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source: tags/ms_r16q2/EDIT4/ED4_visualizeSAI.cxx

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Last change on this file was 14453, checked in by westram, 8 years ago
do not cast AW_POPDOWN
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File size: 28.2 KB

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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 //
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 "current" // 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	// --------------------------------------------------------------------------------
49
50	extern GBDATA *GLOBAL_gb_main;
51
52	static bool clrDefinitionsChanged = false;
53	static bool inCallback = false; // used to avoid multiple refreshes
54	static bool in_colorDefChanged_callback = false; // used to avoid colorDef correction
55
56	// --------------------------------------------------------------------------------
57
58	#define BUFSIZE 100
59	static const char *getAwarName(int awarNo) {
60	static char buf[BUFSIZE];
61
62	strcpy(buf, AWAR_SAI_CLR);
63	(strchr(buf, 0)-1)[0] = '0'+awarNo;
64
65	return buf;
66	}
67
68	static const char getClrDefAwar(const char awarName) {
69	static char buf[BUFSIZE];
70
71	e4_assert(awarName);
72	e4_assert(awarName[0]); // empty awar is bad
73
74	IF_ASSERTION_USED(int size =) sprintf(buf, AWAR_SAI_CLR_DEF "%s", awarName);
75	e4_assert(size<BUFSIZE);
76	return buf;
77	}
78	#undef BUFSIZE
79
80	// ---------------------------------------------------------
81
82	static void setVisualizeSAI_cb(AW_root *awr) {
83	ED4_ROOT->visualizeSAI = awr->awar(AWAR_SAI_ENABLE)->read_int();
84	ED4_ROOT->request_refresh_for_sequence_terminals();
85	}
86
87	static void setVisualizeSAI_options_cb(AW_root *awr) {
88	ED4_ROOT->visualizeSAI_allSpecies = awr->awar(AWAR_SAI_ALL_SPECIES)->read_int();
89	ED4_ROOT->request_refresh_for_sequence_terminals();
90	}
91
92	static bool colorTransTable_exists(AW_root awr, const char name) {
93	char *tableNames = awr->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES)->read_string();
94	const char *searchFrom = tableNames;
95	int len = strlen(name);
96
97	while (searchFrom) {
98	const char *found = strstr(searchFrom, name);
99
100	if (found) {
101	if ((found == tableNames \|\| found[-1] == '\n') && // found start of entry
102	(found[len] == '\n' \|\| found[len] == 0)) // avoid partial entry
103	{
104	break; // exists!
105	}
106	else { // search next match
107	searchFrom = found+1;
108	}
109	}
110	else {
111	searchFrom = 0;
112	}
113	}
114
115	free(tableNames);
116	return searchFrom != 0;
117	}
118
119	static void colorDefChanged_callback(AW_root *awr, int awarNo) {
120	clrDefinitionsChanged = true;
121
122	if (!in_colorDefChanged_callback) { // this callback is special, because it may change all other color defs
123	LocallyModify<bool> flag(in_colorDefChanged_callback, true);
124
125	{
126	LocallyModify<bool> in_cb(inCallback, true);
127
128	char *clrTabName = awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
129	if (clrTabName[0]) {
130	unsigned char charUsed[256]; memset(charUsed, 255, 256);
131
132	{
133	for (int i=0; i<10; i++) {
134	char *awarString_next = awr->awar_string(getAwarName(i))->read_string();
135	for (int c=0; awarString_next[c]; ++c) {
136	charUsed[(unsigned char)awarString_next[c]] = i;
137	}
138	free(awarString_next);
139	}
140
