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source: branches/tree/EDIT4/ED4_ProteinViewer.cxx

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Last change on this file was 18352, checked in by westram, 5 years ago
full update from child 'fix' into 'trunk' adds: log:branches/fix@18339:18351
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1	// =======================================================================================
2	//
3	// File : ED4_ProteinViewer.cxx
4	// Purpose : Protein Viewer: Dynamical translation and display of
5	// aminoacid sequences in the dna alignment.
6	// Author : Yadhu Kumar (yadhu@arb-home.de)
7	// web site : http://www.arb-home.de/
8	//
9	// Copyright Department of Microbiology (Technical University Munich)
10	//
11	// =======================================================================================
12
13	#include "ed4_ProteinViewer.hxx"
14	#include "ed4_edit_string.hxx"
15	#include "ed4_seq_colors.hxx"
16	#include "ed4_class.hxx"
17
18	#include <AP_pro_a_nucs.hxx>
19	#include <AP_codon_table.hxx>
20	#include <Translate.hxx>
21	#include <aw_question.hxx>
22	#include <aw_preset.hxx>
23	#include <aw_awars.hxx>
24	#include <aw_msg.hxx>
25	#include <aw_root.hxx>
26	#include <arbdbt.h>
27
28	#include <iostream>
29
30	using namespace std;
31
32	// Definitions used
33	#define FORWARD_STRAND 1
34	#define COMPLEMENTARY_STRAND 2
35	#define DB_FIELD_STRAND 3
36
37	#define FORWARD_STRANDS 3
38	#define COMPLEMENTARY_STRANDS 3
39	#define DB_FIELD_STRANDS 1
40
41	enum {
42	PV_MARKED = 0,
43	PV_SELECTED,
44	PV_CURSOR,
45	PV_ALL
46	};
47
48	// Global Variables
49	static bool gTerminalsCreated = false;
50	static int PV_AA_Terminals4Species = 0;
51	static int gMissingTransTable = 0;
52	static int gMissingCodonStart = 0;
53	static bool gbWritingData = false;
54	static int giNewAlignments = 0;
55
56	static AW_repeated_question *ASKtoOverWriteData = NULp;
57
58	static bool PV_LookForNewTerminals(AW_root *root) {
59	bool bTerminalsFound = true;
60
61	int all = root->awar(AWAR_PV_DISPLAY_ALL)->read_int();
62	int all_f1 = root->awar(AWAR_PROTVIEW_FORWARD_STRAND_1)->read_int();
63	int all_f2 = root->awar(AWAR_PROTVIEW_FORWARD_STRAND_2)->read_int();
64	int all_f3 = root->awar(AWAR_PROTVIEW_FORWARD_STRAND_3)->read_int();
65	int all_c1 = root->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1)->read_int();
66	int all_c2 = root->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2)->read_int();
67	int all_c3 = root->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3)->read_int();
68	int all_db = root->awar(AWAR_PROTVIEW_DEFINED_FIELDS)->read_int();
69
70	int sel = root->awar(AWAR_PV_SELECTED)->read_int();
71	int sel_db = root->awar(AWAR_PV_SELECTED_DB)->read_int();
72	int sel_f1 = root->awar(AWAR_PV_SELECTED_FS_1)->read_int();
73	int sel_f2 = root->awar(AWAR_PV_SELECTED_FS_2)->read_int();
74	int sel_f3 = root->awar(AWAR_PV_SELECTED_FS_3)->read_int();
75	int sel_c1 = root->awar(AWAR_PV_SELECTED_CS_1)->read_int();
76	int sel_c2 = root->awar(AWAR_PV_SELECTED_CS_2)->read_int();
77	int sel_c3 = root->awar(AWAR_PV_SELECTED_CS_3)->read_int();
78
79	int mrk = root->awar(AWAR_PV_MARKED)->read_int();
80	int mrk_db = root->awar(AWAR_PV_MARKED_DB)->read_int();
81	int mrk_f1 = root->awar(AWAR_PV_MARKED_FS_1)->read_int();
82	int mrk_f2 = root->awar(AWAR_PV_MARKED_FS_2)->read_int();
83	int mrk_f3 = root->awar(AWAR_PV_MARKED_FS_3)->read_int();
84	int mrk_c1 = root->awar(AWAR_PV_MARKED_CS_1)->read_int();
85	int mrk_c2 = root->awar(AWAR_PV_MARKED_CS_2)->read_int();
86	int mrk_c3 = root->awar(AWAR_PV_MARKED_CS_3)->read_int();
87
88	int cur = root->awar(AWAR_PV_CURSOR)->read_int();
89	int cur_db = root->awar(AWAR_PV_CURSOR_DB)->read_int();
90	int cur_f1 = root->awar(AWAR_PV_CURSOR_FS_1)->read_int();
91	int cur_f2 = root->awar(AWAR_PV_CURSOR_FS_2)->read_int();
92	int cur_f3 = root->awar(AWAR_PV_CURSOR_FS_3)->read_int();
93	int cur_c1 = root->awar(AWAR_PV_CURSOR_CS_1)->read_int();
94	int cur_c2 = root->awar(AWAR_PV_CURSOR_CS_2)->read_int();
95	int cur_c3 = root->awar(AWAR_PV_CURSOR_CS_3)->read_int();
96
97	// Test whether any of the options are selected or not?
