1 | /*=======================================================================================*/ |
---|
2 | /* */ |
---|
3 | /* File : ED4_visualizeSAI.cxx */ |
---|
4 | /* Purpose : To Visualise the Sequence Associated Information (SAI) in the Editor */ |
---|
5 | /* Author : Yadhu Kumar (yadhu@mikro.biologie.tu-muenchen.de) */ |
---|
6 | /* web site : http://www.arb-home.de/ */ |
---|
7 | /* */ |
---|
8 | /* Copyright Department of Microbiology (Technical University Munich) */ |
---|
9 | /* */ |
---|
10 | /*=======================================================================================*/ |
---|
11 | |
---|
12 | #include <stdio.h> |
---|
13 | #include <stdlib.h> |
---|
14 | #include <iostream> |
---|
15 | |
---|
16 | #include <arbdb.h> |
---|
17 | #include <arbdbt.h> |
---|
18 | #include <aw_root.hxx> |
---|
19 | #include <aw_window.hxx> |
---|
20 | #include <aw_awars.hxx> |
---|
21 | #include <awt.hxx> |
---|
22 | #include <awt_canvas.hxx> |
---|
23 | #include <awt_sel_boxes.hxx> |
---|
24 | #include <aw_preset.hxx> |
---|
25 | |
---|
26 | #include <ed4_extern.hxx> |
---|
27 | |
---|
28 | #include "ed4_class.hxx" |
---|
29 | #include "ed4_visualizeSAI.hxx" |
---|
30 | |
---|
31 | // -------------------------------------------------------------------------------- |
---|
32 | |
---|
33 | #define AWAR_SAI_CLR_TAB "saicolors/" |
---|
34 | #define AWAR_SAI_SELECT 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" // ;-seperated 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 refreshs |
---|
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 | #ifdef DEBUG |
---|
78 | int size = |
---|
79 | #endif |
---|
80 | sprintf(buf,AWAR_SAI_CLR_DEF "%s", awarName); |
---|
81 | e4_assert(size<BUFSIZE); |
---|
82 | return buf; |
---|
83 | } |
---|
84 | #undef BUFSIZE |
---|
85 | |
---|
86 | /* --------------------------------------------------------- */ |
---|
87 | |
---|
88 | static void setVisualizeSAI_cb(AW_root *awr) { |
---|
89 | ED4_ROOT->visualizeSAI = awr->awar(AWAR_SAI_ENABLE)->read_int(); |
---|
90 | ED4_ROOT->refresh_all_windows(1); //refresh editor |
---|
91 | } |
---|
92 | |
---|
93 | static void setVisualizeSAI_options_cb(AW_root *awr) { |
---|
94 | ED4_ROOT->visualizeSAI_allSpecies = awr->awar(AWAR_SAI_ALL_SPECIES)->read_int(); |
---|
95 | ED4_ROOT->refresh_all_windows(1); //refresh editor |
---|
96 | } |
---|
97 | |
---|
98 | static bool colorTransTable_exists(AW_root *awr, const char *name) { |
---|
99 | char *tableNames = awr->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES)->read_string(); |
---|
100 | const char *searchFrom = tableNames; |
---|
101 | int len = strlen(name); |
---|
102 | |
---|
103 | while (searchFrom) { |
---|
104 | const char *found = strstr(searchFrom, name); |
---|
105 | |
---|
106 | if (found) { |
---|
107 | if ((found == tableNames || found[-1] == '\n') && // found start of entry |
---|
108 | (found[len] == '\n' || found[len] == 0)) // avoid partial entry |
---|
109 | { |
---|
110 | break; // exists! |
---|
111 | } |
---|
112 | else { // search next match |
---|
113 | searchFrom = found+1; |
---|
114 | } |
---|
115 | } |
---|
116 | else { |
---|
117 | searchFrom = 0; |
---|
118 | } |
---|
119 | } |
---|
120 | |
---|
121 | free(tableNames); |
---|
122 | return searchFrom != 0; |
---|
123 | } |
---|
124 | |
---|
125 | static void colorDefChanged_callback(AW_root *awr, AW_CL cl_awarNo) { |
---|
126 | clrDefinitionsChanged = true; |
---|
127 | |
---|
128 | if (!in_colorDefChanged_callback) { // this callback is special, because it may change all other color defs |
---|
129 | in_colorDefChanged_callback = true; |
---|
130 | |
---|
131 | bool old_inCallback = inCallback; |
---|
132 | inCallback = true; |
---|
133 | |
---|
134 | char *clrTabName = awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string(); |
---|
135 | if (clrTabName[0]) { |
---|
136 | unsigned char charUsed[256]; memset(charUsed,255,256); |
---|
137 | |
---|
138 | { |
---|
139 | for (int i=0; i<10 ; i++){ |
---|
140 | char *awarString_next = awr->awar_string(getAwarName(i))->read_string(); |
---|
141 | for(int c=0; awarString_next[c]; ++c){ |
