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source: tags/arb-6.0-rc1/EDIT4/ED4_visualizeSAI.cxx

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Last change on this file was 11464, checked in by westram, 12 years ago
un-dummy-fied transaction (renames only)
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1	// =============================================================== //
2	// //
3	// File : ED4_visualizeSAI.cxx //
4	// Purpose : Visualize sequence associated information (SAI) //
5	// in the Editor //
6	// //
7	// Coded by Yadhu Kumar (yadhu@mikro.biologie.tu-muenchen.de) //
8	// Institute of Microbiology (Technical University Munich) //
9	// http://www.arb-home.de/ //
10	// //
11	// =============================================================== //
12
13	#include <ed4_extern.hxx>
14	#include "ed4_class.hxx"
15
16	#include <aw_awars.hxx>
17	#include <awt_canvas.hxx>
18	#include <awt_sel_boxes.hxx>
19	#include <aw_preset.hxx>
20	#include <aw_msg.hxx>
21	#include <aw_root.hxx>
22	#include <aw_question.hxx>
23	#include <aw_select.hxx>
24
25	#include <arbdbt.h>
26	#include <ad_cb.h>
27	#include <arb_strbuf.h>
28
29	#include <iostream>
30
31	// --------------------------------------------------------------------------------
32
33	#define AWAR_SAI_CLR_TAB "saicolors/"
34	#define AWAR_SAI_VISUALIZED AWAR_SAI_CLR_TAB "select" // current visualized SAI
35	#define AWAR_SAI_CLR_DEF AWAR_SAI_CLR_TAB "clr_trans_tab/" // container for definitions
36	#define AWAR_SAI_ENABLE AWAR_SAI_CLR_TAB "enable" // global enable of visualization
37	#define AWAR_SAI_ALL_SPECIES AWAR_SAI_CLR_TAB "all_species" // 1 = all / 0 = marked
38	#define AWAR_SAI_AUTO_SELECT AWAR_SAI_CLR_TAB "auto_select" // 1 = auto select / 0 = manual select
39	#define AWAR_SAI_CLR_TRANS_TABLE AWAR_SAI_CLR_TAB "clr_trans_table" // current translation table
40	#define AWAR_SAI_CLR_TRANS_TAB_NAMES AWAR_SAI_CLR_TAB "clr_trans_tab_names" // ;-separated list of existing translation tables
41	#define AWAR_SAI_CLR_TRANS_TAB_REL AWAR_SAI_CLR_TAB "sai_relation/" // container to store trans tables for each SAI
42	#define AWAR_SAI_CLR_DEFAULTS_CREATED AWAR_SAI_CLR_TAB "defaults_created" // whether defaults have been created (create only once)
43
44	#define AWAR_SAI_CLR_TRANS_TAB_NEW_NAME "tmp/sai/clr_trans_tab_new_name" // textfield to enter translation table name
45	#define AWAR_SAI_CLR "tmp/sai/color_0" // the definition of the current translation table (number runs from 0 to 9)
46	#define AWAR_SAI_CLR_COUNT 10
47
48	#define ED4_VIS_CREATE 1
49	#define ED4_VIS_COPY 0
50
51	// --------------------------------------------------------------------------------
52
53	extern GBDATA *GLOBAL_gb_main;
54
55	static bool clrDefinitionsChanged = false;
56	static bool inCallback = false; // used to avoid multiple refreshes
57	static bool in_colorDefChanged_callback = false; // used to avoid colorDef correction
58
59	// --------------------------------------------------------------------------------
60
61	#define BUFSIZE 100
62	static const char *getAwarName(int awarNo) {
63	static char buf[BUFSIZE];
64
65	strcpy(buf, AWAR_SAI_CLR);
66	(strchr(buf, 0)-1)[0] = '0'+awarNo;
67
68	return buf;
69	}
70
71	static const char getClrDefAwar(const char awarName) {
72	static char buf[BUFSIZE];
73
74	e4_assert(awarName);
