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source: tags/ms_r16q3/ARBDB/adlang1.cxx

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Last change on this file was 15176, checked in by westram, 9 years ago
reintegrates 'fixres' into 'trunk' fixes #715 adds: log:branches/fixres@15127:15175
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 90.6 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.h"
12	#include "gb_key.h"
13	#include "gb_localdata.h"
14
15	#include <adGene.h>
16	#include "TreeNode.h"
17	#include <ad_cb.h>
18
19	#include <arb_defs.h>
20	#include <arb_strbuf.h>
21	#include <arb_file.h>
22	#include <aw_awar_defs.hxx>
23
24	#include <cctype>
25	#include <cmath>
26	#include <algorithm>
27
28	// hook for 'export_sequence'
29
30	static gb_export_sequence_cb get_export_sequence = 0;
31
32	NOT4PERL void GB_set_export_sequence_hook(gb_export_sequence_cb escb) {
33	gb_assert(!get_export_sequence \|\| !escb); // avoid unwanted overwrite
34	get_export_sequence = escb;
35	}
36
37	// global ACI/SRT debug switch
38	static int trace = 0;
39
40	void GB_set_ACISRT_trace(int enable) { trace = enable; }
41	int GB_get_ACISRT_trace() { return trace; }
42
43
44	// export stream
45
46	#define PASS_2_OUT(args,s) (args)->output.insert(s)
47	#define COPY_2_OUT(args,s) PASS_2_OUT(args, ARB_strdup(s))
48	#define IN_2_OUT(args,i) PASS_2_OUT(args, args->input.get_smart(i))
49	#define PARAM_2_OUT(args,i) PASS_2_OUT(args, args->param.get_smart(i))
50
51	// ----------------------------
52	// Parameter functions
53
54	struct gbl_param {
55	gbl_param *next;
56	GB_TYPES type; // type of variable
57	void *varaddr; // address of variable where value gets stored
58	const char *param_name; // parameter name (e.g. 'include=')
59	const char *help_text; // help text for parameter
60	};
61
62	#define GBL_BEGIN_PARAMS gbl_param *params = 0
63
64	static void gbl_new_param(gbl_param *pp, GB_TYPES type, void vaddr, const char param_name, const char help_text) {
65	gbl_param *gblp = ARB_calloc<gbl_param>(1);
66
67	gblp->next = *pp;
68	*pp = gblp;
69
70	gblp->type = type;
71	gblp->varaddr = vaddr;
72	gblp->param_name = param_name;
73	gblp->help_text = help_text;
74	}
75
76	typedef const char *String;
77	typedef int bit;
78	typedef unsigned int uint;
79
80	static int gbl_param_int(const char param_name, int def, const char help_text, gbl_param *pp, int vaddr) {
81	gbl_new_param(pp, GB_INT, vaddr, param_name, help_text);
82	return def;
83	}
84
85	static char gbl_param_char(const char param_name, char def, const char help_text, gbl_param *pp, char vaddr) {
86	gbl_new_param(pp, GB_BYTE, vaddr, param_name, help_text);
87	return def;
88	}
89
90	static uint gbl_param_uint(const char param_name, uint def, const char help_text, gbl_param *pp, uint vaddr) {
91	gbl_new_param(pp, GB_INT, vaddr, param_name, help_text);
92	return def;
93	}
94
95	static const char gbl_param_String(const char param_name, const char def, const char help_text, gbl_param *pp, String vaddr) {
96	gbl_new_param(pp, GB_STRING, vaddr, param_name, help_text);
97	return def;
98	}
99
100	static int gbl_param_bit(const char param_name, int def, const char help_text, gbl_param *pp, bit vaddr) {
101	gbl_new_param(pp, GB_BIT, vaddr, param_name, help_text);
102	return def;
103	}
104
105	#define GBL_PARAM_TYPE(type, var, param_name, def, help_text) type var = gbl_param_##type(param_name, def, help_text, &params, &var)
106	#define GBL_STRUCT_PARAM_TYPE(type, strct, member, param_name, def, help_text) strct.member = gbl_param_##type(param_name, def, help_text, &params, &strct.member)
107
108	// use PARAM_IF for parameters whose existence depends on condition
109	#define PARAM_IF(cond,param) ((cond) ? (param) : NULL)
110
111	#define GBL_PARAM_INT(var, param_name, def, help_text) GBL_PARAM_TYPE(int, var, param_name, def, help_text)
112	#define GBL_PARAM_CHAR(var, param_name, def, help_text) GBL_PARAM_TYPE(char, var, param_name, def, help_text)
113	#define GBL_PARAM_UINT(var, param_name, def, help_text) GBL_PARAM_TYPE(uint, var, param_name, def, help_text)
114	#define GBL_PARAM_STRING(var, param_name, def, help_text) GBL_PARAM_TYPE(String, var, param_name, def, help_text)
115	#define GBL_PARAM_BIT(var, param_name, def, help_text) GBL_PARAM_TYPE(bit, var, param_name, def, help_text)
116
117	#define GBL_STRUCT_PARAM_INT(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(int, strct, member, param_name, def, help_text)
118	#define GBL_STRUCT_PARAM_CHAR(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(char, strct, member, param_name, def, help_text)
119	#define GBL_STRUCT_PARAM_UINT(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(uint, strct, member, param_name, def, help_text)
120	#define GBL_STRUCT_PARAM_STRING(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(String, strct, member, param_name, def, help_text)
121	#define GBL_STRUCT_PARAM_BIT(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(bit, strct, member, param_name, def, help_text)
122
123	#define GBL_TRACE_PARAMS(args) \
124	do { \
125	GB_ERROR def_error = \
126	trace_params((args)->param, params, (args)->command); \
127	if (def_error) { GBL_END_PARAMS; return def_error; } \
128	} while(0)
129
130	#define GBL_END_PARAMS \
131	do { \
132	gbl_param *_gblp; \
133	while (params) { \
134	_gblp = params; \
135	params = params->next; \
136	free(_gblp); \
137	} \
138	} while (0)
139
140	#define GBL_CHECK_FREE_PARAM(nr, cnt) \
141	do { \
142	if ((nr)+(cnt) >= GBL_MAX_ARGUMENTS) { \
143	/* gb_assert(0); */ \
144	return "max. parameters exceeded"; \
145	} \
146	} while (0)
147
148	#if defined(WARN_TODO)
149	#warning remove GBL_MAX_ARGUMENTS - instead allocate dynamic
150	#endif
151
152	static GB_ERROR trace_params(const GBL_streams& param, gbl_param ppara, const char com) {
153	GB_ERROR error = 0;
154	int i;
155
156	int argc = param.size();
157	for (i=0; i<argc; i++) {
158	gbl_param *para;
159	const char *argument = param.get(i);
160
161	for (para = ppara; para && !error; para = para->next) {
162	if (para->param_name) { // NULL means param is inactive (see PARAM_IF)
163	int len = strlen(para->param_name);
164
165	if (strncmp(argument, para->param_name, len) == 0) {
166	const char *value = argument+len; // set to start of value
167
168	if (para->type == GB_BIT) {
169	// GB_BIT is special cause param_name does NOT contain trailing '='
170
171	if (!value[0]) { // only 'name' -> handle like 'name=1'
172	;
173	}
174	else if (value[0] == '=') {
175	value++;
176	}
177	}
178
179	switch (para->type) {
180	case GB_STRING:
181	(const char *)para->varaddr = value;
182	break;
183
184	case GB_INT:
185	STATIC_ASSERT(sizeof(int) == sizeof(uint)); // assumed by GBL_PARAM_UINT
186	(int )para->varaddr = atoi(value);
187	break;
188
189	case GB_BIT:
190	// 'param=' is same as 'param' or 'param=1' (historical reason, don't change)
191	(int )para->varaddr = (value[0] ? atoi(value) : 1);
192	break;
193
194	case GB_BYTE:
195	(char )para->varaddr = *value; // this may use the terminal zero-byte (e.g. for p1 in 'p0=0,p1=,p2=2' )
196	if (value[0] && value[1]) { // found at least 2 chars
197	GB_warningf("Only one character expected in value '%s' of param '%s' - rest is ignored", value, para->param_name);
198	}
199	break;
200
201	default:
202	gb_assert(0);
203	error = GBS_global_string("Parameter '%s': Unknown type %i (internal error)", para->param_name, para->type);
204	break;
205	}
206	break; // accept parameter
207	}
208	}
209	}
210
211	if (!error && !para) { // no parameter found for argument
212	int pcount = 0;
213	gbl_param **params;
214	int k;
215	char *res;
216	GBS_strstruct *str = GBS_stropen(1000);
217	GB_ERROR err;
218
219
220	for (para = ppara; para; para = para->next) pcount++;
221	ARB_calloc(params, pcount);
222	for (k = 0, para = ppara; para; para = para->next) params[k++] = para;
223
224
225	for (pcount--; pcount>=0; pcount--) {
226	para = params[pcount];
227	if (para->param_name) {
228	GBS_strcat(str, " ");
229	GBS_strcat(str, para->param_name);
230	switch (para->type) {
231	case GB_STRING: GBS_strcat(str, "STRING"); break;
232	case GB_INT: GBS_strcat(str, "INT"); break;
233	case GB_FLOAT: GBS_strcat(str, "FLOAT"); break;
234	case GB_BYTE: GBS_strcat(str, "CHAR"); break;
235	case GB_BIT: GBS_strcat(str, " "); break;
236	default: gb_assert (0); GBS_strcat(str, "????"); break;
237	}
238	GBS_strcat(str, "\t\t;");
239	GBS_strcat(str, para->help_text);
240	GBS_strcat(str, "\n");
241	}
242	}
243	freenull(params);
244	res = GBS_strclose(str);
245	err = GB_export_errorf("Unknown Parameter '%s' in command '%s'\n PARAMETERS:\n%s", argument, com, res);
246	free(res);
247	return err;
248	}
249	}
250
251	return error;
252	}
253
254	inline char interpret_subcommand(const GBL_reference& ref, const char input, const char *command) {
255	return GB_command_interpreter(ref.get_main(), input, command, ref.get_ref(), ref.get_tree_name());
256	}
257
258	// --------------------------------
259	// parameter/stream checks
260
261	inline GB_ERROR check_no_parameter(GBL_command_arguments *args) {
262	if (args->param.size() == 0) return NULL;
263	return GBS_global_string("syntax: %s (no parameters)", args->command);
264	}
265	inline GB_ERROR check_parameters(GBL_command_arguments args, int expected, const char parameterList) {
266	if (args->param.size() == expected) return NULL;
267	return GBS_global_string("syntax: %s(%s)", args->command, parameterList);
268	}
269	inline GB_ERROR check_optional_parameters(GBL_command_arguments args, int fix, const char fixParam, int opt, const char *optParam, bool opt_trailing = true) {
270	int params = args->param.size();
271	if (params >= fix && params <= (fix+opt)) return NULL;
272	if (!fix) return GBS_global_string("syntax: %s[(%s)]", args->command, optParam);
273	if (opt_trailing) return GBS_global_string("syntax: %s(%s[,%s])", args->command, fixParam, optParam);
274	return GBS_global_string("syntax: %s([%s,]%s)", args->command, optParam, fixParam);
275	}
276
277	inline GB_ERROR check_valid_index(int number, const char *what, int min, int max) {
278	if (number >= min && number <= max) return NULL;
279	return GBS_global_string("Illegal %s number '%i' (allowed [%i..%i])", what, number, min, max);
280	}
281	inline GB_ERROR check_valid_stream_index(GBL_command_arguments *args, int number) { return check_valid_index(number, "stream", 1, args->input.size()); }
282	inline GB_ERROR check_valid_param_index (GBL_command_arguments *args, int number) { return check_valid_index(number, "param", 0, args->param.size()-1); }