141	char *awarString = awr->awar_string(getAwarName(awarNo))->read_string();
142	for (int c=0; awarString[c]; ++c) {
143	charUsed[(unsigned char)awarString[c]] = awarNo;
144	}
145	free(awarString);
146	}
147
148	typedef unsigned char mystr[256];
149	mystr s[10];
150	for (int i=0; i<10; i++) s[i][0]=0; // initializing the strings
151
152	for (int i=0; i<256; i++) {
153	int table = charUsed[i];
154	if (table != 255) {
155	char eos = strchr((char )s[table], 0); // get pointer to end of string
156	eos[0] = char(i);
157	eos[1] = 0;
158	}
159	}
160
161	{
162	GBS_strstruct *clrDefStr = GBS_stropen(500); // create output stream
163	for (int i=0; i<10; i++) {
164	awr->awar_string(getAwarName(i))->write_string((char *)s[i]);
165
166	char escaped = GBS_escape_string((char)s[i], ";", '&');
167	GBS_strcat(clrDefStr, escaped);
168	free(escaped);
169	GBS_chrcat(clrDefStr, ';');
170	}
171
172	char *colorDef = GBS_strclose(clrDefStr);
173	AW_awar *awar_def = awr->awar_string(getClrDefAwar(clrTabName), "", AW_ROOT_DEFAULT);
174	awar_def->write_string(colorDef); // writing clr definition to clr trans table awar
175	free(colorDef);
176	}
177	}
178	else {
179	if (!in_cb.old_value()) { // only warn when user really changed the setting
180	aw_message("Please select a VALID Color Translation Table to EDIT.");
181	}
182	}
183	free(clrTabName);
184	}
185
186	if (!inCallback) ED4_ROOT->request_refresh_for_sequence_terminals();
187	}
188	}
189
190	static void colorDefTabNameChanged_callback(AW_root *awr) {
191	char *clrTabName = awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
192	{
193	LocallyModify<bool> flag(inCallback, true);
194	{
195	LocallyModify<bool> flag2(in_colorDefChanged_callback, true); // avoid correction
196
197	// clear current translation table definition
198	for (int i=0; i<10; i++) {
199	AW_awar *transDef_awar = awr->awar_string(getAwarName(i), "", AW_ROOT_DEFAULT);
200	transDef_awar->write_string("");
201	}
202
203	if (clrTabName[0]) {
204	AW_awar *clrTabDef_awar = awr->awar_string(getClrDefAwar(clrTabName), "", AW_ROOT_DEFAULT);
205	char *clrTabDef = clrTabDef_awar->read_string();
206
207	if (clrTabDef[0]) {
208	int i = 0;
209	int tokStart = 0;
210
211	for (int si = 0; clrTabDef[si]; ++si) {
212	if (clrTabDef[si] == ';') {
213	e4_assert(i >= 0 && i<10);
214	AW_awar *awar = awr->awar(getAwarName(i));
215
216	if (tokStart == si) { // empty definition
217	awar->write_string("");
218	}
219	else {
220	int toklen = si-tokStart;
221
222	e4_assert(toklen > 0);
223	e4_assert(clrTabDef[tokStart+toklen] == ';');
224	clrTabDef[tokStart+toklen] = 0;
225
226	char *unescaped = GBS_unescape_string(clrTabDef+tokStart, ";", '&');
227	awar->write_string(unescaped);
228	free(unescaped);
229
230	clrTabDef[tokStart+toklen] = ';';
231	}
232	++i;
233	tokStart = si+1;
234	}
235	}
236	e4_assert(i == 10);
237	}
238	free(clrTabDef);
239	}
240	}
241	colorDefChanged_callback(awr, 0); // correct first def manually
242	{
243	// store the selected table as default for this SAI:
244	char *saiName = awr->awar(AWAR_SAI_VISUALIZED)->read_string();
245	if (saiName[0]) {
246	char buf[100];
247	sprintf(buf, AWAR_SAI_CLR_TRANS_TAB_REL "%s", saiName);
248	awr->awar_string(buf, "", AW_ROOT_DEFAULT); // create an AWAR for the selected SAI and
249	awr->awar(buf)->write_string(clrTabName); // write the existing clr trans table names to the same
250	}
251	free(saiName);
252	}
253	}
254	free(clrTabName);
255