---|
142 | charUsed[(unsigned char)awarString_next[c]] = i; |
---|
143 | } |
---|
144 | free(awarString_next); |
---|
145 | } |
---|
146 | |
---|
147 | int awarNo = (int)cl_awarNo; |
---|
148 | char *awarString = awr->awar_string(getAwarName(awarNo))->read_string(); |
---|
149 | for(int c=0; awarString[c]; ++c){ |
---|
150 | charUsed[(unsigned char)awarString[c]] = awarNo; |
---|
151 | } |
---|
152 | free(awarString); |
---|
153 | } |
---|
154 | |
---|
155 | typedef unsigned char mystr[256]; |
---|
156 | mystr s[10]; |
---|
157 | for (int i=0; i<10; i++) s[i][0]=0; //initializing the strings |
---|
158 | |
---|
159 | for (int i=0; i<256; i++) { |
---|
160 | int table = charUsed[i]; |
---|
161 | if (table != 255) { |
---|
162 | char *eos = strchr((char *)s[table],0); // get pointer to end of string |
---|
163 | eos[0] = char(i); |
---|
164 | eos[1] = 0; |
---|
165 | } |
---|
166 | } |
---|
167 | |
---|
168 | { |
---|
169 | GBS_strstruct *clrDefStr = GBS_stropen(500); /* create output stream */ |
---|
170 | for(int i=0; i<10; i++){ |
---|
171 | awr->awar_string(getAwarName(i))->write_string((char *)s[i]); |
---|
172 | |
---|
173 | char *escaped = GBS_escape_string((char*)s[i], ";", '&'); |
---|
174 | GBS_strcat(clrDefStr, escaped); |
---|
175 | free(escaped); |
---|
176 | GBS_chrcat(clrDefStr, ';'); |
---|
177 | } |
---|
178 | |
---|
179 | char *colorDef = GBS_strclose(clrDefStr); |
---|
180 | AW_awar *awar_def = awr->awar_string(getClrDefAwar(clrTabName), "", AW_ROOT_DEFAULT); |
---|
181 | awar_def->write_string(colorDef); // writing clr defnition to clr trans table awar |
---|
182 | free(colorDef); |
---|
183 | } |
---|
184 | } |
---|
185 | else { |
---|
186 | if (!old_inCallback) { // only warn when user really changed the setting |
---|
187 | aw_message("Please select a VALID Color Translation Table to EDIT."); |
---|
188 | } |
---|
189 | } |
---|
190 | free(clrTabName); |
---|
191 | inCallback = old_inCallback; |
---|
192 | |
---|
193 | if (!inCallback) { |
---|
194 | ED4_ROOT->refresh_all_windows(1); //refresh editor |
---|
195 | } |
---|
196 | |
---|
197 | in_colorDefChanged_callback = false; |
---|
198 | } |
---|
199 | } |
---|
200 | |
---|
201 | static void colorDefTabNameChanged_callback(AW_root *awr) { |
---|
202 | char *clrTabName = awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string(); |
---|
203 | bool old_inCallback = inCallback; |
---|
204 | inCallback = true; |
---|
205 | { |
---|
206 | bool old_in_colorDefChanged_callback = in_colorDefChanged_callback; |
---|
207 | in_colorDefChanged_callback = true; // avoid correction |
---|
208 | |
---|
209 | // clear current translation table definition |
---|
210 | for(int i=0; i<10 ; i++) { |
---|
211 | AW_awar *transDef_awar = awr->awar_string(getAwarName(i), "", AW_ROOT_DEFAULT); |
---|
212 | transDef_awar->write_string(""); |
---|
213 | } |
---|
214 | |
---|
215 | if (clrTabName[0]) { |
---|
216 | AW_awar *clrTabDef_awar = awr->awar_string(getClrDefAwar(clrTabName), "", AW_ROOT_DEFAULT); |
---|
217 | char *clrTabDef = clrTabDef_awar->read_string(); |
---|
218 | |
---|
219 | if (clrTabDef[0]) { |
---|
220 | int i = 0; |
---|
221 | int tokStart = 0; |
---|
222 | |
---|
223 | for (int si = 0; clrTabDef[si]; ++si) { |
---|
224 | if (clrTabDef[si] == ';') { |
---|
225 | e4_assert(i >= 0 && i<10); |
---|
226 | AW_awar *awar = awr->awar(getAwarName(i)); |
---|
227 | |
---|
228 | if (tokStart == si) { // empty definition |
---|
229 | awar->write_string(""); |
---|
230 | } |
---|
231 | else { |
---|
232 | int toklen = si-tokStart; |
---|
233 | |
---|
234 | e4_assert(toklen > 0); |
---|
235 | e4_assert(clrTabDef[tokStart+toklen] == ';'); |
---|
236 | clrTabDef[tokStart+toklen] = 0; |
---|
237 | |
---|
238 | char *unescaped = GBS_unescape_string(clrTabDef+tokStart, ";", '&'); |
---|
239 | awar->write_string(unescaped); |
---|
240 | free(unescaped); |
---|
241 | |
---|
242 | clrTabDef[tokStart+toklen] = ';'; |
---|
243 | } |
---|
244 | ++i; |
---|
245 | tokStart = si+1; |
---|
246 | } |
---|
247 | } |
---|
248 | e4_assert(i == 10); |
---|
249 | } |
---|
250 | free(clrTabDef); |
---|
251 | } |
---|
