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adlang1.c

Revision 6143, 92.9 KB (checked in by westram, 3 years ago)
backport [6141] (parts changing code, but only strings and comments)
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1	#include <stdio.h>
2	#include <stdlib.h>
3	#include <unistd.h>
4	#include <string.h>
5	/* #include <malloc.h> */
6	#include <ctype.h>
7
8	#include "adlocal.h"
9	#include "arbdbt.h"
10	#include "adGene.h"
11
12	#define AWAR_TREE_REFRESH "tmp/focus/tree_refresh" // touch this awar to refresh the tree display
13
14	/* hook for 'export_sequence' */
15
16	static gb_export_sequence_cb get_export_sequence = 0;
17
18	NOT4PERL void GB_set_export_sequence_hook(gb_export_sequence_cb escb) {
19	ad_assert(!get_export_sequence \|\| !escb); // avoid unwanted overwrite
20	get_export_sequence = escb;
21	}
22
23	/* global ACI/SRT debug switch */
24	static int trace = 0;
25
26	void GB_set_ACISRT_trace(int enable) { trace = enable; }
27	int GB_get_ACISRT_trace() { return trace; }
28
29
30	/* export stream */
31
32	#define PASS_2_OUT(args, s) do { (((args)->voutput))[(((args)->coutput))++].str = (s); } while(0)
33	#define COPY_2_OUT(args, s) PASS_2_OUT(args, strdup(s));
34	#define IN_2_OUT(args, i) COPY_2_OUT(args, args->vinput[i].str);
35
36	/********************************************************************************************
37	Parameter Functions
38	********************************************************************************************/
39
40	struct gbl_param {
41	struct gbl_param *next;
42	GB_TYPES type; // type of variable
43	void *varaddr; // address of variable where value gets stored
44	const char *param_name; // parameter name (e.g. 'include=')
45	const char *help_text; // help text for parameter
46	};
47
48	#define GBL_BEGIN_PARAMS struct gbl_param *params = 0
49
50	static void gbl_new_param(struct gbl_param *pp, GB_TYPES type, void vaddr, const char param_name, const char help_text) {
51	struct gbl_param gblp = (struct gbl_param )GB_calloc(1,sizeof(struct gbl_param));
52
53	gblp->next = *pp;
54	*pp = gblp;
55
56	gblp->type = type;
57	gblp->varaddr = vaddr;
58	gblp->param_name = param_name;
59	gblp->help_text = help_text;
60	}
61
62	typedef const char *String;
63	typedef int bit;
64	typedef unsigned int uint;
65
66	static int gbl_param_int(const char param_name,int def, const char help_text, struct gbl_param *pp, int vaddr) {
67	gbl_new_param(pp, GB_INT, vaddr, param_name, help_text);
68	return def;
69	}
70
71	static char gbl_param_char(const char param_name,char def, const char help_text, struct gbl_param *pp, char vaddr) {
72	gbl_new_param(pp, GB_BYTE, vaddr, param_name, help_text);
73	return def;
74	}
75
76	static uint gbl_param_uint(const char param_name, uint def, const char help_text, struct gbl_param *pp, uint vaddr) {
77	gbl_new_param(pp, GB_INT, vaddr, param_name, help_text);
78	return def;
79	}
80
81	static const char gbl_param_String(const char param_name, const char def, const char help_text, struct gbl_param *pp, String vaddr) {
82	gbl_new_param(pp, GB_STRING, vaddr, param_name, help_text);
83	return def;
84	}
85
86	static int gbl_param_bit(const char param_name, int def, const char help_text, struct gbl_param *pp, bit vaddr) {
87	gbl_new_param(pp, GB_BIT, vaddr, param_name, help_text);
88	return def;
89	}
90
91	#define GBL_PARAM_TYPE(type, var, param_name, def, help_text) type var = gbl_param_##type(param_name, def, help_text, &params, &var)
92	#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)
93
94	#define GBL_PARAM_INT( var, param_name, def, help_text) GBL_PARAM_TYPE(int, var, param_name, def, help_text)
95	#define GBL_PARAM_CHAR( var, param_name, def, help_text) GBL_PARAM_TYPE(char, var, param_name, def, help_text)
96	#define GBL_PARAM_UINT( var, param_name, def, help_text) GBL_PARAM_TYPE(uint, var, param_name, def, help_text)
97	#define GBL_PARAM_STRING(var, param_name, def, help_text) GBL_PARAM_TYPE(String, var, param_name, def, help_text)
98	#define GBL_PARAM_BIT( var, param_name, def, help_text) GBL_PARAM_TYPE(bit, var, param_name, def, help_text)
99
100	#define GBL_STRUCT_PARAM_INT( strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(int, strct, member, param_name, def, help_text)
101	#define GBL_STRUCT_PARAM_CHAR( strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(char, strct, member, param_name, def, help_text)
102	#define GBL_STRUCT_PARAM_UINT( strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(uint, strct, member, param_name, def, help_text)
103	#define GBL_STRUCT_PARAM_STRING(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(String, strct, member, param_name, def, help_text)
104	#define GBL_STRUCT_PARAM_BIT( strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(bit, strct, member, param_name, def, help_text)
105
106	#define GBL_TRACE_PARAMS(argc,argv) { \
107	GB_ERROR def_error = trace_params(argc,argv,params,args->command); \
108	if (def_error) { GBL_END_PARAMS; return def_error; }; };
109
110	#define GBL_END_PARAMS { struct gbl_param *_gblp; while (params) { \
111	_gblp = params; params = params->next; \
112	free((char *)_gblp); } };
113
114	#define GBL_CHECK_FREE_PARAM(nr,cnt) do { \
115	if ((nr)+(cnt) >= GBL_MAX_ARGUMENTS) { \
116	/* ad_assert(0); */ \
117	return "max. parameters exceeded"; \
118	} \
119	}while(0)
120
121	#if defined(DEVEL_RALF)
122	#warning remove GBL_MAX_ARGUMENTS - instead allocate dynamic
123	#endif /* DEVEL_RALF */
124
125
126	static GB_ERROR trace_params(int argc, const GBL argv, struct gbl_param ppara, const char *com) {
127	GB_ERROR error = 0;
128	int i;
129
130	for (i=0;i<argc;i++) {
131	struct gbl_param *para;
132	const char *argument = argv[i].str;
133
134	for (para = ppara; para && !error; para = para->next) {
135	int len = strlen(para->param_name);
136
137	if (strncmp(argument, para->param_name, len) == 0) {
138	const char *value = argument+len; // set to start of value;
139
140	if (para->type == GB_BIT) {
141	// GB_BIT is special cause param_name does NOT contain trailing '='
142
143	if (!value[0]) { // only 'name' -> handle like 'name=1'
144	;
145	}
146	else if (value[0] == '=') {
147	value++;
148	}
149	}
150
151	switch (para->type) {
152	case GB_STRING:
153	(const char *)para->varaddr = value;
154	break;
155
156	case GB_INT:
157	gb_assert(sizeof(int) == sizeof(uint)); // assumed by GBL_PARAM_UINT
158	(int )para->varaddr = atoi(value);
159	break;
160
161	case GB_BIT:
162	// 'param=' is same as 'param' or 'param=1' (historical reason, don't change)
163	(int )para->varaddr = (value[0] ? atoi(value) : 1);
164	break;
165
166	case GB_BYTE:
167	(char )para->varaddr = *value; // this may use the terminal zero-byte (e.g. for p1 in 'p0=0,p1=,p2=2' )
168	if (value[0] && value[1]) { // found at least 2 chars
169	GB_warningf("Only one character expected in value '%s' of param '%s' - rest is ignored", value, para->param_name);
170	}
171	break;
172
173	default:
174	gb_assert(0);
175	error = GBS_global_string("Parameter '%s': Unknown type %i (internal error)", para->param_name, para->type);
176	break;
177	}
178	break; // accept parameter
179	}
180	}
181
182	if (!error && !para) { // no parameter found for argument
183	int pcount = 0;
184	struct gbl_param **params;
185	int k;
186	char *res;
187	void *str = GBS_stropen(1000);
188	GB_ERROR err;
189
190
191	for (para = ppara; para; para = para->next) pcount++;
192	params = (struct gbl_param *)GB_calloc(sizeof(void ),pcount);
193	for (k = 0, para = ppara; para; para = para->next) params[k++] = para;
194
195
196	for (pcount--; pcount>=0; pcount--) {
197	para = params[pcount];
198	GBS_strcat(str,"\t");
199	GBS_strcat(str,para->param_name);
200	switch(para->type) {
201	case GB_STRING: GBS_strcat(str, "STRING"); break;
202	case GB_INT: GBS_strcat(str, "INT"); break;
203	case GB_FLOAT: GBS_strcat(str, "FLOAT"); break;
204	case GB_BYTE: GBS_strcat(str, "CHAR"); break;
205	case GB_BIT: GBS_strcat(str, " "); break;
206	default: gb_assert (0); GBS_strcat(str, "????"); break;
207	}
208	GBS_strcat(str,"\t\t;");
209	GBS_strcat(str,para->help_text);
210	GBS_strcat(str,"\n");
211	}
212	freeset(params, NULL);
213	res = GBS_strclose(str);
214	err = GB_export_errorf("Unknown Parameter '%s' in command '%s'\n\tPARAMETERS:\n%s",argv[i].str,com,res);
215	free(res);
216	return err;
217	}
218	}
219
220	return error;
221	}
222
223
224	/********************************************************************************************
225	String Functions
226	********************************************************************************************/
227
228	static char unEscapeString(const char escapedString) {
229	/* replaces all \x by x */
230	char *result = nulldup(escapedString);
231	char *to = result;
232	char *from = result;
233
234	while (1) {
235	char c = *from++;
236	if (!c) break;
237
238	if (c=='\\') {
239	to++ = from++;
240	}
241	else {
242	*to++ = c;
243	}
244	}
245	*to = 0;
246	return result;
247	}
248
249	static int gbl_stricmp(const char s1, const char s2) {
250	/* case insensitive strcmp */
251	int i;
252	for (i = 0; ; ++i) {
253	char c1 = tolower(s1[i]);
254	char c2 = tolower(s2[i]);
255
256	if (c1 == c2) {
257	if (!c1) break; // equal strings
258	}
259	else {
260	if (c1<c2) return -1;
261	return 1;
262	}
263	}
264	return 0;
265	}
266	static int gbl_strincmp(const char s1, const char s2, int size2) {
267	/* case insensitive strcmp */
268	int i;
269	for (i = 0; i<size2; ++i) {
270	char c1 = tolower(s1[i]);
271	char c2 = tolower(s2[i]);
272
273	if (c1 == c2) {
274	if (!c1) break; // equal strings
275	}
276	else {
277	if (c1<c2) return -1;
278	return 1;
279	}
280	}
281	return 0;
282	}
283	static const char gbl_stristr(const char haystack, const char *needle) {
284	/* case insensitive strstr */
285	const char *hp = haystack;
286	char c1 = toupper(needle[0]);
287	char c2 = tolower(c1);
288	int needle_size = strlen(needle);
289
290	if (c1 == c2) {
291	hp = strchr(hp, c1);
292	while (hp) {
293	if (gbl_strincmp(hp, needle, needle_size) == 0) return hp;
294	hp = strchr(hp+1, c1);
295	}
296	}
297	else {
298	while (hp) {
299	const char *h1 = strchr(hp, c1);
300	const char *h2 = strchr(hp, c2);
301
302	if (h1 && h2) {
303	if (h1<h2) {
304	if (gbl_strincmp(h1, needle, needle_size) == 0) return h1;
305	hp = h1+1;
306	}
307	else {
308	gb_assert(h1>h2);
309	if (gbl_strincmp(h2, needle, needle_size) == 0) return h2;
310	hp = h2+1;
311	}
312	}
313	else {
314	if (h1) { hp = h1; }
315	else if (h2) { hp = h2; c1 = c2; }
316	else { hp = 0; }
317
318	while (hp) {
319	if (gbl_strincmp(hp, needle, needle_size) == 0) return hp;
320	hp = strchr(hp+1, c1);
321	}
322	}
323	}
324	}
325	return 0;
326	}
327
328	/* *************************** gbl_mid_streams ***************************
329	* used as well to copy all streams (e.g. by 'dd')
330	*/
331
332	static GB_ERROR gbl_mid_streams(int arg_cinput, const GBL *arg_vinput,
333	int arg_cout, GBL *arg_vout,
334	int start,int mstart,int end,int relend)
335	{
336	int i;
337	GBL_CHECK_FREE_PARAM(*arg_cout,arg_cinput);
338	for (i=0;i<arg_cinput;i++) { /* go through all in streams */
339	char *p;
340	int c;
341
342	int len;
343	int nstart = start;
344	int nend = end;
345
346	p = arg_vinput[i].str;
347	len = strlen(p);
348	if (nstart<0) nstart = len - mstart;
349	if (nend<0) nend = len - relend; /* check rel len */
350
351	if (nstart>len ) nstart = len; /* check boundaries */
352	if (nstart<0) nstart = 0;
353	if (nend>len) nend = len;
354	if (nend<nstart) nend = nstart;
355
356	c = p[nend];
357	p[nend] =0;
358	(arg_vout)[(arg_cout)++].str = strdup(p+nstart); /* export result string */
359	p[nend] = c;
360	}
361	return 0;
362	}
363
364	/* *************************** trace *************************** */
365
366	static GB_ERROR gbl_trace(GBL_command_arguments *args) {
367	int tmp_trace;
368
369	if (args->cparam!=1) return "syntax: trace(0\|1)";
370
371	tmp_trace = atoi(args->vparam[0].str);
372	if (tmp_trace<0 \|\| tmp_trace>1) return GBS_global_string("Illegal value %i to trace", tmp_trace);
373
374	if (tmp_trace != GB_get_ACISRT_trace()) {
375	printf("* %sctivated ACI trace *\n", tmp_trace ? "A" : "De-a");
376	GB_set_ACISRT_trace(tmp_trace);
377	}
378
379	return gbl_mid_streams(args->cinput, args->vinput,args->coutput, args->voutput, 0, 0, -1, 0); /* copy all streams */
380	}
381
382	/********************************************************************************************
383	Binary operators:
384	********************************************************************************************/
385	/*
386	* Binary operators work on pairs of values.