98	if ((all && (all_f1 \|\| all_f2 \|\| all_f3 \|\| all_c1 \|\| all_c2 \|\| all_c3 \|\| all_db)) \|\|
99	(sel && (sel_db \|\| sel_f1 \|\| sel_f2 \|\| sel_f3 \|\| sel_c1 \|\| sel_c2 \|\| sel_c3)) \|\|
100	(mrk && (mrk_db \|\| mrk_f1 \|\| mrk_f2 \|\| mrk_f3 \|\| mrk_c1 \|\| mrk_c2 \|\| mrk_c3)) \|\|
101	(cur && (cur_db \|\| cur_f1 \|\| cur_f2 \|\| cur_f3 \|\| cur_c1 \|\| cur_c2 \|\| cur_c3)))
102	{
103	// if so, then test whether the terminals are created already or not?
104	if (gTerminalsCreated) {
105	// if yes, then set the flag to true
106	bTerminalsFound = true;
107	}
108	else {
109	// if not, then new terminals has to be created
110	bTerminalsFound = false;
111	}
112	}
113	return bTerminalsFound;
114	}
115
116	static void PV_HideTerminal(ED4_orf_terminal *orfTerm) {
117	ED4_sequence_manager *seqManager = orfTerm->get_parent(LEV_SEQUENCE)->to_sequence_manager();
118	seqManager->hide_children();
119	}
120
121	static void PV_UnHideTerminal(ED4_orf_terminal *orfTerm) {
122	ED4_sequence_manager *seqManager = orfTerm->get_parent(LEV_SEQUENCE)->to_sequence_manager();
123	seqManager->unhide_children();
124	}
125
126	static void PV_HideAllTerminals() {
127	ED4_terminal *terminal = NULp;
128	for (terminal = ED4_ROOT->root_group_man->get_first_terminal();
129	terminal;
130	terminal = terminal->get_next_terminal())
131	{
132	if (terminal->is_orf_terminal()) {
133	ED4_orf_terminal *orfTerm = terminal->to_orf_terminal();
134	PV_HideTerminal(orfTerm);
135	}
136	}
137	}
138
139
140	static void PV_ManageTerminalDisplay(AW_root root, ED4_orf_terminal orfTerm, long int DispMode) {
141	int all, af_1, af_2, af_3, ac_1, ac_2, ac_3, adb;
142	all = root->awar(AWAR_PV_DISPLAY_ALL)->read_int();
143	adb = root->awar(AWAR_PROTVIEW_DEFINED_FIELDS)->read_int();
144	af_1 = root->awar(AWAR_PROTVIEW_FORWARD_STRAND_1)->read_int();
145	af_2 = root->awar(AWAR_PROTVIEW_FORWARD_STRAND_2)->read_int();
146	af_3 = root->awar(AWAR_PROTVIEW_FORWARD_STRAND_3)->read_int();
147	ac_1 = root->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1)->read_int();
148	ac_2 = root->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2)->read_int();
149	ac_3 = root->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3)->read_int();
150
151	int mrk, mf_1, mf_2, mf_3, mc_1, mc_2, mc_3, mdb;
152	mrk = root->awar(AWAR_PV_MARKED)->read_int();
153	mdb = root->awar(AWAR_PV_MARKED_DB)->read_int();
154	mf_1 = root->awar(AWAR_PV_MARKED_FS_1)->read_int();
155	mf_2 = root->awar(AWAR_PV_MARKED_FS_2)->read_int();
156	mf_3 = root->awar(AWAR_PV_MARKED_FS_3)->read_int();
157	mc_1 = root->awar(AWAR_PV_MARKED_CS_1)->read_int();
158	mc_2 = root->awar(AWAR_PV_MARKED_CS_2)->read_int();
159	mc_3 = root->awar(AWAR_PV_MARKED_CS_3)->read_int();
160
161	int sel, sf_1, sf_2, sf_3, sc_1, sc_2, sc_3, sdb;
162	sel = root->awar(AWAR_PV_SELECTED)->read_int();
163	sdb = root->awar(AWAR_PV_SELECTED_DB)->read_int();
164	sf_1 = root->awar(AWAR_PV_SELECTED_FS_1)->read_int();
165	sf_2 = root->awar(AWAR_PV_SELECTED_FS_2)->read_int();
166	sf_3 = root->awar(AWAR_PV_SELECTED_FS_3)->read_int();
167	sc_1 = root->awar(AWAR_PV_SELECTED_CS_1)->read_int();
168	sc_2 = root->awar(AWAR_PV_SELECTED_CS_2)->read_int();
169	sc_3 = root->awar(AWAR_PV_SELECTED_CS_3)->read_int();
170
171	int cur, cf_1, cf_2, cf_3, cc_1, cc_2, cc_3, cdb;
172	cur = root->awar(AWAR_PV_CURSOR)->read_int();
173	cdb = root->awar(AWAR_PV_CURSOR_DB)->read_int();
174	cf_1 = root->awar(AWAR_PV_CURSOR_FS_1)->read_int();
175	cf_2 = root->awar(AWAR_PV_CURSOR_FS_2)->read_int();
176	cf_3 = root->awar(AWAR_PV_CURSOR_FS_3)->read_int();