256	if (!inCallback && clrDefinitionsChanged) ED4_ROOT->request_refresh_for_sequence_terminals();
257	}
258
259	static void refresh_display_cb(GB_CB_TYPE cb_type) {
260	if ((cb_type & GB_CB_CHANGED) &&
261	ED4_ROOT->aw_root->awar(AWAR_SAI_ENABLE)->read_int())
262	{
263	clrDefinitionsChanged = 1;
264	ED4_ROOT->request_refresh_for_sequence_terminals();
265	}
266	}
267
268	static void saiChanged_callback(AW_root *awr) {
269	char *saiName = 0;
270	{
271	LocallyModify<bool> flag(inCallback, true);
272	{
273	static GBDATA *gb_last_SAI = 0;
274
275	if (gb_last_SAI) {
276	GB_transaction ta(GLOBAL_gb_main);
277	GB_remove_callback(gb_last_SAI, GB_CB_CHANGED, makeDatabaseCallback(refresh_display_cb));
278	gb_last_SAI = 0;
279	}
280
281	saiName = awr->awar(AWAR_SAI_VISUALIZED)->read_string();
282	char *transTabName = 0;
283
284	if (saiName[0]) {
285	char buf[100];
286	sprintf(buf, AWAR_SAI_CLR_TRANS_TAB_REL "%s", saiName);
287	awr->awar_string(buf, "", AW_ROOT_DEFAULT);
288	transTabName = awr->awar(buf)->read_string();
289	}
290
291	{
292	GB_transaction ta(GLOBAL_gb_main);
293	gb_last_SAI = GBT_find_SAI(GLOBAL_gb_main, saiName);
294	if (gb_last_SAI) {
295	GB_add_callback(gb_last_SAI, GB_CB_CHANGED, makeDatabaseCallback(refresh_display_cb));
296	}
297	}
298	awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->write_string(transTabName ? transTabName : "");
299	free(transTabName);
300
301	clrDefinitionsChanged = true; // SAI changed -> update needed
302	}
303	}
304
305	if (!inCallback && clrDefinitionsChanged) {
306	// SAI changed notify Global SAI Awar AWAR_SAI_GLOBAL
307	awr->awar(AWAR_SAI_GLOBAL)->write_string(saiName);
308	ED4_ROOT->request_refresh_for_sequence_terminals();
309	}
310	free(saiName);
311	}
312
313	static void update_ClrTransTabNamesList_cb(AW_root awr, AW_selection_list colorTransList) {
314	char *clrTransTabNames = awr->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES)->read_string();
315
316	colorTransList->clear();
317
318	for (char *tok = strtok(clrTransTabNames, "\n"); tok; tok = strtok(0, "\n")) {
319	colorTransList->insert(tok, tok);
320	}
321	colorTransList->insert_default("????", "");
322	colorTransList->update();
323
324	free(clrTransTabNames);
325	}
326
327	static void autoselect_cb(AW_root *aw_root) {
328	char *curr_sai = aw_root->awar(AWAR_SAI_NAME)->read_string();
329	#if defined(DEBUG)
330	printf("curr_sai='%s'\n", curr_sai);
331	#endif // DEBUG
332	aw_root->awar(AWAR_SAI_VISUALIZED)->write_string(curr_sai);
333	free(curr_sai);
334	}
335
336	static void set_autoselect_cb(AW_root *aw_root) {
337	static bool callback_active = false;
338
339	if (aw_root->awar(AWAR_SAI_AUTO_SELECT)->read_int()) { // auto select is activated
340	aw_root->awar(AWAR_SAI_NAME)->add_callback(autoselect_cb);
341	callback_active = true;
342	}
343	else {
344	if (callback_active) { // only remove if added
345	aw_root->awar(AWAR_SAI_NAME)->remove_callback(autoselect_cb);
346	callback_active = false;
347	}
348	}
349	}
350
351	static void addOrUpdateTransTable(AW_root aw_root, const char newClrTransTabName, const char *defaultDefinition, bool autoselect) {
352	AW_awar *table_def_awar = aw_root->awar_string(getClrDefAwar(newClrTransTabName), defaultDefinition, AW_ROOT_DEFAULT);
353	table_def_awar->write_string(defaultDefinition);
354
355	if (!colorTransTable_exists(aw_root, newClrTransTabName)) {
356	AW_awar *names_awar = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES);
357	const char *old_names = names_awar->read_char_pntr();