387	* Three different operational modes are implemented for all binary operators:
388	*
389	* 1. inputstreams\|operator
390	*
391	* The number of inputstreams has to be even and the operator will be
392	* applied to pairs of them.
393	*
394	* Example : a;b;c;d;e;f \| plus
395	* Result : a+b;c+d;e+f
396	*
397	* 2. inputstreams\|operator(x)
398	*
399	* The number of inputstreams has to be at least 1.
400	* The operator is applied to each inputstream.
401	*
402	* Example : a;b;c \| plus(d)
403	* Result : a+d;b+d;c+d
404	*
405	* 3. operator(x, y)
406	*
407	* Inputstreams will be ignored and the operator is applied
408	* to the arguments
409	*
410	* Example : a;b \| plus(c,d)
411	* Result : c+d
412	*/
413
414	typedef char* (gbl_binary_operator)(const char arg1, const char arg2, void client_data);
415
416	static GB_ERROR gbl_apply_binary_operator(GBL_command_arguments args, gbl_binary_operator op, void client_data)
417	{
418	GB_ERROR error = 0;
419
420	switch (args->cparam) {
421	case 0:
422	if (args->cinput == 0) error = "Expect at least two input streams if called with 0 parameters";
423	else if (args->cinput%2) error = "Expect an even number of input streams if called with 0 parameters";
424	else {
425	int inputpairs = args->cinput/2;
426	int i;
427	for (i = 0; i<inputpairs; ++i) {
428	PASS_2_OUT(args, op(args->vinput[i2].str, args->vinput[i2+1].str, client_data));
429	}
430	}
431	break;
432
433	case 1:
434	if (args->cinput == 0) error = "Expect at least one input stream if called with 1 parameter";
435	else {
436	int i;
437	const char *argument = args->vparam[0].str;
438	for (i = 0; i<args->cinput; ++i) {
439	PASS_2_OUT(args, op(args->vinput[i].str, argument, client_data));
440	}
441	}
442	break;
443
444	case 2:
445	{
446	GBDATA gb_main = (GBDATA)GB_MAIN(args->gb_ref)->data;
447	int i;
448
449	for (i = 0; i<args->cinput; ++i) {
450	char *result1 = GB_command_interpreter(gb_main, args->vinput[i].str, args->vparam[0].str, args->gb_ref, args->default_tree_name);
451	if (!result1) error = GB_await_error();
452	else {
453	char *result2 = GB_command_interpreter(gb_main, args->vinput[i].str, args->vparam[1].str, args->gb_ref, args->default_tree_name);
454	if (!result2) error = GB_await_error();
455	else {
456	PASS_2_OUT(args, op(result1, result2, client_data));
457	free(result2);
458	}
459	free(result1);
460	}
461	}
462
463	break;
464	}
465	default :
466	error = "0 to 2 arguments expected";
467	break;
468	}
469
470	return error;
471	}
472
473	/********************************************************************************************
474	the commands themselves:
475	********************************************************************************************/
476
477	static GB_ERROR gbl_command(GBL_command_arguments *args) {
478	GB_ERROR error = NULL;
479
480	if (args->cparam!=1) {
481	error = "syntax: command(\"escaped command\")";
482	}
483	else {
484	GBDATA gb_main = (GBDATA)GB_MAIN(args->gb_ref)->data;
485	int i;
486	char *command;
487
488	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
489	command = unEscapeString(args->vparam[0].str);
490	#if defined(DEBUG)
491	printf("executing command '%s'\n", command);
492	#endif /* DEBUG */
493
494	for (i=0; i<args->cinput && !error; i++) { /* go through all orig streams */
495	char *result = GB_command_interpreter(gb_main, args->vinput[i].str, command, args->gb_ref, args->default_tree_name);
496	if (!result) error = GB_await_error();
497	else PASS_2_OUT(args, result);
498	}
499	free(command);
500	}
501	return error;
502	}
503
504	static GB_ERROR gbl_eval(GBL_command_arguments *args) {
505	GB_ERROR error = NULL;
506
507	if (args->cparam!=1) {
508	error = "eval syntax: eval(\"escaped command evaluating to command\")";
509	}
510	else {
511	GBDATA gb_main = (GBDATA)GB_MAIN(args->gb_ref)->data;
512	char *command;
513	char *to_eval;
514
515	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
516
517	to_eval = unEscapeString(args->vparam[0].str);
518	command = GB_command_interpreter(gb_main, "", to_eval, args->gb_ref, args->default_tree_name); // evaluate independent
519
520	if (!command) error = GB_await_error();
521	else {
522	int i;
523
524	if (GB_get_ACISRT_trace()) {
525	printf("evaluating '%s'\n", to_eval);
526	printf("executing '%s'\n", command);
527	}
528
529	for (i=0; i<args->cinput && !error; i++) { /* go through all orig streams */
530	char *result = GB_command_interpreter(gb_main, args->vinput[i].str, command, args->gb_ref, args->default_tree_name);
531	if (!result) error = GB_await_error();
532	else PASS_2_OUT(args, result);
533	}
534	free(command);
535	}
536	free(to_eval);
537	}
538	return error;
539	}
540
541	static GB_HASH *definedCommands = 0;
542
543	static GB_ERROR gbl_define(GBL_command_arguments *args) {
544	GB_ERROR error = 0;
545
546	if (args->cparam!=2) {
547	error = "syntax: define(name, \"escaped command\")";
548	}
549	else {
550	const char *name = args->vparam[0].str;
551	char *cmd = unEscapeString(args->vparam[1].str);
552	char *oldcmd;
553
554	if (!definedCommands) definedCommands = GBS_create_hash(100, GB_MIND_CASE);
555
556	oldcmd = (char*)GBS_read_hash(definedCommands, name);
557	if (oldcmd) free(oldcmd);
558	GBS_write_hash(definedCommands, name, (long)cmd);
559
560	if (GB_get_ACISRT_trace()) {
561	printf("defining command '%s'='%s'\n", name, cmd);
562	}
563	}
564
565	return error;
566	}
567
568	static GB_ERROR gbl_do(GBL_command_arguments *args) {
569	GB_ERROR error = 0;
570
571	if (args->cparam!=1) {
572	error = "syntax: do(name)";
573	}
574	else {
575	const char *name = args->vparam[0].str;
576	const char *cmd = 0;
577
578	if (definedCommands) cmd = (const char*)GBS_read_hash(definedCommands, name);
579	if (!cmd) {
580	error = GBS_global_string("Can't do undefined command '%s' - use define(%s, ...) first", name, name);
581	}
582	else {
583	GBDATA gb_main = (GBDATA)GB_MAIN(args->gb_ref)->data;
584	int i;
585
586	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
587
588	if (GB_get_ACISRT_trace()) {
589	printf("executing defined command '%s'='%s' on %i streams\n", name, cmd, args->cinput);
590	}
591
592	for (i=0; i<args->cinput && !error; i++) { /* go through all orig streams */
593	char *result = GB_command_interpreter(gb_main, args->vinput[i].str, cmd, args->gb_ref, args->default_tree_name);
594	if (!result) error = GB_await_error();
595	else PASS_2_OUT(args, result);
596	}
597	}
598	}
599	return error;
600	}
601
602	static GB_ERROR gbl_streams(GBL_command_arguments *args) {
603	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
604	PASS_2_OUT(args, GBS_global_string_copy("%i", args->cinput));
605	return 0;
606	}
607
608	static GB_ERROR gbl_origin(GBL_command_arguments *args) {
609	GB_ERROR error = NULL;
610
611	if (args->cparam!=1) error = GBS_global_string("syntax: %s(\"escaped command\")", args->command);
612	else if (!GEN_is_pseudo_gene_species(args->gb_ref)) {
613	error = GBS_global_string("'%s' applies to gene-species only", args->command);
614	}
615	else {
616	GBDATA *gb_origin = NULL;
617
618	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
619
620	if (strcmp(args->command, "origin_organism") == 0) {
621	gb_origin = GEN_find_origin_organism(args->gb_ref, 0);
622	}
623	else {
624	ad_assert(strcmp(args->command, "origin_gene") == 0);
625	gb_origin = GEN_find_origin_gene(args->gb_ref, 0);
626	}
627
628	if (!error && !gb_origin) error = GB_await_error();
629
630	if (!error) {
631	char *command = unEscapeString(args->vparam[0].str);
632	int i;
633	GBDATA gb_main = (GBDATA)GB_MAIN(args->gb_ref)->data;
634
635	for (i=0; i<args->cinput && !error; i++) { /* go through all orig streams */
636	char *result = GB_command_interpreter(gb_main, args->vinput[i].str, command, gb_origin, args->default_tree_name);
637	if (!result) error = GB_await_error();
638	else PASS_2_OUT(args, result);
639	}
640
641	free(command);
642	}
643	}
644
645	return error;
646	}
647
648	static GB_ERROR gbl_count(GBL_command_arguments *args)
649	{
650	int i;
651	char tab[256]; /* if tab[char] count 'char' */
652
653	if (args->cparam!=1) return "count syntax: count(\"characters to count\")";
654
655	for (i=0;i<256;i++) {
656	if (strchr(args->vparam[0].str,i)) tab[i] = 1;
657	else tab[i] = 0;
658	}
659	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
660	for (i=0;i<args->cinput;i++) { /* go through all orig streams */
661	long sum = 0; /* count frequencies */
662	unsigned char p = (unsigned char )args->vinput[i].str;
663	while (*p){
664	sum += tab[*(p++)];
665	}
666	PASS_2_OUT(args, GBS_global_string_copy("%li", sum));
667	}
668	return 0;
669	}
670
671	static GB_ERROR gbl_len(GBL_command_arguments *args)
672	{
673	int i;
674	char tab[256]; /* if tab[char] count 'char' */
675	const char *option;
676
677	if (args->cparam == 0) option = "";
678	else option = args->vparam[0].str;
679	if (args->cparam>=2) return "len syntax: len[(\"characters not to count\")]";
680
681	for (i=0;i<256;i++) {
682	if (strchr(option,i)) tab[i] = 0;
683	else tab[i] = 1;
684	}
685	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
686	for (i=0;i<args->cinput;i++) { /* go through all orig streams */
687	char *p;
688	long sum = 0; /* count frequencies */
689	p = args->vinput[i].str;
690	while (*p){
691	sum += tab[(unsigned int)*(p++)];
692	}
693	PASS_2_OUT(args, GBS_global_string_copy("%li", sum));
694	}
695	return 0;
696	}
697
698	static GB_ERROR gbl_remove(GBL_command_arguments *args)
699	{
700	int i;
701	char tab[256]; /* if tab[char] count 'char' */
702
703
704	if (args->cparam!=1) return "remove syntax: remove(\"characters to remove\")";
705
706	for (i=0;i<256;i++) {
707	if (strchr(args->vparam[0].str,i)) tab[i] = 1;
708	else tab[i] = 0;
709	}
710
711	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
712	for (i=0;i<args->cinput;i++) { /* go through all orig streams */
713	void *strstruct;
714	char *p;
715	strstruct = GBS_stropen(1000);
716	for (p = args->vinput[i].str;*p;p++){
