131	gb_assert(res);
1132	PASS_2_OUT(args, res);
1133	}
1134	return 0;
1135	}
1136
1137	static GB_ERROR gbl_checksum(GBL_command_arguments *args) {
1138	GBL_BEGIN_PARAMS;
1139	GBL_PARAM_STRING(exclude, "exclude=", "", "Remove given characters before calculating");
1140	GBL_PARAM_BIT (upper, "toupper", 0, "Convert all characters to uppercase before calculating");
1141	GBL_TRACE_PARAMS(args);
1142	GBL_END_PARAMS;
1143
1144	for (int i=0; i<args->input.size(); i++) {
1145	long id = GBS_checksum(args->input.get(i), upper, exclude);
1146	FORMAT_2_OUT(args, "%lX", id);
1147	}
1148	return 0;
1149	}
1150
1151	static GB_ERROR gbl_gcgchecksum(GBL_command_arguments *args) {
1152	EXPECT_NO_PARAM(args);
1153
1154	for (int i=0; i<args->input.size(); i++) {
1155	long id = GBS_gcgchecksum(args->input.get(i));
1156	FORMAT_2_OUT(args, "%li", id);
1157	}
1158	return 0;
1159	}
1160
1161	// ------------
1162	// SRT
1163
1164	static GB_ERROR gbl_srt(GBL_command_arguments *args) {
1165	EXPECT_PARAMS_PASSED(args, "expr[,expr]+");
1166
1167	GB_ERROR error = NULL;
1168	for (int i=0; i<args->input.size() && !error; i++) {
1169	char *modsource = 0;
1170
1171	for (int j=0; j<args->param_count() && !error; j++) {
1172	char *hs = GBS_string_eval_in_env(modsource ? modsource : args->input.get(i), args->get_param(j), args->get_callEnv());
1173
1174	if (hs) freeset(modsource, hs);
1175	else {
1176	error = GB_await_error();
1177	free(modsource);
1178	}
1179	}
1180
1181	if (!error) {
1182	if (modsource) PASS_2_OUT(args, modsource);
1183	else IN_2_OUT(args, i);
1184	}
1185	}
1186	return error;
1187	}
1188
1189	// -----------------------------
1190	// Calculator Functions
1191
1192	struct binop_pair {
1193	int (*INT) (int, int);
1194	double (*DOUBLE)(double, double);
1195	binop_pair(int (INT_)(int, int), double (DOUBLE_)(double, double)) : INT(INT_), DOUBLE(DOUBLE_) {}
1196	};
1197
1198	static char apply_numeric_binop(const char arg1, const char arg2, int (num_bin_op)(int,int)) {
1199	int v1 = atoi(arg1);
1200	int v2 = atoi(arg2);
1201	int result = num_bin_op(v1, v2);
1202
1203	return GBS_global_string_copy("%i", result);
1204	}
1205
1206	static char apply_double_binop(const char arg1, const char arg2, double (num_bin_op)(double,double)) {
1207	double v1 = strtod(arg1, NULL);
1208	double v2 = strtod(arg2, NULL);
1209	double result = num_bin_op(v1, v2);
1210
1211	return GBS_global_string_copy("%g", result);
1212	}
1213
1214	static char apply_auto_numeric_binop(const char arg1, const char *arg2, binop_pair multiop) {
1215	// argument type detection (int vs double)
1216	int i1 = atoi(arg1);
1217	int i2 = atoi(arg2);
1218	double d1 = strtod(arg1, NULL);
1219	double d2 = strtod(arg2, NULL);
1220
1221	if (double(i1) == d1 \|\| double(i2) == d2) {
1222	int result = multiop.INT(i1, i2);
1223	return GBS_global_string_copy("%i", result);
1224	}
1225	else {
1226	double result = multiop.DOUBLE(d1, d2);
1227	return GBS_global_string_copy("%g", result);
1228	}
1229	}
1230
1231
1232
1233	template <typename T> static T binop_plus (T v1, T v2) { return v1+v2; }
1234	template <typename T> static T binop_minus (T v1, T v2) { return v1-v2; }
1235	template <typename T> static T binop_mult (T v1, T v2) { return v1*v2; }
1236	template <typename T> static T binop_div (T v1, T v2) { return v2 ? v1/v2 : 0; }
1237	template <typename T> static T binop_per_cent(T v1, T v2) { return v2 ? (v1*100)/v2 : 0; }
1238
1239	static int binop_rest(int i1, int i2) { return i2 ? i1%i2 : 0; }
1240
1241
1242	static GB_ERROR gbl_plus (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_numeric_binop, binop_plus<int>); }
1243	static GB_ERROR gbl_fplus (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_double_binop, binop_plus<double>); }
1244	static GB_ERROR gbl_minus (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_numeric_binop, binop_minus<int>); }
1245	static GB_ERROR gbl_fminus (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_double_binop, binop_minus<double>); }
1246	static GB_ERROR gbl_mult (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_numeric_binop, binop_mult<int>); }
1247	static GB_ERROR gbl_fmult (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_double_binop, binop_mult<double>); }
1248	static GB_ERROR gbl_div (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_numeric_binop, binop_div<int>); }
1249	static GB_ERROR gbl_fdiv (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_double_binop, binop_div<double>); }
1250	static GB_ERROR gbl_rest (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_numeric_binop, binop_rest); }
1251	static GB_ERROR gbl_per_cent (GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_numeric_binop, binop_per_cent<int>); }
1252	static GB_ERROR gbl_fper_cent(GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_double_binop, binop_per_cent<double>); }
1253
1254	template <typename T> static T binop_isAbove(T i1, T i2) { return i1>i2; }
1255	template <typename T> static T binop_isBelow(T i1, T i2) { return i1<i2; }
1256	template <typename T> static T binop_isEqual(T i1, T i2) { return i1 == i2; }
1257
1258	static GB_ERROR gbl_isAbove(GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_auto_numeric_binop, binop_pair(binop_isAbove<int>, binop_isAbove<double>)); }
1259	static GB_ERROR gbl_isBelow(GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_auto_numeric_binop, binop_pair(binop_isBelow<int>, binop_isBelow<double>)); }
1260	static GB_ERROR gbl_isEqual(GBL_command_arguments *args) { return gbl_apply_binary_operator(args, apply_auto_numeric_binop, binop_pair(binop_isEqual<int>, binop_isEqual<double>)); }
1261
1262	inline double float_shift_factor(int digits) {
1263	if (digits<0) {
1264	return 1.0/float_shift_factor(-digits);
1265	}
1266	int factor = 1;
1267	while (digits>0) {
1268	factor *= 10;
1269	--digits;
1270	}
1271	return factor;
1272	}
1273
1274	static GB_ERROR gbl_round(GBL_command_arguments *args) {
1275	EXPECT_PARAMS(args, 1, "digits");
1276	int digits = atoi(args->get_param(0));
1277
1278	double factor = float_shift_factor(digits);
1279	for (int i=0; i<args->input.size(); ++i) {