283
284	#define EXPECT_NO_PARAM(args) do { \
285	GB_ERROR perr = check_no_parameter(args); \
286	if (perr) return perr; \
287	} while(0)
288
289	#define EXPECT_PARAMS(args,count,help) do { \
290	GB_ERROR perr = check_parameters(args, count, help); \
291	if (perr) return perr; \
292	} while(0)
293
294	#define EXPECT_OPTIONAL_PARAMS(args,fixcount,fixhelp,optcount,opthelp) do { \
295	GB_ERROR perr = check_optional_parameters(args, fixcount, fixhelp, optcount, opthelp); \
296	if (perr) return perr; \
297	} while(0)
298
299	#define EXPECT_LEGAL_STREAM_INDEX(args,number) do { \
300	GB_ERROR serr = check_valid_stream_index(args, number); \
301	if (serr) return serr; \
302	} while(0)
303
304	#define COMMAND_DROPS_INPUT_STREAMS(args) do { \
305	if (trace && args->input.size()>0) { \
306	if (args->input.size()>1 \|\| args->input.get(0)[0]) { \
307	printf("Warning: Dropped %i input streams\n", \
308	args->input.size()); \
309	} \
310	} \
311	} while(0)
312
313	// -------------------------
314	// String functions
315
316	static int gbl_stricmp(const char s1, const char s2) {
317	// case insensitive strcmp
318	int i;
319	for (i = 0; ; ++i) {
320	char c1 = tolower(s1[i]);
321	char c2 = tolower(s2[i]);
322
323	if (c1 == c2) {
324	if (!c1) break; // equal strings
325	}
326	else {
327	if (c1<c2) return -1;
328	return 1;
329	}
330	}
331	return 0;
332	}
333	static int gbl_strincmp(const char s1, const char s2, int size2) {
334	// case insensitive strcmp
335	int i;
336	for (i = 0; i<size2; ++i) {
337	char c1 = tolower(s1[i]);
338	char c2 = tolower(s2[i]);
339
340	if (c1 == c2) {
341	if (!c1) break; // equal strings
342	}
343	else {
344	if (c1<c2) return -1;
345	return 1;
346	}
347	}
348	return 0;
349	}
350	static const char gbl_stristr(const char haystack, const char *needle) {
351	// case insensitive strstr
352	const char *hp = haystack;
353	char c1 = toupper(needle[0]);
354	char c2 = tolower(c1);
355	int needle_size = strlen(needle);
356
357	if (c1 == c2) {
358	hp = strchr(hp, c1);
359	while (hp) {
360	if (gbl_strincmp(hp, needle, needle_size) == 0) return hp;
361	hp = strchr(hp+1, c1);
362	}
363	}
364	else {
365	while (hp) {
366	const char *h1 = strchr(hp, c1);
367	const char *h2 = strchr(hp, c2);
368
369	if (h1 && h2) {
370	if (h1<h2) {
371	if (gbl_strincmp(h1, needle, needle_size) == 0) return h1;
372	hp = h1+1;
373	}
374	else {
375	gb_assert(h1>h2);
376	if (gbl_strincmp(h2, needle, needle_size) == 0) return h2;
377	hp = h2+1;
378	}
379	}
380	else {
381	if (h1) { hp = h1; }
382	else if (h2) { hp = h2; c1 = c2; }
383	else { hp = 0; }
384
385	while (hp) {
386	if (gbl_strincmp(hp, needle, needle_size) == 0) return hp;
387	hp = strchr(hp+1, c1);
388	}
389	}
390	}
391	}
392	return 0;
393	}
394
395	inline int approve_pos(int pos, int len) { return pos<0 ? (-pos<len ? len+pos : 0) : pos; }
396
397	static GB_ERROR gbl_mid_streams(const GBL_streams& arg_input, GBL_streams& arg_out, int start, int end) {
398	// used as well to copy all streams (e.g. by 'dd')
399	for (int i=0; i<arg_input.size(); i++) {
400	const char *p = arg_input.get(i);
401	int len = strlen(p);
402
403	int s = approve_pos(start, len);
404	int e = approve_pos(end, len);
405
406	char *res;
407	if (s >= len \|\| e<s) {
408	res = ARB_strdup("");
409	}
410	else {
411	gb_assert(s >= 0);
412	res = ARB_strpartdup(p+s, p+e);
413	}
414	arg_out.insert(res);
415	}
416	return 0;
417	}
418
419	static GB_ERROR gbl_trace(GBL_command_arguments *args) {
420	int tmp_trace;
421
422	EXPECT_PARAMS(args, 1, "0\|1");
423
424	tmp_trace = atoi(args->param.get(0));
425	if (tmp_trace<0 \|\| tmp_trace>1) return GBS_global_string("Illegal value %i to trace", tmp_trace);
426
427	if (tmp_trace != GB_get_ACISRT_trace()) {
428	printf("* %sctivated ACI trace *\n", tmp_trace ? "A" : "De-a");
429	GB_set_ACISRT_trace(tmp_trace);
430	}
431
432	return gbl_mid_streams(args->input, args->output, 0, -1); // copy all streams
433	}
434
435	/* ---------------------------------------------------------------------------------------
436	* Binary operators work on pairs of values.
437	* Three different operational modes are implemented for all binary operators:
438	*
439	* 1. inputstreams\|operator
440	*
441	* The number of inputstreams has to be even and the operator will be
442	* applied to pairs of them.
443	*
444	* Example : a;b;c;d;e;f \| plus
445	* Result : a+b;c+d;e+f
446	*
447	* 2. inputstreams\|operator(x)
448	*
449	* The number of inputstreams has to be at least 1.
450	* The operator is applied to each inputstream.
451	*
452	* Example : a;b;c \| plus(d)
453	* Result : a+d;b+d;c+d
454	*
455	* 3. operator(x, y)
456	*
457	* @@@ this decription does not match behavior!
458	* @@@ check description in helpfile as well
459	*
460	* Inputstreams will be ignored and the operator is applied
461	* to the arguments
462	*
463	* Example : a;b \| plus(c,d)
464	* Result : c+d
465	*/
466
467	typedef char* (gbl_binary_operator)(const char arg1, const char arg2, void client_data);
468
469	static GB_ERROR gbl_apply_binary_operator(GBL_command_arguments args, gbl_binary_operator op, void client_data) {
470	GB_ERROR error = 0;
471	switch (args->param.size()) {
472	case 0:
473	if (args->input.size() == 0) error = "Expect at least two input streams if called with 0 parameters";
474	else if (args->input.size()%2) error = "Expect an even number of input streams if called with 0 parameters";
475	else {
476	int inputpairs = args->input.size()/2;
477	int i;
478	for (i = 0; i<inputpairs; ++i) {
479	PASS_2_OUT(args, op(args->input.get(i2), args->input.get(i2+1), client_data));
480	}
481	}
482	break;
483
484	case 1:
485	if (args->input.size() == 0) error = "Expect at least one input stream if called with 1 parameter";
486	else {
487	int i;
488	const char *argument = args->param.get(0);
489	for (i = 0; i<args->input.size(); ++i) {
490	PASS_2_OUT(args, op(args->input.get(i), argument, client_data));
491	}
492	}
493	break;
494
495	case 2:
496	for (int i = 0; i<args->input.size(); ++i) {
497	char result1 = interpret_subcommand(args, args->input.get(i), args->param.get(0));
498	if (!result1) error = GB_await_error();
499	else {
500	char result2 = interpret_subcommand(args, args->input.get(i), args->param.get(1));
501	if (!result2) error = GB_await_error();
502	else {
503	PASS_2_OUT(args, op(result1, result2, client_data));
504	free(result2);
505	}
506	free(result1);
507	}
508	}
509	break;
510
511	default:
512	error = check_optional_parameters(args, 0, NULL, 2, "Expr1[,Expr2]");
513	break;
514	}
515
516	return error;
517	}
518
519	// --------------------------------
520	// escape/unescape strings
521
522	static char unEscapeString(const char escapedString) {
523	// replaces all \x by x
524	char *result = nulldup(escapedString);
525	char *to = result;
526	char *from = result;
527
528	while (1) {
529	char c = *from++;
530	if (!c) break;
531
532	if (c=='\\') {
533	to++ = from++;
534	}
535	else {
536	*to++ = c;
537	}
538	}
539	*to = 0;
540	return result;
541	}
542	static char escapeString(const char unescapedString) {
543	// replaces all '\' and '"' by '\\' and '\"'
544	int len = strlen(unescapedString);
545	char result = ARB_alloc<char>(2len+1);
546	char *to = result;
547	const char *from = unescapedString;
548
549	while (1) {
550	char c = *from++;
551	if (!c) break;
552
553	if (c=='\\' \|\| c == '\"') {
554	*to++ = '\\';
555	*to++ = c;
556	}
557	else {
558	*to++ = c;
559	}
560	}
561	*to = 0;
562	return result;
563	}
564
565	// ---------------------------------
566	// the commands themselves:
567
568	static GB_ERROR gbl_quote(GBL_command_arguments *args) {
569	EXPECT_NO_PARAM(args);
570
571	for (int i=0; i<args->input.size(); i++) {
572	char *quoted = GBS_global_string_copy("\"%s\"", args->input.get(i));
573	PASS_2_OUT(args, quoted);
574	}
575	return NULL;
576	}
577	static GB_ERROR gbl_unquote(GBL_command_arguments *args) {
578	EXPECT_NO_PARAM(args);
579
580	for (int i=0; i<args->input.size(); i++) {
581	const char *str = args->input.get(i);
582	int len = strlen(str);
583
584	if (str[0] == '\"' && str[len-1] == '\"') {
585	PASS_2_OUT(args, ARB_strpartdup(str+1, str+len-2));
586	}
587	else {
588	IN_2_OUT(args, i);
589	}
590	}
591	return NULL;
592	}
593
594	static GB_ERROR gbl_escape(GBL_command_arguments *args) {
595	EXPECT_NO_PARAM(args);
596
597	for (int i=0; i<args->input.size(); i++) {
598	char *escaped = escapeString(args->input.get(i));
599	PASS_2_OUT(args, escaped);
600	}
601	return NULL;
602	}
603	static GB_ERROR gbl_unescape(GBL_command_arguments *args) {
604	EXPECT_NO_PARAM(args);
605
606	for (int i=0; i<args->input.size(); i++) {
607	char *unescaped = unEscapeString(args->input.get(i));
608	PASS_2_OUT(args, unescaped);
609	}
610	return NULL;
611	}
612
613	static GB_ERROR gbl_command(GBL_command_arguments *args) {
614	EXPECT_PARAMS(args, 1, "\"ACI command\"");
615
616	GB_ERROR error = NULL;
617	char *command = unEscapeString(args->param.get(0));
618	#if defined(DEBUG)
619	printf("executing command '%s'\n", command);
620	#endif
621
622	for (int i=0; i<args->input.size() && !error; i++) {
623	char result = interpret_subcommand(args, args->input.get(i), command);
624	if (!result) error = GB_await_error();
625	else PASS_2_OUT(args, result);
626	}
627	free(command);
628	return error;
629	}
630
631	static GB_ERROR gbl_eval(GBL_command_arguments *args) {
632	EXPECT_PARAMS(args, 1, "\"expression evaluating to ACI command\"");
633
634	GB_ERROR error = NULL;
635	char *to_eval = unEscapeString(args->param.get(0));
636	char command = interpret_subcommand(args, "", to_eval); // evaluate independent
637
638	if (!command) error = GB_await_error();
639	else {
640	if (GB_get_ACISRT_trace()) {
641	printf("evaluating '%s'\n", to_eval);
642	printf("executing '%s'\n", command);
643	}
644
645	for (int i=0; i<args->input.size() && !error; i++) {
646	char result = interpret_subcommand(args, args->input.get(i), command);
647	if (!result) error = GB_await_error();
648	else PASS_2_OUT(args, result);
649	}
650	free(command);
651	}
652	free(to_eval);
653	return error;
654	}
655
656	class DefinedCommands : virtual Noncopyable {
657	GB_HASH *cmds;
658	public:
659	DefinedCommands() { cmds = GBS_create_dynaval_hash(100, GB_MIND_CASE, GBS_dynaval_free); }
660	~DefinedCommands() { GBS_free_hash(cmds); }
661
662	void set(const char name, char cmd) { GBS_dynaval_free(GBS_write_hash(cmds, name, (long)cmd)); } // takes ownership of 'cmd'!