252 | in_colorDefChanged_callback = old_in_colorDefChanged_callback; |
---|
253 | colorDefChanged_callback(awr, 0); // correct first def manually |
---|
254 | } |
---|
255 | { |
---|
256 | // store the selected tabel as default for this SAI: |
---|
257 | char *saiName = awr->awar(AWAR_SAI_SELECT)->read_string(); |
---|
258 | if (saiName[0]) { |
---|
259 | char buf[100]; |
---|
260 | sprintf(buf, AWAR_SAI_CLR_TRANS_TAB_REL "%s", saiName); |
---|
261 | awr->awar_string(buf, "", AW_ROOT_DEFAULT); // create an AWAR for the selected SAI and |
---|
262 | awr->awar(buf)->write_string(clrTabName); // write the existing clr trans table names to the same |
---|
263 | } |
---|
264 | free(saiName); |
---|
265 | } |
---|
266 | inCallback = old_inCallback; |
---|
267 | free(clrTabName); |
---|
268 | |
---|
269 | if (!inCallback && clrDefinitionsChanged) { |
---|
270 | ED4_ROOT->refresh_all_windows(1); //refresh editor |
---|
271 | } |
---|
272 | } |
---|
273 | |
---|
274 | static void refresh_display_cb(GBDATA *, int *, GB_CB_TYPE cb_type) { |
---|
275 | if ((cb_type & GB_CB_CHANGED) && |
---|
276 | ED4_ROOT->aw_root->awar(AWAR_SAI_ENABLE)->read_int()) |
---|
277 | { |
---|
278 | clrDefinitionsChanged = 1; |
---|
279 | ED4_ROOT->refresh_all_windows(1); //refresh editor when current SAI is changed |
---|
280 | } |
---|
281 | } |
---|
282 | |
---|
283 | static void saiChanged_callback(AW_root *awr) { |
---|
284 | bool old_inCallback = inCallback; |
---|
285 | inCallback = true; |
---|
286 | char *saiName = 0; |
---|
287 | { |
---|
288 | static GBDATA *gb_last_SAI = 0; |
---|
289 | |
---|
290 | if (gb_last_SAI) { |
---|
291 | GB_transaction dummy(GLOBAL_gb_main); |
---|
292 | GB_remove_callback(gb_last_SAI, GB_CB_CHANGED, refresh_display_cb, 0); |
---|
293 | gb_last_SAI = 0; |
---|
294 | } |
---|
295 | |
---|
296 | saiName = awr->awar(AWAR_SAI_SELECT)->read_string(); |
---|
297 | char *transTabName = 0; |
---|
298 | |
---|
299 | if (saiName[0]) { |
---|
300 | char buf[100]; |
---|
301 | sprintf(buf, AWAR_SAI_CLR_TRANS_TAB_REL "%s", saiName); |
---|
302 | awr->awar_string(buf, "", AW_ROOT_DEFAULT); |
---|
303 | transTabName = awr->awar(buf)->read_string(); |
---|
304 | } |
---|
305 | |
---|
306 | { |
---|
307 | GB_transaction dummy(GLOBAL_gb_main); |
---|
308 | gb_last_SAI = GBT_find_SAI(GLOBAL_gb_main, saiName); |
---|
309 | if (gb_last_SAI) { |
---|
310 | GB_add_callback(gb_last_SAI, GB_CB_CHANGED, refresh_display_cb, 0); |
---|
311 | } |
---|
312 | } |
---|
313 | awr->awar(AWAR_SAI_CLR_TRANS_TABLE)->write_string(transTabName ? transTabName : ""); |
---|
314 | free(transTabName); |
---|
315 | |
---|
316 | clrDefinitionsChanged = true; // SAI changed -> update needed |
---|
317 | } |
---|
318 | inCallback = old_inCallback; |
---|
319 | |
---|
320 | if (!inCallback && clrDefinitionsChanged) { |
---|
321 | ED4_ROOT->refresh_all_windows(1); //refresh editor |
---|
322 | // SAI changed notify Global SAI Awar AWAR_SAI_GLOBAL |
---|
323 | awr->awar(AWAR_SAI_GLOBAL)->write_string(saiName); |
---|
324 | } |
---|
325 | free(saiName); |
---|
326 | } |
---|
327 | |
---|
328 | static void update_ClrTransTabNamesList_cb(AW_root *awr, AW_CL cl_aws, AW_CL cl_id) { |
---|
329 | AW_window *aws = (AW_window*)cl_aws; |
---|
330 | AW_selection_list *id = (AW_selection_list*)cl_id; |
---|
331 | char *clrTransTabNames = awr->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES)->read_string(); |
---|
332 | |
---|
333 | aws->clear_selection_list(id); |
---|
334 | |
---|
335 | for (char *tok = strtok(clrTransTabNames,"\n"); tok; tok = strtok(0,"\n")) { |
---|
336 | aws->insert_selection(id,tok,tok); |
---|
337 | } |
---|
338 | aws->insert_default_selection(id, "????", ""); |
---|
339 | aws->update_selection_list(id); |
---|
340 | |
---|
341 | free(clrTransTabNames); |
---|
342 | } |
---|
343 | |
---|
344 | static void autoselect_cb(AW_root *aw_root) { |
---|
345 | char *curr_sai = aw_root->awar(AWAR_SAI_NAME)->read_string(); |
---|
346 | #if defined(DEBUG) |
---|
347 | printf("curr_sai='%s'\n", curr_sai); |
---|
348 | #endif // DEBUG |
---|
349 | aw_root->awar(AWAR_SAI_SELECT)->write_string(curr_sai); |