1280	double val = strtod(args->input.get(i), NULL);
1281	val = round(val*factor)/factor;
1282	FORMAT_2_OUT(args, "%g", val);
1283	}
1284	return NULL;
1285	}
1286
1287
1288
1289	// boolean operators
1290
1291	static GB_ERROR gbl_not(GBL_command_arguments *args) {
1292	EXPECT_NO_PARAM(args);
1293
1294	for (int i=0; i<args->input.size(); ++i) {
1295	const char *s = args->input.get(i);
1296	int val = atoi(s);
1297	FORMAT_2_OUT(args, "%i", !val);
1298	}
1299	return NULL;
1300	}
1301
1302	static GB_ERROR gbl_and(GBL_command_arguments *args) {
1303	EXPECT_NO_PARAM(args);
1304	bool conjunction = true;
1305	for (int i=0; conjunction && i<args->input.size(); ++i) {
1306	const char *s = args->input.get(i);
1307	conjunction = conjunction && atoi(s);
1308	}
1309	FORMAT_2_OUT(args, "%i", conjunction);
1310	return NULL;
1311	}
1312	static GB_ERROR gbl_or(GBL_command_arguments *args) {
1313	EXPECT_NO_PARAM(args);
1314	bool disjunction = false;
1315	for (int i=0; !disjunction && i<args->input.size(); ++i) {
1316	const char *s = args->input.get(i);
1317	disjunction = disjunction \|\| atoi(s);
1318	}
1319	FORMAT_2_OUT(args, "%i", disjunction);
1320	return NULL;
1321	}
1322
1323	static GB_ERROR gbl_select(GBL_command_arguments *args) {
1324	ACCEPT_ANY_PARAMS(args);
1325
1326	GB_ERROR error = NULL;
1327	for (int i=0; i<args->input.size() && !error; i++) {
1328	int paraidx = atoi(args->input.get(i));
1329	error = check_valid_param_index(args, paraidx);
1330	if (!error) {
1331	char *result = args->get_callEnv().interpret_subcommand("", args->get_param(paraidx)); // @@@ EVALUATED_PARAM (#768)
1332	if (!result) error = GB_await_error();
1333	else PASS_2_OUT(args, result);
1334	}
1335	}
1336	return error;
1337	}
1338
1339	static GB_ERROR gbl_readdb(GBL_command_arguments *args) {
1340	EXPECT_PARAMS_PASSED(args, "fieldname[,fieldname]+");
1341	COMMAND_DROPS_INPUT_STREAMS(args);
1342
1343	GBS_strstruct *strstr = GBS_stropen(1024);
1344	for (int i=0; i<args->param_count(); i++) {
1345	char *val = GBT_read_as_string(args->get_ref(), args->get_param(i));
1346	if (val) {
1347	GBS_strcat(strstr, val);
1348	free(val);
1349	}
1350	}
1351	PASS_2_OUT(args, GBS_strclose(strstr));
1352	return 0;
1353	}
1354
1355
1356	enum GBT_ITEM_TYPE {
1357	GBT_ITEM_UNKNOWN,
1358	GBT_ITEM_SPECIES,
1359	GBT_ITEM_GENE
1360	};
1361
1362	static GBT_ITEM_TYPE identify_gb_item(GBDATA *gb_item) {
1363	/* returns: GBT_ITEM_UNKNOWN -> unknown database_item
1364	* GBT_ITEM_SPECIES -> /species_data/species
1365	* GBT_ITEM_GENE -> /species_data/species/gene_data/gene */
1366
1367	GBT_ITEM_TYPE res = GBT_ITEM_UNKNOWN;
1368	if (gb_item) {
1369	GBDATA *gb_father = GB_get_father(gb_item);
1370	if (gb_father) {
1371	const char *key = GB_KEY(gb_item);
1372
1373	if (strcmp(key, "species") == 0 &&
1374	strcmp(GB_KEY(gb_father), "species_data") == 0) {
1375	res = GBT_ITEM_SPECIES;
1376	}
1377	else if (strcmp(key, "gene") == 0 &&
1378	strcmp(GB_KEY(gb_father), "gene_data") == 0 &&
1379	identify_gb_item(GB_get_father(gb_father)) == GBT_ITEM_SPECIES) {
1380	res = GBT_ITEM_GENE;
1381	}
1382	}
1383	}
1384	return res;
1385	}
1386
1387	// --------------------------------------------------------------------------------
1388	// taxonomy caching
1389
1390	#if defined(DEBUG)
1391	// #define DUMP_TAXONOMY_CACHING
1392	#endif
1393
1394
1395	#define GROUP_COUNT_CHARS 6 // characters in taxonomy-key reserved for group-counter (hex number)
1396	#define BITS_PER_HEXCHAR 4
1397	#define MAX_GROUPS (1 << (GROUP_COUNT_CHARS*BITS_PER_HEXCHAR)) // resulting number of groups
1398
1399	struct cached_taxonomy {
1400	char *tree_name; // tree for which taxonomy is cached here
1401	int groups; // number of named groups in tree (at time of caching)
1402	GB_HASH taxonomy; / keys: "!species", ">XXXXgroup" and "<root>".
1403	* Species and groups contain their first parent (i.e. '>XXXXgroup' or '<root>').
1404	* Species not in hash are not members of tree.
1405	* The 'XXXX' in groupname is simply a counter to avoid multiple groups with same name.
1406	* The group-db-entries are stored in hash as pointers ('>>%p') and
1407	* point to their own group entry ('>XXXXgroup')
1408	*
1409	* Note: the number of 'X's in 'XXXX' above is defined by GROUP_COUNT_CHARS!
1410	*/
1411	};
1412
1413	static void free_cached_taxonomy(cached_taxonomy *ct) {
1414	free(ct->tree_name);
1415	GBS_free_hash(ct->taxonomy);
1416	free(ct);
1417	}
1418
1419	static void build_taxonomy_rek(TreeNode node, GB_HASH tax_hash, const char parent_group, int group_counter) {
1420	if (node->is_leaf) {
1421	GBDATA *gb_species = node->gb_node;
1422	if (gb_species) { // not zombie
1423	GBS_write_hash(tax_hash, GBS_global_string("!%s", GBT_read_name(gb_species)), (long)ARB_strdup(parent_group));
1424	}
1425	}
1426	else {
1427	if (node->name) { // named group
1428	char *hash_entry;
1429	const char *hash_binary_entry;
1430	(*group_counter)++;
1431
1432	gb_assert((*group_counter)<MAX_GROUPS); // overflow - increase GROUP_COUNT_CHARS
1433
1434	hash_entry = GBS_global_string_copy(">%0x%s", GROUP_COUNT_CHARS, group_counter, node->name);
1435	GBS_write_hash(tax_hash, hash_entry, (long)ARB_strdup(parent_group));
1436
1437	hash_binary_entry = GBS_global_string(">>%p", node->gb_node);
1438	GBS_write_hash(tax_hash, hash_binary_entry, (long)ARB_strdup(hash_entry));
1439
1440	build_taxonomy_rek(node->get_leftson(), tax_hash, hash_entry, group_counter);
1441	build_taxonomy_rek(node->get_rightson(), tax_hash, hash_entry, group_counter);
1442	free(hash_entry);
1443	}
1444	else {
1445	build_taxonomy_rek(node->get_leftson(), tax_hash, parent_group, group_counter);
1446	build_taxonomy_rek(node->get_rightson(), tax_hash, parent_group, group_counter);
1447	}
1448	}
1449	}
1450
1451	static GB_HASH *cached_taxonomies = 0;
1452
1453	static bool is_cached_taxonomy(const char /key/, long val, void cl_ct) {
1454	cached_taxonomy ct1 = (cached_taxonomy )val;
1455	cached_taxonomy ct2 = (cached_taxonomy )cl_ct;
1456
1457	return ct1 == ct2;
1458	}
1459
1460	static const char tree_of_cached_taxonomy(cached_taxonomy ct) {
1461	/* search the hash to find the correct cached taxonomy.