663	const char get(const char name) const { return (const char *)GBS_read_hash(cmds, name); }
664	};
665
666	static DefinedCommands defined_commands;
667
668	static GB_ERROR gbl_define(GBL_command_arguments *args) {
669	COMMAND_DROPS_INPUT_STREAMS(args);
670	EXPECT_PARAMS(args, 2, "name, \"ACI command\"");
671
672	const char *name = args->param.get(0);
673	char *cmd = unEscapeString(args->param.get(1));
674
675	defined_commands.set(name, cmd);
676	if (GB_get_ACISRT_trace()) printf("defining command '%s'='%s'\n", name, cmd);
677	return NULL;
678	}
679
680	static GB_ERROR gbl_do(GBL_command_arguments *args) {
681	EXPECT_PARAMS(args, 1, "definedCommandName");
682
683	GB_ERROR error = 0;
684	const char *name = args->param.get(0);
685	const char *cmd = defined_commands.get(name);
686
687	if (!cmd) {
688	error = GBS_global_string("Can't do undefined command '%s' - use define(%s, ...) first", name, name);
689	}
690	else {
691	if (GB_get_ACISRT_trace()) {
692	printf("executing defined command '%s'='%s' on %i streams\n", name, cmd, args->input.size());
693	}
694
695	for (int i=0; i<args->input.size() && !error; i++) {
696	char result = interpret_subcommand(args, args->input.get(i), cmd);
697	if (!result) error = GB_await_error();
698	else PASS_2_OUT(args, result);
699	}
700	}
701	return error;
702	}
703
704	static GB_ERROR gbl_streams(GBL_command_arguments *args) {
705	EXPECT_NO_PARAM(args);
706	PASS_2_OUT(args, GBS_global_string_copy("%i", args->input.size()));
707	return 0;
708	}
709
710	static GB_ERROR gbl_origin(GBL_command_arguments *args) {
711	EXPECT_PARAMS(args, 1, "\"ACI command\"");
712
713	GB_ERROR error = NULL;
714	if (!GEN_is_pseudo_gene_species(args->get_ref())) {
715	error = GBS_global_string("'%s' applies to gene-species only", args->command);
716	}
717	else {
718	GBDATA *gb_origin = NULL;
719	if (strcmp(args->command, "origin_organism") == 0) {
720	gb_origin = GEN_find_origin_organism(args->get_ref(), 0);
721	}
722	else {
723	gb_assert(strcmp(args->command, "origin_gene") == 0);
724	gb_origin = GEN_find_origin_gene(args->get_ref(), 0);
725	}
726
727	if (!error && !gb_origin) error = GB_await_error();
728
729	if (!error) {
730	char *command = unEscapeString(args->param.get(0));
731	GBL_reference ref(gb_origin, args->get_tree_name()); // refer to gb_origin for subcommands
732
733	for (int i=0; i<args->input.size() && !error; i++) {
734	char *result = interpret_subcommand(ref, args->input.get(i), command);
735	if (!result) error = GB_await_error();
736	else PASS_2_OUT(args, result);
737	}
738
739	free(command);
740	}
741	}
742
743	return error;
744	}
745
746	class Tab {
747	bool tab[256];
748	public:
749	Tab(bool take, const char *invert) {
750	bool init = !take;
751	for (int i = 0; i<256; ++i) tab[i] = init;
752	for (int i = 0; invert[i]; ++i) tab[safeCharIndex(invert[i])] = take;
753	}
754	bool operator[](int i) const { return tab[i]; }
755	};
756
757	inline GB_ERROR count_by_tab(GBL_command_arguments *args, const Tab& tab) {
758	for (int i=0; i<args->input.size(); ++i) {
759	long sum = 0; // count frequencies
760	const char *p = args->input.get(i);
761
762	while (p) sum += tab[safeCharIndex((p++))];
763	PASS_2_OUT(args, GBS_global_string_copy("%li", sum));
764	}
765	return NULL;
766	}
767	inline GB_ERROR remove_by_tab(GBL_command_arguments *args, const Tab& tab) {
768	for (int i=0; i<args->input.size(); ++i) {
769	GBS_strstruct *strstruct = GBS_stropen(1000);
770	for (const char p = args->input.get(i); p; p++) {
771	if (!tab[(unsigned int)*p]) {
772	GBS_chrcat(strstruct, *p);
773	}
774	}
775	PASS_2_OUT(args, GBS_strclose(strstruct));
776	}
777	return NULL;
778	}
779
780	static GB_ERROR gbl_count(GBL_command_arguments *args) {
781	EXPECT_PARAMS(args, 1, "\"characters to count\"");
782	return count_by_tab(args, Tab(true, args->param.get(0)));
783	}
784	static GB_ERROR gbl_len(GBL_command_arguments *args) {
785	EXPECT_OPTIONAL_PARAMS(args, 0, NULL, 1, "\"characters not to count\"");
786	const char *exclude = args->param.size() ? args->param.get(0) : "";
787	return count_by_tab(args, Tab(false, exclude));
788	}
789	static GB_ERROR gbl_remove(GBL_command_arguments *args) {
790	EXPECT_PARAMS(args, 1, "\"characters to remove\"");
791	return remove_by_tab(args, Tab(true, args->param.get(0)));
792	}
793	static GB_ERROR gbl_keep(GBL_command_arguments *args) {
794	EXPECT_PARAMS(args, 1, "\"characters to keep\"");
795	return remove_by_tab(args, Tab(false, args->param.get(0)));
796	}
797
798
799	static char binop_compare(const char arg1, const char arg2, void client_data) {
800	long case_sensitive = (long)client_data;
801	int result;
802
803	if (case_sensitive) result = strcmp(arg1, arg2);
804	else result = gbl_stricmp(arg1, arg2);
805
806	return GBS_global_string_copy("%i", result<0 ? -1 : (result>0 ? 1 : 0));
807	}
808	static char binop_equals(const char arg1, const char arg2, void client_data) {
809	long case_sensitive = (long)client_data;
810	int result;
811
812	if (case_sensitive) result = strcmp(arg1, arg2);
813	else result = gbl_stricmp(arg1, arg2);
814
815	return GBS_global_string_copy("%i", result == 0 ? 1 : 0);
816	}
817	static char binop_contains(const char arg1, const char arg2, void client_data) {
818	long case_sensitive = (long)client_data;
819	const char *found = 0;
820
821	if (case_sensitive) found = strstr(arg1, arg2);
822	else found = gbl_stristr(arg1, arg2);
823
824	return GBS_global_string_copy("%ti", found == 0 ? 0 : (found-arg1)+1);
825	}
826	static char binop_partof(const char arg1, const char arg2, void client_data) {
827	return binop_contains(arg2, arg1, client_data);
828	}
829
830	static GB_ERROR gbl_compare (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_compare, (void)1); }
831	static GB_ERROR gbl_icompare (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_compare, (void)0); }
832	static GB_ERROR gbl_equals (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_equals, (void)1); }
833	static GB_ERROR gbl_iequals (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_equals, (void)0); }
834	static GB_ERROR gbl_contains (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_contains, (void)1); }
835	static GB_ERROR gbl_icontains(GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_contains, (void)0); }
836	static GB_ERROR gbl_partof (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_partof, (void)1); }
837	static GB_ERROR gbl_ipartof (GBL_command_arguments args) { return gbl_apply_binary_operator(args, binop_partof, (void)0); }
838
839	static GB_ERROR gbl_translate(GBL_command_arguments *args) {
840	EXPECT_OPTIONAL_PARAMS(args, 2, "old,new", 1, "other");
841
842	char replace_other = 0;
843	if (args->param.size() == 3) {
844	const char *other = args->param.get(2);
845	if (other[0] == 0 \|\| other[1] != 0) {
846	return "third parameter of translate has to be one character (i.e. \"-\")";
847	}
848	replace_other = other[0];
849	}
850
851	// build translation table :
852	unsigned char tab[256];
853	{
854	const unsigned char o = (const unsigned char )args->param.get(0);
855	const unsigned char n = (const unsigned char )args->param.get(1);
856	char used[256];
857
858	if (strlen((const char )o) != strlen((const char )n)) {
859	return "arguments 1 and 2 of translate should be strings with identical length";
860	}
861
862	for (int i = 0; i<256; ++i) {
863	tab[i] = replace_other ? replace_other : i; // replace unused or identity translation
864	used[i] = 0;
865	}
866
867	for (int i = 0; o[i]; ++i) {
868	if (used[o[i]]) return GBS_global_string("character '%c' used twice in argument 1 of translate", o[i]);
869	used[o[i]] = 1;
870	tab[o[i]] = n[i]; // real translation
871	}
872	}
873
874	for (int i=0; i<args->input.size(); i++) {
875	GBS_strstruct *strstruct = GBS_stropen(1000);
876	for (const char p = args->input.get(i); p; p++) {
877	GBS_chrcat(strstruct, tab[(unsigned char)*p]);
878	}
879	PASS_2_OUT(args, GBS_strclose(strstruct));
880	}
881	return 0;
882	}
883
884
885	static GB_ERROR gbl_echo(GBL_command_arguments *args) {
886	COMMAND_DROPS_INPUT_STREAMS(args);
887	for (int i=0; i<args->param.size(); i++) PARAM_2_OUT(args, i);
888	return 0;
889	}
890
891	static GB_ERROR gbl_dd(GBL_command_arguments *args) {
892	EXPECT_NO_PARAM(args);
893	return gbl_mid_streams(args->input, args->output, 0, -1); // copy all streams
894	}
895
896	static GB_ERROR gbl_string_convert(GBL_command_arguments *args) {
897	EXPECT_NO_PARAM(args);
898
899	int mode = -1;
900	if (strcmp(args->command, "lower") == 0) mode = 0;
901	else if (strcmp(args->command, "upper") == 0) mode = 1;
902	else if (strcmp(args->command, "caps") == 0) mode = 2;
903	else return GB_export_errorf("Unknown command '%s'", args->command);
904
905	for (int i=0; i<args->input.size(); i++) {
906	char *p = ARB_strdup(args->input.get(i));
907	bool last_was_alnum = false;
908
909	for (char *pp = p; pp[0]; ++pp) {
910	switch (mode) {
911	case 0: pp[0] = tolower(pp[0]); break;
912	case 1: pp[0] = toupper(pp[0]); break;
913	case 2: { // caps
914	bool alnum = isalnum(pp[0]);
915	if (alnum) pp[0] = (last_was_alnum ? tolower : toupper)(pp[0]);
916	last_was_alnum = alnum;
917	break;
918	}
919	default: gb_assert(0); break;
920	}
921	}
922
923	PASS_2_OUT(args, p);
924	}
925
926	return 0;
927	}
928
929	static GB_ERROR gbl_head(GBL_command_arguments *args) {
930	EXPECT_PARAMS(args, 1, "length_of_head");
931	int start = atoi(args->param.get(0));
932	if (start <= 0) return gbl_mid_streams(args->input, args->output, 1, 0); // empty all streams
933	return gbl_mid_streams(args->input, args->output, 0, start-1);
934	}
935	static GB_ERROR gbl_tail(GBL_command_arguments *args) {
936	EXPECT_PARAMS(args, 1, "length_of_tail");
937	int end = atoi(args->param.get(0));
938	if (end <= 0) return gbl_mid_streams(args->input, args->output, 1, 0); // empty all streams
939	return gbl_mid_streams(args->input, args->output, -end, -1);
940	}
941
942	inline GB_ERROR mid(GBL_command_arguments *args, int start_index) {
943	EXPECT_PARAMS(args, 2, "start,end");
944	return gbl_mid_streams(args->input, args->output, atoi(args->param.get(0))-start_index, atoi(args->param.get(1))-start_index);
945	}
946	static GB_ERROR gbl_mid0(GBL_command_arguments *args) { return mid(args, 0); }
947	static GB_ERROR gbl_mid (GBL_command_arguments *args) { return mid(args, 1); }
948
949	static GB_ERROR tab(GBL_command_arguments *args, bool pretab) {
950	EXPECT_PARAMS(args, 1, "tabstop");
951
952	int tab = atoi(args->param.get(0));
953	for (int i=0; i<args->input.size(); i++) {
954	int len = strlen(args->input.get(i));
955	if (len >= tab) IN_2_OUT(args, i);
956	else {
957	char *p = ARB_alloc<char>(tab+1);
958	if (pretab) {
959	int spaces = tab-len;
960	for (int j = 0; j<spaces; ++j) p[j] = ' ';
961	strcpy(p+spaces, args->input.get(i));
962	}
963	else {
964	strcpy(p, args->input.get(i));
965	for (int j=len; j<tab; j++) p[j] = ' ';
966	p[tab] = 0;
967	}
968	PASS_2_OUT(args, p);
969	}
970	}
971	return 0;
972	}
973	static GB_ERROR gbl_tab (GBL_command_arguments *args) { return tab(args, false); }
974	static GB_ERROR gbl_pretab(GBL_command_arguments *args) { return tab(args, true); }
975
976	static GB_ERROR gbl_crop(GBL_command_arguments *args) {
977	EXPECT_PARAMS(args, 1, "\"chars_to_crop\"");
978
979	const char *chars_to_crop = args->param.get(0);
980	for (int i=0; i<args->input.size(); i++) {
981	const char *s = args->input.get(i);
982	while (s[0] && strchr(chars_to_crop, s[0]) != 0) s++; // crop at beg of line
983
984	int len = strlen(s);
985	char *p = ARB_alloc<char>(len+1);
986	strcpy(p, s);
987
988	{
989	char *pe = p+len-1;
990
991	while (pe >= p && strchr(chars_to_crop, pe[0]) != 0) { // crop at end of line
992	--pe;
993	}
994	gb_assert(pe >= (p-1));
995	pe[1] = 0;
996	}
997	PASS_2_OUT(args, p);
998	}
999	return 0;
1000	}
1001
1002
1003
1004	static GB_ERROR gbl_cut(GBL_command_arguments *args) {