---|
350 | free(curr_sai); |
---|
351 | } |
---|
352 | |
---|
353 | static void set_autoselect_cb(AW_root *aw_root) { |
---|
354 | static bool callback_active = false; |
---|
355 | |
---|
356 | if (aw_root->awar(AWAR_SAI_AUTO_SELECT)->read_int()) { // auto select is avtivated |
---|
357 | aw_root->awar(AWAR_SAI_NAME)->add_callback(autoselect_cb); |
---|
358 | callback_active = true; |
---|
359 | } |
---|
360 | else { |
---|
361 | if (callback_active) { // only remove if added |
---|
362 | aw_root->awar(AWAR_SAI_NAME)->remove_callback(autoselect_cb); |
---|
363 | callback_active = false; |
---|
364 | } |
---|
365 | } |
---|
366 | } |
---|
367 | |
---|
368 | static void addNewTransTable(AW_root *aw_root, const char *newClrTransTabName, const char *defaultDefinition, bool autoselect) { |
---|
369 | AW_awar *table_def_awar = aw_root->awar_string(getClrDefAwar(newClrTransTabName), defaultDefinition , AW_ROOT_DEFAULT); |
---|
370 | table_def_awar->write_string(defaultDefinition); |
---|
371 | |
---|
372 | e4_assert(!colorTransTable_exists(aw_root, newClrTransTabName)); |
---|
373 | |
---|
374 | AW_awar *names_awar = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES); |
---|
375 | char *old_names = names_awar->read_string(); |
---|
376 | names_awar->write_string(old_names[0] |
---|
377 | ? GBS_global_string("%s\n%s", old_names, newClrTransTabName) |
---|
378 | : newClrTransTabName); // add new name |
---|
379 | free(old_names); |
---|
380 | |
---|
381 | if (autoselect) { |
---|
382 | aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->write_string(newClrTransTabName); // select new |
---|
383 | } |
---|
384 | } |
---|
385 | |
---|
386 | static void addDefaultTransTable(AW_root *aw_root, const char *newClrTransTabName, const char *defaultDefinition) { |
---|
387 | if (!colorTransTable_exists(aw_root, newClrTransTabName)) { |
---|
388 | addNewTransTable(aw_root, newClrTransTabName, defaultDefinition, false); |
---|
389 | } |
---|
390 | } |
---|
391 | |
---|
392 | void ED4_createVisualizeSAI_Awars(AW_root *aw_root, AW_default aw_def) { // --- Creating and initializing AWARS ----- |
---|
393 | aw_root->awar_int (AWAR_SAI_ENABLE, 0, aw_def); |
---|
394 | aw_root->awar_int (AWAR_SAI_ALL_SPECIES, 0, aw_def); |
---|
395 | aw_root->awar_int (AWAR_SAI_AUTO_SELECT, 0, aw_def); |
---|
396 | aw_root->awar_string(AWAR_SAI_SELECT, "", aw_def); |
---|
397 | aw_root->awar_string(AWAR_SAI_CLR_TRANS_TABLE, "", aw_def); |
---|
398 | aw_root->awar_string(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME, "", aw_def); |
---|
399 | aw_root->awar_string(AWAR_SAI_CLR_TRANS_TAB_NAMES, "", aw_def); |
---|
400 | |
---|
401 | for (int i=0;i<10;i++){ // initialising 10 color definition string AWARS |
---|
402 | AW_awar *def_awar = aw_root->awar_string(getAwarName(i),"",aw_def); |
---|
403 | def_awar->add_callback(colorDefChanged_callback, (AW_CL)i); |
---|
404 | } |
---|
405 | aw_root->awar(AWAR_SAI_ENABLE)->add_callback(setVisualizeSAI_cb); |
---|
406 | aw_root->awar(AWAR_SAI_ALL_SPECIES)->add_callback(setVisualizeSAI_options_cb); |
---|
407 | aw_root->awar(AWAR_SAI_AUTO_SELECT)->add_callback(set_autoselect_cb); |
---|
408 | aw_root->awar(AWAR_SAI_SELECT)->add_callback(saiChanged_callback); |
---|
409 | aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->add_callback(colorDefTabNameChanged_callback); |
---|
410 | |
---|
411 | ED4_ROOT->visualizeSAI = aw_root->awar(AWAR_SAI_ENABLE)->read_int(); |
---|
412 | ED4_ROOT->visualizeSAI_allSpecies = aw_root->awar(AWAR_SAI_ALL_SPECIES)->read_int(); |
---|
413 | |
---|
414 | // create some defaults: |
---|
415 | AW_awar *awar_defaults_created = aw_root->awar_int(AWAR_SAI_CLR_DEFAULTS_CREATED, 0, aw_def); |
---|
416 | |
---|
417 | if (awar_defaults_created->read_int() == 0) { |
---|
418 | addDefaultTransTable(aw_root, "numeric", "0;1;2;3;4;5;6;7;8;9;"); |
---|
419 | addDefaultTransTable(aw_root, "binary", ".;+;;;;;;;;;"); |
---|
420 | addDefaultTransTable(aw_root, "consensus", "=ACGTU;;acgtu;.;;;;;;;"); |
---|
421 | addDefaultTransTable(aw_root, "helix", ";;<>;;;;;[];;;"); |
---|
422 | addDefaultTransTable(aw_root, "xstring", ";x;;;;;;;;;"); |