717	if (!tab[(unsigned int)*p]) {
718	GBS_chrcat(strstruct,*p);
719	}
720	}
721	PASS_2_OUT(args, GBS_strclose(strstruct));
722	}
723	return 0;
724	}
725
726	static GB_ERROR gbl_keep(GBL_command_arguments *args)
727	{
728	int i;
729	char tab[256]; /* if tab[char] != 0 then keep'char' */
730
731
732	if (args->cparam!=1) return "keep syntax: keep(\"characters not to remove\")";
733
734	memset(tab, 0, 256); // keep none
735	{
736	unsigned char keep = (unsigned char)args->vparam[0].str;
737	for (i = 0; keep[i]; ++i) {
738	tab[keep[i]] = 1; // keep all members of argument
739	}
740	}
741
742	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
743	for (i=0;i<args->cinput;i++) { /* go through all orig streams */
744	void *strstruct;
745	char *p;
746	strstruct = GBS_stropen(1000);
747	for (p = args->vinput[i].str;*p;p++){
748	if (tab[(unsigned int)*p]) {
749	GBS_chrcat(strstruct,*p);
750	}
751	}
752	PASS_2_OUT(args, GBS_strclose(strstruct));
753	}
754	return 0;
755	}
756
757	static char binop_compare(const char arg1, const char arg2, void client_data) {
758	long case_sensitive = (long)client_data;
759	int result;
760
761	if (case_sensitive) result = strcmp(arg1, arg2);
762	else result = gbl_stricmp(arg1, arg2);
763
764	return GBS_global_string_copy("%i", result<0 ? -1 : (result>0 ? 1 : 0));
765	}
766	static char binop_equals(const char arg1, const char arg2, void client_data) {
767	long case_sensitive = (long)client_data;
768	int result;
769
770	if (case_sensitive) result = strcmp(arg1, arg2);
771	else result = gbl_stricmp(arg1, arg2);
772
773	return GBS_global_string_copy("%i", result == 0 ? 1 : 0);
774	}
775	static char binop_contains(const char arg1, const char arg2, void client_data) {
776	long case_sensitive = (long)client_data;
777	const char *found = 0;
778
779	if (case_sensitive) found = strstr(arg1, arg2);
780	else found = gbl_stristr(arg1, arg2);
781
782	return GBS_global_string_copy("%ti", found == 0 ? 0 : (found-arg1)+1);
783	}
784	static char binop_partof(const char arg1, const char arg2, void client_data) {
785	return binop_contains(arg2, arg1, client_data);
786	}
787
788	static GB_ERROR gbl_compare (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_compare, (void)1); }
789	static GB_ERROR gbl_icompare (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_compare, (void)0); }
790	static GB_ERROR gbl_equals (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_equals, (void)1); }
791	static GB_ERROR gbl_iequals (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_equals, (void)0); }
792	static GB_ERROR gbl_contains (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_contains, (void)1); }
793	static GB_ERROR gbl_icontains(GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_contains, (void)0); }
794	static GB_ERROR gbl_partof (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_partof, (void)1); }
795	static GB_ERROR gbl_ipartof (GBL_command_arguments args){ return gbl_apply_binary_operator(args, binop_partof, (void)0); }
796
797	static GB_ERROR gbl_translate(GBL_command_arguments *args)
798	{
799	unsigned char tab[256];
800	int i;
801	char replace_other = 0;
802
803	if (args->cparam<2 \|\| args->cparam>3) return "translate syntax: translate(#old, #new [,#other])";
804
805	if (args->cparam == 3) {
806	const char *other = args->vparam[2].str;
807	if (other[0] == 0 \|\| other[1] != 0) {
808	return "third parameter of translate has to be one character (i.e. \"-\")";
809	}
810	replace_other = other[0];
811	}
812
813	/* build translation table : */
814	{
815	const unsigned char o = (const unsigned char )args->vparam[0].str;
816	const unsigned char n = (const unsigned char )args->vparam[1].str;
817	char used[256];
818
819	if (strlen((const char )o) != strlen((const char )n)) {
820	return "arguments 1 and 2 of translate should be strings with identical length";
821	}
822
823	for (i = 0; i<256; ++i) {
824	tab[i] = replace_other ? replace_other : i; // replace unused or identity translation
825	used[i] = 0;
826	}
827
828	for (i = 0; o[i]; ++i) {
829	if (used[o[i]]) return GBS_global_string("character '%c' used twice in argument 1 of translate", o[i]);
830	used[o[i]] = 1;
831	tab[o[i]] = n[i]; // real translation
832	}
833	}
834
835	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
836	for (i=0;i<args->cinput;i++) { /* go through all orig streams */
837	void *strstruct;
838	char *p;
839	strstruct = GBS_stropen(1000);
840	for (p = args->vinput[i].str;*p;p++){
841	GBS_chrcat(strstruct, tab[(unsigned char)*p]);
842	}
843	PASS_2_OUT(args, GBS_strclose(strstruct));
844	}
845	return 0;
846	}
847
848
849	static GB_ERROR gbl_echo(GBL_command_arguments *args)
850	{
851	int i;
852	args->cinput = args->cinput;
853	args->vinput = args->vinput;
854	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
855	for (i=0;i<args->cparam;i++) { /* go through all in streams */
856	char *p;
857	p = args->vparam[i].str;
858	COPY_2_OUT(args, p);
859	}
860	return 0;
861	}
862
863	static GB_ERROR gbl_dd(GBL_command_arguments *args)
864	{
865	if (args->cparam!=0) return "syntax: dd (no parameters)";
866	return gbl_mid_streams(args->cinput, args->vinput,args->coutput, args->voutput, 0, 0, -1, 0); /* copy all streams */
867	}
868
869	static GB_ERROR gbl_string_convert(GBL_command_arguments *args)
870	{
871	int mode = -1;
872	int i;
873
874	if (strcmp(args->command, "lower") == 0) mode = 0;
875	else if (strcmp(args->command, "upper") == 0) mode = 1;
876	else if (strcmp(args->command, "caps") == 0) mode = 2;
877	else return GB_export_errorf("Unknown command '%s'", args->command);
878
879	if (args->cparam!=0) return GBS_global_string("syntax: %s (no parameters)", args->command);
880
881	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
882	for (i=0;i<args->cinput;i++) { /* go through all in streams */
883	char *p = strdup(args->vinput[i].str);
884	char *pp;
885	int last_was_alnum = 0;
886
887	for (pp = p; pp[0]; ++pp) {
888	switch (mode) {
889	case 0: pp[0] = tolower(pp[0]); break;
890	case 1: pp[0] = toupper(pp[0]); break;
891	case 2: /* caps */
892	if (isalnum(pp[0])) {
893	if (last_was_alnum) pp[0] = tolower(pp[0]);
894	else pp[0] = toupper(pp[0]);
895	last_was_alnum = 1;
896	}
897	else {
898	last_was_alnum = 0;
899	}
900	break;
901	default : ad_assert(0); break;
902	}
903	}
904
905	PASS_2_OUT(args, p);
906	}
907
908	return 0;
909	}
910
911	static GB_ERROR gbl_head(GBL_command_arguments *args)
912	{
913	int start;
914	if (args->cparam!=1) return "head syntax: head(#start)";
915	start = atoi(args->vparam[0].str);
916	return gbl_mid_streams(args->cinput, args->vinput,args->coutput, args->voutput, 0,0, start, -start);
917	}
918
919	static GB_ERROR gbl_tail(GBL_command_arguments *args)
920	{
921	int end;
922	if (args->cparam!=1) return "tail syntax: tail(#length_of_tail)";
923	end = atoi(args->vparam[0].str);
924	return gbl_mid_streams(args->cinput, args->vinput,args->coutput, args->voutput, -1, end, -1, 0);
925	}
926
927	static GB_ERROR gbl_mid0(GBL_command_arguments *args)
928	{
929	int start;
930	int end;
931	if (args->cparam!=2) return "mid0 syntax: mid0(#start;#end)";
932	start = atoi(args->vparam[0].str);
933	end = atoi(args->vparam[1].str);
934	return gbl_mid_streams(args->cinput, args->vinput, args->coutput, args->voutput, start, -start, end, -end);
935	}
936
937	static GB_ERROR gbl_mid(GBL_command_arguments *args)
938	{
939	int start;
940	int end;
941	if (args->cparam!=2) return "mid syntax: mid(#start;#end)";
942	start = atoi(args->vparam[0].str)-1;
943	end = atoi(args->vparam[1].str)-1;
944	return gbl_mid_streams(args->cinput, args->vinput, args->coutput, args->voutput, start, -start, end, -end);
945	}
946
947	static GB_ERROR gbl_tab(GBL_command_arguments *args)
948	{
949	int i,j;
950	int tab;
951	if (args->cparam!=1) return "tab syntax: tab(#tab)";
952	tab = atoi(args->vparam[0].str);
953	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
954	for (i=0;i<args->cinput;i++) { /* go through all in streams */
955	char *p;
956	int len = strlen(args->vinput[i].str);
957
958	if (len >= tab) {
959	IN_2_OUT(args, i);
960	}
961	else {
962	p = (char *)GB_calloc(sizeof(char),tab+1);
963	strcpy(p, args->vinput[i].str);
964	for (j=len; j<tab; j++) p[j] = ' ';
965
966	PASS_2_OUT(args, p);
967	}
968	}
969	return 0;
970	}
971
972	static GB_ERROR gbl_pretab(GBL_command_arguments *args)
973	{
974	int i,j;
975	int tab;
976	if (args->cparam!=1) return "pretab syntax: pretab(#tab)";
977	tab = atoi(args->vparam[0].str);
978	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
979	for (i=0;i<args->cinput;i++) { /* go through all in streams */
980	char *p;
981	int len = strlen(args->vinput[i].str);
982
983	if (len >= tab) {
984	IN_2_OUT(args, i);
985	}
986	else {
987	int spaces = tab-len;
988
989	p = (char *)GB_calloc(sizeof(char),tab+1);
990	for (j = 0; j<spaces; ++j) p[j] = ' ';
991	strcpy(p+j, args->vinput[i].str);
992
993	PASS_2_OUT(args, p);
994	}
995	}
996	return 0;
997	}
998
999	static GB_ERROR gbl_crop(GBL_command_arguments *args)
1000	{
1001	int i;
1002	const char *chars_to_crop;
1003
1004	if (args->cparam != 1) return "crop syntax: pretab(chars_to_crop)";
1005
1006	chars_to_crop = args->vparam[0].str;
1007	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
1008	for (i=0;i<args->cinput;i++) { /* go through all in streams */
1009	const char *s = args->vinput[i].str;
1010	char *p;
1011	int len;
1012
1013	while (s[0] && strchr(chars_to_crop, s[0]) != 0) s++; /* crop at beg of line */
1014
1015	len = strlen(s);
1016	p = (char*)GB_calloc(sizeof(char), len+1);
1017	memcpy(p, s, len);
1018
1019	{
1020	char *pe = p+len-1;
1021
1022	while (pe >= p && strchr(chars_to_crop, pe[0]) != 0) { /* crop at end of line */
1023	--pe;
1024	}
1025	ad_assert(pe >= (p-1));
1026	pe[1] = 0;
1027	}
1028
1029	PASS_2_OUT(args, p);
1030	}
1031	return 0;
1032	}
1033
1034	static GB_ERROR gbl_cut(GBL_command_arguments *args)
1035	{
1036	int i;
1037
1038	GBL_CHECK_FREE_PARAM(*args->coutput,args->cparam);