1005	for (int i=0; i<args->param.size(); i++) {
1006	int stream = atoi(args->param.get(i));
1007	EXPECT_LEGAL_STREAM_INDEX(args, stream);
1008	IN_2_OUT(args, bio2info(stream));
1009	}
1010	return 0;
1011	}
1012	static GB_ERROR gbl_drop(GBL_command_arguments *args) {
1013	GB_ERROR error = 0;
1014	bool *dropped = ARB_alloc<bool>(args->input.size());
1015
1016	for (int i=0; i<args->input.size(); ++i) dropped[i] = false;
1017
1018	for (int i=0; i<args->param.size() && !error; ++i) {
1019	int stream = atoi(args->param.get(i));
1020	error = check_valid_stream_index(args, stream);
1021	if (!error) dropped[bio2info(stream)] = true;
1022	}
1023
1024	if (!error) {
1025	for (int i=0; i<args->input.size(); ++i) {
1026	if (!dropped[i]) IN_2_OUT(args, i);
1027	}
1028	}
1029	free(dropped);
1030
1031	return error;
1032	}
1033
1034	static GB_ERROR gbl_dropempty(GBL_command_arguments *args) {
1035	EXPECT_NO_PARAM(args);
1036
1037	for (int i=0; i<args->input.size(); ++i) {
1038	if (args->input.get(i)[0]) { // if non-empty
1039	IN_2_OUT(args, i);
1040	}
1041	}
1042	return 0;
1043	}
1044
1045	static GB_ERROR gbl_dropzero(GBL_command_arguments *args) {
1046	EXPECT_NO_PARAM(args);
1047
1048	for (int i=0; i<args->input.size(); ++i) {
1049	if (atoi(args->input.get(i))) { // if non-zero
1050	IN_2_OUT(args, i);
1051	}
1052	}
1053	return 0;
1054	}
1055
1056	static GB_ERROR gbl_swap(GBL_command_arguments *args) {
1057	if (args->input.size()<2) return "need at least two input streams";
1058
1059	int swap1;
1060	int swap2;
1061	if (args->param.size() == 0) {
1062	swap1 = args->input.size()-1;
1063	swap2 = args->input.size()-2;
1064	}
1065	else if (args->param.size() == 2) {
1066	swap1 = atoi(args->param.get(0));
1067	swap2 = atoi(args->param.get(1));
1068
1069	EXPECT_LEGAL_STREAM_INDEX(args, swap1);
1070	EXPECT_LEGAL_STREAM_INDEX(args, swap2);
1071
1072	swap1 = bio2info(swap1);
1073	swap2 = bio2info(swap2);
1074	}
1075	else {
1076	return "expected 0 or 2 parameters";
1077	}
1078
1079	for (int i = 0; i<args->input.size(); ++i) {
1080	int j = i == swap1 ? swap2 : (i == swap2 ? swap1 : i);
1081	IN_2_OUT(args, j);
1082	}
1083
1084	return 0;
1085	}
1086
1087	static GB_ERROR backfront_stream(GBL_command_arguments *args, int toback) {
1088	if (args->input.size()<1) return "need at least one input stream";
1089	if (args->param.size() != 1) return "expecting one parameter";
1090
1091	int stream_to_move = atoi(args->param.get(0));
1092	EXPECT_LEGAL_STREAM_INDEX(args, stream_to_move);
1093	stream_to_move = bio2info(stream_to_move);
1094
1095	if (!toback) IN_2_OUT(args, stream_to_move);
1096	for (int i = 0; i<args->input.size(); ++i) {
1097	if (i != stream_to_move) IN_2_OUT(args, i);
1098	}
1099	if (toback) IN_2_OUT(args, stream_to_move);
1100
1101	return 0;
1102	}
1103	static GB_ERROR gbl_toback (GBL_command_arguments *args) { return backfront_stream(args, 1); }
1104	static GB_ERROR gbl_tofront(GBL_command_arguments *args) { return backfront_stream(args, 0); }
1105
1106	static GB_ERROR gbl_merge(GBL_command_arguments *args) {
1107	const char *separator;
1108	switch (args->param.size()) {
1109	case 0: separator = 0; break;
1110	case 1: separator = args->param.get(0); break;
1111	default: return check_optional_parameters(args, 0, NULL, 1, "\"separator\"");
1112	}
1113
1114	if (args->input.size()) {
1115	GBS_strstruct *str = GBS_stropen(1000);
1116	GBS_strcat(str, args->input.get(0));
1117
1118	for (int i = 1; i<args->input.size(); ++i) {
1119	if (separator) GBS_strcat(str, separator);
1120	GBS_strcat(str, args->input.get(i));
1121	}
1122
1123	PASS_2_OUT(args, GBS_strclose(str));
1124	}
1125	return 0;
1126	}
1127
1128	static GB_ERROR gbl_split(GBL_command_arguments *args) {
1129	const char *separator;
1130	int split_mode = 0; // 0 = remove separator, 1 = split before separator, 2 = split behind separator
1131
1132	switch (args->param.size()) {
1133	case 0: // default behavior: split into lines and remove LF
1134	separator = "\n";
1135	break;
1136	case 2:
1137	split_mode = atoi(args->param.get(1));
1138	if (split_mode<0 \|\| split_mode>2) {
1139	return GBS_global_string("Illegal split mode '%i' (valid: 0..2)", split_mode);
1140	}
1141	// fall-through
1142	case 1:
1143	separator = args->param.get(0);
1144	break;
1145	default:
1146	return check_optional_parameters(args, 0, NULL, 2, "\"separator\"[,mode]");
1147	}
1148
1149	{
1150	size_t sepLen = strlen(separator);
1151
1152	for (int i = 0; i<args->input.size(); ++i) {
1153	const char *in = args->input.get(i);
1154	const char *from = in; // search from here
1155
1156	while (in) {
1157	const char *splitAt = strstr(from, separator);
1158	if (splitAt) {
1159	size_t len;
1160	char *copy;
1161
1162	if (split_mode == 2) splitAt += sepLen; // split behind separator
1163
1164	len = splitAt-in;
1165	copy = ARB_strndup(in, len);
1166
1167	PASS_2_OUT(args, copy);
1168
1169	in = splitAt + (split_mode == 0 ? sepLen : 0);
1170	from = in+(split_mode == 1 ? sepLen : 0);
1171	}
1172	else {
1173	COPY_2_OUT(args, in); // last part
1174	in = 0;
1175	}
1176	}
1177	}
1178	}
1179
1180	return 0;
1181	}
1182
1183	// ----------------------------------
1184	// Extended string functions
1185
1186	static GB_ERROR gbl_extract_words(GBL_command_arguments *args) {
1187	EXPECT_PARAMS(args, 2, "\"chars\", minchars");
1188
1189	float len = atof(args->param.get(1));
1190	for (int i=0; i<args->input.size(); i++) {
1191	char *res = GBS_extract_words(args->input.get(i), args->param.get(0), len, 1);
1192	gb_assert(res);
1193	PASS_2_OUT(args, res);
1194	}
1195	return 0;
1196	}
1197
1198	static GB_ERROR gbl_extract_sequence(GBL_command_arguments *args) {
1199	EXPECT_PARAMS(args, 2, "\"chars\",minFrequency");
1200
1201	const char *chars = args->param.get(0);
1202	float minFreq = atof(args->param.get(1));
1203
1204	if (minFreq <0.0 \|\| minFreq > 1.0) return GBS_global_string("Illegal minFrequency=%f", minFreq);
1205
1206	for (int i=0; i<args->input.size(); i++) {
1207	char *res = GBS_extract_words(args->input.get(i), chars, minFreq, 0);
1208	gb_assert(res);
1209	PASS_2_OUT(args, res);
1210	}
1211	return 0;
1212	}
1213
1214	static GB_ERROR gbl_checksum(GBL_command_arguments *args) {
1215	GBL_BEGIN_PARAMS;
1216	GBL_PARAM_STRING(exclude, "exclude=", "", "Remove given characters before calculating");
1217	GBL_PARAM_BIT (upper, "toupper", 0, "Convert all characters to uppercase before calculating");
1218	GBL_TRACE_PARAMS(args);
1219	GBL_END_PARAMS;
1220
1221	for (int i=0; i<args->input.size(); i++) {
1222	long id = GBS_checksum(args->input.get(i), upper, exclude);
1223	PASS_2_OUT(args, GBS_global_string_copy("%lX", id));
1224	}
1225	return 0;
1226	}
1227
1228	static GB_ERROR gbl_gcgcheck(GBL_command_arguments *args) {
1229	GBL_BEGIN_PARAMS;
1230	GBL_TRACE_PARAMS(args);
1231	GBL_END_PARAMS;
1232
1233	for (int i=0; i<args->input.size(); i++) {
1234	long id = GBS_gcgchecksum(args->input.get(i));
1235	PASS_2_OUT(args, GBS_global_string_copy("%li", id));
1236	}
1237	return 0;
1238	}
1239
1240	// ------------
1241	// SRT
1242
1243	static GB_ERROR gbl_srt(GBL_command_arguments *args) {
1244	GB_ERROR error = NULL;
1245	for (int i=0; i<args->input.size() && !error; i++) {
1246	char *modsource = 0;
1247
1248	for (int j=0; j<args->param.size() && !error; j++) {
1249	char *hs = GBS_string_eval(modsource ? modsource : args->input.get(i),
1250	args->param.get(j),
1251	args->get_ref());
1252
1253	if (hs) freeset(modsource, hs);
1254	else {
1255	error = GB_await_error();
1256	free(modsource);
1257	}
1258	}
1259
1260	if (!error) {
1261	if (modsource) PASS_2_OUT(args, modsource);
1262	else IN_2_OUT(args, i);
1263	}
1264	}
1265	return error;
1266	}
1267
1268	// -----------------------------
1269	// Calculator Functions
1270
1271
1272	// numeric binary operators
1273
1274	typedef int (*numeric_binary_operator)(int i1, int i2);
1275
1276	static char apply_numeric_binop(const char arg1, const char arg2, void client_data) {
1277	numeric_binary_operator nbo = (numeric_binary_operator)client_data;
1278
1279	int i1 = atoi(arg1);
1280	int i2 = atoi(arg2);
1281	int result = nbo(i1, i2);
1282
1283	return GBS_global_string_copy("%i", result);
1284	}
1285
1286	static int binop_plus (int i1, int i2) { return i1+i2; }
1287	static int binop_minus (int i1, int i2) { return i1-i2; }
1288	static int binop_mult (int i1, int i2) { return i1*i2; }
1289	static int binop_div (int i1, int i2) { return i2 ? i1/i2 : 0; }
1290	static int binop_rest (int i1, int i2) { return i2 ? i1%i2 : 0; }
1291	static int binop_per_cent(int i1, int i2) { return i2 ? (i1*100)/i2 : 0; }
1292
1293	static GB_ERROR gbl_plus (GBL_command_arguments args) { return gbl_apply_binary_operator(args, apply_numeric_binop, (void)binop_plus); }
1294	static GB_ERROR gbl_minus (GBL_command_arguments args) { return gbl_apply_binary_operator(args, apply_numeric_binop, (void)binop_minus); }
1295	static GB_ERROR gbl_mult (GBL_command_arguments args) { return gbl_apply_binary_operator(args, apply_numeric_binop, (void)binop_mult); }
1296	static GB_ERROR gbl_div (GBL_command_arguments args) { return gbl_apply_binary_operator(args, apply_numeric_binop, (void)binop_div); }
1297	static GB_ERROR gbl_rest (GBL_command_arguments args) { return gbl_apply_binary_operator(args, apply_numeric_binop, (void)binop_rest); }
1298	static GB_ERROR gbl_per_cent(GBL_command_arguments args) { return gbl_apply_binary_operator(args, apply_numeric_binop, (void)binop_per_cent); }
1299
1300
1301	static GB_ERROR gbl_select(GBL_command_arguments *args) {
1302	GB_ERROR error = NULL;
1303	for (int i=0; i<args->input.size() && !error; i++) {
1304	int paraidx = atoi(args->input.get(i));
1305	error = check_valid_param_index(args, paraidx);
1306	if (!error) {
1307	char result = interpret_subcommand(args, "", args->param.get(paraidx));
1308	if (!result) error = GB_await_error();
1309	else PASS_2_OUT(args, result);
1310	}
1311	}
1312	return error;
1313	}
1314
1315	static GB_ERROR gbl_readdb(GBL_command_arguments *args) {
1316	COMMAND_DROPS_INPUT_STREAMS(args);
1317
1318	GBS_strstruct *strstr = GBS_stropen(1024);
1319	for (int i=0; i<args->param.size(); i++) {
1320	char *val = GBT_read_as_string(args->get_ref(), args->param.get(i));
1321	if (val) {
1322	GBS_strcat(strstr, val);
1323	free(val);
1324	}
1325	}
1326	PASS_2_OUT(args, GBS_strclose(strstr));
1327	return 0;
1328	}
1329
1330
1331	enum GBT_ITEM_TYPE {
1332	GBT_ITEM_UNKNOWN,
1333	GBT_ITEM_SPECIES,
1334	GBT_ITEM_GENE
1335	};
1336
1337	static GBT_ITEM_TYPE identify_gb_item(GBDATA *gb_item) {
1338	/* returns: GBT_ITEM_UNKNOWN -> unknown database_item
1339	* GBT_ITEM_SPECIES -> /species_data/species
1340	* GBT_ITEM_GENE -> /species_data/species/gene_data/gene */
1341
1342	GBT_ITEM_TYPE res = GBT_ITEM_UNKNOWN;
1343	if (gb_item) {
1344	GBDATA *gb_father = GB_get_father(gb_item);
1345	if (gb_father) {
1346	const char *key = GB_KEY(gb_item);
1347
1348	if (strcmp(key, "species") == 0 &&
1349	strcmp(GB_KEY(gb_father), "species_data") == 0) {
1350	res = GBT_ITEM_SPECIES;
1351	}
1352	else if (strcmp(key, "gene") == 0 &&
1353	strcmp(GB_KEY(gb_father), "gene_data") == 0 &&
1354	identify_gb_item(GB_get_father(gb_father)) == GBT_ITEM_SPECIES) {
1355	res = GBT_ITEM_GENE;
1356	}
1357	}
1358	}
1359	return res;
1360	}
1361
1362	// --------------------------------------------------------------------------------
1363	// taxonomy caching
1364
1365	#if defined(DEBUG)
1366	// #define DUMP_TAXONOMY_CACHING
1367	#endif
1368
1369
1370	#define GROUP_COUNT_CHARS 6 // characters in taxonomy-key reserved for group-counter (hex number)
1371	#define BITS_PER_HEXCHAR 4
1372	#define MAX_GROUPS (1 << (GROUP_COUNT_CHARS*BITS_PER_HEXCHAR)) // resulting number of groups
1373
1374	struct cached_taxonomy {
1375	char *tree_name; // tree for which taxonomy is cached here
1376	int groups; // number of named groups in tree (at time of caching)