---|
423 | addDefaultTransTable(aw_root, "gaps", ";-.;;;;;;;;;"); |
---|
424 | |
---|
425 | awar_defaults_created->write_int(1); |
---|
426 | } |
---|
427 | |
---|
428 | inCallback = true; // avoid refresh |
---|
429 | saiChanged_callback(aw_root); |
---|
430 | colorDefTabNameChanged_callback(aw_root); // init awars for selected table |
---|
431 | set_autoselect_cb(aw_root); |
---|
432 | inCallback = false; |
---|
433 | } |
---|
434 | |
---|
435 | static void createCopyClrTransTable(AW_window *aws, AW_CL cl_mode) { |
---|
436 | // mode = ED4_VIS_COPY copies the selected color translation table |
---|
437 | // mode = ED4_VIS_CREATE creates a new (empty) color translation table |
---|
438 | |
---|
439 | int mode = (int)cl_mode; |
---|
440 | AW_root *aw_root = aws->get_root(); |
---|
441 | char *newClrTransTabName = 0; |
---|
442 | char *clrTabSourceName = 0; |
---|
443 | |
---|
444 | switch(mode){ |
---|
445 | case ED4_VIS_CREATE: |
---|
446 | newClrTransTabName = GBS_string_2_key(aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME)->read_string()); |
---|
447 | |
---|
448 | if (strcmp(newClrTransTabName, "__") == 0) { // user entered nothing |
---|
449 | aw_message("Please enter a translation table name"); |
---|
450 | } |
---|
451 | else if (colorTransTable_exists(aw_root, newClrTransTabName)) { |
---|
452 | aw_message(GBS_global_string("Color translation table '%s' already exists.", newClrTransTabName)); |
---|
453 | } |
---|
454 | else { |
---|
455 | addNewTransTable(aw_root, newClrTransTabName, "", true); |
---|
456 | } |
---|
457 | break; |
---|
458 | |
---|
459 | case ED4_VIS_COPY: |
---|
460 | newClrTransTabName = GBS_string_2_key(aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME)->read_string()); |
---|
461 | clrTabSourceName = aw_root->awar(AWAR_SAI_CLR_TRANS_TABLE)->read_string(); |
---|
462 | |
---|
463 | if (!clrTabSourceName[0]) { |
---|
464 | aw_message("Please select a valid Color Translation Table to COPY!"); |
---|
465 | } |
---|
466 | else if (colorTransTable_exists(aw_root, newClrTransTabName)) { |
---|
467 | aw_message(GBS_global_string("Color Translation Table \"%s\" EXISTS! Please enter a different name.", newClrTransTabName)); |
---|
468 | } |
---|
469 | else { |
---|
470 | char *old_def = aw_root->awar(getClrDefAwar(clrTabSourceName))->read_string(); |
---|
471 | addNewTransTable(aw_root, newClrTransTabName, old_def, true); |
---|
472 | free(old_def); |
---|
473 | } |
---|
474 | break; |
---|
475 | |
---|
476 | default: |
---|
477 | break; |
---|
478 | } |
---|
479 | free(clrTabSourceName); |
---|
480 | free(newClrTransTabName); |
---|
481 | } |
---|
482 | |
---|
483 | static void deleteColorTranslationTable(AW_window *aws) { |
---|
484 | bool delete_table = aw_ask_sure("Are you sure you want to delete the selected COLOR TRANSLATION TABLE?"); |
---|
485 | if (delete_table) { |
---|
486 | AW_root *aw_root = aws->get_root(); |
---|
487 | char *clrTabName = aw_root->awar_string(AWAR_SAI_CLR_TRANS_TABLE)->read_string(); |
---|
488 | |
---|
489 | if (clrTabName[0]) { |
---|
490 | AW_awar *awar_tabNames = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES); |
---|
491 | char *clrTransTabNames = awar_tabNames->read_string(); |
---|
492 | GBS_strstruct *newTransTabName = GBS_stropen(strlen(clrTransTabNames)); |
---|
493 | |
---|
494 | for (const char *tok = strtok(clrTransTabNames,"\n"); tok; tok = strtok(0,"\n")) { |
---|
495 | if (strcmp(clrTabName, tok) != 0) { // merge all not to delete |
---|
496 | GBS_strcat(newTransTabName, tok); |
---|
497 | GBS_strcat(newTransTabName, "\n"); |
---|
498 | } |
---|
499 | } |
---|
500 | |
---|
501 | aw_root->awar_string(getClrDefAwar(clrTabName))->write_string(""); |
---|
502 | char *new_name = GBS_strclose(newTransTabName); |
---|
503 | awar_tabNames->write_string(new_name); // updates selection list |
---|
504 | free(new_name); |
---|
505 | |
---|
506 | free(clrTransTabNames); |
---|
507 | } |
---|
508 | else { |
---|
509 | aw_message("Selected Color Translation Table is not VALID and cannot be DELETED!"); |
---|
510 | } |
---|
511 | free(clrTabName); |
---|
512 | } |