75	e4_assert(awarName[0]); // empty awar is bad
76
77	IF_ASSERTION_USED(int size =) sprintf(buf, AWAR_SAI_CLR_DEF "%s", awarName);
78	e4_assert(size<BUFSIZE);
79	return buf;
80	}
81	#undef BUFSIZE
82
83	// ---------------------------------------------------------
84
85	static void setVisualizeSAI_cb(AW_root *awr) {
86	ED4_ROOT->visualizeSAI = awr->awar(AWAR_SAI_ENABLE)->read_int();
87	ED4_ROOT->request_refresh_for_sequence_terminals();
88	}
89
90	static void setVisualizeSAI_options_cb(AW_root *awr) {
91	ED4_ROOT->visualizeSAI_allSpecies = awr->awar(AWAR_SAI_ALL_SPECIES)->read_int();
92	ED4_ROOT->request_refresh_for_sequence_terminals();
93	}
94
95	static bool colorTransTable_exists(AW_root awr, const char name) {
96	char *tableNames = awr->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES)->read_string();
97	const char *searchFrom = tableNames;
98	int len = strlen(name);
99
100	while (searchFrom) {
101	const char *found = strstr(searchFrom, name);
102
103	if (found) {
104	if ((found == tableNames \|\| found[-1] == '\n') && // found start of entry
105	(found[len] == '\n' \|\| found[len] == 0)) // avoid partial entry
106	{
107	break; // exists!
108	}
109	else { // search next match
110	searchFrom = found+1;
111	}
112	}
113	else {
114	searchFrom = 0;
115	}
116	}
117
118	free(tableNames);
119	return searchFrom != 0;
120	}
121
122	static void colorDefChanged_callback(AW_root *awr, AW_CL cl_awarNo) {
123	clrDefinitionsChanged = true;
124
125	if (!in_colorDefChanged_callback) { // this callback is special, because it may change all other color defs
126	LocallyModify<bool> flag(in_colorDefChanged_callback, true);
127
128	{
129	LocallyModify<bool> in_cb(inCallback, true);
130
131	char *clrTabName = awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
132	if (clrTabName[0]) {
133	unsigned char charUsed[256]; memset(charUsed, 255, 256);
134
135	{
136	for (int i=0; i<10; i++) {
137	char *awarString_next = awr->awar_string(getAwarName(i))->read_string();
138	for (int c=0; awarString_next[c]; ++c) {
139	charUsed[(unsigned char)awarString_next[c]] = i;
140	}
141	free(awarString_next);
142	}
143
144	int awarNo = (int)cl_awarNo;
145	char *awarString = awr->awar_string(getAwarName(awarNo))->read_string();
146	for (int c=0; awarString[c]; ++c) {
147	charUsed[(unsigned char)awarString[c]] = awarNo;
148	}
149	free(awarString);
150	}
151
152	typedef unsigned char mystr[256];
153	mystr s[10];
154	for (int i=0; i<10; i++) s[i][0]=0; // initializing the strings
155
156	for (int i=0; i<256; i++) {
157	int table = charUsed[i];
158	if (table != 255) {
159	char eos = strchr((char )s[table], 0); // get pointer to end of string
160	eos[0] = char(i);
161	eos[1] = 0;
162	}
163	}
164
165	{
166	GBS_strstruct *clrDefStr = GBS_stropen(500); // create output stream
167	for (int i=0; i<10; i++) {
168	awr->awar_string(getAwarName(i))->write_string((char *)s[i]);
169
170	char escaped = GBS_escape_string((char)s[i], ";", '&');
171	GBS_strcat(clrDefStr, escaped);
172	free(escaped);
173	GBS_chrcat(clrDefStr, ';');
174	}
175
176	char *colorDef = GBS_strclose(clrDefStr);
177	AW_awar *awar_def = awr->awar_string(getClrDefAwar(clrTabName), "", AW_ROOT_DEFAULT);
178	awar_def->write_string(colorDef); // writing clr definition to clr trans table awar
179	free(colorDef);
180	}
181	}
182	else {