358	names_awar->write_string(old_names[0]
359	? GBS_global_string("%s\n%s", old_names, newClrTransTabName)
360	: newClrTransTabName); // add new name
361	}
362
363	if (autoselect) {
364	aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->write_string(newClrTransTabName); // select new
365	}
366	}
367
368	static void addDefaultTransTable(AW_root aw_root, const char newClrTransTabName, const char *defaultDefinition) {
369	addOrUpdateTransTable(aw_root, newClrTransTabName, defaultDefinition, false);
370	}
371
372	void ED4_createVisualizeSAI_Awars(AW_root *aw_root, AW_default aw_def) { // --- Creating and initializing AWARS -----
373	aw_root->awar_int(AWAR_SAI_ENABLE, 0, aw_def);
374	aw_root->awar_int(AWAR_SAI_ALL_SPECIES, 0, aw_def);
375	aw_root->awar_int(AWAR_SAI_AUTO_SELECT, 0, aw_def);
376
377	aw_root->awar_string(AWAR_SAI_VISUALIZED, "", aw_def);
378	aw_root->awar_string(AWAR_SAI_CLR_TRANS_TABLE, "", aw_def);
379	aw_root->awar_string(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, "", aw_def);
380	aw_root->awar_string(AWAR_SAI_CLR_TRANS_TAB_NAMES, "", aw_def);
381
382	for (int i=0; i<10; i++) { // initializing 10 color definition string AWARS
383	AW_awar *def_awar = aw_root->awar_string(getAwarName(i), "", aw_def);
384	def_awar->add_callback(makeRootCallback(colorDefChanged_callback, i));
385	}
386	aw_root->awar(AWAR_SAI_ENABLE) ->add_callback(setVisualizeSAI_cb);
387	aw_root->awar(AWAR_SAI_ALL_SPECIES) ->add_callback(setVisualizeSAI_options_cb);
388	aw_root->awar(AWAR_SAI_AUTO_SELECT) ->add_callback(set_autoselect_cb);
389	aw_root->awar(AWAR_SAI_VISUALIZED) ->add_callback(saiChanged_callback);
390	aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->add_callback(colorDefTabNameChanged_callback);
391
392	ED4_ROOT->visualizeSAI = aw_root->awar(AWAR_SAI_ENABLE)->read_int();
393	ED4_ROOT->visualizeSAI_allSpecies = aw_root->awar(AWAR_SAI_ALL_SPECIES)->read_int();
394
395	// create some defaults:
396	aw_root->awar_int(AWAR_SAI_CLR_DEFAULTS_CREATED, 1, aw_def); // @@@ Feb 2012 - remove me in some years
397
398	addDefaultTransTable(aw_root, "numeric", "0;1;2;3;4;5;6;7;8;9;");
399	addDefaultTransTable(aw_root, "binary", ".0;;+1;;;;;;;;");
400	addDefaultTransTable(aw_root, "consensus", "=ACGTU;;acgtu;.;;;;;;;");
401	addDefaultTransTable(aw_root, "helix", ";;<>;;;;;[];;;");
402	addDefaultTransTable(aw_root, "xstring", ";x;;;;;;;;;");
403	addDefaultTransTable(aw_root, "gaps", ";-.;;;;;;;;;");
404
405	LocallyModify<bool> flag(inCallback, true); // avoid refresh
406	saiChanged_callback(aw_root);
407	colorDefTabNameChanged_callback(aw_root); // init awars for selected table
408	set_autoselect_cb(aw_root);
409	}
410
411	enum CreationMode {
412	ED4_VIS_CREATE, // creates a new (empty) color translation table
413	ED4_VIS_COPY, // copies the selected color translation table
414	};
415
416	static void createCopyClrTransTable(AW_window *aws, CreationMode mode) {
417	AW_root *aw_root = aws->get_root();
418
419	char *newClrTransTabName = 0;
420	char *clrTabSourceName = 0;
421
422	switch (mode) {
423	case ED4_VIS_CREATE:
424	newClrTransTabName = GBS_string_2_key(aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME)->read_char_pntr());
425
426	if (strcmp(newClrTransTabName, "__") == 0) { // user entered nothing
427	aw_message("Please enter a translation table name");
428	}
429	else if (colorTransTable_exists(aw_root, newClrTransTabName)) {