1377	GB_HASH taxonomy; / keys: "!species", ">XXXXgroup" and "<root>".
1378	* Species and groups contain their first parent (i.e. '>XXXXgroup' or '<root>').
1379	* Species not in hash are not members of tree.
1380	* The 'XXXX' in groupname is simply a counter to avoid multiple groups with same name.
1381	* The group-db-entries are stored in hash as pointers ('>>%p') and
1382	* point to their own group entry ('>XXXXgroup')
1383	*
1384	* Note: the number of 'X's in 'XXXX' above is defined by GROUP_COUNT_CHARS!
1385	*/
1386	};
1387
1388	static void free_cached_taxonomy(cached_taxonomy *ct) {
1389	free(ct->tree_name);
1390	GBS_free_hash(ct->taxonomy);
1391	free(ct);
1392	}
1393
1394	static void build_taxonomy_rek(TreeNode node, GB_HASH tax_hash, const char parent_group, int group_counter) {
1395	if (node->is_leaf) {
1396	GBDATA *gb_species = node->gb_node;
1397	if (gb_species) { // not zombie
1398	GBS_write_hash(tax_hash, GBS_global_string("!%s", GBT_read_name(gb_species)), (long)ARB_strdup(parent_group));
1399	}
1400	}
1401	else {
1402	if (node->name) { // named group
1403	char *hash_entry;
1404	const char *hash_binary_entry;
1405	(*group_counter)++;
1406
1407	gb_assert((*group_counter)<MAX_GROUPS); // overflow - increase GROUP_COUNT_CHARS
1408
1409	hash_entry = GBS_global_string_copy(">%0x%s", GROUP_COUNT_CHARS, group_counter, node->name);
1410	GBS_write_hash(tax_hash, hash_entry, (long)ARB_strdup(parent_group));
1411
1412	hash_binary_entry = GBS_global_string(">>%p", node->gb_node);
1413	GBS_write_hash(tax_hash, hash_binary_entry, (long)ARB_strdup(hash_entry));
1414
1415	build_taxonomy_rek(node->get_leftson(), tax_hash, hash_entry, group_counter);
1416	build_taxonomy_rek(node->get_rightson(), tax_hash, hash_entry, group_counter);
1417	free(hash_entry);
1418	}
1419	else {
1420	build_taxonomy_rek(node->get_leftson(), tax_hash, parent_group, group_counter);
1421	build_taxonomy_rek(node->get_rightson(), tax_hash, parent_group, group_counter);
1422	}
1423	}
1424	}
1425
1426	static GB_HASH *cached_taxonomies = 0;
1427
1428	static bool is_cached_taxonomy(const char /key/, long val, void cl_ct) {
1429	cached_taxonomy ct1 = (cached_taxonomy )val;
1430	cached_taxonomy ct2 = (cached_taxonomy )cl_ct;
1431
1432	return ct1 == ct2;
1433	}
1434
1435	static const char tree_of_cached_taxonomy(cached_taxonomy ct) {
1436	/* search the hash to find the correct cached taxonomy.
1437	* searching for tree name does not work, because the tree possibly already was deleted
1438	*/
1439	const char *tree = GBS_hash_next_element_that(cached_taxonomies, NULL, is_cached_taxonomy, ct);
1440	#ifdef DUMP_TAXONOMY_CACHING
1441	if (tree) printf("tree_of_cached_taxonomy: tree='%s' ct->tree_name='%s'\n", tree, ct->tree_name);
1442	#endif // DUMP_TAXONOMY_CACHING
1443	return tree;
1444	}
1445
1446	static void flush_taxonomy_cb(GBDATA gbd, cached_taxonomy ct) {
1447	/* this cb is bound all tree db members below "/tree_data/tree_xxx" which
1448	* may have an effect on the displayed taxonomy
1449	* it invalidates cached taxonomies for that tree (when changed or deleted)
1450	*/
1451
1452	GB_ERROR error = 0;
1453	const char *found = tree_of_cached_taxonomy(ct);
1454
1455	if (found) {
1456	#ifdef DUMP_TAXONOMY_CACHING
1457	fprintf(stderr, "Deleting cached taxonomy ct=%p (tree='%s')\n", ct, found);
1458	#endif // DUMP_TAXONOMY_CACHING
1459	GBS_write_hash(cached_taxonomies, found, 0); // delete cached taxonomy from hash
1460	free_cached_taxonomy(ct);
1461	}
1462	#ifdef DUMP_TAXONOMY_CACHING
1463	else {
1464	fprintf(stderr, "No tree found for cached_taxonomies ct=%p (already deleted?)\n", ct);
1465	}
1466	#endif // DUMP_TAXONOMY_CACHING
1467
1468	if (!GB_inside_callback(gbd, GB_CB_DELETE)) {
1469	GB_remove_all_callbacks_to(gbd, GB_CB_CHANGED_OR_DELETED, (GB_CB)flush_taxonomy_cb);
1470	}
1471
1472	if (found && !error) {
1473	GBDATA *gb_main = GB_get_gb_main_during_cb();
1474	if (gb_main) {
1475	GBDATA *gb_tree_refresh = GB_search(gb_main, AWAR_TREE_REFRESH, GB_INT);
1476	if (!gb_tree_refresh) {
1477	error = GBS_global_string("%s (while trying to force refresh)", GB_await_error());
1478	}
1479	else {
1480	GB_touch(gb_tree_refresh); // Note : force tree update
1481	}
1482	}
1483	}
1484
1485	if (error) {
1486	fprintf(stderr, "Error in flush_taxonomy_cb: %s\n", error);
1487	}
1488	}
1489
1490	static void flush_taxonomy_if_new_group_cb(GBDATA gb_tree, cached_taxonomy ct) {
1491	// detects the creation of new groups and call flush_taxonomy_cb() manually
1492	#ifdef DUMP_TAXONOMY_CACHING
1493	fputs("flush_taxonomy_if_new_group_cb() has been called\n", stderr);
1494	#endif // DUMP_TAXONOMY_CACHING
1495
1496	const char *tree_name = tree_of_cached_taxonomy(ct);
1497	if (tree_name) {
1498	int groups = 0;
1499	GBDATA *gb_group_node;
1500
1501	for (gb_group_node = GB_entry(gb_tree, "node");
1502	gb_group_node;
1503	gb_group_node = GB_nextEntry(gb_group_node))
1504	{
1505	if (GB_entry(gb_group_node, "group_name")) {
1506	groups++; // count named groups only
1507	}
1508	}
1509
1510	#ifdef DUMP_TAXONOMY_CACHING
1511	fprintf(stderr, "cached_groups=%i counted_groups=%i\n", ct->groups, groups);
1512	#endif // DUMP_TAXONOMY_CACHING
1513	if (groups != ct->groups) {
1514	#ifdef DUMP_TAXONOMY_CACHING
1515	fprintf(stderr, "Number of groups changed -> invoking flush_taxonomy_cb() manually\n");
1516	#endif // DUMP_TAXONOMY_CACHING
1517	flush_taxonomy_cb(gb_tree, ct);
1518	}
1519	}
1520	#ifdef DUMP_TAXONOMY_CACHING
1521	else {
1522	fprintf(stderr, "cached taxonomy no longer valid.\n");
1523	}
1524	#endif // DUMP_TAXONOMY_CACHING
1525	}
1526
1527	static cached_taxonomy get_cached_taxonomy(GBDATA gb_main, const char tree_name, GB_ERROR error) {
1528	long cached;
1529	*error = 0;
1530	if (!cached_taxonomies) {
1531	cached_taxonomies = GBS_create_hash(20, GB_IGNORE_CASE);
1532	}
1533	cached = GBS_read_hash(cached_taxonomies, tree_name);
1534	if (!cached) {
1535	TreeNode *tree = GBT_read_tree(gb_main, tree_name, new SimpleRoot);
1536	if (!tree) *error = GB_await_error();
1537	else *error = GBT_link_tree(tree, gb_main, false, 0, 0);
1538
1539	if (!*error) {
1540	GBDATA *gb_tree = GBT_find_tree(gb_main, tree_name);
1541	if (!gb_tree) {
1542	*error = GBS_global_string("Can't find tree '%s'", tree_name);
1543	}
1544	else {
1545	cached_taxonomy *ct = ARB_alloc<cached_taxonomy>(1);
1546	long nodes = GBT_count_leafs(tree);
1547	int group_counter = 0;
1548
1549	ct->tree_name = ARB_strdup(tree_name);
1550	ct->taxonomy = GBS_create_dynaval_hash(int(nodes), GB_IGNORE_CASE, GBS_dynaval_free);
1551	ct->groups = 0; // counted below
1552
1553	build_taxonomy_rek(tree, ct->taxonomy, "<root>", &group_counter);
1554	cached = (long)ct;
1555	GBS_write_hash(cached_taxonomies, tree_name, (long)ct);
1556
1557	GB_remove_all_callbacks_to(gb_tree, GB_CB_SON_CREATED, (GB_CB)flush_taxonomy_if_new_group_cb);
1558	GB_add_callback(gb_tree, GB_CB_SON_CREATED, makeDatabaseCallback(flush_taxonomy_if_new_group_cb, ct));
1559
1560	{
1561	GBDATA *gb_tree_entry = GB_entry(gb_tree, "tree");
1562	GBDATA *gb_group_node;
1563
1564	if (gb_tree_entry) {
1565	GB_remove_all_callbacks_to(gb_tree_entry, GB_CB_CHANGED_OR_DELETED, (GB_CB)flush_taxonomy_cb);
1566	GB_add_callback(gb_tree_entry, GB_CB_CHANGED_OR_DELETED, makeDatabaseCallback(flush_taxonomy_cb, ct));
1567	}
1568
1569	// add callbacks for all node/group_name subentries
1570	for (gb_group_node = GB_entry(gb_tree, "node");
1571	gb_group_node;
1572	gb_group_node = GB_nextEntry(gb_group_node))
1573	{
1574	GBDATA *gb_group_name = GB_entry(gb_group_node, "group_name");
1575	if (gb_group_name) { // group with id = 0 has no name
1576	GB_remove_all_callbacks_to(gb_group_name, GB_CB_CHANGED_OR_DELETED, (GB_CB)flush_taxonomy_cb);
1577	GB_add_callback(gb_group_name, GB_CB_CHANGED_OR_DELETED, makeDatabaseCallback(flush_taxonomy_cb, ct));
1578	ct->groups++;
1579	}
1580	}
1581	}
1582	#ifdef DUMP_TAXONOMY_CACHING
1583	fprintf(stderr, "Created taxonomy hash for '%s' (ct=%p)\n", tree_name, ct);
1584	#endif // DUMP_TAXONOMY_CACHING
1585	}
1586	}
1587
1588	destroy(tree);
1589	}
1590
1591	if (!*error) {
1592	cached_taxonomy ct = (cached_taxonomy)cached;
1593	gb_assert(ct);
1594	return ct;
1595	}
1596
1597	return 0;
1598	}
1599
1600	static char get_taxonomy_string(GB_HASH tax_hash, const char group_key, int depth, GB_ERROR error) {
1601	long found;
1602	char *result = 0;
1603
1604	gb_assert(depth>0);
1605	gb_assert(!(group_key[0] == '>' && group_key[1] == '>')); // internal group-pointers not allowed here!