183	if (!in_cb.old_value()) { // only warn when user really changed the setting
184	aw_message("Please select a VALID Color Translation Table to EDIT.");
185	}
186	}
187	free(clrTabName);
188	}
189
190	if (!inCallback) ED4_ROOT->request_refresh_for_sequence_terminals();
191	}
192	}
193
194	static void colorDefTabNameChanged_callback(AW_root *awr) {
195	char *clrTabName = awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
196	{
197	LocallyModify<bool> flag(inCallback, true);
198	{
199	LocallyModify<bool> flag2(in_colorDefChanged_callback, true); // avoid correction
200
201	// clear current translation table definition
202	for (int i=0; i<10; i++) {
203	AW_awar *transDef_awar = awr->awar_string(getAwarName(i), "", AW_ROOT_DEFAULT);
204	transDef_awar->write_string("");
205	}
206
207	if (clrTabName[0]) {
208	AW_awar *clrTabDef_awar = awr->awar_string(getClrDefAwar(clrTabName), "", AW_ROOT_DEFAULT);
209	char *clrTabDef = clrTabDef_awar->read_string();
210
211	if (clrTabDef[0]) {
212	int i = 0;
213	int tokStart = 0;
214
215	for (int si = 0; clrTabDef[si]; ++si) {
216	if (clrTabDef[si] == ';') {
217	e4_assert(i >= 0 && i<10);
218	AW_awar *awar = awr->awar(getAwarName(i));
219
220	if (tokStart == si) { // empty definition
221	awar->write_string("");
222	}
223	else {
224	int toklen = si-tokStart;
225
226	e4_assert(toklen > 0);
227	e4_assert(clrTabDef[tokStart+toklen] == ';');
228	clrTabDef[tokStart+toklen] = 0;
229
230	char *unescaped = GBS_unescape_string(clrTabDef+tokStart, ";", '&');
231	awar->write_string(unescaped);
232	free(unescaped);
233
234	clrTabDef[tokStart+toklen] = ';';
235	}
236	++i;
237	tokStart = si+1;
238	}
239	}
240	e4_assert(i == 10);
241	}
242	free(clrTabDef);
243	}
244	}
245	colorDefChanged_callback(awr, 0); // correct first def manually
246	{
247	// store the selected table as default for this SAI:
248	char *saiName = awr->awar(AWAR_SAI_VISUALIZED)->read_string();
249	if (saiName[0]) {
250	char buf[100];
251	sprintf(buf, AWAR_SAI_CLR_TRANS_TAB_REL "%s", saiName);
252	awr->awar_string(buf, "", AW_ROOT_DEFAULT); // create an AWAR for the selected SAI and
253	awr->awar(buf)->write_string(clrTabName); // write the existing clr trans table names to the same
254	}
255	free(saiName);
256	}
257	}
258	free(clrTabName);
259
260	if (!inCallback && clrDefinitionsChanged) ED4_ROOT->request_refresh_for_sequence_terminals();
261	}
262
263	static void refresh_display_cb(GB_CB_TYPE cb_type) {
264	if ((cb_type & GB_CB_CHANGED) &&
265	ED4_ROOT->aw_root->awar(AWAR_SAI_ENABLE)->read_int())
266	{
267	clrDefinitionsChanged = 1;
268	ED4_ROOT->request_refresh_for_sequence_terminals();
269	}
270	}
271
272	static void saiChanged_callback(AW_root *awr) {
273	char *saiName = 0;
274	{
275	LocallyModify<bool> flag(inCallback, true);
276	{
277	static GBDATA *gb_last_SAI = 0;
278
279	if (gb_last_SAI) {
280	GB_transaction ta(GLOBAL_gb_main);
281	GB_remove_callback(gb_last_SAI, GB_CB_CHANGED, makeDatabaseCallback(refresh_display_cb));
282	gb_last_SAI = 0;
283	}
284
285	saiName = awr->awar(AWAR_SAI_VISUALIZED)->read_string();
286	char *transTabName = 0;
287
288	if (saiName[0]) {
289	char buf[100];
290	sprintf(buf, AWAR_SAI_CLR_TRANS_TAB_REL "%s", saiName);
291	awr->awar_string(buf, "", AW_ROOT_DEFAULT);
292	transTabName = awr->awar(buf)->read_string();
293	}
294
295	{