1462	* searching for tree name does not work, because the tree possibly already was deleted
1463	*/
1464	const char *tree = GBS_hash_next_element_that(cached_taxonomies, NULL, is_cached_taxonomy, ct);
1465	#ifdef DUMP_TAXONOMY_CACHING
1466	if (tree) printf("tree_of_cached_taxonomy: tree='%s' ct->tree_name='%s'\n", tree, ct->tree_name);
1467	#endif // DUMP_TAXONOMY_CACHING
1468	return tree;
1469	}
1470
1471	static void flush_taxonomy_cb(GBDATA gbd, cached_taxonomy ct) {
1472	/* this cb is bound all tree db members below "/tree_data/tree_xxx" which
1473	* may have an effect on the displayed taxonomy
1474	* it invalidates cached taxonomies for that tree (when changed or deleted)
1475	*/
1476
1477	GB_ERROR error = 0;
1478	const char *found = tree_of_cached_taxonomy(ct);
1479
1480	if (found) {
1481	#ifdef DUMP_TAXONOMY_CACHING
1482	fprintf(stderr, "Deleting cached taxonomy ct=%p (tree='%s')\n", ct, found);
1483	#endif // DUMP_TAXONOMY_CACHING
1484	GBS_write_hash(cached_taxonomies, found, 0); // delete cached taxonomy from hash
1485	free_cached_taxonomy(ct);
1486	}
1487	#ifdef DUMP_TAXONOMY_CACHING
1488	else {
1489	fprintf(stderr, "No tree found for cached_taxonomies ct=%p (already deleted?)\n", ct);
1490	}
1491	#endif // DUMP_TAXONOMY_CACHING
1492
1493	if (!GB_inside_callback(gbd, GB_CB_DELETE)) {
1494	GB_remove_all_callbacks_to(gbd, GB_CB_CHANGED_OR_DELETED, (GB_CB)flush_taxonomy_cb);
1495	}
1496
1497	if (found && !error) {
1498	GBDATA *gb_main = GB_get_gb_main_during_cb();
1499	if (gb_main) {
1500	GBDATA *gb_tree_refresh = GB_search(gb_main, AWAR_TREE_REFRESH, GB_INT);
1501	if (!gb_tree_refresh) {
1502	error = GBS_global_string("%s (while trying to force refresh)", GB_await_error());
1503	}
1504	else {
1505	GB_touch(gb_tree_refresh); // Note : force tree update
1506	}
1507	}
1508	}
1509
1510	if (error) {
1511	fprintf(stderr, "Error in flush_taxonomy_cb: %s\n", error);
1512	}
1513	}
1514
1515	static void flush_taxonomy_if_new_group_cb(GBDATA gb_tree, cached_taxonomy ct) {
1516	// detects the creation of new groups and call flush_taxonomy_cb() manually
1517	#ifdef DUMP_TAXONOMY_CACHING
1518	fputs("flush_taxonomy_if_new_group_cb() has been called\n", stderr);
1519	#endif // DUMP_TAXONOMY_CACHING
1520
1521	const char *tree_name = tree_of_cached_taxonomy(ct);
1522	if (tree_name) {
1523	int groups = 0;
1524	GBDATA *gb_group_node;
1525
1526	for (gb_group_node = GB_entry(gb_tree, "node");
1527	gb_group_node;
1528	gb_group_node = GB_nextEntry(gb_group_node))
1529	{
1530	if (GB_entry(gb_group_node, "group_name")) {
1531	groups++; // count named groups only
1532	}
1533	}
1534
1535	#ifdef DUMP_TAXONOMY_CACHING
1536	fprintf(stderr, "cached_groups=%i counted_groups=%i\n", ct->groups, groups);
1537	#endif // DUMP_TAXONOMY_CACHING
1538	if (groups != ct->groups) {
1539	#ifdef DUMP_TAXONOMY_CACHING
1540	fprintf(stderr, "Number of groups changed -> invoking flush_taxonomy_cb() manually\n");
1541	#endif // DUMP_TAXONOMY_CACHING
1542	flush_taxonomy_cb(gb_tree, ct);
1543	}
1544	}
1545	#ifdef DUMP_TAXONOMY_CACHING
1546	else {
1547	fprintf(stderr, "cached taxonomy no longer valid.\n");
1548	}
1549	#endif // DUMP_TAXONOMY_CACHING
1550	}
1551
1552	static cached_taxonomy get_cached_taxonomy(GBDATA gb_main, const char tree_name, GB_ERROR error) {
1553	long cached;
1554	*error = 0;
1555	if (!cached_taxonomies) {
1556	cached_taxonomies = GBS_create_hash(20, GB_IGNORE_CASE);
1557	}
1558	cached = GBS_read_hash(cached_taxonomies, tree_name);
1559	if (!cached) {
1560	TreeNode *tree = GBT_read_tree(gb_main, tree_name, new SimpleRoot);
1561	if (!tree) *error = GB_await_error();
1562	else *error = GBT_link_tree(tree, gb_main, false, 0, 0);
1563
1564	if (!*error) {
1565	GBDATA *gb_tree = GBT_find_tree(gb_main, tree_name);
1566	if (!gb_tree) {
1567	*error = GBS_global_string("Can't find tree '%s'", tree_name);
1568	}
1569	else {
1570	cached_taxonomy *ct = ARB_alloc<cached_taxonomy>(1);
1571	long nodes = GBT_count_leafs(tree);
1572	int group_counter = 0;
1573
1574	ct->tree_name = ARB_strdup(tree_name);
1575	ct->taxonomy = GBS_create_dynaval_hash(int(nodes), GB_IGNORE_CASE, GBS_dynaval_free);
1576	ct->groups = 0; // counted below
1577
1578	build_taxonomy_rek(tree, ct->taxonomy, "<root>", &group_counter);
1579	cached = (long)ct;
1580	GBS_write_hash(cached_taxonomies, tree_name, (long)ct);
1581
1582	GB_remove_all_callbacks_to(gb_tree, GB_CB_SON_CREATED, (GB_CB)flush_taxonomy_if_new_group_cb);
1583	GB_add_callback(gb_tree, GB_CB_SON_CREATED, makeDatabaseCallback(flush_taxonomy_if_new_group_cb, ct));
1584
1585	{
1586	GBDATA *gb_tree_entry = GB_entry(gb_tree, "tree");
1587	GBDATA *gb_group_node;
1588
1589	if (gb_tree_entry) {
1590	GB_remove_all_callbacks_to(gb_tree_entry, GB_CB_CHANGED_OR_DELETED, (GB_CB)flush_taxonomy_cb);
1591	GB_add_callback(gb_tree_entry, GB_CB_CHANGED_OR_DELETED, makeDatabaseCallback(flush_taxonomy_cb, ct));
1592	}
1593
1594	// add callbacks for all node/group_name subentries
1595	for (gb_group_node = GB_entry(gb_tree, "node");
1596	gb_group_node;
1597	gb_group_node = GB_nextEntry(gb_group_node))
1598	{
1599	GBDATA *gb_group_name = GB_entry(gb_group_node, "group_name");
1600	if (gb_group_name) { // group with id = 0 has no name
1601	GB_remove_all_callbacks_to(gb_group_name, GB_CB_CHANGED_OR_DELETED, (GB_CB)flush_taxonomy_cb);
1602	GB_add_callback(gb_group_name, GB_CB_CHANGED_OR_DELETED, makeDatabaseCallback(flush_taxonomy_cb, ct));
1603	ct->groups++;
1604	}
1605	}
1606	}
1607	#ifdef DUMP_TAXONOMY_CACHING
1608	fprintf(stderr, "Created taxonomy hash for '%s' (ct=%p)\n", tree_name, ct);
1609	#endif // DUMP_TAXONOMY_CACHING
1610	}
1611	}
1612
1613	destroy(tree);
1614	}
1615
1616	if (!*error) {
1617	cached_taxonomy ct = (cached_taxonomy)cached;
1618	gb_assert(ct);
1619	return ct;
1620	}
1621
1622	return 0;
1623	}
1624
1625	static char get_taxonomy_string(GB_HASH tax_hash, const char group_key, int depth, GB_ERROR error) {
1626	long found;
1627	char *result = 0;
1628
1629	gb_assert(depth>0);
1630	gb_assert(!(group_key[0] == '>' && group_key[1] == '>')); // internal group-pointers not allowed here!