1606
1607	found = GBS_read_hash(tax_hash, group_key);
1608	if (found) {
1609	const char parent_group_key = (const char )found;
1610	if (strcmp(parent_group_key, "<root>") == 0) { // root reached
1611	result = ARB_strdup(group_key+(GROUP_COUNT_CHARS+1)); // return own group name
1612	}
1613	else {
1614	if (depth>1) {
1615	char *parent_name = get_taxonomy_string(tax_hash, parent_group_key, depth-1, error);
1616	if (parent_name) {
1617	result = GBS_global_string_copy("%s/%s", parent_name, group_key+(GROUP_COUNT_CHARS+1));
1618	free(parent_name);
1619	}
1620	else {
1621	error = GBS_global_string("In get_taxonomy_string(%s): %s", group_key, error);
1622	result = 0;
1623	}
1624	}
1625	else {
1626	result = ARB_strdup(group_key+(GROUP_COUNT_CHARS+1)); // return own group name
1627	}
1628	}
1629	}
1630	else {
1631	*error = GBS_global_string("Not in tax_hash: '%s'", group_key);
1632	}
1633	return result;
1634	}
1635
1636	static const char get_taxonomy(GBDATA gb_species_or_group, const char tree_name, bool is_current_tree, int depth, GB_ERROR error) {
1637	GBDATA *gb_main = GB_get_root(gb_species_or_group);
1638	cached_taxonomy *tax = get_cached_taxonomy(gb_main, tree_name, error);
1639	const char *result = 0;
1640
1641	if (tax) {
1642	GBDATA *gb_name = GB_entry(gb_species_or_group, "name");
1643	GBDATA *gb_group_name = GB_entry(gb_species_or_group, "group_name");
1644
1645	if (gb_name && !gb_group_name) { // it's a species
1646	char *name = GB_read_string(gb_name);
1647	if (name) {
1648	GB_HASH *tax_hash = tax->taxonomy;
1649	long found = GBS_read_hash(tax_hash, GBS_global_string("!%s", name));
1650
1651	if (found) {
1652	const char parent_group = (const char )found;
1653
1654	if (strcmp(parent_group, "<root>") == 0) {
1655	result = ""; // not member of any group
1656	}
1657	else {
1658	static char *parent = 0;
1659
1660	freeset(parent, get_taxonomy_string(tax_hash, parent_group, depth, error));
1661	result = parent;
1662	}
1663	}
1664	else {
1665	result = GBS_global_string("Species '%s' not in '%s'", name, tree_name);
1666	}
1667	free(name);
1668	}
1669	else {
1670	*error = GBS_global_string("Species without 'name' entry!");
1671	}
1672	}
1673	else if (gb_group_name && !gb_name) { // it's a group
1674	char *group_name = GB_read_string(gb_group_name);
1675	if (group_name) {
1676	if (is_current_tree) {
1677	GB_HASH *tax_hash = tax->taxonomy;
1678	long found = GBS_read_hash(tax_hash, GBS_global_string(">>%p", gb_species_or_group));
1679
1680	if (found) {
1681	static char *full_group = 0;
1682	const char group_id = (const char )found;
1683
1684	freeset(full_group, get_taxonomy_string(tax_hash, group_id, depth, error));
1685	result = full_group;
1686	}
1687	else {
1688	result = GBS_global_string("Group '%s' not in '%s'", group_name, tree_name);
1689	}
1690	}
1691	else {
1692	*error = "It's not possible to specify the tree name in taxonomy() for groups";
1693	}
1694	free(group_name);
1695	}
1696	else {
1697	*error = "Group without 'group_name' entry";
1698	}
1699	}
1700	else if (gb_group_name) {
1701	*error = "Container has 'name' and 'group_name' entry - can't detect container type";
1702	}
1703	else {
1704	*error = "Container has neither 'name' nor 'group_name' entry - can't detect container type";
1705	}
1706	}
1707
1708	return result;
1709	}
1710
1711	static GB_ERROR gbl_taxonomy(GBL_command_arguments *args) {
1712	COMMAND_DROPS_INPUT_STREAMS(args);
1713
1714	GB_ERROR error = check_optional_parameters(args, 1, "count", 1, "tree_name", false);
1715	if (!error) {
1716	char *tree_name = 0;
1717	bool is_current_tree = false;
1718	int depth = -1;
1719	char *result = 0;
1720
1721	if (args->param.size() == 1) { // only 'depth'
1722	if (!args->get_tree_name()) {
1723	result = ARB_strdup("No default tree");
1724	}
1725	else {
1726	tree_name = ARB_strdup(args->get_tree_name());
1727	depth = atoi(args->param.get(0));
1728	is_current_tree = true;
1729	}
1730	}
1731	else { // 'tree_name', 'depth'
1732	tree_name = ARB_strdup(args->param.get(0));
1733	depth = atoi(args->param.get(1));
1734	}
1735
1736	if (!result) {
1737	if (depth<1) {
1738	error = GBS_global_string("Illegal depth '%i' (allowed 1..n)", depth);
1739	}
1740	if (!error) {
1741	const char *taxonomy_string = get_taxonomy(args->get_ref(), tree_name, is_current_tree, depth, &error);
1742	if (taxonomy_string) result = ARB_strdup(taxonomy_string);
1743	}
1744	}
1745
1746	gb_assert(contradicted(result, error));
1747	if (result) PASS_2_OUT(args, result);
1748	free(tree_name);
1749	}
1750	return error;
1751	}
1752
1753	static GB_ERROR gbl_sequence(GBL_command_arguments *args) {
1754	COMMAND_DROPS_INPUT_STREAMS(args);
1755
1756	GB_ERROR error = check_no_parameter(args);
1757	if (!error) {
1758	switch (identify_gb_item(args->get_ref())) {
1759	case GBT_ITEM_UNKNOWN: {
1760	error = "'sequence' used for unknown item";
1761	break;
1762	}
1763	case GBT_ITEM_SPECIES: {
1764	char *use = GBT_get_default_alignment(args->get_main());
1765
1766	if (!use) error = GB_await_error();
1767	else {
1768	GBDATA *gb_seq = GBT_find_sequence(args->get_ref(), use);
1769
1770	if (gb_seq) PASS_2_OUT(args, GB_read_string(gb_seq));
1771	else COPY_2_OUT(args, ""); // if current alignment does not exist -> return empty string
1772
1773	free(use);
1774	}
1775	break;
1776	}
1777	case GBT_ITEM_GENE: {
1778	char *seq = GBT_read_gene_sequence(args->get_ref(), true, 0);
1779
1780	if (!seq) error = GB_await_error();
1781	else PASS_2_OUT(args, seq);
1782
1783	break;
1784	}
1785	}
1786	}
1787	return error;
1788	}
1789
1790	static GB_ERROR gbl_export_sequence(GBL_command_arguments *args) {
1791	COMMAND_DROPS_INPUT_STREAMS(args);
1792
1793	GB_ERROR error = check_no_parameter(args);
1794	if (!error) {
1795	switch (identify_gb_item(args->get_ref())) {
1796	case GBT_ITEM_UNKNOWN: {
1797	error = "'export_sequence' used for unknown item";
1798	break;
1799	}
1800	case GBT_ITEM_SPECIES: {
1801	if (get_export_sequence == 0) {
1802	error = "No export-sequence-hook defined (can't use 'export_sequence' here)";
1803	}
1804	else {
1805	size_t len;
1806	const char *seq = get_export_sequence(args->get_ref(), &len, &error);
1807
1808	gb_assert(error \|\| seq);
1809
1810	if (seq) PASS_2_OUT(args, ARB_strduplen(seq, len));
1811	}
1812	break;
1813	}
1814	case GBT_ITEM_GENE: {
1815	error = "'export_sequence' cannot be used for gene";
1816	break;
1817	}
1818	}
1819	}
1820	return error;
1821	}
1822
1823	static GB_ERROR gbl_ali_name(GBL_command_arguments *args) {
1824	COMMAND_DROPS_INPUT_STREAMS(args);
1825
1826	GB_ERROR error = check_no_parameter(args);
1827	if (!error) {
1828	GBDATA *gb_main = args->get_main();
1829	char *use = GBT_get_default_alignment(gb_main);
1830	PASS_2_OUT(args, use);
1831	}
1832	return error;
1833	}
1834
1835	static GB_ERROR gbl_sequence_type(GBL_command_arguments *args) {
1836	COMMAND_DROPS_INPUT_STREAMS(args);
1837
1838	GB_ERROR error = check_no_parameter(args);
1839	if (!error) {
1840	GBDATA *gb_main = args->get_main();
1841	char *use = GBT_get_default_alignment(gb_main);
1842	PASS_2_OUT(args, GBT_get_alignment_type_string(gb_main, use));
1843	free(use);
1844	}
1845
1846	return error;
1847	}
1848
1849	static GB_ERROR gbl_format_sequence(GBL_command_arguments *args) {
1850	GB_ERROR error = 0;
1851	int ic;
1852
1853	int simple_format = (strcmp(args->command, "format") == 0); // "format_sequence" == !simple_format
1854
1855	GBL_BEGIN_PARAMS;
1856	GBL_PARAM_UINT (firsttab, "firsttab=", 10, "Indent first line");
1857	GBL_PARAM_UINT (tab, "tab=", 10, "Indent not first line");
1858	GBL_PARAM_UINT (width, "width=", 50, "Sequence width (bases only)");
1859
1860	// "format_sequence"-only
1861	GBL_PARAM_BIT (numleft, PARAM_IF(!simple_format, "numleft"), 0, "Numbers left of sequence");
1862	GBL_PARAM_INT (numright, PARAM_IF(!simple_format, "numright="), 0, "Numbers right of sequence (specifies width; -1 -> auto-width)");
1863	GBL_PARAM_UINT(gap, PARAM_IF(!simple_format, "gap="), 10, "Insert ' ' every n sequence characters");
1864
1865	// "format"-only
1866	GBL_PARAM_STRING(nl, PARAM_IF(simple_format, "nl="), " ", "Break line at characters 'str' if wrapping needed");