296	GB_transaction ta(GLOBAL_gb_main);
297	gb_last_SAI = GBT_find_SAI(GLOBAL_gb_main, saiName);
298	if (gb_last_SAI) {
299	GB_add_callback(gb_last_SAI, GB_CB_CHANGED, makeDatabaseCallback(refresh_display_cb));
300	}
301	}
302	awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->write_string(transTabName ? transTabName : "");
303	free(transTabName);
304
305	clrDefinitionsChanged = true; // SAI changed -> update needed
306	}
307	}
308
309	if (!inCallback && clrDefinitionsChanged) {
310	// SAI changed notify Global SAI Awar AWAR_SAI_GLOBAL
311	awr->awar(AWAR_SAI_GLOBAL)->write_string(saiName);
312	ED4_ROOT->request_refresh_for_sequence_terminals();
313	}
314	free(saiName);
315	}
316
317	static void update_ClrTransTabNamesList_cb(AW_root *awr, AW_CL cl_colorTransList) {
318	AW_selection_list colorTransList = (AW_selection_list)cl_colorTransList;
319	char *clrTransTabNames = awr->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES)->read_string();
320
321	colorTransList->clear();
322
323	for (char *tok = strtok(clrTransTabNames, "\n"); tok; tok = strtok(0, "\n")) {
324	colorTransList->insert(tok, tok);
325	}
326	colorTransList->insert_default("????", "");
327	colorTransList->update();
328
329	free(clrTransTabNames);
330	}
331
332	static void autoselect_cb(AW_root *aw_root) {
333	char *curr_sai = aw_root->awar(AWAR_SAI_NAME)->read_string();
334	#if defined(DEBUG)
335	printf("curr_sai='%s'\n", curr_sai);
336	#endif // DEBUG
337	aw_root->awar(AWAR_SAI_VISUALIZED)->write_string(curr_sai);
338	free(curr_sai);
339	}
340
341	static void set_autoselect_cb(AW_root *aw_root) {
342	static bool callback_active = false;
343
344	if (aw_root->awar(AWAR_SAI_AUTO_SELECT)->read_int()) { // auto select is activated
345	aw_root->awar(AWAR_SAI_NAME)->add_callback(autoselect_cb);
346	callback_active = true;
347	}
348	else {
349	if (callback_active) { // only remove if added
350	aw_root->awar(AWAR_SAI_NAME)->remove_callback(autoselect_cb);
351	callback_active = false;
352	}
353	}
354	}
355
356	static void addOrUpdateTransTable(AW_root aw_root, const char newClrTransTabName, const char *defaultDefinition, bool autoselect) {
357	AW_awar *table_def_awar = aw_root->awar_string(getClrDefAwar(newClrTransTabName), defaultDefinition, AW_ROOT_DEFAULT);
358	table_def_awar->write_string(defaultDefinition);
359
360	if (!colorTransTable_exists(aw_root, newClrTransTabName)) {
361	AW_awar *names_awar = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES);
362	const char *old_names = names_awar->read_char_pntr();
363	names_awar->write_string(old_names[0]
364	? GBS_global_string("%s\n%s", old_names, newClrTransTabName)
365	: newClrTransTabName); // add new name
366	}
367
368	if (autoselect) {
369	aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->write_string(newClrTransTabName); // select new
370	}
371	}
372
373	static void addDefaultTransTable(AW_root aw_root, const char newClrTransTabName, const char *defaultDefinition) {
374	addOrUpdateTransTable(aw_root, newClrTransTabName, defaultDefinition, false);
375	}
376
377	void ED4_createVisualizeSAI_Awars(AW_root *aw_root, AW_default aw_def) { // --- Creating and initializing AWARS -----
378	aw_root->awar_int(AWAR_SAI_ENABLE, 0, aw_def);
379	aw_root->awar_int(AWAR_SAI_ALL_SPECIES, 0, aw_def);
380	aw_root->awar_int(AWAR_SAI_AUTO_SELECT, 0, aw_def);