1631
1632	found = GBS_read_hash(tax_hash, group_key);
1633	if (found) {
1634	const char parent_group_key = (const char )found;
1635	if (strcmp(parent_group_key, "<root>") == 0) { // root reached
1636	result = ARB_strdup(group_key+(GROUP_COUNT_CHARS+1)); // return own group name
1637	}
1638	else {
1639	if (depth>1) {
1640	char *parent_name = get_taxonomy_string(tax_hash, parent_group_key, depth-1, error);
1641	if (parent_name) {
1642	result = GBS_global_string_copy("%s/%s", parent_name, group_key+(GROUP_COUNT_CHARS+1));
1643	free(parent_name);
1644	}
1645	else {
1646	error = GBS_global_string("In get_taxonomy_string(%s): %s", group_key, error);
1647	result = 0;
1648	}
1649	}
1650	else {
1651	result = ARB_strdup(group_key+(GROUP_COUNT_CHARS+1)); // return own group name
1652	}
1653	}
1654	}
1655	else {
1656	*error = GBS_global_string("Not in tax_hash: '%s'", group_key);
1657	}
1658	return result;
1659	}
1660
1661	static const char get_taxonomy(GBDATA gb_species_or_group, const char tree_name, bool is_current_tree, int depth, GB_ERROR error) {
1662	GBDATA *gb_main = GB_get_root(gb_species_or_group);
1663	cached_taxonomy *tax = get_cached_taxonomy(gb_main, tree_name, error);
1664	const char *result = 0;
1665
1666	if (tax) {
1667	GBDATA *gb_name = GB_entry(gb_species_or_group, "name");
1668	GBDATA *gb_group_name = GB_entry(gb_species_or_group, "group_name");
1669
1670	if (gb_name && !gb_group_name) { // it's a species
1671	char *name = GB_read_string(gb_name);
1672	if (name) {
1673	GB_HASH *tax_hash = tax->taxonomy;
1674	long found = GBS_read_hash(tax_hash, GBS_global_string("!%s", name));
1675
1676	if (found) {
1677	const char parent_group = (const char )found;
1678
1679	if (strcmp(parent_group, "<root>") == 0) {
1680	result = ""; // not member of any group
1681	}
1682	else {
1683	static char *parent = 0;
1684
1685	freeset(parent, get_taxonomy_string(tax_hash, parent_group, depth, error));
1686	result = parent;
1687	}
1688	}
1689	else {
1690	result = GBS_global_string("Species '%s' not in '%s'", name, tree_name);
1691	}
1692	free(name);
1693	}
1694	else {
1695	*error = GBS_global_string("Species without 'name' entry!");
1696	}
1697	}
1698	else if (gb_group_name && !gb_name) { // it's a group
1699	char *group_name = GB_read_string(gb_group_name);
1700	if (group_name) {
1701	if (is_current_tree) {
1702	GB_HASH *tax_hash = tax->taxonomy;
1703	long found = GBS_read_hash(tax_hash, GBS_global_string(">>%p", gb_species_or_group));
1704
1705	if (found) {
1706	static char *full_group = 0;
1707	const char group_id = (const char )found;
1708
1709	freeset(full_group, get_taxonomy_string(tax_hash, group_id, depth, error));
1710	result = full_group;
1711	}
1712	else {
1713	result = GBS_global_string("Group '%s' not in '%s'", group_name, tree_name);
1714	}
1715	}
1716	else {
1717	*error = "It's not possible to specify the tree name in taxonomy() for groups";
1718	}
1719	free(group_name);
1720	}
1721	else {
1722	*error = "Group without 'group_name' entry";
1723	}
1724	}
1725	else if (gb_group_name) {
1726	*error = "Container has 'name' and 'group_name' entry - can't detect container type";
1727	}
1728	else {
1729	*error = "Container has neither 'name' nor 'group_name' entry - can't detect container type";
1730	}
1731	}
1732
1733	return result;
1734	}
1735
1736	static GB_ERROR gbl_taxonomy(GBL_command_arguments *args) {
1737	GB_ERROR error = check_optional_parameters(args, 1, "count", 1, "tree_name", false, true);
1738	if (!error) {
1739	COMMAND_DROPS_INPUT_STREAMS(args);
1740
1741	char *tree_name = 0;
1742	bool is_current_tree = false;
1743	int depth = -1;
1744	char *result = 0;
1745
1746	if (args->param_count() == 1) { // only 'depth'
1747	if (!args->get_treename()) {
1748	result = ARB_strdup("No default tree");
1749	}
1750	else {
1751	tree_name = ARB_strdup(args->get_treename());
1752	depth = atoi(args->get_param(0));
1753	is_current_tree = true;
1754	}
1755	}
1756	else { // 'tree_name', 'depth'
1757	tree_name = ARB_strdup(args->get_param(0));
1758	depth = atoi(args->get_param(1));
1759	}
1760
1761	if (!result) {
1762	if (depth<1) {
1763	error = GBS_global_string("Illegal depth '%i' (allowed 1..n)", depth);
1764	}
1765	if (!error) {
1766	const char *taxonomy_string = get_taxonomy(args->get_ref(), tree_name, is_current_tree, depth, &error);
1767	if (taxonomy_string) result = ARB_strdup(taxonomy_string);
1768	}
1769	}
1770
1771	gb_assert(contradicted(result, error));
1772	if (result) PASS_2_OUT(args, result);
1773	free(tree_name);
1774	}
1775	return error;
1776	}
1777
1778	static GB_ERROR gbl_sequence(GBL_command_arguments *args) {
1779	COMMAND_DROPS_INPUT_STREAMS(args);
1780
1781	GB_ERROR error = check_no_parameter(args);
1782	if (!error) {
1783	switch (identify_gb_item(args->get_ref())) {
1784	case GBT_ITEM_UNKNOWN: {
1785	error = "'sequence' used for unknown item";
1786	break;
1787	}
1788	case GBT_ITEM_SPECIES: {
1789	char *use = GBT_get_default_alignment(args->get_gb_main());
1790
1791	if (!use) {
1792	error = GB_have_error() ? GB_await_error() : "no default alignment defined";
1793	}
1794	else {
1795	GBDATA *gb_seq = GBT_find_sequence(args->get_ref(), use);
1796
1797	if (gb_seq) PASS_2_OUT(args, GB_read_string(gb_seq));
1798	else COPY_2_OUT(args, ""); // if current alignment does not exist -> return empty string
1799
1800	free(use);
1801	}
1802	break;
1803	}
1804	case GBT_ITEM_GENE: {
1805	char *seq = GBT_read_gene_sequence(args->get_ref(), true, 0);
1806
1807	if (!seq) error = GB_await_error();
1808	else PASS_2_OUT(args, seq);
1809
1810	break;
1811	}
1812	}
1813	}
1814	return error;
1815	}
1816
1817	static GB_ERROR gbl_export_sequence(GBL_command_arguments *args) {
1818	COMMAND_DROPS_INPUT_STREAMS(args);
1819
1820	GB_ERROR error = check_no_parameter(args);
1821	if (!error) {