177	cc_1 = root->awar(AWAR_PV_CURSOR_CS_1)->read_int();
178	cc_2 = root->awar(AWAR_PV_CURSOR_CS_2)->read_int();
179	cc_3 = root->awar(AWAR_PV_CURSOR_CS_3)->read_int();
180
181	// Get the AA sequence flag - says which strand we are in
182	int aaStrandType = int(orfTerm->GET_aaStrandType());
183	// Check the display options and make visible or hide the AA seq terminal
184	switch (aaStrandType) {
185	case FORWARD_STRAND: {
186	int aaStartPos = int(orfTerm->GET_aaStartPos());
187	switch (aaStartPos) {
188	case 1:
189	switch (DispMode) {
190	case PV_ALL: (all && af_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
191	case PV_MARKED: (mrk && mf_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
192	case PV_SELECTED: (sel && sf_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
193	case PV_CURSOR: (cur && cf_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
194	}
195	break;
196	case 2:
197	switch (DispMode) {
198	case PV_ALL: (all && af_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
199	case PV_MARKED: (mrk && mf_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
200	case PV_SELECTED: (sel && sf_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
201	case PV_CURSOR: (cur && cf_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
202	}
203	break;
204	case 3:
205	switch (DispMode) {
206	case PV_ALL: (all && af_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
207	case PV_MARKED: (mrk && mf_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
208	case PV_SELECTED: (sel && sf_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
209	case PV_CURSOR: (cur && cf_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
210	}
211	break;
212	}
213	break;
214	}
215	case COMPLEMENTARY_STRAND: {
216	int aaStartPos = int(orfTerm->GET_aaStartPos());
217	switch (aaStartPos) {
218	case 1:
219	switch (DispMode) {
220	case PV_ALL: (all && ac_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
221	case PV_MARKED: (mrk && mc_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
222	case PV_SELECTED: (sel && sc_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
223	case PV_CURSOR: (cur && cc_1) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
224	}
225	break;
226	case 2:
227	switch (DispMode) {
228	case PV_ALL: (all && ac_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
229	case PV_MARKED: (mrk && mc_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
230	case PV_SELECTED: (sel && sc_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
231	case PV_CURSOR: (cur && cc_2) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
232	}
233	break;
234	case 3:
235	switch (DispMode) {
236	case PV_ALL: (all && ac_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
237	case PV_MARKED: (mrk && mc_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
238	case PV_SELECTED: (sel && sc_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
239	case PV_CURSOR: (cur && cc_3) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
240	}
241	break;
242	}
243	break;
244	}
245	case DB_FIELD_STRAND:
246	switch (DispMode) {
247	case PV_ALL: (all && adb) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
248	case PV_MARKED: (mrk && mdb) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
249	case PV_SELECTED: (sel && sdb) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
250	case PV_CURSOR: (cur && cdb) ? PV_UnHideTerminal(orfTerm) : PV_HideTerminal(orfTerm); break;
251	}
252	break;
253	}
254	}
255
256	static void PV_ManageTerminals(AW_root *root) {
257
258	// First Hide all orf Terminals
259	PV_HideAllTerminals();
260