381
382	aw_root->awar_string(AWAR_SAI_VISUALIZED, "", aw_def);
383	aw_root->awar_string(AWAR_SAI_CLR_TRANS_TABLE, "", aw_def);
384	aw_root->awar_string(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, "", aw_def);
385	aw_root->awar_string(AWAR_SAI_CLR_TRANS_TAB_NAMES, "", aw_def);
386
387	for (int i=0; i<10; i++) { // initializing 10 color definition string AWARS
388	AW_awar *def_awar = aw_root->awar_string(getAwarName(i), "", aw_def);
389	def_awar->add_callback(colorDefChanged_callback, (AW_CL)i);
390	}
391	aw_root->awar(AWAR_SAI_ENABLE) ->add_callback(setVisualizeSAI_cb);
392	aw_root->awar(AWAR_SAI_ALL_SPECIES) ->add_callback(setVisualizeSAI_options_cb);
393	aw_root->awar(AWAR_SAI_AUTO_SELECT) ->add_callback(set_autoselect_cb);
394	aw_root->awar(AWAR_SAI_VISUALIZED) ->add_callback(saiChanged_callback);
395	aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->add_callback(colorDefTabNameChanged_callback);
396
397	ED4_ROOT->visualizeSAI = aw_root->awar(AWAR_SAI_ENABLE)->read_int();
398	ED4_ROOT->visualizeSAI_allSpecies = aw_root->awar(AWAR_SAI_ALL_SPECIES)->read_int();
399
400	// create some defaults:
401	aw_root->awar_int(AWAR_SAI_CLR_DEFAULTS_CREATED, 1, aw_def); // @@@ Feb 2012 - remove me in some years
402
403	addDefaultTransTable(aw_root, "numeric", "0;1;2;3;4;5;6;7;8;9;");
404	addDefaultTransTable(aw_root, "binary", ".0;;+1;;;;;;;;");
405	addDefaultTransTable(aw_root, "consensus", "=ACGTU;;acgtu;.;;;;;;;");
406	addDefaultTransTable(aw_root, "helix", ";;<>;;;;;[];;;");
407	addDefaultTransTable(aw_root, "xstring", ";x;;;;;;;;;");
408	addDefaultTransTable(aw_root, "gaps", ";-.;;;;;;;;;");
409
410	LocallyModify<bool> flag(inCallback, true); // avoid refresh
411	saiChanged_callback(aw_root);
412	colorDefTabNameChanged_callback(aw_root); // init awars for selected table
413	set_autoselect_cb(aw_root);
414	}
415
416	static void createCopyClrTransTable(AW_window *aws, AW_CL cl_mode) {
417	// mode = ED4_VIS_COPY copies the selected color translation table
418	// mode = ED4_VIS_CREATE creates a new (empty) color translation table
419
420	int mode = (int)cl_mode;
421	AW_root *aw_root = aws->get_root();
422	char *newClrTransTabName = 0;
423	char *clrTabSourceName = 0;
424
425	switch (mode) {
426	case ED4_VIS_CREATE:
427	newClrTransTabName = GBS_string_2_key(aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME)->read_char_pntr());
428
429	if (strcmp(newClrTransTabName, "__") == 0) { // user entered nothing
430	aw_message("Please enter a translation table name");
431	}
432	else if (colorTransTable_exists(aw_root, newClrTransTabName)) {
433	aw_message(GBS_global_string("Color translation table '%s' already exists.", newClrTransTabName));
434	}
435	else {
436	addOrUpdateTransTable(aw_root, newClrTransTabName, "", true);
437	}
438	break;
439
440	case ED4_VIS_COPY:
441	newClrTransTabName = GBS_string_2_key(aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME)->read_char_pntr());
442	clrTabSourceName = aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
443
444	if (!clrTabSourceName[0]) {
445	aw_message("Please select a valid Color Translation Table to COPY!");
446	}
447	else if (colorTransTable_exists(aw_root, newClrTransTabName)) {
448	aw_message(GBS_global_string("Color Translation Table \"%s\" EXISTS! Please enter a different name.", newClrTransTabName));