1822	switch (identify_gb_item(args->get_ref())) {
1823	case GBT_ITEM_UNKNOWN: {
1824	error = "'export_sequence' used for unknown item";
1825	break;
1826	}
1827	case GBT_ITEM_SPECIES: {
1828	if (get_export_sequence == 0) {
1829	error = "No export-sequence-hook defined (can't use 'export_sequence' here)";
1830	}
1831	else {
1832	size_t len;
1833	const char *seq = get_export_sequence(args->get_ref(), &len, &error);
1834
1835	gb_assert(error \|\| seq);
1836
1837	if (seq) PASS_2_OUT(args, ARB_strduplen(seq, len));
1838	}
1839	break;
1840	}
1841	case GBT_ITEM_GENE: {
1842	error = "'export_sequence' cannot be used for gene";
1843	break;
1844	}
1845	}
1846	}
1847	return error;
1848	}
1849
1850	static GB_ERROR gbl_ali_name(GBL_command_arguments *args) {
1851	COMMAND_DROPS_INPUT_STREAMS(args);
1852
1853	GB_ERROR error = check_no_parameter(args);
1854	if (!error) {
1855	GBDATA *gb_main = args->get_gb_main();
1856	char *use = GBT_get_default_alignment(gb_main);
1857	PASS_2_OUT(args, use);
1858	}
1859	return error;
1860	}
1861
1862	static GB_ERROR gbl_sequence_type(GBL_command_arguments *args) {
1863	COMMAND_DROPS_INPUT_STREAMS(args);
1864
1865	GB_ERROR error = check_no_parameter(args);
1866	if (!error) {
1867	GBDATA *gb_main = args->get_gb_main();
1868	char *use = GBT_get_default_alignment(gb_main);
1869	PASS_2_OUT(args, GBT_get_alignment_type_string(gb_main, use));
1870	free(use);
1871	}
1872
1873	return error;
1874	}
1875
1876	static GB_ERROR format(GBL_command_arguments *args, bool simple_format) {
1877	// simple_format: true = "format", false="format_sequence"
1878
1879	GB_ERROR error = 0;
1880	int ic;
1881
1882	GBL_BEGIN_PARAMS;
1883	GBL_PARAM_INT(firsttab, "firsttab=", 10, "Indent first line");
1884	GBL_PARAM_INT(tab, "tab=", 10, "Indent not first line");
1885	GBL_PARAM_INT(width, "width=", 50, "Sequence width (bases only)");
1886
1887	// "format_sequence"-only
1888	GBL_PARAM_BIT (numleft, PARAM_IF(!simple_format, "numleft"), 0, "Numbers left of sequence");
1889	GBL_PARAM_INT (numright, PARAM_IF(!simple_format, "numright="), 0, "Numbers right of sequence (specifies width; -1 -> auto-width)");
1890	GBL_PARAM_UINT(gap, PARAM_IF(!simple_format, "gap="), 10, "Insert ' ' every n sequence characters");
1891
1892	// "format"-only
1893	GBL_PARAM_STRING(nl, PARAM_IF(simple_format, "nl="), " ", "Break line at characters 'str' if wrapping needed");
1894	GBL_PARAM_STRING(forcenl, PARAM_IF(simple_format, "forcenl="), "\n", "Always break line at characters 'str'");
1895
1896	GBL_TRACE_PARAMS(args);
1897	GBL_END_PARAMS;
1898
1899	if (tab < 0) tab = 0;
1900	if (firsttab < 0) firsttab = 0;
1901
1902	if (width == 0) return "Illegal zero width";
1903	if (numleft && numright != 0) return "You may only specify 'numleft' OR 'numright', not both.";
1904
1905	if (gap<1) gap = UINT_MAX;
1906
1907	for (ic = 0; ic<args->input.size(); ++ic) {
1908	{
1909	const char *src = args->input.get(ic);
1910	size_t data_size = strlen(src);
1911	size_t needed_size;
1912	size_t line_size;
1913	int numright_used = numright;
1914
1915	if (numright_used<0) {
1916	numright_used = calc_digits(data_size);
1917	}
1918
1919	{
1920	size_t lines;
1921
1922	if (simple_format) {
1923	lines = data_size/2 + 1; // worst case
1924	line_size = tab + (width>0 ? width : data_size) + 1;
1925	}
1926	else {
1927	size_t gapsPerLine = (width-1)/gap;
1928	lines = data_size/width+1;
1929	line_size = tab + width + gapsPerLine + 1;
1930
1931	if (numright_used) {
1932	// add space for numright
1933	line_size += numright_used+1; // plus space
1934	}
1935	}
1936
1937	needed_size = lines*line_size + firsttab + 1 + 10;
1938	}
1939
1940	char *result = ARB_alloc<char>(needed_size);
1941	if (!result) {
1942	error = GBS_global_string("Out of memory (tried to alloc %zu bytes)", needed_size);
1943	}
1944	else {
1945	char *dst = result;
1946	size_t rest_data = data_size;
1947
1948	if (simple_format) {
1949	/* format string w/o gaps or numleft
1950	* does word-wrapping at chars in nl
1951	*/
1952
1953	// build wrap table
1954	unsigned char isWrapChar[256];
1955	memset(isWrapChar, 0, sizeof(isWrapChar));
1956	for (int i = 0; nl[i]; ++i) isWrapChar[(unsigned char)nl[i]] = 1;
1957	for (int i = 0; forcenl[i]; ++i) isWrapChar[(unsigned char)forcenl[i]] = 2;
1958
1959	if (firsttab>0) {
1960	memset(dst, ' ', firsttab);
1961	dst += firsttab;
1962	}
1963
1964	while (width>0 && rest_data>unsigned(width)) {
1965	int take;
1966	int move;
1967	int took;
1968
1969	for (take = width; take > 0; --take) {
1970	if (isWrapChar[(unsigned char)src[take]]) break;
1971	}
1972	if (take <= 0) { // no wrap character found -> hard wrap at width
1973	take = move = width;
1974	}
1975	else { // soft wrap at last found wrap character
1976	move = take+1;
1977	}
1978
1979	for (took = 0; took<take; took++) {
1980	char c = src[took];
1981	if (isWrapChar[(unsigned char)c] == 2) { // forced newline
1982	take = took;
1983	move = take+1;
1984	break;
1985	}
1986	dst[took] = c;
1987	}
1988
1989	dst += take;
1990	src += move;
1991	rest_data -= move;
1992
1993	if (rest_data>0) {
1994	*dst++ = '\n';
1995	if (tab>0) {
1996	memset(dst, ' ', tab);
1997	dst += tab;
1998	}
1999	}
2000	}
2001
2002	if (rest_data>0) {
2003	size_t j, k;
2004	for (j = 0, k = 0; j<rest_data; ++j) {
2005	char c = src[j];
2006
2007	if (isWrapChar[(unsigned char)c] == 2) {
2008	dst[k++] = '\n';
2009	if (tab>0) {
2010	memset(dst+k, ' ', tab);
2011	k += tab;
2012	}
2013	}
2014	else {
2015	dst[k++] = c;
2016	}
2017	}
2018	src += j;
2019	dst += k;
2020	rest_data = 0;
2021	}
2022	}
2023	else {
2024	// "format_sequence" with gaps and numleft
2025	char *format = 0;
2026	const char *src_start = src;
2027	const char *dst_linestart = dst;
2028
2029	if (numleft) {
2030	/* Warning: Be very careful, when you change format strings here!