---|
513 | } |
---|
514 | |
---|
515 | static AW_selection_list *buildClrTransTabNamesList(AW_window *aws) { |
---|
516 | AW_root *awr = aws->get_root(); |
---|
517 | AW_selection_list *id = aws->create_selection_list(AWAR_SAI_CLR_TRANS_TABLE); |
---|
518 | |
---|
519 | update_ClrTransTabNamesList_cb(awr, (AW_CL)aws, (AW_CL)id); |
---|
520 | |
---|
521 | return id; |
---|
522 | } |
---|
523 | |
---|
524 | const char *ED4_getSaiColorString(AW_root *awr, int start, int end) { |
---|
525 | static int seqBufferSize = 0; |
---|
526 | static char *saiColors = 0; |
---|
527 | static int lastStart = -1; |
---|
528 | static int lastEnd = -1; |
---|
529 | static bool lastVisualize = false; |
---|
530 | |
---|
531 | e4_assert(start<=end); |
---|
532 | |
---|
533 | if(lastStart==start && lastEnd==end && !clrDefinitionsChanged && lastVisualize) { |
---|
534 | return saiColors-start; //if start and end positions are same as the previous positions and no settings |
---|
535 | } //were changed return the last calculated saiColors string |
---|
536 | |
---|
537 | lastStart = start; lastEnd = end; clrDefinitionsChanged = false; // storing start and end positions |
---|
538 | |
---|
539 | int seqSize = end-start+1; |
---|
540 | |
---|
541 | if(seqSize>seqBufferSize){ |
---|
542 | free(saiColors); |
---|
543 | seqBufferSize = seqSize; |
---|
544 | saiColors = (char*)GB_calloc(seqBufferSize, sizeof(char)); |
---|
545 | } |
---|
546 | else memset(saiColors,0,sizeof(char)*seqSize); |
---|
547 | |
---|
548 | char *saiSelected = awr->awar(AWAR_SAI_SELECT)->read_string(); |
---|
549 | |
---|
550 | GB_push_transaction(GLOBAL_gb_main); |
---|
551 | char *alignment_name = GBT_get_default_alignment(GLOBAL_gb_main); |
---|
552 | GBDATA *gb_extended = GBT_find_SAI(GLOBAL_gb_main, saiSelected); |
---|
553 | bool visualize = false; // set to true if all goes fine |
---|
554 | |
---|
555 | if (gb_extended) { |
---|
556 | GBDATA *gb_ali = GB_entry(gb_extended, alignment_name); |
---|
557 | if (gb_ali) { |
---|
558 | const char *saiData = 0; |
---|
559 | bool free_saiData = false; |
---|
560 | |
---|
561 | { |
---|
562 | GBDATA *saiSequence = GB_entry(gb_ali, "data"); // search "data" entry (normal SAI) |
---|
563 | if (saiSequence) { |
---|
564 | saiData = GB_read_char_pntr(saiSequence); // not allocated |
---|
565 | } |
---|
566 | else { |
---|
567 | saiSequence = GB_entry(gb_ali, "bits"); // search "bits" entry (binary SAI) |
---|
568 | if (saiSequence) { |
---|
569 | saiData = GB_read_as_string(saiSequence); // allocated |
---|
570 | free_saiData = true; // free saiData below |
---|
571 | } |
---|
572 | } |
---|
573 | } |
---|
574 | |
---|
575 | if (saiData) { |
---|
576 | char trans_table[256]; |
---|
577 | { |
---|
578 | // build the translation table: |
---|
579 | memset(trans_table, 0, 256); |
---|
580 | for (int i = 0; i<AWAR_SAI_CLR_COUNT; ++i) { |
---|
581 | char *def = awr->awar(getAwarName(i))->read_string(); |
---|
582 | int clrRange = ED4_G_CBACK_0 + i; |
---|
583 | |
---|
584 | for (char *d = def; *d; ++d) { |
---|
585 | trans_table[(unsigned char)*d] = clrRange; |
---|
586 | } |
---|
587 | free(def); |
---|
588 | } |
---|
589 | } |
---|
590 | |
---|
591 | // translate SAI to colors |
---|
592 | for (int i = start; i <= end; ++i) { |
---|
593 | saiColors[i-start] = trans_table[(unsigned char)saiData[i]]; |
---|
594 | } |
---|
595 | |
---|
596 | visualize = true; |
---|
597 | } |
---|
598 | |
---|
599 | if (free_saiData) { |
---|
600 | free(const_cast<char*>(saiData)); // in this case saiData is allocated (see above) |
---|
601 | } |
---|
602 | } |
---|
603 | } |
---|
604 | free(alignment_name); |
---|
605 | free(saiSelected); |
---|
606 | GB_pop_transaction(GLOBAL_gb_main); |
---|
607 | |
---|
608 | lastVisualize = visualize; |
---|
609 | if (visualize) { |
---|
610 | e4_assert(saiColors); |
---|
611 | return saiColors-start; |
---|
612 | } |
---|
613 | |
---|
614 | return 0; // don't visualize (sth went wrong) |
---|
615 | } |
---|
616 | |
---|
617 | |
---|
618 | /* -------------------- Creating Windows and Display dialogs -------------------- */ |
---|
619 | |
---|