430	aw_message(GBS_global_string("Color translation table '%s' already exists.", newClrTransTabName));
431	}
432	else {
433	addOrUpdateTransTable(aw_root, newClrTransTabName, "", true);
434	}
435	break;
436
437	case ED4_VIS_COPY:
438	newClrTransTabName = GBS_string_2_key(aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME)->read_char_pntr());
439	clrTabSourceName = aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
440
441	if (!clrTabSourceName[0]) {
442	aw_message("Please select a valid Color Translation Table to COPY!");
443	}
444	else if (colorTransTable_exists(aw_root, newClrTransTabName)) {
445	aw_message(GBS_global_string("Color Translation Table \"%s\" EXISTS! Please enter a different name.", newClrTransTabName));
446	}
447	else {
448	char *old_def = aw_root->awar(getClrDefAwar(clrTabSourceName))->read_string();
449	addOrUpdateTransTable(aw_root, newClrTransTabName, old_def, true);
450	free(old_def);
451	}
452	break;
453	}
454
455	free(clrTabSourceName);
456	free(newClrTransTabName);
457	}
458
459	static void deleteColorTranslationTable(AW_window *aws) {
460	AW_root *aw_root = aws->get_root();
461	char *clrTabName = aw_root->awar_string(AWAR_SAI_CLR_TRANS_TABLE)->read_string();
462
463	if (clrTabName[0]) {
464	AW_awar *awar_tabNames = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES);
465	char *clrTransTabNames = awar_tabNames->read_string();
466	GBS_strstruct *newTransTabName = GBS_stropen(strlen(clrTransTabNames));
467
468	for (const char *tok = strtok(clrTransTabNames, "\n"); tok; tok = strtok(0, "\n")) {
469	if (strcmp(clrTabName, tok) != 0) { // merge all not to delete
470	GBS_strcat(newTransTabName, tok);
471	GBS_strcat(newTransTabName, "\n");
472	}
473	}
474
475	aw_root->awar_string(getClrDefAwar(clrTabName))->write_string("");
476	char *new_name = GBS_strclose(newTransTabName);
477	awar_tabNames->write_string(new_name); // updates selection list
478	free(new_name);
479
480	free(clrTransTabNames);
481	}
482	else {
483	aw_message("Selected Color Translation Table is not VALID and cannot be DELETED!");
484	}
485	free(clrTabName);
486	}
487
488	static AW_selection_list buildClrTransTabNamesList(AW_window aws) {
489	AW_root *awr = aws->get_root();
490	AW_selection_list *colorTransList = aws->create_selection_list(AWAR_SAI_CLR_TRANS_TABLE, true);
491
492	update_ClrTransTabNamesList_cb(awr, colorTransList);
493
494	return colorTransList;
495	}
496
497	const char ED4_getSaiColorString(AW_root awr, int start, int end) {
498	static int seqBufferSize = 0;
499	static char *saiColors = 0;
500	static int lastStart = -1;
501	static int lastEnd = -1;
502	static bool lastVisualize = false;
503
504	e4_assert(start<=end);
505
506	if (lastStart==start && lastEnd==end && !clrDefinitionsChanged && lastVisualize) {
507	return saiColors-start; // if start and end positions are same as the previous positions and no settings
508	} // were changed return the last calculated saiColors string
509
510	lastStart = start; lastEnd = end; clrDefinitionsChanged = false; // storing start and end positions
511
512	int seqSize = end-start+1;
513
514	if (seqSize>seqBufferSize) {
515	free(saiColors);
516	seqBufferSize = seqSize;
517	saiColors = (char*)GB_calloc(seqBufferSize, sizeof(char));
518	}
519	else memset(saiColors, 0, sizeof(char)*seqSize);
520
521	char *saiSelected = awr->awar(AWAR_SAI_VISUALIZED)->read_string();
522
523	GB_push_transaction(GLOBAL_gb_main);
524	char *alignment_name = GBT_get_default_alignment(GLOBAL_gb_main);