2031	* currently all format strings result in '%u' or '%-##u' (where # are digits)
2032	*/
2033	if (firsttab>0) {
2034	char *firstFormat = GBS_global_string_copy("%%-%iu ", firsttab-1);
2035	dst += sprintf(dst, firstFormat, (unsigned)1);
2036	free(firstFormat);
2037	}
2038	else {
2039	dst += sprintf(dst, "%u ", (unsigned)1);
2040	}
2041	format = tab>0 ? GBS_global_string_copy("%%-%iu ", tab-1) : ARB_strdup("%u ");
2042	}
2043	else if (firsttab>0) {
2044	memset(dst, ' ', firsttab);
2045	dst += firsttab;
2046	}
2047
2048	while (rest_data>0) {
2049	size_t take = (width>0 && rest_data>unsigned(width)) ? width : rest_data;
2050
2051	rest_data -= take;
2052
2053	while (take>gap) {
2054	memcpy(dst, src, gap);
2055	dst += gap;
2056	src += gap;
2057	*dst++ = ' ';
2058	take -= gap;
2059	}
2060
2061	memcpy(dst, src, take);
2062	dst += take;
2063	src += take;
2064
2065	if (numright_used) {
2066	if (rest_data) *dst++ = ' ';
2067	else {
2068	// fill in missing spaces for proper alignment of numright
2069	size_t currSize = dst-dst_linestart;
2070	size_t wantSize = line_size-numright_used-1;
2071	if (currSize<wantSize) {
2072	size_t spaces = wantSize-currSize;
2073	memset(dst, ' ', spaces);
2074	dst += spaces;
2075	}
2076	}
2077	unsigned int num = (src-src_start);
2078	dst += sprintf(dst, "%*u", numright_used, num);
2079	}
2080
2081	if (rest_data>0) {
2082	*dst++ = '\n';
2083	dst_linestart = dst;
2084	if (numleft) {
2085	unsigned int num = (src-src_start)+1; // this goes to the '%u' (see comment above)
2086	dst += sprintf(dst, format, num);
2087	}
2088	else if (tab>0) {
2089	memset(dst, ' ', tab);
2090	dst += tab;
2091	}
2092	}
2093	}
2094
2095	free(format);
2096	}
2097
2098	*dst++ = 0; // close str
2099
2100	#if defined(DEBUG)
2101	{ // check for array overflow
2102	size_t used_size = dst-result;
2103	gb_assert(used_size <= needed_size);
2104	ARB_realloc(result, used_size);
2105	}
2106	#endif // DEBUG
2107	}
2108
2109	if (!error) PASS_2_OUT(args, result);
2110	else free(result);
2111	}
2112	}
2113	return error;
2114	}
2115
2116	static GB_ERROR gbl_format (GBL_command_arguments *args) { return format(args, true); }
2117	static GB_ERROR gbl_format_sequence(GBL_command_arguments *args) { return format(args, false); }
2118
2119
2120	static char gbl_read_seq_sai_or_species(GBDATA gb_main, const char species, const char sai, const char ali, size_t seqLen) {
2121	/* Reads the alignment 'ali' of 'species' or 'sai'.
2122	* If 'ali' is NULL, use default alignment.
2123	* Returns NULL in case of error (which is exported then)
2124	*/
2125
2126	char *seq = NULL;
2127	GB_ERROR error = 0;
2128
2129	int sources = !!species + !!sai;
2130	if (sources != 1) {
2131	error = "Either parameters 'species' or 'SAI' must be specified";
2132	}
2133	else {
2134	GBDATA *gb_item = 0;
2135	const char *what = 0;
2136	const char *name = 0;
2137
2138	if (species) {
2139	gb_item = GBT_find_species(gb_main, species);
2140	what = "species";
2141	name = species;
2142	}
2143	else {
2144	gb_item = GBT_find_SAI(gb_main, sai);
2145	what = "SAI";
2146	name = sai;
2147	}
2148
2149	if (!gb_item) error = GBS_global_string("Can't find %s '%s'", what, name);
2150	else {
2151	char *freeMe = 0;
2152
2153	if (!ali) {
2154	ali = freeMe = GBT_get_default_alignment(gb_main);
2155	if (!ali) error = "can't detect default alignment";
2156	}
2157
2158	if (ali) {
2159	GBDATA *gb_ali = GB_entry(gb_item, ali);
2160
2161	if (gb_ali) {
2162	GBDATA *gb_seq;
2163
2164	for (gb_seq = GB_child(gb_ali); gb_seq; gb_seq = GB_nextChild(gb_seq)) {
2165	long type = GB_read_type(gb_seq);
2166	if (type == GB_BITS) {
2167	seq = GB_read_bits(gb_seq, '-', '+');
2168	if (seqLen) *seqLen = GB_read_bits_count(gb_seq);
2169	break;
2170	}
2171	if (type == GB_STRING) {
2172	seq = GB_read_string(gb_seq);
2173	if (seqLen) *seqLen = GB_read_string_count(gb_seq);
2174	break;
2175	}
2176	}
2177	}
2178
2179	if (!seq) error = GBS_global_string("%s '%s' has no (usable) data in alignment '%s'", what, name, ali);
2180	}
2181	free(freeMe);
2182	}
2183	}
2184
2185	if (error) {
2186	gb_assert(!seq);
2187	GB_export_error(error);
2188	}
2189
2190	return seq;
2191	}
2192
2193	struct common_filter_params {
2194	const char *align;
2195	const char *sai;
2196	const char *species;
2197	int first;
2198	int pairwise;
2199	};
2200
2201	#define GBL_COMMON_FILTER_PARAMS \
2202	common_filter_params common_param; \
2203	GBL_STRUCT_PARAM_STRING(common_param, align, "align=", 0, "alignment to use (defaults to default alignment)"); \
2204	GBL_STRUCT_PARAM_STRING(common_param, sai, "SAI=", 0, "Use default sequence of given SAI as a filter"); \
2205	GBL_STRUCT_PARAM_STRING(common_param, species, "species=", 0, "Use default sequence of given species as a filter"); \
2206	GBL_STRUCT_PARAM_BIT (common_param, first, "first=", 0, "Use 1st stream as filter for other streams"); \
2207	GBL_STRUCT_PARAM_BIT (common_param, pairwise, "pairwise=", 0, "Use 1st stream as filter for 2nd, 3rd for 4th, ...")
2208
2209	typedef char* (filter_fun)(const char seq, const char filter, size_t flen, void param);
2210	/* Note:
2211	* filter_fun has to return a heap copy of the filter-result.