620 | static AW_window *create_copyColorTranslationTable_window(AW_root *aw_root){ // creates copy color tranlation table window |
---|
621 | AW_window_simple *aws = new AW_window_simple; |
---|
622 | aws->init( aw_root, "COPY_CLR_TR_TABLE", "Copy Color Translation Table"); |
---|
623 | aws->load_xfig("ad_al_si.fig"); |
---|
624 | |
---|
625 | aws->at("close"); |
---|
626 | aws->callback( (AW_CB0)AW_POPDOWN); |
---|
627 | aws->create_button("CLOSE","CLOSE","C"); |
---|
628 | |
---|
629 | aws->at("label"); |
---|
630 | aws->create_autosize_button(0,"Please enter the new name\nfor the Color Translation Table"); |
---|
631 | |
---|
632 | aws->at("input"); |
---|
633 | aws->create_input_field(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME,15); |
---|
634 | |
---|
635 | aws->at("ok"); |
---|
636 | aws->callback(createCopyClrTransTable, (AW_CL)ED4_VIS_COPY); |
---|
637 | aws->create_button("GO","GO","G"); |
---|
638 | |
---|
639 | return (AW_window *)aws; |
---|
640 | } |
---|
641 | |
---|
642 | static AW_window *create_createColorTranslationTable_window(AW_root *aw_root){ // creates create color tranlation table window |
---|
643 | AW_window_simple *aws = new AW_window_simple; |
---|
644 | aws->init( aw_root, "CREATE_CLR_TR_TABLE", "Create Color Translation Table"); |
---|
645 | aws->load_xfig("ad_al_si.fig"); |
---|
646 | |
---|
647 | aws->at("close"); |
---|
648 | aws->callback( (AW_CB0)AW_POPDOWN); |
---|
649 | aws->create_button("CLOSE","CLOSE","C"); |
---|
650 | |
---|
651 | aws->at("label"); |
---|
652 | aws->create_autosize_button(0,"Please enter the name\nfor the Color Translation Table"); |
---|
653 | |
---|
654 | aws->at("input"); |
---|
655 | aws->create_input_field(AWAR_SAI_CLR_TRANS_TAB_NEW_NAME,15); |
---|
656 | |
---|
657 | aws->at("ok"); |
---|
658 | aws->callback(createCopyClrTransTable, (AW_CL)ED4_VIS_CREATE); |
---|
659 | aws->create_button("GO","GO","G"); |
---|
660 | |
---|
661 | return (AW_window *)aws; |
---|
662 | } |
---|
663 | |
---|
664 | static void reverseColorTranslationTable(AW_window *aww) { |
---|
665 | AW_root *aw_root = aww->get_root(); |
---|
666 | |
---|
667 | int j = AWAR_SAI_CLR_COUNT-1; |
---|
668 | for (int i = 0; i<AWAR_SAI_CLR_COUNT/2+1; ++i, --j) { |
---|
669 | if (i<j) { |
---|
670 | AW_awar *aw_i = aw_root->awar(getAwarName(i)); |
---|
671 | AW_awar *aw_j = aw_root->awar(getAwarName(j)); |
---|
672 | |
---|
673 | char *ci = aw_i->read_string(); |
---|
674 | char *cj = aw_j->read_string(); |
---|
675 | |
---|
676 | aw_i->write_string(cj); |
---|
677 | aw_j->write_string(ci); |
---|
678 | |
---|
679 | free(ci); |
---|
680 | free(cj); |
---|
681 | } |
---|
682 | } |
---|
683 | } |
---|
684 | |
---|
685 | static AW_window *create_editColorTranslationTable_window(AW_root *aw_root){ // creates edit color tranlation table window |
---|
686 | static AW_window_simple *aws = 0; |
---|
687 | if(aws) return (AW_window *)aws; |
---|
688 | |
---|
689 | aws = new AW_window_simple; |
---|
690 | aws->init( aw_root, "EDIT_CTT", "Color Translation Table"); |
---|
691 | aws->load_xfig("saiColorRange.fig"); |
---|
692 | |
---|
693 | char at_name[] = "rangex"; |
---|
694 | char *dig = strchr(at_name, 0)-1; |
---|
695 | |
---|
696 | for (int i = 0; i<AWAR_SAI_CLR_COUNT; ++i) { |
---|
697 | dig[0] = '0'+i; |
---|
698 | aws->at(at_name); |
---|
699 | aws->create_input_field(getAwarName(i), 20); |
---|
700 | } |
---|
701 | |
---|
702 | aws->at("close"); |
---|
703 | aws->callback(AW_POPDOWN); |
---|
704 | aws->create_button("CLOSE","CLOSE","C"); |
---|
705 | |
---|
706 | aws->at("reverse"); |
---|
707 | aws->callback(reverseColorTranslationTable); |
---|
708 | aws->create_button("REVERSE", "Reverse", "R"); |
---|
709 | |
---|
710 | aws->at("colors"); |
---|
711 | aws->callback(AW_POPUP,(AW_CL)AW_create_gc_window, (AW_CL)ED4_ROOT->aw_gc_manager); |
---|
712 | aws->button_length(0); |
---|
713 | aws->create_button("COLORS","#colors.xpm"); |
---|
714 | |
---|
715 | return (AW_window *)aws; |
---|
716 | } |
---|
717 | |
---|
718 | static AW_window *openSelectSAI_window(AW_root *aw_root, AW_CL cl_awar_name){ |
---|