449	}
450	else {
451	char *old_def = aw_root->awar(getClrDefAwar(clrTabSourceName))->read_string();
452	addOrUpdateTransTable(aw_root, newClrTransTabName, old_def, true);
453	free(old_def);
454	}
455	break;
456
457	default:
458	break;
459	}
460	free(clrTabSourceName);
461	free(newClrTransTabName);
462	}
463
464	static void deleteColorTranslationTable(AW_window *aws) {
465	bool delete_table = aw_ask_sure("del_color_table", "Are you sure you want to delete the selected COLOR TRANSLATION TABLE?");
466	if (delete_table) {
467	AW_root *aw_root = aws->get_root();
468	char *clrTabName = aw_root->awar_string(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
469
470	if (clrTabName[0]) {
471	AW_awar *awar_tabNames = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES);
472	char *clrTransTabNames = awar_tabNames->read_string();
473	GBS_strstruct *newTransTabName = GBS_stropen(strlen(clrTransTabNames));
474
475	for (const char *tok = strtok(clrTransTabNames, "\n"); tok; tok = strtok(0, "\n")) {
476	if (strcmp(clrTabName, tok) != 0) { // merge all not to delete
477	GBS_strcat(newTransTabName, tok);
478	GBS_strcat(newTransTabName, "\n");
479	}
480	}
481
482	aw_root->awar_string(getClrDefAwar(clrTabName))->write_string("");
483	char *new_name = GBS_strclose(newTransTabName);
484	awar_tabNames->write_string(new_name); // updates selection list
485	free(new_name);
486
487	free(clrTransTabNames);
488	}
489	else {
490	aw_message("Selected Color Translation Table is not VALID and cannot be DELETED!");
491	}
492	free(clrTabName);
493	}
494	}
495
496	static AW_selection_list buildClrTransTabNamesList(AW_window aws) {
497	AW_root *awr = aws->get_root();
498	AW_selection_list *colorTransList = aws->create_selection_list(AWAR_SAI_CLR_TRANS_TABLE);
499
500	update_ClrTransTabNamesList_cb(awr, (AW_CL)colorTransList);
501
502	return colorTransList;
503	}
504
505	const char ED4_getSaiColorString(AW_root awr, int start, int end) {
506	static int seqBufferSize = 0;
507	static char *saiColors = 0;
508	static int lastStart = -1;
509	static int lastEnd = -1;
510	static bool lastVisualize = false;
511
512	e4_assert(start<=end);
513
514	if (lastStart==start && lastEnd==end && !clrDefinitionsChanged && lastVisualize) {
515	return saiColors-start; // if start and end positions are same as the previous positions and no settings
516	} // were changed return the last calculated saiColors string
517
518	lastStart = start; lastEnd = end; clrDefinitionsChanged = false; // storing start and end positions
519
520	int seqSize = end-start+1;
521
522	if (seqSize>seqBufferSize) {
523	free(saiColors);
524	seqBufferSize = seqSize;
525	saiColors = (char*)GB_calloc(seqBufferSize, sizeof(char));
526	}
527	else memset(saiColors, 0, sizeof(char)*seqSize);
528
529	char *saiSelected = awr->awar(AWAR_SAI_VISUALIZED)->read_string();
530
531	GB_push_transaction(GLOBAL_gb_main);
532	char *alignment_name = GBT_get_default_alignment(GLOBAL_gb_main);
533	GBDATA *gb_extended = GBT_find_SAI(GLOBAL_gb_main, saiSelected);
534	bool visualize = false; // set to true if all goes fine
535
536	if (gb_extended) {
537	GBDATA *gb_ali = GB_entry(gb_extended, alignment_name);
538	if (gb_ali) {
539	const char *saiData = 0;
540	bool free_saiData = false;
541
542	{