2212	* if 'flen' != 0, it contains the length of 'filter'
2213	* 'param' may be any client data
2214	*/
2215
2216	static GB_ERROR apply_filters(GBL_command_arguments args, common_filter_params common, filter_fun filter_one, void *param) {
2217	GB_ERROR error = 0;
2218
2219	if (args->input.size()==0) error = "No input stream";
2220	else {
2221	int methodCount = !!common->sai + !!common->species + !!common->pairwise + !!common->first;
2222
2223	if (methodCount != 1) error = "Need exactly one of the parameters 'SAI', 'species', 'pairwise' or 'first'";
2224	else {
2225	if (common->pairwise) {
2226	if (args->input.size() % 2) error = "Using 'pairwise' requires an even number of input streams";
2227	else {
2228	int i;
2229	for (i = 1; i<args->input.size(); i += 2) {
2230	PASS_2_OUT(args, filter_one(args->input.get(i), args->input.get(i-1), 0, param));
2231	}
2232	}
2233	}
2234	else {
2235	int i = 0;
2236	char *filter = 0;
2237	size_t flen = 0;
2238
2239	if (common->first) {
2240	if (args->input.size()<2) error = "Using 'first' needs at least 2 input streams";
2241	else {
2242	const char *in = args->input.get(i++);
2243	gb_assert(in);
2244
2245	flen = strlen(in);
2246	filter = ARB_strduplen(in, flen);
2247	}
2248	}
2249	else {
2250	filter = gbl_read_seq_sai_or_species(args->get_gb_main(), common->species, common->sai, common->align, &flen);
2251	if (!filter) error = GB_await_error();
2252	}
2253
2254	gb_assert(filter \|\| error);
2255	if (filter) {
2256	for (; i<args->input.size(); ++i) {
2257	PASS_2_OUT(args, filter_one(args->input.get(i), filter, flen, param));
2258	}
2259	}
2260	free(filter);
2261	}
2262	}
2263	}
2264	return error;
2265	}
2266
2267	// -------------------------
2268	// calculate diff
2269
2270	struct diff_params {
2271	char equalC;
2272	char diffC;
2273	};
2274	static char calc_diff(const char seq, const char filter, size_t /flen/, void paramP) {
2275	// filters 'seq' through 'filter'
2276	// - replace all equal positions by 'equal_char' (if != 0)
2277	// - replace all differing positions by 'diff_char' (if != 0)
2278
2279	diff_params param = (diff_params)paramP;
2280	char equal_char = param->equalC;
2281	char diff_char = param->diffC;
2282
2283	char *result = ARB_strdup(seq);
2284	int p;
2285
2286	for (p = 0; result[p] && filter[p]; ++p) {
2287	if (result[p] == filter[p]) {
2288	if (equal_char) result[p] = equal_char;
2289	}
2290	else {
2291	if (diff_char) result[p] = diff_char;
2292	}
2293	}
2294
2295	// if 'seq' is longer than 'filter' and diff_char is given
2296	// -> fill rest of 'result' with 'diff_char'
2297	if (diff_char) {
2298	for (; result[p]; ++p) {
2299	result[p] = diff_char;
2300	}
2301	}
2302
2303	return result;
2304	}
2305	static GB_ERROR gbl_diff(GBL_command_arguments *args) {
2306	GBL_BEGIN_PARAMS;
2307	GBL_COMMON_FILTER_PARAMS;
2308
2309	diff_params param;
2310	GBL_STRUCT_PARAM_CHAR(param, equalC, "equal=", '.', "symbol for equal characters");
2311	GBL_STRUCT_PARAM_CHAR(param, diffC, "differ=", 0, "symbol for diff characters (default: use char from input stream)");
2312
2313	GBL_TRACE_PARAMS(args);
2314	GBL_END_PARAMS;
2315
2316	return apply_filters(args, &common_param, calc_diff, &param);
2317	}
2318
2319	// -------------------------
2320	// standard filter
2321
2322	enum filter_function { FP_FILTER, FP_MODIFY };
2323
2324	struct filter_params { // used by gbl_filter and gbl_change_gc
2325	filter_function function;
2326
2327	const char *include;
2328	const char *exclude;
2329
2330	// FP_MODIFY only:
2331	int change_pc;
2332	const char *change_to;
2333	};
2334
2335	static char filter_seq(const char seq, const char filter, size_t flen, void paramP) {
2336	filter_params param = (filter_params)paramP;
2337
2338	size_t slen = strlen(seq);
2339	if (!flen) flen = strlen(filter);
2340	size_t mlen = slen<flen ? slen : flen;
2341
2342	GBS_strstruct *out = GBS_stropen(mlen+1); // +1 to avoid invalid, zero-length buffer
2343
2344	const char *charset;
2345	int include;
2346
2347	if (param->include) {
2348	charset = param->include;
2349	include = 1;
2350	}
2351	else {
2352	gb_assert(param->exclude);
2353	charset = param->exclude;
2354	include = 0;
2355	}
2356
2357	size_t pos = 0;
2358	size_t rest = slen;
2359	size_t ctl = 0;
2360	if (param->function == FP_MODIFY) ctl = strlen(param->change_to);
2361
2362	int inset = 1; // 1 -> check chars in charset, 0 -> check chars NOT in charset
2363	while (rest) {
2364	size_t count;
2365	if (pos >= flen) { // behind filter
2366	// trigger last loop
2367	count = rest;
2368	inset = 0; // if 'include' -> 'applies' will get false, otherwise true
2369	// (meaning is: behind filter nothing can match 'include' or 'exclude')
2370	}
2371	else {
2372	count = (inset ? strspn : strcspn)(filter+pos, charset); // count how many chars are 'inset'
2373	}
2374	if (count) {
2375	int applies = !!include == !!inset; // true -> 'filter' matches 'include' or doesn't match 'exclude'
2376	if (count>rest) count = rest;
2377
2378	switch (param->function) {
2379	case FP_FILTER:
2380	if (applies) GBS_strncat(out, seq+pos, count);
2381	break;
2382
2383	case FP_MODIFY:
2384	if (applies) { // then modify
2385	size_t i;
2386	for (i = 0; i<count; i++) {
2387	char c = seq[pos+i];
2388	if (isalpha(c) && GB_random(100)<param->change_pc) c = param->change_to[GB_random(ctl)];
2389	GBS_chrcat(out, c);
2390	}
2391	}
2392	else { // otherwise simply copy
2393	GBS_strncat(out, seq+pos, count);
2394	}
2395	break;
2396	}
2397
2398	pos += count;
2399	rest -= count;
2400	}
2401	inset = 1-inset; // toggle
2402	}
2403	return GBS_strclose(out);
2404	}
2405
2406	static GB_ERROR gbl_filter(GBL_command_arguments *args) {
2407	GBL_BEGIN_PARAMS;
2408	GBL_COMMON_FILTER_PARAMS;
2409
2410	filter_params param;
2411	GBL_STRUCT_PARAM_STRING(param, exclude, "exclude=", 0, "Exclude colums");
2412	GBL_STRUCT_PARAM_STRING(param, include, "include=", 0, "Include colums");
2413	param.function = FP_FILTER;
2414
2415	GBL_TRACE_PARAMS(args);
2416	GBL_END_PARAMS;
2417
2418	GB_ERROR error = 0;
2419	int inOrEx = !!param.include + !!param.exclude;
2420
2421	if (inOrEx != 1) error = "Need exactly one parameter of: 'include', 'exclude'";
2422	else error = apply_filters(args, &common_param, filter_seq, &param);
2423
2424	return error;
2425	}
2426
2427	static GB_ERROR gbl_change_gc(GBL_command_arguments *args) {
2428	GBL_BEGIN_PARAMS;
2429	GBL_COMMON_FILTER_PARAMS;
2430
2431	filter_params param;
2432	GBL_STRUCT_PARAM_STRING(param, exclude, "exclude=", 0, "Exclude colums");
2433	GBL_STRUCT_PARAM_STRING(param, include, "include=", 0, "Include colums");
2434	GBL_STRUCT_PARAM_INT (param, change_pc, "change=", 0, "percentage of changed columns (default: silently change nothing)");
2435	GBL_STRUCT_PARAM_STRING(param, change_to, "to=", "GC", "change to one of this");
2436	param.function = FP_MODIFY;
2437
2438	GBL_TRACE_PARAMS(args);
2439	GBL_END_PARAMS;
2440
2441	GB_ERROR error = 0;
2442	int inOrEx = !!param.include + !!param.exclude;
2443
2444	if (inOrEx != 1) error = "Need exactly one parameter of: 'include', 'exclude'";
2445	else {
2446	error = apply_filters(args, &common_param, filter_seq, &param);
2447	}
2448
2449	return error;
2450	}
2451
2452	static GB_ERROR gbl_exec(GBL_command_arguments *args) {
2453	EXPECT_PARAMS_PASSED(args, "command[,arguments]+");
2454
2455	// write inputstreams to temp file:
2456	GB_ERROR error = 0;
2457	char *inputname;
2458	int i;
2459	{
2460	char *filename = GB_unique_filename("arb_exec_input", "tmp");
2461	FILE *out = GB_fopen_tempfile(filename, "wt", &inputname);
2462
2463	if (!out) error = GB_await_error();
2464	else {
2465	for (i=0; i<args->input.size(); i++) {
2466	fprintf(out, "%s\n", args->input.get(i));
2467	}
2468	fclose(out);
2469	}
2470	free(filename);
2471	}
2472
2473	if (!error) {
2474	// build shell command to execute
2475	char *sys;