1039	for (i=0; i<args->cparam;i++) {
1040	int j = atoi(args->vparam[i].str);
1041	if (j<1 \|\| j>args->cinput) {
1042	return GBS_global_string("Illegal stream number '%i'", j);
1043	}
1044	--j; // user numbers streams from 1 to N
1045
1046	IN_2_OUT(args, j);
1047	}
1048	return 0;
1049	}
1050	static GB_ERROR gbl_drop(GBL_command_arguments *args)
1051	{
1052	int i;
1053	int *dropped;
1054	GB_ERROR error = 0;
1055
1056	GBL_CHECK_FREE_PARAM(*args->coutput, args->cinput-args->cparam);
1057
1058	dropped = malloc(args->cinput*sizeof(dropped));
1059	for (i=0; i<args->cinput;++i) {
1060	dropped[i] = 0;
1061	}
1062
1063	for (i=0; i<args->cparam;++i) {
1064	int j = atoi(args->vparam[i].str);
1065	if (j<1 \|\| j>args->cinput) {
1066	error = GBS_global_string("Illegal stream number '%i'", j);
1067	break;
1068	}
1069	--j; // user numbers streams from 1 to N
1070	dropped[j] = 1;
1071	}
1072
1073	if (!error) {
1074	for (i=0; i<args->cinput;++i) {
1075	if (dropped[i] == 0) {
1076	IN_2_OUT(args, i);
1077	}
1078	}
1079	}
1080	free(dropped);
1081
1082	return error;
1083	}
1084
1085	static GB_ERROR gbl_dropempty(GBL_command_arguments *args)
1086	{
1087	int i;
1088	GBL_CHECK_FREE_PARAM(*args->coutput, args->cinput);
1089	if (args->cparam != 0) return "expect no parameters";
1090
1091	for (i=0; i<args->cinput;++i) {
1092	if (args->vinput[i].str[0]) { /* if non-empty */
1093	IN_2_OUT(args, i);
1094	}
1095	}
1096	return 0;
1097	}
1098
1099	static GB_ERROR gbl_dropzero(GBL_command_arguments *args)
1100	{
1101	int i;
1102	GBL_CHECK_FREE_PARAM(*args->coutput, args->cinput);
1103	if (args->cparam != 0) return "expect no parameters";
1104
1105	for (i=0; i<args->cinput;++i) {
1106	if (atoi(args->vinput[i].str)) { /* if non-zero */
1107	IN_2_OUT(args, i);
1108	}
1109	}
1110	return 0;
1111	}
1112
1113	static GB_ERROR gbl_swap(GBL_command_arguments *args)
1114	{
1115	int swap1;
1116	int swap2;
1117	int firstout = *args->coutput;
1118	int i;
1119
1120	GBL_CHECK_FREE_PARAM(*args->coutput, args->cinput);
1121	if (args->cinput<2) return "need at least two input streams";
1122
1123	if (args->cparam == 0) {
1124	swap1 = args->cinput-1;
1125	swap2 = args->cinput-2;
1126	}
1127	else if (args->cparam == 2) {
1128	int illegal = 0;
1129
1130	swap1 = atoi(args->vparam[0].str);
1131	swap2 = atoi(args->vparam[1].str);
1132
1133	if (swap1<1 \|\| swap1>args->cinput) illegal = swap1;
1134	else if (swap2<1 \|\| swap2>args->cinput) illegal = swap2;
1135
1136	if (illegal) return GBS_global_string("illegal stream number '%i'", illegal);
1137
1138	swap1--;
1139	swap2--;
1140	}
1141	else {
1142	return "expected 0 or 2 parameters";
1143	}
1144
1145	for (i = 0; i<args->cinput; ++i) {
1146	IN_2_OUT(args, i);
1147	}
1148
1149	if (swap1 != swap2) {
1150	char temp = (args->voutput)[firstout+swap1].str;
1151	(args->voutput)[firstout+swap1].str = (args->voutput)[firstout+swap2].str;
1152	(*args->voutput)[firstout+swap2].str = temp;
1153	}
1154
1155	return 0;
1156	}
1157
1158	static GB_ERROR backfront_stream(GBL_command_arguments *args, int toback)
1159	{
1160	int i;
1161	int stream_to_move;
1162	int firstout = *args->coutput;
1163
1164	GBL_CHECK_FREE_PARAM(*args->coutput, args->cinput);
1165	if (args->cinput<1) return "need at least one input stream";
1166	if (args->cparam != 1) return "expecting one parameter";
1167
1168	stream_to_move = atoi(args->vparam[0].str);
1169	if (stream_to_move<1 \|\| stream_to_move>args->cinput) {
1170	return GBS_global_string("Illegal stream number '%i'", stream_to_move);
1171	}
1172	--stream_to_move;
1173
1174	for (i = 0; i<args->cinput; ++i) {
1175	IN_2_OUT(args, i);
1176	}
1177
1178	if (toback) {
1179	if (stream_to_move<(args->cinput-1)) { /* not last */
1180	GBL new_last = (*args->voutput)[firstout+stream_to_move];
1181	/* char new_last = (args->voutput)[firstout+stream_to_move].str; */
1182	for (i = stream_to_move+1; i<args->cinput; ++i) {
1183	(args->voutput)[firstout+i-1] = (args->voutput)[firstout+i];
1184	/* (args->voutput)[firstout+i-1].str = (args->voutput)[firstout+i].str; */
1185	}
1186	(*args->voutput)[firstout+args->cinput-1] = new_last;
1187	}
1188	}
1189	else { /* to front */
1190	if (stream_to_move != 0) { /* not first */
1191	GBL new_first = (*args->voutput)[firstout+stream_to_move];
1192	for (i = stream_to_move-1; i >= 0; --i) {
1193	(args->voutput)[firstout+i+1] = (args->voutput)[firstout+i];
1194	}
1195	(*args->voutput)[0] = new_first;
1196	}
1197	}
1198	return 0;
1199	}
1200	static GB_ERROR gbl_toback (GBL_command_arguments *args) { return backfront_stream(args, 1); }
1201	static GB_ERROR gbl_tofront(GBL_command_arguments *args) { return backfront_stream(args, 0); }
1202
1203	static GB_ERROR gbl_merge(GBL_command_arguments *args)
1204	{
1205	const char *separator;
1206
1207	switch (args->cparam) {
1208	case 0: separator = 0; break;
1209	case 1: separator = args->vparam[0].str; break;
1210	default : return "expect 0 or 1 parameter";
1211	}
1212
1213	GBL_CHECK_FREE_PARAM(*args->coutput, 1);
1214
1215	if (args->cinput) {
1216	int i;
1217	void *str;
1218
1219	str = GBS_stropen(1000);
1220	GBS_strcat(str, args->vinput[0].str);
1221
1222	for (i = 1; i<args->cinput; ++i) {
1223	if (separator) GBS_strcat(str, separator);
1224	GBS_strcat(str, args->vinput[i].str);
1225	}
1226
1227	PASS_2_OUT(args, GBS_strclose(str));
1228	}
1229
1230	return 0;
1231	}
1232
1233	static GB_ERROR gbl_split(GBL_command_arguments *args) {
1234	const char *separator;
1235	int split_mode = 0; /* 0 = remove separator, 1 = split before separator, 2 = split behind separator */
1236
1237	switch (args->cparam) {
1238	case 0: /* default behavior: split into lines and remove LF */
1239	separator = "\n";
1240	break;
1241	case 2:
1242	split_mode = atoi(args->vparam[1].str);
1243	if (split_mode<0 \|\| split_mode>2) {
1244	return GBS_global_string("Illegal split mode '%i' (valid: 0..2)", split_mode);
1245	}
1246	/* fall-through */
1247	case 1:
1248	separator = args->vparam[0].str;
1249	break;
1250	default : return "expect 0, 1 or 2 parameters";
1251	}
1252
1253	{
1254	size_t sepLen = strlen(separator);
1255	int i;
1256
1257	for (i = 0; i<args->cinput; ++i) {
1258	char *in = args->vinput[i].str;
1259	char from = in; / search from here */
1260
1261	while (in) {
1262	char *splitAt;
1263	GBL_CHECK_FREE_PARAM(*args->coutput, 1);
1264
1265	splitAt = strstr(from, separator);
1266	if (splitAt) {
1267	size_t len;
1268	char *copy;
1269
1270	if (split_mode == 2) splitAt += sepLen; /* split behind separator */
1271
1272	len = splitAt-in;
1273	copy = (char*)malloc(len+1);
1274
1275	memcpy(copy, in, len);
1276	copy[len] = 0;
1277
1278	PASS_2_OUT(args, copy);
1279
1280	in = splitAt + (split_mode == 0 ? sepLen : 0);
1281	from = in+(split_mode == 1 ? sepLen : 0);
1282	}
1283	else { // last part
1284	COPY_2_OUT(args, in);
1285	in = 0;
1286	}
1287	}
1288	}
1289	}
1290
1291	return 0;
1292	}
1293
1294	/********************************************************************************************
1295	Extended String Functions
1296	********************************************************************************************/
1297
1298	static GB_ERROR gbl_extract_words(GBL_command_arguments *args)
1299	{
1300	int i;
1301	float len;
1302	if (args->cparam != 2) return "extract_words needs two parameters:\nextract_words(\"Characters\",min_characters)";
1303	len = atof(args->vparam[1].str);
1304
1305	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
1306	for (i=0;i<args->cinput;i++) { /* go through all in streams */
1307	char *res = GBS_extract_words(args->vinput[i].str, args->vparam[0].str, len, 1);
1308	ad_assert(res);
1309	PASS_2_OUT(args, res);
1310	}
1311	return 0;
1312	}
1313
1314	static GB_ERROR gbl_extract_sequence(GBL_command_arguments *args)
1315	{
1316	int i;
1317	float len;
1318	GB_ERROR syntax_err = "extract_sequence needs two parameters:\nextract_sequence(\"Characters\",min_rel_characters [0.0-1.0])";
1319
1320	if (args->cparam != 2) return syntax_err;
1321	len = atof(args->vparam[1].str);
1322	if (len <0.0 \|\| len > 1.0) return syntax_err;
1323
1324	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
1325	for (i=0;i<args->cinput;i++) { /* go through all in streams */
1326	char *res = GBS_extract_words(args->vinput[i].str, args->vparam[0].str, len, 0);
1327	ad_assert(res);
1328	PASS_2_OUT(args, res);
1329	}
1330	return 0;
1331	}
1332
1333	static GB_ERROR gbl_check(GBL_command_arguments *args)
1334	{
1335	int i;
1336
1337	GBL_BEGIN_PARAMS;
1338	GBL_PARAM_STRING(exclude, "exclude=", "", "Remove characters 'str' before calculating" );
1339	GBL_PARAM_BIT (upper, "toupper", 0, "Convert all characters to uppercase before calculating");
1340	GBL_TRACE_PARAMS(args->cparam,args->vparam);
1341	GBL_END_PARAMS;
1342
1343	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
1344	for (i=0;i<args->cinput;i++) { /* go through all in streams */
1345	char buf[100];
1346	long id;
1347	id = GBS_checksum(args->vinput[i].str,upper,exclude);
1348	sprintf(buf,"%lX",id);
1349	COPY_2_OUT(args, buf);
1350	}
1351	return 0;
1352	}
1353
1354	static GB_ERROR gbl_gcgcheck(GBL_command_arguments *args)
1355	{
1356	int i;
1357
1358	GBL_BEGIN_PARAMS;
1359	GBL_TRACE_PARAMS(args->cparam,args->vparam);
1360	GBL_END_PARAMS;
1361
1362	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
1363	for (i=0;i<args->cinput;i++) { /* go through all in streams */
1364	char buf[100];
1365	long id;
1366	id = GBS_gcgchecksum(args->vinput[i].str);
1367	sprintf(buf,"%li",id);
1368	COPY_2_OUT(args, buf);
1369	}
1370	return 0;
1371	}
1372
1373	/********************************************************************************************
1374	SRT
1375	********************************************************************************************/
1376
1377	static GB_ERROR gbl_srt(GBL_command_arguments *args) {
1378	GB_ERROR error = NULL;
1379	int i;
1380	int j;
1381
1382	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