543	GBDATA *saiSequence = GB_entry(gb_ali, "data"); // search "data" entry (normal SAI)
544	if (saiSequence) {
545	saiData = GB_read_char_pntr(saiSequence); // not allocated
546	}
547	else {
548	saiSequence = GB_entry(gb_ali, "bits"); // search "bits" entry (binary SAI)
549	if (saiSequence) {
550	saiData = GB_read_as_string(saiSequence); // allocated
551	free_saiData = true; // free saiData below
552	}
553	}
554	}
555
556	if (saiData) {
557	char trans_table[256];
558	{
559	// build the translation table:
560	memset(trans_table, 0, 256);
561	for (int i = 0; i<AWAR_SAI_CLR_COUNT; ++i) {
562	char *def = awr->awar(getAwarName(i))->read_string();
563	int clrRange = ED4_G_CBACK_0 + i;
564
565	for (char d = def; d; ++d) {
566	trans_table[(unsigned char)*d] = clrRange;
567	}
568	free(def);
569	}
570	}
571
572	// translate SAI to colors
573	for (int i = start; i <= end; ++i) {
574	saiColors[i-start] = trans_table[(unsigned char)saiData[i]];
575	}
576
577	visualize = true;
578	}
579
580	if (free_saiData) {
581	free(const_cast<char*>(saiData)); // in this case saiData is allocated (see above)
582	}
583	}
584	}
585	free(alignment_name);
586	free(saiSelected);
587	GB_pop_transaction(GLOBAL_gb_main);
588
589	lastVisualize = visualize;
590	if (visualize) {
591	e4_assert(saiColors);
592	return saiColors-start;
593	}
594
595	return 0; // don't visualize (sth went wrong)
596	}
597
598
599	// -------------------- Creating Windows and Display dialogs --------------------
600
601	static AW_window create_copyColorTranslationTable_window(AW_root aw_root) { // creates copy color translation table window
602	AW_window_simple *aws = new AW_window_simple;
603	aws->init(aw_root, "COPY_CLR_TR_TABLE", "Copy Color Translation Table");
604	aws->load_xfig("ad_al_si.fig");
605
606	aws->at("close");
607	aws->callback((AW_CB0)AW_POPDOWN);
608	aws->create_button("CLOSE", "CLOSE", "C");
609
610	aws->at("label");
611	aws->create_autosize_button(0, "Please enter the new name\nfor the Color Translation Table");
612
613	aws->at("input");
614	aws->create_input_field(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, 15);
615
616	aws->at("ok");
617	aws->callback(createCopyClrTransTable, (AW_CL)ED4_VIS_COPY);
618	aws->create_button("GO", "GO", "G");
619
620	return (AW_window *)aws;
621	}
622
623	static AW_window create_createColorTranslationTable_window(AW_root aw_root) { // creates create color translation table window
624	AW_window_simple *aws = new AW_window_simple;
625	aws->init(aw_root, "CREATE_CLR_TR_TABLE", "Create Color Translation Table");
626	aws->load_xfig("ad_al_si.fig");
627
628	aws->at("close");
629	aws->callback((AW_CB0)AW_POPDOWN);
630	aws->create_button("CLOSE", "CLOSE", "C");
631
632	aws->at("label");
633	aws->create_autosize_button(0, "Please enter the name\nfor the Color Translation Table");
634
635	aws->at("input");
636	aws->create_input_field(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, 15);
637
638	aws->at("ok");
639	aws->callback(createCopyClrTransTable, (AW_CL)ED4_VIS_CREATE);
640	aws->create_button("GO", "GO", "G");
641
642	return (AW_window *)aws;
643	}
644
645	static void reverseColorTranslationTable(AW_window *aww) {
646	AW_root *aw_root = aww->get_root();
647
648	int j = AWAR_SAI_CLR_COUNT-1;
649	for (int i = 0; i<AWAR_SAI_CLR_COUNT/2+1; ++i, --j) {
650	if (i<j) {