261	int dispAll = root->awar(AWAR_PV_DISPLAY_ALL)->read_int();
262	if (dispAll) {
263	for (ED4_terminal *terminal = ED4_ROOT->root_group_man->get_first_terminal();
264	terminal;
265	terminal = terminal->get_next_terminal())
266	{
267	if (terminal->is_orf_terminal()) {
268	ED4_orf_terminal *orfTerm = terminal->to_orf_terminal();
269	PV_ManageTerminalDisplay(root, orfTerm, PV_ALL);
270	}
271	}
272	}
273
274	int dispMarked = root->awar(AWAR_PV_MARKED)->read_int();
275	if (dispMarked) {
276	GBDATA *gb_main = ED4_ROOT->get_gb_main();
277	GB_transaction ta(gb_main);
278	int marked = GBT_count_marked_species(gb_main);
279	if (marked) {
280	for (GBDATA *gbSpecies = GBT_first_marked_species(gb_main);
281	gbSpecies;
282	gbSpecies = GBT_next_marked_species(gbSpecies))
283	{
284	ED4_species_name_terminal *spNameTerm = ED4_find_species_name_terminal(GBT_get_name_or_description(gbSpecies));
285	if (spNameTerm) {
286	ED4_terminal *terminal = spNameTerm->corresponding_sequence_terminal();
287	for (int i=0; i<PV_AA_Terminals4Species; i++) {
288	// get the corresponding orf_terminal skipping sequence_info terminal
289	// $$$$$ sequence_terminal->sequence_info_terminal->aa_sequence_terminal $$$$$$
290	terminal = terminal->get_next_terminal()->get_next_terminal();
291	// Make sure it is ORF terminal
292	if (terminal->is_orf_terminal()) {
293	ED4_orf_terminal *orfTerm = terminal->to_orf_terminal();
294	PV_ManageTerminalDisplay(root, orfTerm, PV_MARKED);
295	}
296	}
297	}
298	}
299	}
300	}
301
302	int dispSelected = root->awar(AWAR_PV_SELECTED)->read_int();
303	if (dispSelected) {
304	for (ED4_terminal *terminal = ED4_ROOT->root_group_man->get_first_terminal();
305	terminal;
306	terminal = terminal->get_next_terminal())
307	{
308	if (terminal->is_sequence_terminal()) {
309	ED4_species_manager *speciesManager = terminal->get_parent(LEV_SPECIES)->to_species_manager();
310	if (speciesManager->is_species_seq_terminal()) {
311	// we are in the sequence terminal section of a species
312	// walk through all the corresponding ORF terminals for the species and
313	// hide or unhide the terminals based on the display options set by the user
314	if (speciesManager->is_selected()) {
315	for (int i=0; i<PV_AA_Terminals4Species; i++) {
316	// get the corresponding orf_terminal skipping sequence_info terminal
317	// $$$$$ sequence_terminal->sequence_info_terminal->aa_sequence_terminal $$$$$$
318	terminal = terminal->get_next_terminal()->get_next_terminal();
319	// Make sure it is ORF terminal
320	if (terminal->is_orf_terminal()) {
321	ED4_orf_terminal *orfTerm = terminal->to_orf_terminal();
322	PV_ManageTerminalDisplay(root, orfTerm, PV_SELECTED);
323	}
324	}
325	}
326	}
327	}
328	}
329	}
330
331	int dispAtCursor = root->awar(AWAR_PV_CURSOR)->read_int();
332	if (dispAtCursor) {
333	// only display terminals for species at cursor
334	if (ED4_ROOT->get_most_recently_used_window()) {
335	ED4_MostRecentWinContext context;
336	ED4_cursor& cursor = current_cursor();
337
338	if (cursor.owner_of_cursor) {
339	// Get The Cursor Terminal And The Corresponding Aa_Sequence Terminals And Set The Display Options
340	ED4_terminal *cursorTerminal = cursor.owner_of_cursor;
341	if (cursorTerminal->is_species_seq_terminal()) {
342	for (int i=0; i<PV_AA_Terminals4Species; i++) {
343	// get the corresponding orf_terminal skipping sequence_info terminal
344	// $$$$$ sequence_terminal->sequence_info_terminal->aa_sequence_terminal $$$$$$
345	cursorTerminal = cursorTerminal->get_next_terminal()->get_next_terminal();
346	// Make sure it is ORF terminal
347	if (cursorTerminal->is_orf_terminal()) {