525	GBDATA *gb_extended = GBT_find_SAI(GLOBAL_gb_main, saiSelected);
526	bool visualize = false; // set to true if all goes fine
527
528	if (gb_extended) {
529	GBDATA *gb_ali = GB_entry(gb_extended, alignment_name);
530	if (gb_ali) {
531	const char *saiData = 0;
532	bool free_saiData = false;
533
534	{
535	GBDATA *saiSequence = GB_entry(gb_ali, "data"); // search "data" entry (normal SAI)
536	if (saiSequence) {
537	saiData = GB_read_char_pntr(saiSequence); // not allocated
538	}
539	else {
540	saiSequence = GB_entry(gb_ali, "bits"); // search "bits" entry (binary SAI)
541	if (saiSequence) {
542	saiData = GB_read_as_string(saiSequence); // allocated
543	free_saiData = true; // free saiData below
544	}
545	}
546	}
547
548	if (saiData) {
549	char trans_table[256];
550	{
551	// build the translation table:
552	memset(trans_table, 0, 256);
553	for (int i = 0; i<AWAR_SAI_CLR_COUNT; ++i) {
554	char *def = awr->awar(getAwarName(i))->read_string();
555	int clrRange = ED4_G_CBACK_0 + i;
556
557	for (char d = def; d; ++d) {
558	trans_table[(unsigned char)*d] = clrRange;
559	}
560	free(def);
561	}
562	}
563
564	// translate SAI to colors
565	for (int i = start; i <= end; ++i) {
566	saiColors[i-start] = trans_table[(unsigned char)saiData[i]];
567	}
568
569	visualize = true;
570	}
571
572	if (free_saiData) {
573	free(const_cast<char*>(saiData)); // in this case saiData is allocated (see above)
574	}
575	}
576	}
577	free(alignment_name);
578	free(saiSelected);
579	GB_pop_transaction(GLOBAL_gb_main);
580
581	lastVisualize = visualize;
582	if (visualize) {
583	e4_assert(saiColors);
584	return saiColors-start;
585	}
586
587	return 0; // don't visualize (sth went wrong)
588	}
589
590
591	// -------------------- Creating Windows and Display dialogs --------------------
592
593	static AW_window create_copyColorTranslationTable_window(AW_root aw_root) { // creates copy color translation table window
594	AW_window_simple *aws = new AW_window_simple;
595	aws->init(aw_root, "COPY_CLR_TR_TABLE", "Copy Color Translation Table");
596	aws->load_xfig("ad_al_si.fig");
597
598	aws->at("close");
599	aws->callback(AW_POPDOWN);
600	aws->create_button("CLOSE", "CLOSE", "C");
601
602	aws->at("label");
603	aws->create_autosize_button(0, "Please enter the new name\nfor the Color Translation Table");
604
605	aws->at("input");
606	aws->create_input_field(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, 15);
607
608	aws->at("ok");
609	aws->callback(makeWindowCallback(createCopyClrTransTable, ED4_VIS_COPY));
610	aws->create_button("GO", "GO", "G");
611
612	return (AW_window *)aws;
613	}
614
615	static AW_window create_createColorTranslationTable_window(AW_root aw_root) { // creates create color translation table window
616	AW_window_simple *aws = new AW_window_simple;
617	aws->init(aw_root, "CREATE_CLR_TR_TABLE", "Create Color Translation Table");
618	aws->load_xfig("ad_al_si.fig");
619
620	aws->at("close");
621	aws->callback(AW_POPDOWN);
622	aws->create_button("CLOSE", "CLOSE", "C");
623
624	aws->at("label");
625	aws->create_autosize_button(0, "Please enter the name\nfor the Color Translation Table");
626
627	aws->at("input");
628	aws->create_input_field(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, 15);
629
630	aws->at("ok");
631	aws->callback(makeWindowCallback(createCopyClrTransTable, ED4_VIS_CREATE));
632	aws->create_button("GO", "GO", "G");
633
634	return (AW_window *)aws;
635	}