1383
1384	for (i=0; i<args->cinput && !error; i++) { /* go through all in streams */
1385	const char *source = args->vinput[i].str;
1386	char *modsource = 0;
1387
1388	for (j=0; j<args->cparam && !error; j++) {
1389	char *hs = GBS_string_eval(modsource ? modsource : source,
1390	args->vparam[j].str,
1391	args->gb_ref);
1392
1393	if (!hs) error = GB_await_error();
1394	else freeset(modsource, hs);
1395	}
1396
1397	if (!error) {
1398	if (modsource) {
1399	PASS_2_OUT(args, modsource);
1400	}
1401	else {
1402	COPY_2_OUT(args, source);
1403	}
1404	}
1405	}
1406	return error;
1407	}
1408
1409	/********************************************************************************************
1410	Calculator Functions
1411	********************************************************************************************/
1412
1413	/* numeric binary operators */
1414
1415	typedef int (*numeric_binary_operator)(int i1, int i2);
1416	static char apply_numeric_binop(const char arg1, const char arg2, void client_data) {
1417	int i1 = atoi(arg1);
1418	int i2 = atoi(arg2);
1419	numeric_binary_operator nbo = (numeric_binary_operator)client_data;
1420	int result = nbo(i1, i2);
1421
1422	return GBS_global_string_copy("%i", result);
1423	}
1424
1425	static int binop_plus(int i1, int i2) { return i1+i2; }
1426	static int binop_minus(int i1, int i2) { return i1-i2; }
1427	static int binop_mult(int i1, int i2) { return i1*i2; }
1428	static int binop_div(int i1, int i2) { return i2 ? i1/i2 : 0; }
1429	static int binop_rest(int i1, int i2) { return i2 ? i1%i2 : 0; }
1430	static int binop_per_cent(int i1, int i2) { return i2 ? (i1*100)/i2 : 0; }
1431
1432	static GB_ERROR gbl_plus (GBL_command_arguments *args){ return gbl_apply_binary_operator(args, apply_numeric_binop, binop_plus ); }
1433	static GB_ERROR gbl_minus (GBL_command_arguments *args){ return gbl_apply_binary_operator(args, apply_numeric_binop, binop_minus ); }
1434	static GB_ERROR gbl_mult (GBL_command_arguments *args){ return gbl_apply_binary_operator(args, apply_numeric_binop, binop_mult ); }
1435	static GB_ERROR gbl_div (GBL_command_arguments *args){ return gbl_apply_binary_operator(args, apply_numeric_binop, binop_div ); }
1436	static GB_ERROR gbl_rest (GBL_command_arguments *args){ return gbl_apply_binary_operator(args, apply_numeric_binop, binop_rest ); }
1437	static GB_ERROR gbl_per_cent(GBL_command_arguments *args){ return gbl_apply_binary_operator(args, apply_numeric_binop, binop_per_cent); }
1438
1439
1440	/********************************************************************************************
1441	Logical Functions
1442	********************************************************************************************/
1443
1444	static GB_ERROR gbl_select(GBL_command_arguments *args) {
1445	int i;
1446	GB_ERROR error = 0;
1447
1448	GBL_CHECK_FREE_PARAM(*args->coutput, args->cinput);
1449
1450	for (i=0;i<args->cinput && !error;i++) { /* go through all in streams */
1451	int value = atoi(args->vinput[i].str);
1452	if (value<0 \|\| value >= args->cparam) {
1453	error = GBS_global_string("Input stream value (%i) is out of bounds (0 to %i)", value, args->cparam-1);
1454	}
1455	else {
1456	GBDATA gb_main = (GBDATA)GB_MAIN(args->gb_ref)->data;
1457	char *result = GB_command_interpreter(gb_main, "", args->vparam[value].str, args->gb_ref, args->default_tree_name);
1458	if (!result) error = GB_await_error();
1459	else PASS_2_OUT(args, result);
1460	}
1461	}
1462	return error;
1463	}
1464
1465	/********************************************************************************************
1466	Database Functions
1467	********************************************************************************************/
1468	static GB_ERROR gbl_readdb(GBL_command_arguments *args)
1469	{
1470	int i;
1471	void *strstr = GBS_stropen(1024);
1472
1473
1474	for (i=0;i<args->cparam;i++){
1475	char *val = GBT_read_as_string(args->gb_ref, args->vparam[i].str);
1476	if (val) {
1477	GBS_strcat(strstr, val);
1478	free(val);
1479	}
1480	}
1481	PASS_2_OUT(args, GBS_strclose(strstr));
1482	return 0;
1483	}
1484
1485
1486	/********************************************************************************************
1487	Sequence Functions
1488	********************************************************************************************/
1489
1490	typedef enum enum_gbt_item_type {
1491	GBT_ITEM_UNKNOWN,
1492	GBT_ITEM_SPECIES,
1493	GBT_ITEM_GENE
1494	} gbt_item_type;
1495
1496	static gbt_item_type identify_gb_item(GBDATA *gb_item) {
1497	/* returns: GBT_ITEM_UNKNOWN -> unknown database_item
1498	* GBT_ITEM_SPECIES -> /species_data/species
1499	* GBT_ITEM_GENE -> /species_data/species/gene_data/gene */
1500
1501	GBDATA *gb_father;
1502	const char *key;
1503
1504	if (!gb_item) return GBT_ITEM_UNKNOWN;
1505	gb_father = GB_get_father(gb_item);
1506	if (!gb_father) return GBT_ITEM_UNKNOWN;
1507
1508	key = GB_KEY(gb_item);
1509
1510	if (strcmp(key, "species") == 0 &&
1511	strcmp(GB_KEY(gb_father), "species_data") == 0) {
1512	return GBT_ITEM_SPECIES;
1513	}
1514
1515	if (strcmp(key, "gene") == 0 &&
1516	strcmp(GB_KEY(gb_father), "gene_data") == 0 &&
1517	identify_gb_item(GB_get_father(gb_father)) == GBT_ITEM_SPECIES) {
1518	return GBT_ITEM_GENE;
1519	}
1520
1521	return GBT_ITEM_UNKNOWN;
1522	}
1523
1524	/* -------------------------------------------------------------------------------- */
1525	/* taxonomy caching */
1526
1527	struct cached_taxonomy {
1528	char tree_name; / tree for which taxonomy is cached here */
1529	int groups; /* number of named groups in tree (at time of caching) */
1530	GB_HASH taxonomy; / keys: "!species", ">XXXXgroup" and "<root>".
1531	Species and groups contain their first parent (i.e. '>XXXXgroup' or '<root>').
1532	Species not in hash are not members of tree.
1533	The 'XXXX' in groupname is simply a counter to avoid multiple groups with same name.
1534	The group-db-entries are stored in hash as pointers ('>>%p') and
1535	point to their own group entry ('>XXXXgroup')
1536	*/
1537	};
1538
1539	static void free_cached_taxonomy(struct cached_taxonomy *ct) {
1540	free(ct->tree_name);
1541	GBS_free_hash(ct->taxonomy);
1542	free(ct);
1543	}
1544
1545	static void build_taxonomy_rek(GBT_TREE node, GB_HASH tax_hash, const char parent_group, int group_counter) {
1546	if (node->is_leaf) {
1547	GBDATA *gb_species = node->gb_node;
1548	if (gb_species) { /* not zombie */
1549	GBS_write_hash(tax_hash, GBS_global_string("!%s", GBT_read_name(gb_species)), (long)strdup(parent_group));
1550	}
1551	}
1552	else {
1553	if (node->name) { /* named group */
1554	char *hash_entry;
1555	const char *hash_binary_entry;
1556	(*group_counter)++;
1557
1558	hash_entry = GBS_global_string_copy(">%04x%s", *group_counter, node->name);
1559	/* printf("hash_entry='%s' gb_node=%p\n", hash_entry, node->gb_node); */
1560	GBS_write_hash(tax_hash, hash_entry, (long)strdup(parent_group));
1561
1562	hash_binary_entry = GBS_global_string(">>%p", node->gb_node);
1563	/* printf("hash_entry='%s' gb_node=%p\n", hash_binary_entry, node->gb_node); */
1564	GBS_write_hash(tax_hash, hash_binary_entry, (long)strdup(hash_entry));
1565
1566	build_taxonomy_rek(node->leftson, tax_hash, hash_entry, group_counter);
1567	build_taxonomy_rek(node->rightson, tax_hash, hash_entry, group_counter);
1568	free(hash_entry);
1569	}
1570	else {
1571	build_taxonomy_rek(node->leftson, tax_hash, parent_group, group_counter);
1572	build_taxonomy_rek(node->rightson, tax_hash, parent_group, group_counter);
1573	}
1574	}
1575	}
1576
1577	static GB_HASH *cached_taxonomies = 0;
1578
1579	static GB_BOOL is_cached_taxonomy(const char key, long val, void cl_ct) {
1580	GBUSE(key);
1581	struct cached_taxonomy ct1 = (struct cached_taxonomy )val;
1582	struct cached_taxonomy ct2 = (struct cached_taxonomy )cl_ct;
1583
1584	return ct1 == ct2 ? GB_TRUE : GB_FALSE;
1585	}
1586
1587	static const char tree_of_cached_taxonomy(struct cached_taxonomy ct) {
1588	/* search the hash to find the correct cached taxonomy.
1589	* searching for tree name does not work, because the tree possibly already was deleted
1590	*/
1591	const char *tree = GBS_hash_next_element_that(cached_taxonomies, NULL, is_cached_taxonomy, ct);
1592	#if defined(DEBUG)
1593	if (tree) printf("tree_of_cached_taxonomy: tree='%s' ct->tree_name='%s'\n", tree, ct->tree_name);
1594	#endif /* DEBUG */
1595	return tree;
1596	}
1597
1598	static void flush_taxonomy_cb(GBDATA gbd, int cd_ct, GB_CB_TYPE cbt) {
1599	/* this cb is bound all tree db members below "/tree_data/tree_xxx" which
1600	* may have an effect on the displayed taxonomy
1601	* it invalidates cached taxonomies for that tree (when changed or deleted)
1602	*/
1603
1604	struct cached_taxonomy ct = (struct cached_taxonomy )cd_ct;
1605	const char *found = 0;
1606	GB_ERROR error = 0;
1607
1608	GBUSE(cbt);
1609
1610	found = tree_of_cached_taxonomy(ct);
1611
1612	if (found) {
1613	#if defined(DEBUG) && 0
1614	fprintf(stderr, "Deleting cached taxonomy ct=%p (tree='%s')\n", ct, found);
1615	#endif /* DEBUG */
1616	GBS_write_hash(cached_taxonomies, found, 0); /* delete cached taxonomy from hash */
1617	free_cached_taxonomy(ct);
1618	}
1619	#if defined(DEBUG) && 0
1620	else {
1621	fprintf(stderr, "No tree found for cached_taxonomies ct=%p (already deleted?)\n", ct);
1622	}
1623	#endif /* DEBUG */
1624
1625	if (!GB_inside_callback(gbd, GB_CB_DELETE)) {
1626	GB_remove_all_callbacks_to(gbd, (GB_CB_TYPE)(GB_CB_CHANGED\|GB_CB_DELETE), flush_taxonomy_cb);
1627	}
1628
1629	if (found && !error) {
1630	GBDATA *gb_main = GB_get_gb_main_during_cb();
1631	if (gb_main) {
1632	GBDATA *gb_tree_refresh = GB_search(gb_main, AWAR_TREE_REFRESH, GB_INT);
1633	if (!gb_tree_refresh) {
1634	error = GBS_global_string("%s (while trying to force refresh)", GB_await_error());
1635	}
1636	else {
1637	GB_touch(gb_tree_refresh); /* Note : force tree update */
1638	}
1639	}
1640	}
1641
1642	if (error) {