651	AW_awar *aw_i = aw_root->awar(getAwarName(i));
652	AW_awar *aw_j = aw_root->awar(getAwarName(j));
653
654	char *ci = aw_i->read_string();
655	char *cj = aw_j->read_string();
656
657	aw_i->write_string(cj);
658	aw_j->write_string(ci);
659
660	free(ci);
661	free(cj);
662	}
663	}
664	}
665
666	static AW_window create_editColorTranslationTable_window(AW_root aw_root) { // creates edit color translation table window
667	static AW_window_simple *aws = 0;
668	if (aws) return (AW_window *)aws;
669
670	aws = new AW_window_simple;
671	aws->init(aw_root, "EDIT_CTT", "Color Translation Table");
672	aws->load_xfig("saiColorRange.fig");
673
674	char at_name[] = "rangex";
675	char *dig = strchr(at_name, 0)-1;
676
677	for (int i = 0; i<AWAR_SAI_CLR_COUNT; ++i) {
678	dig[0] = '0'+i;
679	aws->at(at_name);
680	aws->create_input_field(getAwarName(i), 20);
681	}
682
683	aws->at("close");
684	aws->callback(AW_POPDOWN);
685	aws->create_button("CLOSE", "CLOSE", "C");
686
687	aws->at("reverse");
688	aws->callback(reverseColorTranslationTable);
689	aws->create_button("REVERSE", "Reverse", "R");
690
691	aws->at("colors");
692	aws->callback(makeCreateWindowCallback(AW_create_gc_window, ED4_ROOT->gc_manager));
693	aws->button_length(0);
694	aws->create_button("COLORS", "#colors.xpm");
695
696	return (AW_window *)aws;
697	}
698
699	AW_window ED4_createVisualizeSAI_window(AW_root aw_root) {
700	static AW_window_simple *aws = 0;
701	if (!aws) {
702
703	aws = new AW_window_simple;
704
705	aws->init(aw_root, "VISUALIZE_SAI", "Visualize SAIs");
706	aws->load_xfig("visualizeSAI.fig");
707
708	aws->callback(makeHelpCallback("visualizeSAI.hlp"));
709	aws->at("help");
710	aws->create_button("HELP", "HELP", "H");
711
712	aws->at("close");
713	aws->callback((AW_CB0)AW_POPDOWN);
714	aws->create_button("CLOSE", "CLOSE", "C");
715
716	aws->at("enable");
717	aws->create_toggle(AWAR_SAI_ENABLE);
718
719	aws->at("sai");
720	aws->button_length(30);
721	awt_create_SAI_selection_button(GLOBAL_gb_main, aws, AWAR_SAI_VISUALIZED);
722
723	aws->at("auto_select");
724	aws->create_toggle(AWAR_SAI_AUTO_SELECT);
725
726	aws->at("clrTrList");
727	AW_selection_list *clrTransTableLst = buildClrTransTabNamesList(aws);
728
729	aws->at("edit");
730	aws->button_length(10);
731	aws->callback(AW_POPUP, (AW_CL)create_editColorTranslationTable_window, 0);
732	aws->create_button("EDIT", "EDIT");
733
734	aws->at("create");
735	aws->callback(AW_POPUP, (AW_CL)create_createColorTranslationTable_window, 0);
736	aws->create_button("CREATE", "CREATE");
737
738	aws->at("copy");
739	aws->callback(AW_POPUP, (AW_CL)create_copyColorTranslationTable_window, 0);
740	aws->create_button("COPY", "COPY");
741
742	aws->at("delete");
743	aws->callback((AW_CB1)deleteColorTranslationTable, 0);
744	aws->create_button("DELETE", "DELETE");
745
746	aws->at("marked");
747	aws->create_toggle_field(AWAR_SAI_ALL_SPECIES, 1);
748	aws->insert_toggle("MARKED SPECIES", "M", 0);
749	aws->insert_toggle("ALL SPECIES", "A", 1);
750	aws->update_toggle_field();
751
752	AW_awar *trans_tabs = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES);
753	trans_tabs->add_callback(update_ClrTransTabNamesList_cb, (AW_CL)clrTransTableLst);
754	trans_tabs->touch(); // force update
755	}
756	aws->show();
757
758	return aws;
759	}
760

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