636
637	static void reverseColorTranslationTable(AW_window *aww) {
638	AW_root *aw_root = aww->get_root();
639
640	int j = AWAR_SAI_CLR_COUNT-1;
641	for (int i = 0; i<AWAR_SAI_CLR_COUNT/2+1; ++i, --j) {
642	if (i<j) {
643	AW_awar *aw_i = aw_root->awar(getAwarName(i));
644	AW_awar *aw_j = aw_root->awar(getAwarName(j));
645
646	char *ci = aw_i->read_string();
647	char *cj = aw_j->read_string();
648
649	aw_i->write_string(cj);
650	aw_j->write_string(ci);
651
652	free(ci);
653	free(cj);
654	}
655	}
656	}
657
658	static AW_window create_editColorTranslationTable_window(AW_root aw_root) { // creates edit color translation table window
659	static AW_window_simple *aws = 0;
660	if (!aws) {
661	aws = new AW_window_simple;
662	aws->init(aw_root, "EDIT_CTT", "Color Translation Table");
663	aws->load_xfig("saiColorRange.fig");
664
665	char at_name[] = "rangex";
666	char *dig = strchr(at_name, 0)-1;
667
668	for (int i = 0; i<AWAR_SAI_CLR_COUNT; ++i) {
669	dig[0] = '0'+i;
670	aws->at(at_name);
671	aws->create_input_field(getAwarName(i), 20);
672	}
673
674	aws->at("close");
675	aws->callback(AW_POPDOWN);
676	aws->create_button("CLOSE", "CLOSE", "C");
677
678	aws->at("reverse");
679	aws->callback(reverseColorTranslationTable);
680	aws->create_button("REVERSE", "Reverse", "R");
681
682	aws->at("colors");
683	aws->callback(makeWindowCallback(ED4_popup_gc_window, ED4_ROOT->gc_manager));
684	aws->button_length(0);
685	aws->create_button("COLORS", "#colors.xpm");
686	}
687	return aws;
688	}
689
690	AW_window ED4_createVisualizeSAI_window(AW_root aw_root) {
691	static AW_window_simple *aws = 0;
692	if (!aws) {
693	aws = new AW_window_simple;
694
695	aws->init(aw_root, "VISUALIZE_SAI", "Visualize SAIs");
696	aws->load_xfig("visualizeSAI.fig");
697
698	aws->callback(makeHelpCallback("visualizeSAI.hlp"));
699	aws->at("help");
700	aws->create_button("HELP", "HELP", "H");
701
702	aws->at("close");
703	aws->callback(AW_POPDOWN);
704	aws->create_button("CLOSE", "CLOSE", "C");
705
706	aws->at("enable");
707	aws->create_toggle(AWAR_SAI_ENABLE);
708
709	aws->at("sai");
710	aws->button_length(30);
711	awt_create_SAI_selection_button(GLOBAL_gb_main, aws, AWAR_SAI_VISUALIZED);
712
713	aws->at("auto_select");
714	aws->create_toggle(AWAR_SAI_AUTO_SELECT);
715
716	aws->at("clrTrList");
717	AW_selection_list *clrTransTableLst = buildClrTransTabNamesList(aws);
718
719	aws->at("edit");
720	aws->button_length(10);
721	aws->callback(create_editColorTranslationTable_window);
722	aws->create_button("EDIT", "EDIT");
723
724	aws->at("create");
725	aws->callback(create_createColorTranslationTable_window);
726	aws->create_button("CREATE", "CREATE");
727
728	aws->at("copy");
729	aws->callback(create_copyColorTranslationTable_window);
730	aws->create_button("COPY", "COPY");
731
732	aws->at("delete");
733	aws->callback(deleteColorTranslationTable);
734	aws->create_button("DELETE", "DELETE");
735
736	aws->at("marked");
737	aws->create_toggle_field(AWAR_SAI_ALL_SPECIES, 1);
738	aws->insert_toggle("MARKED SPECIES", "M", 0);
739	aws->insert_toggle("ALL SPECIES", "A", 1);
740	aws->update_toggle_field();
741
742	AW_awar *trans_tabs = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES);
743	trans_tabs->add_callback(makeRootCallback(update_ClrTransTabNamesList_cb, clrTransTableLst));
744	trans_tabs->touch(); // force update
745	}
746	aws->show();
747
748	return aws;
749	}
750

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