2476	{
2477	GBS_strstruct *str = GBS_stropen(1000);
2478
2479	GBS_strcat(str, args->get_param(0));
2480	for (i=1; i<args->param_count(); i++) {
2481	GBS_strcat(str, " \'");
2482	GBS_strcat(str, args->get_param(i)); // @@@ use GBK_singlequote here?
2483	GBS_chrcat(str, '\'');
2484	}
2485	GBS_strcat(str, " <");
2486	GBS_strcat(str, inputname);
2487
2488	sys = GBS_strclose(str);
2489	}
2490
2491	char *result = 0;
2492	{
2493	FILE *in = popen(sys, "r");
2494	if (in) {
2495	GBS_strstruct *str = GBS_stropen(4096);
2496
2497	while ((i=getc(in)) != EOF) { GBS_chrcat(str, i); }
2498	result = GBS_strclose(str);
2499	pclose(in);
2500	}
2501	else {
2502	error = GBS_global_string("Cannot execute shell command '%s'", sys);
2503	}
2504	}
2505
2506	if (!error) {
2507	gb_assert(result);
2508	PASS_2_OUT(args, result);
2509	}
2510
2511	free(sys);
2512	}
2513
2514	gb_assert(GB_is_privatefile(inputname, false));
2515	GB_unlink_or_warn(inputname, &error);
2516	free(inputname);
2517
2518	return error;
2519	}
2520
2521
2522	static GBL_command_definition gbl_command_table[] = {
2523	{ "ali_name", gbl_ali_name },
2524	{ "caps", gbl_caps },
2525	{ "change", gbl_change_gc },
2526	{ "checksum", gbl_checksum },
2527	{ "command", gbl_command },
2528	{ "compare", gbl_compare },
2529	{ "icompare", gbl_icompare },
2530	{ "contains", gbl_contains },
2531	{ "icontains", gbl_icontains },
2532	{ "count", gbl_count },
2533	{ "crop", gbl_crop },
2534	{ "cut", gbl_cut },
2535	{ "dd", gbl_dd },
2536	{ "define", gbl_define },
2537	{ "diff", gbl_diff },
2538	{ "div", gbl_div },
2539	{ "fdiv", gbl_fdiv },
2540	{ "do", gbl_do },
2541	{ "drop", gbl_drop },
2542	{ "dropempty", gbl_dropempty },
2543	{ "dropzero", gbl_dropzero },
2544	{ "echo", gbl_echo },
2545	{ "equals", gbl_equals },
2546	{ "iequals", gbl_iequals },
2547	{ "escape", gbl_escape },
2548	{ "unescape", gbl_unescape },
2549	{ "eval", gbl_eval },
2550	{ "exec", gbl_exec },
2551	{ "export_sequence", gbl_export_sequence },
2552	{ "extract_sequence", gbl_extract_sequence },
2553	{ "extract_words", gbl_extract_words },
2554	{ "filter", gbl_filter },
2555	{ "format", gbl_format },
2556	{ "format_sequence", gbl_format_sequence },
2557	{ "gcgchecksum", gbl_gcgchecksum },
2558	{ "head", gbl_head },
2559	{ "inRange", gbl_inRange },
2560	{ "isAbove", gbl_isAbove },
2561	{ "isBelow", gbl_isBelow },
2562	{ "isEqual", gbl_isEqual },
2563	{ "isEmpty", gbl_isEmpty },
2564	{ "keep", gbl_keep },
2565	{ "left", gbl_head },
2566	{ "len", gbl_len },
2567	{ "lower", gbl_lower },
2568	{ "merge", gbl_merge },
2569	{ "mid", gbl_mid },
2570	{ "mid0", gbl_mid0 },
2571	{ "minus", gbl_minus },
2572	{ "fminus", gbl_fminus },
2573	{ "mult", gbl_mult },
2574	{ "fmult", gbl_fmult },
2575	{ "and", gbl_and },
2576	{ "or", gbl_or },
2577	{ "not", gbl_not },
2578	{ "origin_gene", gbl_origin_gene },
2579	{ "origin_organism", gbl_origin_organism },
2580	{ "partof", gbl_partof },
2581	{ "ipartof", gbl_ipartof },
2582	{ "per_cent", gbl_per_cent },
2583	{ "fper_cent", gbl_fper_cent },
2584	{ "plus", gbl_plus },
2585	{ "fplus", gbl_fplus },
2586	{ "pretab", gbl_pretab },
2587	{ "quote", gbl_quote },
2588	{ "unquote", gbl_unquote },
2589	{ "readdb", gbl_readdb },
2590	{ "remove", gbl_remove },
2591	{ "rest", gbl_rest },
2592	{ "right", gbl_tail },
2593	{ "round", gbl_round },
2594	{ "select", gbl_select },
2595	{ "sequence", gbl_sequence },
2596	{ "sequence_type", gbl_sequence_type },
2597	{ "split", gbl_split },
2598	{ "srt", gbl_srt },
2599	{ "streams", gbl_streams },
2600	{ "swap", gbl_swap },
2601	{ "tab", gbl_tab },
2602	{ "tail", gbl_tail },
2603	{ "taxonomy", gbl_taxonomy },
2604	{ "toback", gbl_toback },
2605	{ "tofront", gbl_tofront },
2606	{ "trace", gbl_trace },
2607	{ "translate", gbl_translate },
2608	{ "upper", gbl_upper },
2609
2610	{ 0, 0 }
2611	};
2612
2613	const GBL_command_lookup_table& ACI_get_standard_commands() {
2614	static GBL_command_lookup_table clt(gbl_command_table, ARRAY_ELEMS(gbl_command_table)-1);
2615	return clt;
2616	}
2617

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