1643	fprintf(stderr, "Error in flush_taxonomy_cb: %s\n", error);
1644	}
1645	}
1646
1647	static void flush_taxonomy_if_new_group_cb(GBDATA gb_tree, int cd_ct, GB_CB_TYPE cbt) {
1648	/* detects the creation of new groups and call flush_taxonomy_cb() manually */
1649	struct cached_taxonomy ct = (struct cached_taxonomy )cd_ct;
1650	const char *tree_name;
1651
1652	#if defined(DEBUG)
1653	fprintf(stderr, "flush_taxonomy_if_new_group_cb() has been called (cbt=%i)\n", cbt);
1654	#endif /* DEBUG */
1655
1656	tree_name = tree_of_cached_taxonomy(ct);
1657	if (tree_name) {
1658	int groups = 0;
1659	GBDATA *gb_group_node;
1660
1661	for (gb_group_node = GB_entry(gb_tree, "node");
1662	gb_group_node;
1663	gb_group_node = GB_nextEntry(gb_group_node))
1664	{
1665	if (GB_entry(gb_group_node, "group_name")) {
1666	groups++; /* count named groups only */
1667	}
1668	}
1669
1670	#if defined(DEBUG)
1671	fprintf(stderr, "cached_groups=%i counted_groups=%i\n", ct->groups, groups);
1672	#endif /* DEBUG */
1673	if (groups != ct->groups) {
1674	#if defined(DEBUG)
1675	fprintf(stderr, "Number of groups changed -> invoking flush_taxonomy_cb() manually\n");
1676	#endif /* DEBUG */
1677	flush_taxonomy_cb(gb_tree, cd_ct, cbt);
1678	}
1679	}
1680	#if defined(DEBUG)
1681	else {
1682	fprintf(stderr, "cached taxonomy no longer valid.\n");
1683	}
1684	#endif /* DEBUG */
1685	}
1686
1687	static struct cached_taxonomy get_cached_taxonomy(GBDATA gb_main, const char tree_name, GB_ERROR error) {
1688	long cached;
1689	*error = 0;
1690	if (!cached_taxonomies) {
1691	cached_taxonomies = GBS_create_hash(20, GB_IGNORE_CASE);
1692	}
1693	cached = GBS_read_hash(cached_taxonomies, tree_name);
1694	if (!cached) {
1695	GBT_TREE tree = GBT_read_tree(gb_main, tree_name, sizeof(tree));
1696	if (!tree) *error = GB_await_error();
1697	else *error = GBT_link_tree(tree, gb_main, GB_FALSE, 0, 0);
1698
1699	if (!*error) {
1700	GBDATA *gb_tree = GBT_get_tree(gb_main, tree_name);
1701	if (!gb_tree) {
1702	*error = GBS_global_string("Can't find tree '%s'", tree_name);
1703	}
1704	else {
1705	struct cached_taxonomy ct = malloc(sizeof(ct));
1706	long nodes = GBT_count_nodes(tree);
1707	int group_counter = 0;
1708
1709	ct->tree_name = strdup(tree_name);
1710	ct->taxonomy = GBS_create_dynaval_hash((int)(nodes*2), GB_IGNORE_CASE, GBS_dynaval_free);
1711	ct->groups = 0; // counted below
1712
1713	build_taxonomy_rek(tree, ct->taxonomy, "<root>", &group_counter);
1714	cached = (long)ct;
1715	GBS_write_hash(cached_taxonomies, tree_name, (long)ct);
1716
1717	GB_remove_all_callbacks_to(gb_tree, GB_CB_SON_CREATED, flush_taxonomy_if_new_group_cb);
1718	GB_add_callback(gb_tree, GB_CB_SON_CREATED, flush_taxonomy_if_new_group_cb, (int*)ct);
1719
1720	{
1721	GBDATA *gb_tree_entry = GB_entry(gb_tree, "tree");
1722	GBDATA *gb_group_node;
1723
1724	if (gb_tree_entry) {
1725	GB_remove_all_callbacks_to(gb_tree_entry, (GB_CB_TYPE)(GB_CB_CHANGED\|GB_CB_DELETE), flush_taxonomy_cb);
1726	GB_add_callback(gb_tree_entry, (GB_CB_TYPE)(GB_CB_CHANGED\|GB_CB_DELETE), flush_taxonomy_cb, (int*)ct);
1727	}
1728
1729	/* add callbacks for all node/group_name subentries */
1730	for (gb_group_node = GB_entry(gb_tree, "node");
1731	gb_group_node;
1732	gb_group_node = GB_nextEntry(gb_group_node))
1733	{
1734	GBDATA *gb_group_name = GB_entry(gb_group_node, "group_name");
1735	if (gb_group_name) { /* group with id = 0 has no name */
1736	GB_remove_all_callbacks_to(gb_group_name, (GB_CB_TYPE)(GB_CB_CHANGED\|GB_CB_DELETE), flush_taxonomy_cb);
1737	GB_add_callback(gb_group_name, (GB_CB_TYPE)(GB_CB_CHANGED\|GB_CB_DELETE), flush_taxonomy_cb, (int*)ct);
1738	ct->groups++;
1739	}
1740	}
1741	}
1742	#if defined(DEBUG)
1743	fprintf(stderr, "Created taxonomy hash for '%s' (ct=%p)\n", tree_name, ct);
1744	#endif /* DEBUG */
1745	}
1746	}
1747
1748	if (tree) GBT_delete_tree(tree);
1749	}
1750
1751	if (!*error) {
1752	struct cached_taxonomy ct = (struct cached_taxonomy)cached;
1753	gb_assert(ct);
1754	return ct;
1755	}
1756
1757	return 0;
1758	}
1759
1760	static char get_taxonomy_string(GB_HASH tax_hash, const char group_key, int depth, GB_ERROR error) {
1761	long found;
1762	char *result = 0;
1763
1764	gb_assert(depth>0);
1765	gb_assert(!(group_key[0] == '>' && group_key[1] == '>')); // internal group-pointers not allowed here!
1766
1767	found = GBS_read_hash(tax_hash, group_key);
1768	if (found) {
1769	const char parent_group_key = (const char )found;
1770	if (strcmp(parent_group_key, "<root>") == 0) { // root reached
1771	result = strdup(group_key+5); // return own group name
1772	}
1773	else {
1774	if (depth>1) {
1775	char *parent_name = get_taxonomy_string(tax_hash, parent_group_key, depth-1, error);
1776	if (parent_name) {
1777	result = GBS_global_string_copy("%s/%s", parent_name, group_key+5);
1778	free(parent_name);
1779	}
1780	else {
1781	error = GBS_global_string("In get_taxonomy_string(%s): %s", group_key, error);
1782	result = 0;
1783	}
1784	}
1785	else {
1786	result = strdup(group_key+5); // return own group name
1787	}
1788	}
1789	}
1790	else {
1791	*error = GBS_global_string("Not in tax_hash: '%s'", group_key);
1792	}
1793	return result;
1794	}
1795
1796	static const char get_taxonomy(GBDATA gb_species_or_group, const char tree_name, int is_current_tree, int depth, GB_ERROR error) {
1797	GBDATA *gb_main = GB_get_root(gb_species_or_group);
1798	struct cached_taxonomy *tax = get_cached_taxonomy(gb_main, tree_name, error);
1799	const char *result = 0;
1800
1801	if (tax) {
1802	GBDATA *gb_name = GB_entry(gb_species_or_group, "name");
1803	GBDATA *gb_group_name = GB_entry(gb_species_or_group, "group_name");
1804
1805	if (gb_name && !gb_group_name) { /* it's a species */
1806	char *name = GB_read_string(gb_name);
1807	if (name) {
1808	GB_HASH *tax_hash = tax->taxonomy;
1809	long found = GBS_read_hash(tax_hash, GBS_global_string("!%s", name));
1810
1811	if (found) {
1812	const char parent_group = (const char )found;
1813
1814	if (strcmp(parent_group, "<root>") == 0) {
1815	result = ""; /* not member of any group */
1816	}
1817	else {
1818	static char *parent = 0;
1819
1820	freeset(parent, get_taxonomy_string(tax_hash, parent_group, depth, error));
1821	result = parent;
1822	}
1823	}
1824	else {
1825	result = GBS_global_string("Species '%s' not in '%s'", name, tree_name);
1826	}
1827	free(name);
1828	}
1829	else {
1830	*error = GBS_global_string("Species without 'name' entry!");
1831	}
1832	}
1833	else if (gb_group_name && !gb_name) { /* it's a group */
1834	char *group_name = GB_read_string(gb_group_name);
1835	if (group_name) {
1836	if (is_current_tree) {
1837	GB_HASH *tax_hash = tax->taxonomy;
1838	long found = GBS_read_hash(tax_hash, GBS_global_string(">>%p", gb_species_or_group));
1839
1840	if (found) {
1841	static char *full_group = 0;
1842	const char group_id = (const char )found;
1843
1844	freeset(full_group, get_taxonomy_string(tax_hash, group_id, depth, error));
1845	result = full_group;
1846	}
1847	else {
1848	result = GBS_global_string("Group '%s' not in '%s'", group_name, tree_name);
1849	}
1850	}
1851	else {
1852	*error = "It's not possible to specify the tree name in taxonomy() for groups";
1853	}
1854	free(group_name);
1855	}
1856	else {
1857	*error = "Group without 'group_name' entry";
1858	}
1859	}
1860	else if (gb_group_name) {
1861	*error = "Container has 'name' and 'group_name' entry - can't detect container type";
1862	}
1863	else {
1864	*error = "Container has neither 'name' nor 'group_name' entry - can't detect container type";
1865	}
1866	}
1867
1868	return result;
1869	}
1870
1871	static GB_ERROR gbl_taxonomy(GBL_command_arguments *args)
1872	{
1873	char *tree_name = 0;
1874	GB_ERROR error = 0;
1875
1876
1877	if (args->cparam<1 \|\| args->cparam>2) {
1878	error = "\"taxonomy\" syntax: \"taxonomy\"([tree_name,] count)";
1879	}
1880	else {
1881	int is_current_tree = 0;
1882	int count = -1;
1883	char *result = 0;
1884
1885	if (args->cparam == 1) { /* only 'count' */
1886	if (!args->default_tree_name) {
1887	result = strdup("No default tree");
1888	}
1889	else {
1890	tree_name = strdup(args->default_tree_name);
1891	count = atoi(args->vparam[0].str);
1892	is_current_tree = 1;
1893	}
1894	}
1895	else { /* 'tree_name', 'count' */
1896	tree_name = strdup(args->vparam[0].str);
1897	count = atoi(args->vparam[1].str);
1898	}
1899
1900	if (!result) {
1901	if (count<1) {
1902	error = GBS_global_string("Illegal count '%i' (allowed 1..n)", count);
1903	}
1904	if (!error) {
1905	const char *taxonomy_string = get_taxonomy(args->gb_ref, tree_name, is_current_tree, count, &error);
1906	if (taxonomy_string) result = strdup(taxonomy_string);
1907	}
1908	}
1909
1910	ad_assert(result \|\| error);
1911	if (result) PASS_2_OUT(args, result);
1912	}
1913	if (tree_name) free(tree_name);
1914	return error;
1915	}
1916
1917	static GB_ERROR gbl_sequence(GBL_command_arguments *args) {
1918	GB_ERROR error = 0;
1919
1920	if (args->cparam!=0) error = "\"sequence\" syntax: \"sequence\" (no parameters)";
1921	else if (args->cinput==0) error = "No input stream";
1922	else {
1923	GBL_CHECK_FREE_PARAM(*args->coutput,1);
1924
1925	switch (identify_gb_item(args->gb_ref)) {
1926	case GBT_ITEM_UNKNOWN: {
1927	error = "'sequence' used for unknown item";
1928	break;
1929	}
1930	case GBT_ITEM_SPECIES: {
1931	char *use = GBT_get_default_alignment(GB_get_root(args->gb_ref));
1932
1933	if (!use) error = GB_await_error();
1934	else {
1935	GBDATA *gb_seq = GBT_read_sequence(args->gb_ref,use);
1936
1937	if (gb_seq) PASS_2_OUT(args, GB_read_string(gb_seq));
1938	else COPY_2_OUT(args, ""); /* if current alignment does not exist -> return empty string */
1939
1940	free(use);
1941	}
1942	break;
1943	}
1944	case GBT_ITEM_GENE: {
1945	char *seq = GBT_read_gene_sequence(args->gb_ref, GB_TRUE, 0);
1946
1947	if (!seq) error = GB_await_error();
1948	else PASS_2_OUT(args, seq);
1949
1950	break;
1951	}
1952	}
1953	}
1954	return error;
1955	}
1956
1957	static GB_ERROR gbl_export_sequence(GBL_command_arguments *args) {