1867	GBL_PARAM_STRING(forcenl, PARAM_IF(simple_format, "forcenl="), "\n", "Always break line at characters 'str'");
1868
1869	GBL_TRACE_PARAMS(args);
1870	GBL_END_PARAMS;
1871
1872	if (width == 0) return "Illegal zero width";
1873	if (numleft && numright != 0) return "You may only specify 'numleft' OR 'numright', not both.";
1874
1875	for (ic = 0; ic<args->input.size(); ++ic) {
1876	{
1877	const char *src = args->input.get(ic);
1878	size_t data_size = strlen(src);
1879	size_t needed_size;
1880	size_t line_size;
1881	int numright_used = numright;
1882
1883	if (numright_used<0) {
1884	numright_used = calc_digits(data_size);
1885	}
1886
1887	{
1888	size_t lines;
1889
1890	if (simple_format) {
1891	lines = data_size/2 + 1; // worst case
1892	line_size = tab + width + 1;
1893	}
1894	else {
1895	size_t gapsPerLine = (width-1)/gap;
1896	lines = data_size/width+1;
1897	line_size = tab + width + gapsPerLine + 1;
1898
1899	if (numright_used) {
1900	// add space for numright
1901	line_size += numright_used+1; // plus space
1902	}
1903	}
1904
1905	needed_size = lines*line_size + firsttab + 1 + 10;
1906	}
1907
1908	char *result = ARB_alloc<char>(needed_size);
1909	if (!result) {
1910	error = GBS_global_string("Out of memory (tried to alloc %zu bytes)", needed_size);
1911	}
1912	else {
1913	char *dst = result;
1914	size_t rest_data = data_size;
1915
1916	if (simple_format) {
1917	/* format string w/o gaps or numleft
1918	* does word-wrapping at chars in nl
1919	*/
1920
1921	// build wrap table
1922	unsigned char isWrapChar[256];
1923	memset(isWrapChar, 0, sizeof(isWrapChar));
1924	for (int i = 0; nl[i]; ++i) isWrapChar[(unsigned char)nl[i]] = 1;
1925	for (int i = 0; forcenl[i]; ++i) isWrapChar[(unsigned char)forcenl[i]] = 2;
1926
1927	if (firsttab>0) {
1928	memset(dst, ' ', firsttab);
1929	dst += firsttab;
1930	}
1931
1932	while (rest_data>width) {
1933	int take;
1934	int move;
1935	int took;
1936
1937	for (take = width; take > 0; --take) {
1938	if (isWrapChar[(unsigned char)src[take]]) break;
1939	}
1940	if (take <= 0) { // no wrap character found -> hard wrap at width
1941	take = move = width;
1942	}
1943	else { // soft wrap at last found wrap character
1944	move = take+1;
1945	}
1946
1947	for (took = 0; took<take; took++) {
1948	char c = src[took];
1949	if (isWrapChar[(unsigned char)c] == 2) { // forced newline
1950	take = took;
1951	move = take+1;
1952	break;
1953	}
1954	dst[took] = c;
1955	}
1956
1957	dst += take;
1958	src += move;
1959	rest_data -= move;
1960
1961	if (rest_data>0) {
1962	*dst++ = '\n';
1963	if (tab>0) {
1964	memset(dst, ' ', tab);
1965	dst += tab;
1966	}
1967	}
1968	}
1969
1970	if (rest_data>0) {
1971	size_t j, k;
1972	for (j = 0, k = 0; j<rest_data; ++j) {
1973	char c = src[j];
1974
1975	if (isWrapChar[(unsigned char)c] == 2) {
1976	dst[k++] = '\n';
1977	if (tab>0) {
1978	memset(dst+k, ' ', tab);
1979	k += tab;
1980	}
1981	}
1982	else {
1983	dst[k++] = c;
1984	}
1985	}
1986	src += j;
1987	dst += k;
1988	rest_data = 0;
1989	}
1990	}
1991	else {
1992	// "format_sequence" with gaps and numleft
1993	char *format = 0;
1994	const char *src_start = src;
1995	const char *dst_linestart = dst;
1996
1997	if (numleft) {
1998	/* Warning: Be very careful, when you change format strings here!
1999	* currently all format strings result in '%u' or '%-##u' (where # are digits)
2000	*/
2001	if (firsttab>0) {
2002	char *firstFormat = GBS_global_string_copy("%%-%iu ", firsttab-1);
2003	dst += sprintf(dst, firstFormat, (unsigned)1);
2004	free(firstFormat);
2005	}
2006	else {
2007	dst += sprintf(dst, "%u ", (unsigned)1);
2008	}
2009	format = tab>0 ? GBS_global_string_copy("%%-%iu ", tab-1) : ARB_strdup("%u ");
2010	}
2011	else if (firsttab>0) {
2012	memset(dst, ' ', firsttab);
2013	dst += firsttab;
2014	}
2015
2016	while (rest_data>0) {
2017	size_t take = rest_data>width ? width : rest_data;
2018
2019	rest_data -= take;
2020
2021	while (take>gap) {
2022	memcpy(dst, src, gap);
2023	dst += gap;
2024	src += gap;
2025	*dst++ = ' ';
2026	take -= gap;
2027	}
2028
2029	memcpy(dst, src, take);
2030	dst += take;
2031	src += take;
2032
2033	if (numright_used) {
2034	if (rest_data) *dst++ = ' ';
2035	else {
2036	// fill in missing spaces for proper alignment of numright
2037	size_t currSize = dst-dst_linestart;
2038	size_t wantSize = line_size-numright_used-1;
2039	if (currSize<wantSize) {
2040	size_t spaces = wantSize-currSize;
2041	memset(dst, ' ', spaces);
2042	dst += spaces;
2043	}
2044	}
2045	unsigned int num = (src-src_start);
2046	dst += sprintf(dst, "%*u", numright_used, num);
2047	}
2048
2049	if (rest_data>0) {
2050	*dst++ = '\n';
2051	dst_linestart = dst;
2052	if (numleft) {
2053	unsigned int num = (src-src_start)+1; // this goes to the '%u' (see comment above)
2054	dst += sprintf(dst, format, num);
2055	}
2056	else if (tab>0) {
2057	memset(dst, ' ', tab);
2058	dst += tab;
2059	}
2060	}
2061	}
2062
2063	free(format);
2064	}
2065
2066	*dst++ = 0; // close str
2067
2068	#if defined(DEBUG)
2069	{ // check for array overflow
2070	size_t used_size = dst-result;
2071	gb_assert(used_size <= needed_size);
2072	ARB_realloc(result, used_size);
2073	}
2074	#endif // DEBUG
2075	}
2076
2077	if (!error) PASS_2_OUT(args, result);
2078	else free(result);
2079	}
2080	}
2081	return error;
2082	}
2083
2084	static char gbl_read_seq_sai_or_species(const char species, const char sai, const char ali, size_t *seqLen) {
2085	/* Reads the alignment 'ali' of 'species' or 'sai'.
2086	* If 'ali' is NULL, use default alignment.
2087	* Returns NULL in case of error (which is exported then)
2088	*/
2089
2090	char *seq = NULL;
2091	GB_ERROR error = 0;
2092
2093	int sources = !!species + !!sai;
2094	if (sources != 1) {
2095	error = "Either parameters 'species' or 'SAI' must be specified";
2096	}
2097	else {
2098	GBDATA *gb_main = gb_local->gbl.gb_main;
2099	GBDATA *gb_item = 0;
2100	const char *what = 0;
2101	const char *name = 0;
2102
2103	if (species) {
2104	gb_item = GBT_find_species(gb_main, species);
2105	what = "species";
2106	name = species;
2107	}
2108	else {
2109	gb_item = GBT_find_SAI(gb_main, sai);
2110	what = "SAI";
2111	name = sai;
2112	}
2113
2114	if (!gb_item) error = GBS_global_string("Can't find %s '%s'", what, name);
2115	else {
2116	char *freeMe = 0;
2117
2118	if (!ali) {
2119	ali = freeMe = GBT_get_default_alignment(gb_main);
2120	if (!ali) error = "can't detect default alignment";
2121	}
2122
2123	if (ali) {
2124	GBDATA *gb_ali = GB_entry(gb_item, ali);
2125
2126	if (gb_ali) {
2127	GBDATA *gb_seq;
2128
2129	for (gb_seq = GB_child(gb_ali); gb_seq; gb_seq = GB_nextChild(gb_seq)) {
2130	long type = GB_read_type(gb_seq);
2131	if (type == GB_BITS) {
2132	seq = GB_read_bits(gb_seq, '-', '+');
2133	if (seqLen) *seqLen = GB_read_bits_count(gb_seq);
2134	break;
2135	}
2136	if (type == GB_STRING) {
2137	seq = GB_read_string(gb_seq);
2138	if (seqLen) *seqLen = GB_read_string_count(gb_seq);
2139	break;
2140	}
2141	}
2142	}
2143
2144	if (!seq) error = GBS_global_string("%s '%s' has no (usable) data in alignment '%s'", what, name, ali);
2145	}
2146	free(freeMe);
2147	}
2148	}
2149
2150	if (error) {
2151	gb_assert(!seq);
2152	GB_export_error(error);
2153	}
2154
2155	return seq;
2156	}
2157
2158	struct common_filter_params {
2159	const char *align;
2160	const char *sai;
2161	const char *species;
2162	int first;
2163	int pairwise;
2164	};
2165
2166	#define GBL_COMMON_FILTER_PARAMS \
2167	common_filter_params common_param; \
2168	GBL_STRUCT_PARAM_STRING(common_param, align, "align=", 0, "alignment to use (defaults to default alignment)"); \
2169	GBL_STRUCT_PARAM_STRING(common_param, sai, "SAI=", 0, "Use default sequence of given SAI as a filter"); \
2170	GBL_STRUCT_PARAM_STRING(common_param, species, "species=", 0, "Use default sequence of given species as a filter"); \
2171	GBL_STRUCT_PARAM_BIT (common_param, first, "first=", 0, "Use 1st stream as filter for other streams"); \
2172	GBL_STRUCT_PARAM_BIT (common_param, pairwise, "pairwise=", 0, "Use 1st stream as filter for 2nd, 3rd for 4th, ...")
2173
2174	typedef char* (filter_fun)(const char seq, const char filter, size_t flen, void param);
2175	/* Note:
2176	* filter_fun has to return a heap copy of the filter-result.