348	ED4_orf_terminal *orfTerm = cursorTerminal->to_orf_terminal();
349	PV_ManageTerminalDisplay(root, orfTerm, PV_CURSOR);
350	}
351	}
352	}
353	}
354	}
355	}
356	}
357
358	void PV_RefreshWindow(AW_root *root) {
359	// Manage the terminals showing only those selected by the user
360	if (gTerminalsCreated) {
361	PV_ManageTerminals(root);
362	}
363	// Refresh all windows
364	// ED4_ROOT->refresh_all_windows(0);
365	}
366
367	static GB_ERROR PV_ComplementarySequence(char *sequence) {
368	char T_or_U;
369	GB_ERROR error = GBT_determine_T_or_U(ED4_ROOT->alignment_type, &T_or_U, "complement");
370	if (!error) {
371	int seqLen = strlen(sequence);
372	char complementarySeq = GBT_complementNucSequence((const char) sequence, seqLen, T_or_U);
373
374	strcpy(sequence, complementarySeq);
375	free(complementarySeq);
376	}
377	return error;
378	}
379
380	static void PV_WriteTranslatedSequenceToDB(ED4_orf_terminal aaSeqTerm, const char spName) {
381	GBDATA *gb_main = ED4_ROOT->get_gb_main();
382	GB_ERROR error = GB_begin_transaction(gb_main);
383	GBDATA *gb_species = GBT_find_species(gb_main, spName);
384	if (!gb_species) error = GBS_global_string("Species '%s' does not exist", spName);
385	else {
386	char *defaultAlignment = GBT_get_default_alignment(gb_main);
387	if (!defaultAlignment) error = GB_await_error();
388	else {
389	GBDATA *gb_SeqData = GBT_find_sequence(gb_species, defaultAlignment);
390	if (!gb_SeqData) {
391	error = GB_have_error()
392	? GB_await_error()
393	: GBS_global_string("Species '%s' has no data in alignment '%s'", spName, defaultAlignment);
394	}
395	else {
396	char *str_SeqData = GB_read_string(gb_SeqData);
397	if (!str_SeqData) error = GB_await_error();
398	else {
399	int aaStrandType = int(aaSeqTerm->GET_aaStrandType());
400	if (aaStrandType == COMPLEMENTARY_STRAND) {
401	GB_ERROR compl_err = PV_ComplementarySequence(str_SeqData);
402	if (compl_err) error = GBS_global_string("Failed to calc complementary strand (Reason: %s)", compl_err);
403	}
404
405	if (!error) {
406	char newAlignmentName[100];
407	int aaStartPos = int(aaSeqTerm->GET_aaStartPos());
408
409	switch (aaStrandType) {
410	case FORWARD_STRAND: sprintf(newAlignmentName, "ali_pro_ProtView_forward_start_pos_%ld", (long)aaStartPos); break;
411	case COMPLEMENTARY_STRAND: sprintf(newAlignmentName, "ali_pro_ProtView_complementary_start_pos_%ld", (long)aaStartPos); break;
412	case DB_FIELD_STRAND: sprintf(newAlignmentName, "ali_pro_ProtView_database_field_start_pos_%ld", (long)aaStartPos); break;
413	}
414
415	int len = GB_read_string_count(gb_SeqData);
416	translate_nuc2aa(AWT_default_protein_type(), str_SeqData, len, aaStartPos-1, false, true, false, NULp);
417
418	// Create alignment data to store the translated sequence
419	GBDATA *gb_presets = GBT_get_presets(gb_main);
420	GBDATA *gb_alignment_exists = GB_find_string(gb_presets, "alignment_name", newAlignmentName, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
421	GBDATA *gb_new_alignment = NULp;
422
423	if (gb_alignment_exists) {
424	int skip_sp = 0;
425	char *question = NULp;
426	GBDATA *gb_seq_data = GBT_find_sequence(gb_species, newAlignmentName);
427	if (gb_seq_data) {
428	e4_assert(ASKtoOverWriteData);
429	question = GBS_global_string_copy("\"%s\" contain data in the alignment \"%s\"!", spName, newAlignmentName);
430	skip_sp = ASKtoOverWriteData->get_answer("overwrite_translated", question, "Overwrite, Skip Species", "all", false);
431	}
432	if (skip_sp) {
433	error = GBS_global_string_copy("%s You chose to skip this Species!", question);
434	}
435	else {
436	gb_new_alignment = GBT_get_alignment(gb_main, newAlignmentName);