719 | const char *awar_name = reinterpret_cast<const char *>(cl_awar_name); |
---|
720 | |
---|
721 | static GB_HASH *SAI_window_hash = 0; |
---|
722 | if (!SAI_window_hash) SAI_window_hash = GBS_create_hash(10, GB_MIND_CASE); |
---|
723 | |
---|
724 | AW_window_simple *aws = reinterpret_cast<AW_window_simple *>(GBS_read_hash(SAI_window_hash, awar_name)); |
---|
725 | |
---|
726 | if (!aws) { |
---|
727 | aws = new AW_window_simple; |
---|
728 | aws->init( aw_root, "SELECT_SAI", "SELECT SAI"); |
---|
729 | aws->load_xfig("selectSAI.fig"); |
---|
730 | |
---|
731 | aws->at("selection"); |
---|
732 | aws->callback((AW_CB0)AW_POPDOWN); |
---|
733 | awt_create_selection_list_on_extendeds(GLOBAL_gb_main, (AW_window *)aws, awar_name); |
---|
734 | |
---|
735 | aws->at("close"); |
---|
736 | aws->callback(AW_POPDOWN); |
---|
737 | aws->create_button("CLOSE","CLOSE","C"); |
---|
738 | |
---|
739 | aws->window_fit(); |
---|
740 | |
---|
741 | GBS_write_hash(SAI_window_hash, awar_name, reinterpret_cast<long>(aws)); |
---|
742 | } |
---|
743 | |
---|
744 | return aws; |
---|
745 | } |
---|
746 | |
---|
747 | void ED4_create_SAI_selection_button(AW_window *aws, const char *cawar_name) { |
---|
748 | char *awar_name = strdup(cawar_name); |
---|
749 | int old_button_length = aws->get_button_length(); |
---|
750 | |
---|
751 | aws->button_length(30); |
---|
752 | |
---|
753 | aws->callback(AW_POPUP, (AW_CL)openSelectSAI_window, (AW_CL)awar_name); |
---|
754 | aws->create_button("SELECT_SAI", awar_name); |
---|
755 | |
---|
756 | aws->button_length(old_button_length); |
---|
757 | } |
---|
758 | |
---|
759 | AW_window *ED4_createVisualizeSAI_window(AW_root *aw_root) { |
---|
760 | static AW_window_simple *aws = 0; |
---|
761 | if (!aws) { |
---|
762 | |
---|
763 | aws = new AW_window_simple; |
---|
764 | |
---|
765 | aws->init( aw_root, "VISUALIZE_SAI", "Visualize SAIs"); |
---|
766 | aws->load_xfig("visualizeSAI.fig"); |
---|
767 | |
---|
768 | aws->callback( AW_POPUP_HELP,(AW_CL)"visualizeSAI.hlp"); |
---|
769 | aws->at("help"); |
---|
770 | aws->create_button("HELP","HELP","H"); |
---|
771 | |
---|
772 | aws->at("close"); |
---|
773 | aws->callback((AW_CB0)AW_POPDOWN); |
---|
774 | aws->create_button("CLOSE","CLOSE","C"); |
---|
775 | |
---|
776 | aws->at("enable"); |
---|
777 | aws->create_toggle(AWAR_SAI_ENABLE); |
---|
778 | |
---|
779 | aws->at("sai"); |
---|
780 | ED4_create_SAI_selection_button(aws, AWAR_SAI_SELECT); |
---|
781 | |
---|
782 | aws->at("auto_select"); |
---|
783 | aws->create_toggle(AWAR_SAI_AUTO_SELECT); |
---|
784 | |
---|
785 | aws->at("clrTrList"); |
---|
786 | AW_selection_list *clrTransTableLst = buildClrTransTabNamesList(aws); |
---|
787 | |
---|
788 | aws->at("edit"); |
---|
789 | aws->button_length(10); |
---|
790 | aws->callback(AW_POPUP,(AW_CL)create_editColorTranslationTable_window,0); |
---|
791 | aws->create_button("EDIT","EDIT"); |
---|
792 | |
---|
793 | aws->at("create"); |
---|
794 | aws->callback(AW_POPUP,(AW_CL)create_createColorTranslationTable_window,0); |
---|
795 | aws->create_button("CREATE","CREATE"); |
---|
796 | |
---|
797 | aws->at("copy"); |
---|
798 | aws->callback(AW_POPUP,(AW_CL)create_copyColorTranslationTable_window,0); |
---|
799 | aws->create_button("COPY","COPY"); |
---|
800 | |
---|
801 | aws->at("delete"); |
---|
802 | aws->callback((AW_CB1)deleteColorTranslationTable,0); |
---|
803 | aws->create_button("DELETE","DELETE"); |
---|
804 | |
---|
805 | aws->at("marked"); |
---|
806 | aws->create_toggle_field(AWAR_SAI_ALL_SPECIES,1); |
---|
807 | aws->insert_toggle("MARKED SPECIES", "M", 0); |
---|
808 | aws->insert_toggle("ALL SPECIES", "A", 1); |
---|
809 | aws->update_toggle_field(); |
---|
810 | |
---|
811 | AW_awar *trans_tabs = aw_root->awar(AWAR_SAI_CLR_TRANS_TAB_NAMES); |
---|
812 | trans_tabs->add_callback(update_ClrTransTabNamesList_cb, (AW_CL)aws, (AW_CL)clrTransTableLst); |
---|
813 | trans_tabs->touch(); // force update |
---|
814 | } |
---|
815 | aws->show(); |
---|
816 | |
---|
817 | return aws; |
---|
818 | } |
---|
819 | |
---|
820 | bool ED4_SAIs_visualized() { |
---|
821 | return ED4_ROOT->visualizeSAI; |
---|
822 | } |
---|