2177	* if 'flen' != 0, it contains the length of 'filter'
2178	* 'param' may be any client data
2179	*/
2180
2181	static GB_ERROR apply_filters(GBL_command_arguments args, common_filter_params common, filter_fun filter_one, void *param) {
2182	GB_ERROR error = 0;
2183
2184	if (args->input.size()==0) error = "No input stream";
2185	else {
2186	int methodCount = !!common->sai + !!common->species + !!common->pairwise + !!common->first;
2187
2188	if (methodCount != 1) error = "Need exactly one of the parameters 'SAI', 'species', 'pairwise' or 'first'";
2189	else {
2190	if (common->pairwise) {
2191	if (args->input.size() % 2) error = "Using 'pairwise' requires an even number of input streams";
2192	else {
2193	int i;
2194	for (i = 1; i<args->input.size(); i += 2) {
2195	PASS_2_OUT(args, filter_one(args->input.get(i), args->input.get(i-1), 0, param));
2196	}
2197	}
2198	}
2199	else {
2200	int i = 0;
2201	char *filter = 0;
2202	size_t flen = 0;
2203
2204	if (common->first) {
2205	if (args->input.size()<2) error = "Using 'first' needs at least 2 input streams";
2206	else {
2207	const char *in = args->input.get(i++);
2208	gb_assert(in);
2209
2210	flen = strlen(in);
2211	filter = ARB_strduplen(in, flen);
2212	}
2213	}
2214	else {
2215	filter = gbl_read_seq_sai_or_species(common->species, common->sai, common->align, &flen);
2216	if (!filter) error = GB_await_error();
2217	}
2218
2219	gb_assert(filter \|\| error);
2220	if (filter) {
2221	for (; i<args->input.size(); ++i) {
2222	PASS_2_OUT(args, filter_one(args->input.get(i), filter, flen, param));
2223	}
2224	}
2225	free(filter);
2226	}
2227	}
2228	}
2229	return error;
2230	}
2231
2232	// -------------------------
2233	// calculate diff
2234
2235	struct diff_params {
2236	char equalC;
2237	char diffC;
2238	};
2239	static char calc_diff(const char seq, const char filter, size_t /flen/, void paramP) {
2240	// filters 'seq' through 'filter'
2241	// - replace all equal positions by 'equal_char' (if != 0)
2242	// - replace all differing positions by 'diff_char' (if != 0)
2243
2244	diff_params param = (diff_params)paramP;
2245	char equal_char = param->equalC;
2246	char diff_char = param->diffC;
2247
2248	char *result = ARB_strdup(seq);
2249	int p;
2250
2251	for (p = 0; result[p] && filter[p]; ++p) {
2252	if (result[p] == filter[p]) {
2253	if (equal_char) result[p] = equal_char;
2254	}
2255	else {
2256	if (diff_char) result[p] = diff_char;
2257	}
2258	}
2259
2260	// if 'seq' is longer than 'filter' and diff_char is given
2261	// -> fill rest of 'result' with 'diff_char'
2262	if (diff_char) {
2263	for (; result[p]; ++p) {
2264	result[p] = diff_char;
2265	}
2266	}
2267
2268	return result;
2269	}
2270	static GB_ERROR gbl_diff(GBL_command_arguments *args) {
2271	GBL_BEGIN_PARAMS;
2272	GBL_COMMON_FILTER_PARAMS;
2273
2274	diff_params param;
2275	GBL_STRUCT_PARAM_CHAR(param, equalC, "equal=", '.', "symbol for equal characters");
2276	GBL_STRUCT_PARAM_CHAR(param, diffC, "differ=", 0, "symbol for diff characters (default: use char from input stream)");
2277
2278	GBL_TRACE_PARAMS(args);
2279	GBL_END_PARAMS;
2280
2281	return apply_filters(args, &common_param, calc_diff, &param);
2282	}
2283
2284	// -------------------------
2285	// standard filter
2286
2287	enum filter_function { FP_FILTER, FP_MODIFY };
2288
2289	struct filter_params { // used by gbl_filter and gbl_change_gc
2290	filter_function function;
2291
2292	const char *include;
2293	const char *exclude;
2294
2295	// FP_MODIFY only:
2296	int change_pc;
2297	const char *change_to;
2298	};
2299
2300	static char filter_seq(const char seq, const char filter, size_t flen, void paramP) {
2301	filter_params param = (filter_params)paramP;
2302
2303	size_t slen = strlen(seq);
2304	if (!flen) flen = strlen(filter);
2305	size_t mlen = slen<flen ? slen : flen;
2306
2307	GBS_strstruct *out = GBS_stropen(mlen+1); // +1 to avoid invalid, zero-length buffer
2308
2309	const char *charset;
2310	int include;
2311
2312	if (param->include) {
2313	charset = param->include;
2314	include = 1;
2315	}
2316	else {
2317	gb_assert(param->exclude);
2318	charset = param->exclude;
2319	include = 0;
2320	}
2321
2322	size_t pos = 0;
2323	size_t rest = slen;
2324	size_t ctl = 0;
2325	if (param->function == FP_MODIFY) ctl = strlen(param->change_to);
2326
2327	int inset = 1; // 1 -> check chars in charset, 0 -> check chars NOT in charset
2328	while (rest) {
2329	size_t count;
2330	if (pos >= flen) { // behind filter
2331	// trigger last loop
2332	count = rest;
2333	inset = 0; // if 'include' -> 'applies' will get false, otherwise true
2334	// (meaning is: behind filter nothing can match 'include' or 'exclude')
2335	}
2336	else {
2337	count = (inset ? strspn : strcspn)(filter+pos, charset); // count how many chars are 'inset'
2338	}
2339	if (count) {
2340	int applies = !!include == !!inset; // true -> 'filter' matches 'include' or doesn't match 'exclude'
2341	if (count>rest) count = rest;
2342
2343	switch (param->function) {
2344	case FP_FILTER:
2345	if (applies) GBS_strncat(out, seq+pos, count);
2346	break;
2347
2348	case FP_MODIFY:
2349	if (applies) { // then modify
2350	size_t i;
2351	for (i = 0; i<count; i++) {
2352	char c = seq[pos+i];
2353	if (isalpha(c) && GB_random(100)<param->change_pc) c = param->change_to[GB_random(ctl)];
2354	GBS_chrcat(out, c);
2355	}
2356	}
2357	else { // otherwise simply copy
2358	GBS_strncat(out, seq+pos, count);
2359	}
2360	break;
2361	}
2362
2363	pos += count;
2364	rest -= count;
2365	}
2366	inset = 1-inset; // toggle
2367	}
2368	return GBS_strclose(out);
2369	}
2370
2371	static GB_ERROR gbl_filter(GBL_command_arguments *args) {
2372	GBL_BEGIN_PARAMS;
2373	GBL_COMMON_FILTER_PARAMS;
2374
2375	filter_params param;
2376	GBL_STRUCT_PARAM_STRING(param, exclude, "exclude=", 0, "Exclude colums");
2377	GBL_STRUCT_PARAM_STRING(param, include, "include=", 0, "Include colums");
2378	param.function = FP_FILTER;
2379
2380	GBL_TRACE_PARAMS(args);
2381	GBL_END_PARAMS;
2382
2383	GB_ERROR error = 0;
2384	int inOrEx = !!param.include + !!param.exclude;
2385
2386	if (inOrEx != 1) error = "Need exactly one parameter of: 'include', 'exclude'";
2387	else error = apply_filters(args, &common_param, filter_seq, &param);
2388
2389	return error;
2390	}
2391
2392	static GB_ERROR gbl_change_gc(GBL_command_arguments *args) {
2393	GBL_BEGIN_PARAMS;
2394	GBL_COMMON_FILTER_PARAMS;
2395
2396	filter_params param;
2397	GBL_STRUCT_PARAM_STRING(param, exclude, "exclude=", 0, "Exclude colums");
2398	GBL_STRUCT_PARAM_STRING(param, include, "include=", 0, "Include colums");
2399	GBL_STRUCT_PARAM_INT (param, change_pc, "change=", 0, "percentage of changed columns (default: silently change nothing)");
2400	GBL_STRUCT_PARAM_STRING(param, change_to, "to=", "GC", "change to one of this");
2401	param.function = FP_MODIFY;
2402
2403	GBL_TRACE_PARAMS(args);
2404	GBL_END_PARAMS;
2405
2406	GB_ERROR error = 0;
2407	int inOrEx = !!param.include + !!param.exclude;
2408
2409	if (inOrEx != 1) error = "Need exactly one parameter of: 'include', 'exclude'";
2410	else {
2411	error = apply_filters(args, &common_param, filter_seq, &param);
2412	}
2413
2414	return error;
2415	}
2416
2417	static GB_ERROR gbl_exec(GBL_command_arguments *args) {
2418	GB_ERROR error = 0;
2419
2420	if (args->param.size()==0) {
2421	error = "exec needs parameters:\nexec(command[,arguments])";
2422	}
2423	else {
2424	// write inputstreams to temp file:
2425	char *inputname;
2426	int i;
2427	{
2428	char *filename = GB_unique_filename("arb_exec_input", "tmp");
2429	FILE *out = GB_fopen_tempfile(filename, "wt", &inputname);
2430
2431	if (!out) error = GB_await_error();
2432	else {
2433	for (i=0; i<args->input.size(); i++) {
2434	fprintf(out, "%s\n", args->input.get(i));
2435	}
2436	fclose(out);
2437	}
2438	free(filename);
2439	}
2440
2441	if (!error) {
2442	// build shell command to execute
2443	char *sys;
2444	{
2445	GBS_strstruct *str = GBS_stropen(1000);
2446
2447	GBS_strcat(str, args->param.get(0));
2448	for (i=1; i<args->param.size(); i++) {
2449	GBS_strcat(str, " \'");
2450	GBS_strcat(str, args->param.get(i));
2451	GBS_chrcat(str, '\'');
2452	}
2453	GBS_strcat(str, " <");
2454	GBS_strcat(str, inputname);
2455
2456	sys = GBS_strclose(str);
2457	}
2458
2459	char *result = 0;
2460	{
2461	FILE *in = popen(sys, "r");
2462	if (in) {
2463	GBS_strstruct *str = GBS_stropen(4096);
2464
2465	while ((i=getc(in)) != EOF) { GBS_chrcat(str, i); }
2466	result = GBS_strclose(str);
2467	pclose(in);
2468	}
2469	else {
2470	error = GBS_global_string("Cannot execute shell command '%s'", sys);
2471	}
2472	}
2473
2474	if (!error) {
2475	gb_assert(result);
2476	PASS_2_OUT(args, result);
2477	}
2478
2479	free(sys);
2480	}
2481
2482	gb_assert(GB_is_privatefile(inputname, false));
2483	GB_unlink_or_warn(inputname, &error);
2484	free(inputname);
2485	}
2486
2487	return error;
2488	}
2489
2490
2491	static GBL_command_table gbl_command_table[] = {
2492	{ "ali_name", gbl_ali_name },
2493	{ "caps", gbl_string_convert },
2494	{ "change", gbl_change_gc },
2495	{ "checksum", gbl_checksum },
2496	{ "command", gbl_command },
2497	{ "compare", gbl_compare },
2498	{ "icompare", gbl_icompare },
2499	{ "contains", gbl_contains },
2500	{ "icontains", gbl_icontains },
2501	{ "count", gbl_count },
2502	{ "crop", gbl_crop },
2503	{ "cut", gbl_cut },
2504	{ "dd", gbl_dd },
2505	{ "define", gbl_define },
2506	{ "diff", gbl_diff },
2507	{ "div", gbl_div },
2508	{ "do", gbl_do },
2509	{ "drop", gbl_drop },
2510	{ "dropempty", gbl_dropempty },
2511	{ "dropzero", gbl_dropzero },
2512	{ "echo", gbl_echo },
2513	{ "equals", gbl_equals },
2514	{ "iequals", gbl_iequals },
2515	{ "escape", gbl_escape },
2516	{ "unescape", gbl_unescape },
2517	{ "eval", gbl_eval },
2518	{ "exec", gbl_exec },
2519	{ "export_sequence", gbl_export_sequence },
2520	{ "extract_sequence", gbl_extract_sequence },
2521	{ "extract_words", gbl_extract_words },
2522	{ "filter", gbl_filter },
2523	{ "format", gbl_format_sequence },
2524	{ "format_sequence", gbl_format_sequence },
2525	{ "gcgchecksum", gbl_gcgcheck },
2526	{ "head", gbl_head },
2527	{ "keep", gbl_keep },
2528	{ "left", gbl_head },
2529	{ "len", gbl_len },
2530	{ "lower", gbl_string_convert },
2531	{ "merge", gbl_merge },
2532	{ "mid", gbl_mid },
2533	{ "mid0", gbl_mid0 },
2534	{ "minus", gbl_minus },
2535	{ "mult", gbl_mult },
2536	{ "origin_gene", gbl_origin },
2537	{ "origin_organism", gbl_origin },
2538	{ "partof", gbl_partof },
2539	{ "ipartof", gbl_ipartof },
2540	{ "per_cent", gbl_per_cent },
2541	{ "plus", gbl_plus },
2542	{ "pretab", gbl_pretab },
2543	{ "quote", gbl_quote },
2544	{ "unquote", gbl_unquote },
2545	{ "readdb", gbl_readdb },
2546	{ "remove", gbl_remove },
2547	{ "rest", gbl_rest },
2548	{ "right", gbl_tail },
2549	{ "select", gbl_select },
2550	{ "sequence", gbl_sequence },
2551	{ "sequence_type", gbl_sequence_type },
2552	{ "split", gbl_split },
2553	{ "srt", gbl_srt },
2554	{ "streams", gbl_streams },
2555	{ "swap", gbl_swap },
2556	{ "tab", gbl_tab },
2557	{ "tail", gbl_tail },
2558	{ "taxonomy", gbl_taxonomy },
2559	{ "toback", gbl_toback },
2560	{ "tofront", gbl_tofront },
2561	{ "trace", gbl_trace },
2562	{ "translate", gbl_translate },
2563	{ "upper", gbl_string_convert },
2564	{ 0, 0 }
2565
2566	};
2567
2568	void gbl_install_standard_commands(GBDATA *gb_main) {
2569	gb_install_command_table(gb_main, gbl_command_table, ARRAY_ELEMS(gbl_command_table));
2570	}

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