1958	GB_ERROR error = 0;
1959
1960	if (args->cparam!=0) {
1961	error = "\"sequence\" syntax: \"export_sequence\" (no parameters)";
1962	}
1963	else if (args->cinput==0) {
1964	error = "No input stream";
1965	}
1966	else {
1967	GBL_CHECK_FREE_PARAM(*args->coutput,1);
1968
1969	switch (identify_gb_item(args->gb_ref)) {
1970	case GBT_ITEM_UNKNOWN: {
1971	error = "'export_sequence' used for unknown item";
1972	break;
1973	}
1974	case GBT_ITEM_SPECIES: {
1975	if (get_export_sequence == 0) {
1976	error = "No export-sequence-hook defined (can't use 'export_sequence' here)";
1977	}
1978	else {
1979	size_t len;
1980	const char *seq = get_export_sequence(args->gb_ref, &len, &error);
1981
1982	ad_assert(error \|\| seq);
1983
1984	if (seq) PASS_2_OUT(args, GB_strduplen(seq, len));
1985	}
1986	break;
1987	}
1988	case GBT_ITEM_GENE: {
1989	error = "'export_sequence' cannot be used for gene";
1990	break;
1991	}
1992	}
1993	}
1994	return error;
1995	}
1996
1997	static GB_ERROR gbl_sequence_type(GBL_command_arguments *args)
1998	{
1999	GB_ERROR error = 0;
2000
2001	if (args->cparam) error = "\"sequence_type\" syntax: \"sequence\" (no parameters)";
2002	else {
2003	GBL_CHECK_FREE_PARAM(*args->coutput,1);
2004	if (!args->cinput) error = "No input stream";
2005	else {
2006	char *use = GBT_get_default_alignment(GB_get_root(args->gb_ref));
2007	PASS_2_OUT(args, GBT_get_alignment_type_string(GB_get_root(args->gb_ref), use));
2008	free(use);
2009	}
2010	}
2011
2012	return error;
2013	}
2014
2015	static GB_ERROR gbl_format_sequence(GBL_command_arguments *args)
2016	{
2017	GB_ERROR error = 0;
2018	int ic;
2019
2020	GBL_BEGIN_PARAMS;
2021	GBL_PARAM_UINT (firsttab, "firsttab=", 10, "Indent first line");
2022	GBL_PARAM_UINT (tab, "tab=", 10, "Indent not first line");
2023	GBL_PARAM_BIT (numleft, "numleft", 0, "Numbers left of sequence");
2024	GBL_PARAM_UINT (gap, "gap=", 10, "Insert ' ' every n sequence characters");
2025	GBL_PARAM_UINT (width, "width=", 50, "Sequence width (bases only)");
2026	GBL_PARAM_STRING(nl, "nl=", " ", "Break line at characters 'str' if wrapping needed");
2027	GBL_PARAM_STRING(forcenl, "forcenl=", "\n", "Always break line at characters 'str'");
2028	GBL_TRACE_PARAMS(args->cparam,args->vparam);
2029	GBL_END_PARAMS;
2030
2031	for (ic = 0; ic<args->cinput; ++ic) {
2032	GBL_CHECK_FREE_PARAM(*args->coutput,1);
2033
2034	{
2035	const char *src = args->vinput[ic].str;
2036	size_t data_size = strlen(src);
2037	size_t needed_size;
2038	char *result = 0;
2039	int simple_format = (strcmp(args->command,"format") == 0);
2040
2041	{
2042	size_t lines;
2043	size_t line_size;
2044
2045	if (simple_format) {
2046	lines = data_size/2 + 1; // worst case
2047	line_size = tab + width + 1;
2048	}
2049	else {
2050	size_t gapsPerLine = (width-1)/gap;
2051	lines = data_size/width+1;
2052	line_size = tab + width + gapsPerLine + 1;
2053	}
2054
2055	needed_size = lines*line_size + firsttab + 1 + 10;
2056	}
2057
2058	result = malloc(needed_size);
2059	if (!result) {
2060	error = GBS_global_string("Out of memory (tried to alloc %zu bytes)", needed_size);
2061	}
2062	else {
2063	char *dst = result;
2064	size_t rest_data = data_size;
2065	int i;
2066
2067	if (simple_format) {
2068	/* format string w/o gaps or numleft
2069	* does word-wrapping at chars in nl
2070	*/
2071
2072	/* build wrap table */
2073	unsigned char isWrapChar[256];
2074	memset(isWrapChar, 0, sizeof(isWrapChar));
2075	for (i = 0; nl[i]; ++i) isWrapChar[(unsigned char)nl[i]] = 1;
2076	for (i = 0; forcenl[i]; ++i) isWrapChar[(unsigned char)forcenl[i]] = 2;
2077
2078	if (firsttab>0) {
2079	memset(dst, ' ', firsttab);
2080	dst += firsttab;
2081	}
2082
2083	while (rest_data>width) {
2084	int take;
2085	int move;
2086	int took;
2087
2088	for (take = width; take > 0; --take) {
2089	if (isWrapChar[(unsigned char)src[take]]) break;
2090	}
2091	if (take <= 0) { /* no wrap character found -> hard wrap at width */
2092	take = move = width;
2093	}
2094	else { /* soft wrap at last found wrap character */
2095	move = take+1;
2096	}
2097
2098	for (took = 0; took<take; took++) {
2099	char c = src[took];
2100	if (isWrapChar[(unsigned char)c] == 2) { /* forced newline */
2101	take = took;
2102	move = take+1;
2103	break;
2104	}
2105	dst[took] = c;
2106	}
2107
2108	/* memcpy(dst, src, take); */
2109	dst += take;
2110	src += move;
2111	rest_data -= move;
2112
2113	if (rest_data>0) {
2114	*dst++ = '\n';
2115	if (tab>0) {
2116	memset(dst, ' ', tab);
2117	dst += tab;
2118	}
2119	}
2120	}
2121
2122	if (rest_data>0) {
2123	size_t j, k;
2124	for (j = 0, k = 0; j<rest_data; ++j) {
2125	char c = src[j];
2126
2127	if (isWrapChar[(unsigned char)c] == 2) {
2128	dst[k++] = '\n';
2129	if (tab>0) {
2130	memset(dst+k, ' ', tab);
2131	k += tab;
2132	}
2133	}
2134	else {
2135	dst[k++] = c;
2136	}
2137	}
2138	src += j;
2139	dst += k;
2140	rest_data = 0;
2141	}
2142	}
2143	else {
2144	/* "format_sequence" with gaps and numleft */
2145	char *format = 0;
2146	const char *src_start = src;
2147
2148	if (numleft) {
2149	/* Warning: Be very careful, when you change format strings here!
2150	* currently all format strings result in '%u' or '%-##u' (where # are digits)
2151	*/
2152	if (firsttab>0) {
2153	char *firstFormat = GBS_global_string_copy("%%-%iu ", firsttab-1);
2154	dst += sprintf(dst, firstFormat, (unsigned)1);
2155	free(firstFormat);
2156	}
2157	else {
2158	dst += sprintf(dst, "%u ", (unsigned)1);
2159	}
2160	format = tab>0 ? GBS_global_string_copy("%%-%iu ", tab-1) : strdup("%u ");
2161	}
2162	else if (firsttab>0) {
2163	memset(dst, ' ', firsttab);
2164	dst += firsttab;
2165	}
2166
2167	while (rest_data>0) {
2168	size_t take = rest_data>width ? width : rest_data;
2169
2170	rest_data -= take;
2171
2172	while (take>gap) {
2173	memcpy(dst, src, gap);
2174	dst += gap;
2175	src += gap;
2176	*dst++ = ' ';
2177	take -= gap;
2178	}
2179
2180	memcpy(dst, src, take);
2181	dst += take;
2182	src += take;
2183
2184	if (rest_data>0) {
2185	*dst++ = '\n';
2186	if (numleft) {
2187	unsigned int num = (src-src_start)+1; /* this goes to the '%u' (see comment above) */
2188	dst += sprintf(dst, format, num);
2189	}
2190	else if (tab>0) {
2191	memset(dst, ' ', tab);
2192	dst += tab;
2193	}
2194	}
2195	}
2196
2197	free(format);
2198	}
2199
2200	dst++ = 0; / close str */
2201
2202	#if defined(DEBUG)
2203	{ /* check for array overflow */
2204	size_t used_size = dst-result;
2205	char *new_result;
2206
2207	gb_assert(used_size <= needed_size);
2208
2209	new_result = realloc(result, used_size);
2210	if (!new_result) {
2211	error = "Out of memory";
2212	}
2213	else {
2214	result = new_result;
2215	}
2216	}
2217	#endif /* DEBUG */
2218	}
2219
2220	if (!error) PASS_2_OUT(args, result);
2221	else free(result);
2222	}
2223	}
2224	return error;
2225	}
2226
2227	/********************************************************************************************
2228	Filter Functions
2229	********************************************************************************************/
2230
2231	static char gbl_read_seq_sai_or_species(const char species, const char sai, const char ali, size_t *seqLen) {
2232	/* Reads the alignment 'ali' of 'species' or 'sai'.
2233	* If 'ali' is NULL, use default alignment.
2234	* Returns NULL in case of error (which is exported then)
2235	*/
2236
2237	char *seq = NULL;
2238	GB_ERROR error = 0;
2239
2240	int sources = !!species + !!sai;
2241	if (sources != 1) {
2242	error = "Either parameters 'species' or 'SAI' must be specified";
2243	}
2244	else {
2245	GBDATA *gb_main = gb_local->gbl.gb_main;
2246	GBDATA *gb_item = 0;
2247	const char *what = 0;
2248	const char *name = 0;
2249
2250	if (species) {
2251	gb_item = GBT_find_species(gb_main, species);
2252	what = "species";
2253	name = species;
2254	}
2255	else {
2256	gb_item = GBT_find_SAI(gb_main, sai);
2257	what = "SAI";
2258	name = sai;
2259	}
2260
2261	if (!gb_item) error = GBS_global_string("Can't find %s '%s'", what, name);
2262	else {
2263	char *freeMe = 0;
2264
2265	if (!ali) {
2266	ali = freeMe = GBT_get_default_alignment(gb_main);
2267	if (!ali) error = "can't detect default alignment";
2268	}
2269
2270	if (ali) {
2271	GBDATA *gb_ali = GB_entry(gb_item, ali);
2272
2273	if (gb_ali) {
2274	GBDATA *gb_seq;
2275
2276	for (gb_seq = GB_child(gb_ali); gb_seq; gb_seq = GB_nextChild(gb_seq)) {
2277	long type = GB_read_type(gb_seq);
2278	if (type == GB_BITS) {
2279	seq = GB_read_bits(gb_seq,'-','+');
2280	if (seqLen) *seqLen = GB_read_bits_count(gb_seq);
2281	break;
2282	}
2283	if (type == GB_STRING) {
2284	seq = GB_read_string(gb_seq);
2285	if (seqLen) *seqLen = GB_read_string_count(gb_seq);
2286	break;
2287	}
2288	}
2289	}
2290
2291	if (!seq) error = GBS_global_string("%s '%s' has no (usable) data in alignment '%s'", what, name, ali);
2292	}
2293	free(freeMe);
2294	}
2295	}
2296
2297	if (error) {
2298	gb_assert(!seq);
2299	GB_export_error(error);
2300	}
2301
2302	return seq;
2303	}
2304
2305	struct common_filter_params {
2306	const char *align;
2307	const char *sai;
2308	const char *species;
2309	int first;
2310	int pairwise;
2311	};
2312
2313	#define GBL_COMMON_FILTER_PARAMS \
2314	struct common_filter_params common_param; \
2315	GBL_STRUCT_PARAM_STRING(common_param, align, "align=", 0, "alignment to use (defaults to default alignment)"); \
2316	GBL_STRUCT_PARAM_STRING(common_param, sai, "SAI=", 0, "Use default sequence of given SAI as a filter"); \
2317	GBL_STRUCT_PARAM_STRING(common_param, species, "species=", 0, "Use default sequence of given species as a filter"); \
2318	GBL_STRUCT_PARAM_BIT (common_param, first, "first=", 0, "Use 1st stream as filter for other streams"); \
2319	GBL_STRUCT_PARAM_BIT (common_param, pairwise, "pairwise=", 0, "Use 1st stream as filter for 2nd, 3rd for 4th, ...")
2320
2321	typedef char* (filter_fun)(const char seq, const char filter, size_t flen, void param);
2322	/* Note:
2323	* filter_fun has to return a heap copy of the filter-result.
2324	* if 'flen' != 0, it contains the length of 'filter'
2325	* 'param' may be any client data
2326	*/
2327
2328	static GB_ERROR apply_filters(GBL_command_arguments args, struct common_filter_params common, filter_fun filter_one, void *param) {
2329	GB_ERROR error = 0;
2330
2331	if (args->cinput==0) error = "No input stream";
2332	else {
2333	int methodCount = !!common->sai + !!common->species + !!common->pairwise + !!common->first;
2334
2335	if (methodCount != 1) error = "Need exactly one of the parameters 'SAI', 'species', 'pairwise' or 'first'";
2336	else {
2337	if (common->pairwise) {
2338	if (args->cinput % 2) error = "Using 'pairwise' requires an even number of input streams";
2339	else {
2340	int i;
2341	for (i = 1; i<args->cinput; i += 2) {
2342	PASS_2_OUT(args, filter_one(args->vinput[i].str, args->vinput[i-1].str, 0, param));
2343	}
2344	}
2345	}
2346	else {
2347	int i = 0;
2348	char *filter = 0;
2349	size_t flen = 0;
2350
2351	if (common->first) {
2352	if (args->cinput<2) error = "Using 'first' needs at least 2 input streams";
2353	else {
2354	const char *in = args->vinput[i++].str;
2355	gb_assert(in);
2356
2357	flen = strlen(in);
2358	filter = GB_strduplen(in, flen);
2359	}
2360	}
2361	else {
2362	filter = gbl_read_seq_sai_or_species(common->species, common->sai, common->align, &flen);
2363	if (!filter) error = GB_await_error();
2364	}
2365
2366	gb_assert(filter \|\| error);
2367	if (filter) {
2368	for (; i<args->cinput; ++i) {
2369	PASS_2_OUT(args, filter_one(args->vinput[i].str, filter, flen, param));
2370	}
2371	}
2372	free(filter);
2373	}
2374	}
2375	}
2376	return error;
2377	}
2378
2379	/* ------------------------- */
2380	/* calculate diff */
2381
2382	struct diff_params {
2383	char equalC;
2384	char diffC;
2385	};
2386	static char calc_diff(const char seq, const char filter, size_t flen, void paramP) {
2387	// filters 'seq' through 'filter'
2388	// - replace all equal positions by 'equal_char' (if != 0)
2389	// - replace all differing positions by 'diff_char' (if != 0)
2390
2391	GBUSE(flen);
2392
2393	struct diff_params param = (struct diff_params)paramP;
2394	char equal_char = param->equalC;
2395	char diff_char = param->diffC;
2396
2397	char *result = strdup(seq);
2398	int p;
2399
2400	for (p = 0; result[p] && filter[p]; ++p) {
2401	if (result[p] == filter[p]) {
2402	if (equal_char) result[p] = equal_char;
2403	}
2404	else {
2405	if (diff_char) result[p] = diff_char;
2406	}
2407	}
2408
2409	// if 'seq' is longer than 'filter' and diff_char is given
2410	// -> fill rest of 'result' with 'diff_char'
2411	if (diff_char) {
2412	for (; result[p]; ++p) {
2413	result[p] = diff_char;
2414	}
2415	}
2416
2417	return result;
2418	}
2419	static GB_ERROR gbl_diff(GBL_command_arguments *args) {
2420	GBL_BEGIN_PARAMS;
2421	GBL_COMMON_FILTER_PARAMS;
2422
2423	struct diff_params param;
2424	GBL_STRUCT_PARAM_CHAR(param, equalC, "equal=", '.', "symbol for equal characters");
2425	GBL_STRUCT_PARAM_CHAR(param, diffC, "differ=", 0, "symbol for diff characters (default: use char from input stream)");
2426
2427	GBL_TRACE_PARAMS(args->cparam,args->vparam);
2428	GBL_END_PARAMS;
2429
2430	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
2431
2432	return apply_filters(args, &common_param, calc_diff, &param);
2433	}
2434
2435	/* ------------------------- */
2436	/* standard filter */
2437
2438	struct filter_params { // used by gbl_filter and gbl_change_gc
2439	enum { FP_FILTER, FP_MODIFY } function;
2440
2441	const char *include;
2442	const char *exclude;
2443
2444	// FP_MODIFY only:
2445	int change_pc;
2446	const char *change_to;
2447	};
2448
2449	static char filter_seq(const char seq, const char filter, size_t flen, void paramP) {
2450	struct filter_params param = (struct filter_params)paramP;
2451
2452	size_t slen = strlen(seq);
2453	if (!flen) flen = strlen(filter);
2454	size_t mlen = slen<flen ? slen : flen;
2455
2456	struct GBS_strstruct *out = GBS_stropen(mlen);
2457
2458	const char *charset;
2459	int include;
2460
2461	if (param->include) {
2462	charset = param->include;
2463	include = 1;
2464	}
2465	else {
2466	gb_assert(param->exclude);
2467	charset = param->exclude;
2468	include = 0;
2469	}
2470
2471	size_t pos = 0;
2472	size_t rest = slen;
2473	size_t ctl = 0;
2474	if (param->function == FP_MODIFY) ctl = strlen(param->change_to);
2475
2476	int inset = 1; // 1 -> check chars in charset, 0 -> check chars NOT in charset
2477	while (rest) {
2478	size_t count;
2479	if (pos >= flen) { // behind filter
2480	// trigger last loop
2481	count = rest;
2482	inset = 0; // if 'include' -> 'applies' will get false, otherwise true
2483	// (meaning is: behind filter nothing can match 'include' or 'exclude')
2484	}
2485	else {
2486	count = (inset ? strspn : strcspn)(filter+pos, charset); // count how many chars are 'inset'
2487	}
2488	if (count) {
2489	int applies = !!include == !!inset; // true -> 'filter' matches 'include' or doesn't match 'exclude'
2490	if (count>rest) count = rest;
2491
2492	switch(param->function) {
2493	case FP_FILTER:
2494	if (applies) GBS_strncat(out, seq+pos, count);
2495	break;
2496
2497	case FP_MODIFY:
2498	if (applies) { // then modify
2499	size_t i;
2500	for (i = 0; i<count; i++) {
2501	char c = seq[pos+i];
2502	if (isalpha(c) && GB_random(100)<param->change_pc) c = param->change_to[GB_random(ctl)];
2503	GBS_chrcat(out, c);
2504	}
2505	}
2506	else { // otherwise simply copy
2507	GBS_strncat(out, seq+pos, count);
2508	}
2509	break;
2510	}
2511
2512	pos += count;
2513	rest -= count;
2514	}
2515	inset = 1-inset; // toggle
2516	}
2517	return GBS_strclose(out);
2518	}
2519
2520	static GB_ERROR gbl_filter(GBL_command_arguments *args) {
2521	GBL_BEGIN_PARAMS;
2522	GBL_COMMON_FILTER_PARAMS;
2523
2524	struct filter_params param;
2525	GBL_STRUCT_PARAM_STRING(param, exclude, "exclude=", 0, "Exclude colums");
2526	GBL_STRUCT_PARAM_STRING(param, include, "include=", 0, "Include colums");
2527	param.function = FP_FILTER;
2528
2529	GBL_TRACE_PARAMS(args->cparam,args->vparam);
2530	GBL_END_PARAMS;
2531
2532	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
2533
2534	GB_ERROR error = 0;
2535	int inOrEx = !!param.include + !!param.exclude;
2536
2537	if (inOrEx != 1) error = "Need exactly one parameter of: 'include', 'exclude'";
2538	else error = apply_filters(args, &common_param, filter_seq, &param);
2539
2540	return error;
2541	}
2542
2543	static GB_ERROR gbl_change_gc(GBL_command_arguments *args) {
2544	GBL_BEGIN_PARAMS;
2545	GBL_COMMON_FILTER_PARAMS;
2546
2547	struct filter_params param;
2548	GBL_STRUCT_PARAM_STRING(param, exclude, "exclude=", 0, "Exclude colums");
2549	GBL_STRUCT_PARAM_STRING(param, include, "include=", 0, "Include colums");
2550	GBL_STRUCT_PARAM_INT (param, change_pc, "change=", 0, "percentage of changed columns (default: silently change nothing)");
2551	GBL_STRUCT_PARAM_STRING(param, change_to, "to=", "GC", "change to one of this");
2552	param.function = FP_MODIFY;
2553
2554	GBL_TRACE_PARAMS(args->cparam,args->vparam);
2555	GBL_END_PARAMS;
2556
2557	GBL_CHECK_FREE_PARAM(*args->coutput,args->cinput);
2558
2559	GB_ERROR error = 0;
2560	int inOrEx = !!param.include + !!param.exclude;
2561
2562	if (inOrEx != 1) error = "Need exactly one parameter of: 'include', 'exclude'";
2563	else {
2564	error = apply_filters(args, &common_param, filter_seq, &param);
2565	}
2566
2567	return error;
2568	}
2569
2570	/********************************************************************************************
2571	Exec Functions
2572	********************************************************************************************/
2573
2574	static GB_ERROR gbl_exec(GBL_command_arguments *args)
2575	{
2576	GB_ERROR error = 0;
2577
2578	if (args->cparam==0) {
2579	error = "exec needs parameters:\nexec(command,...)";
2580	}
2581	else {
2582	// write inputstreams to temp file:
2583	char *inputname;
2584	int i;
2585	{
2586	char *filename = GB_unique_filename("arb_exec_input", "tmp");
2587	FILE *out = GB_fopen_tempfile(filename, "wt", &inputname);
2588
2589	if (!out) error = GB_await_error();
2590	else {
2591	for (i=0; i<args->cinput; i++) { // go through all in streams
2592	fprintf(out,"%s\n",args->vinput[i].str);
2593	}
2594	fclose(out);
2595	}
2596	free(filename);
2597	}
2598
2599	if (!error) {
2600	// build shell command to execute
2601	char *sys;
2602	{
2603	struct GBS_strstruct *str = GBS_stropen(1000);
2604
2605	GBS_strcat(str, args->vparam[0].str);
2606	for (i=1; i<args->cparam; i++) { // go through all in params
2607	GBS_strcat(str," \'");
2608	GBS_strcat(str, args->vparam[i].str);
2609	GBS_chrcat(str,'\'');
2610	}
2611	GBS_strcat(str, " <");
2612	GBS_strcat(str, inputname);
2613
2614	sys = GBS_strclose(str);
2615	}
2616
2617	char *result = 0;
2618	{
2619	FILE *in = popen(sys,"r");
2620	if (in) {
2621	void *str = GBS_stropen(4096);
2622
2623	while ( (i=getc(in)) != EOF ) { GBS_chrcat(str,i); }
2624	result = GBS_strclose(str);
2625	pclose(in);
2626	}
2627	else {
2628	error = GBS_global_string("Cannot execute shell command '%s'", sys);
2629	}
2630	}
2631
2632	if (!error) {
2633	gb_assert(result);
2634	PASS_2_OUT(args, result);
2635	}
2636
2637	free(sys);
2638	}
2639
2640	gb_assert(GB_is_privatefile(inputname, GB_FALSE));
2641	GB_unlink_or_warn(inputname, &error);
2642	free(inputname);
2643	}
2644
2645	return error;
2646	}
2647
2648
2649	static struct GBL_command_table gbl_command_table[] = {
2650	{"caps", gbl_string_convert },
2651	{"change", gbl_change_gc },
2652	{"checksum", gbl_check },
2653	{"command", gbl_command },
2654	{"compare", gbl_compare },
2655	{"icompare", gbl_icompare },
2656	{"contains", gbl_contains },
2657	{"icontains", gbl_icontains },
2658	{"count", gbl_count },
2659	{"crop", gbl_crop },
2660	{"cut", gbl_cut },
2661	{"dd", gbl_dd },
2662	{"define", gbl_define },
2663	{"diff", gbl_diff },
2664	{"div", gbl_div },
2665	{"do", gbl_do },
2666	{"drop", gbl_drop },
2667	{"dropempty", gbl_dropempty },
2668	{"dropzero", gbl_dropzero },
2669	{"echo", gbl_echo },
2670	{"equals", gbl_equals },
2671	{"iequals", gbl_iequals },
2672	{"eval", gbl_eval },
2673	{"exec", gbl_exec },
2674	{"export_sequence", gbl_export_sequence },
2675	{"extract_sequence", gbl_extract_sequence },
2676	{"extract_words", gbl_extract_words },
2677	{"filter", gbl_filter },
2678	{"format", gbl_format_sequence },
2679	{"format_sequence", gbl_format_sequence },
2680	{"gcgchecksum", gbl_gcgcheck },
2681	{"head", gbl_head },
2682	{"keep", gbl_keep },
2683	{"left", gbl_head },
2684	{"len", gbl_len },
2685	{"lower", gbl_string_convert },
2686	{"merge", gbl_merge },
2687	{"mid", gbl_mid },
2688	{"mid0", gbl_mid0 },
2689	{"minus", gbl_minus },
2690	{"mult", gbl_mult },
2691	{"origin_gene", gbl_origin },
2692	{"origin_organism", gbl_origin },
2693	{"partof", gbl_partof },
2694	{"ipartof", gbl_ipartof },
2695	{"per_cent", gbl_per_cent },
2696	{"plus", gbl_plus },
2697	{"pretab", gbl_pretab },
2698	{"readdb", gbl_readdb },
2699	{"remove", gbl_remove },
2700	{"rest", gbl_rest },
2701	{"right", gbl_tail },
2702	{"select", gbl_select },
2703	{"sequence", gbl_sequence },
2704	{"sequence_type", gbl_sequence_type },
2705	{"split", gbl_split },
2706	{"srt", gbl_srt },
2707	{"streams", gbl_streams },
2708	{"swap", gbl_swap },
2709	{"tab", gbl_tab },
2710	{"tail", gbl_tail },
2711	{"taxonomy", gbl_taxonomy },
2712	{"toback", gbl_toback },
2713	{"tofront", gbl_tofront },
2714	{"trace", gbl_trace },
2715	{"translate", gbl_translate },
2716	{"upper", gbl_string_convert },
2717	{0,0}
2718
2719	};
2720
2721	void gbl_install_standard_commands(GBDATA *gb_main)
2722	{
2723	gb_install_command_table(gb_main,gbl_command_table);
2724	}

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