437	if (!gb_new_alignment) error = GB_await_error();
438	}
439	free(question);
440	}
441	else {
442	long aliLen = GBT_get_alignment_len(gb_main, defaultAlignment);
443	gb_new_alignment = GBT_create_alignment(gb_main, newAlignmentName, aliLen/3+1, 0, 1, "ami");
444
445	if (!gb_new_alignment) error = GB_await_error();
446	else giNewAlignments++;
447	}
448
449	if (!error) {
450	GBDATA *gb_ProSeqData = GBT_add_data(gb_species, newAlignmentName, "data", GB_STRING);
451	if (!gb_ProSeqData) error = GB_await_error();
452	else error = GB_write_string(gb_ProSeqData, str_SeqData);
453	}
454
455	if (!error) error = GBT_check_data(gb_main, NULp);
456	}
457
458	free(str_SeqData);
459	}
460	}
461	free(defaultAlignment);
462	}
463	}
464	GB_end_transaction_show_error(gb_main, error, aw_message);
465	}
466
467	static void PV_SaveData(AW_window /aww*/) {
468	// IDEA:
469	// 1. walk thru the orf terminals
470	// 2. check the visibility status
471	// 3. select only the visible terminals
472	// 4. get the corresponding species name
473	// 5. translate the sequence
474	// 6. write to the database
475	gbWritingData = true;
476	if (gTerminalsCreated) {
477	ASKtoOverWriteData = new AW_repeated_question;
478
479	for (ED4_terminal *terminal = ED4_ROOT->root_group_man->get_first_terminal();
480	terminal;
481	terminal = terminal->get_next_terminal())
482	{
483	if (terminal->is_species_seq_terminal()) {
484	const char *speciesName = terminal->to_sequence_terminal()->species_name;
485
486	for (int i=0; i<PV_AA_Terminals4Species; i++) {
487	// get the corresponding orf_terminal skipping sequence_info terminal
488	terminal = terminal->get_next_terminal()->get_next_terminal();
489	// Make sure it is ORF terminal
490	if (terminal->is_orf_terminal()) {
491	ED4_orf_terminal *orfTerm = terminal->to_orf_terminal();
492	ED4_base base = (ED4_base)orfTerm;
493	if (!base->flag.hidden) {
494	PV_WriteTranslatedSequenceToDB(orfTerm, speciesName);
495	}
496	}
497	}
498	}
499	}
500	if (giNewAlignments>0) {
501	char *msg = GBS_global_string_copy("Protein data saved to NEW alignments.\n%d new alignments were created and named ali_prot_ProtView_XXXX", giNewAlignments);
502	aw_message(msg);
503	free(msg);
504
505	giNewAlignments = 0;
506	}
507	}
508	gbWritingData = false;
509	}
510
511	static void TranslateGeneToAminoAcidSequence(AW_root * /* root /, ED4_orf_terminal seqTerm, const char *speciesName, int startPos4Translation, int translationMode) {
512	// This function translates gene sequence to aminoacid sequence and stores translation into the respective AA_Sequence_terminal
513	GB_ERROR error = NULp;
514	GBDATA *gb_main = ED4_ROOT->get_gb_main();
515	GBDATA *gb_species = GBT_find_species(gb_main, speciesName);
516	if (!gb_species) error = GBS_global_string("Species '%s' does not exist", speciesName);
517	else {
518	char *defaultAlignment = GBT_get_default_alignment(gb_main);
519	if (!defaultAlignment) error = GB_await_error();
520	else {
521	GBDATA *gb_SeqData = GBT_find_sequence(gb_species, defaultAlignment);
522	if (!gb_SeqData) {
523	error = GB_have_error()
524	? GB_await_error()
525	: GBS_global_string("Species '%s' has no data in alignment '%s'", speciesName, defaultAlignment);
526	}
527	else {
528	e4_assert(startPos4Translation>=0 && startPos4Translation<=2);
529
530	char *str_SeqData = GB_read_string(gb_SeqData);
531	if (!str_SeqData) error = GB_await_error();
532	else {
533	int len = GB_read_string_count(gb_SeqData);
534	int translationTable = AWT_default_protein_type(gb_main);
535
536	switch (translationMode) {
537	case FORWARD_STRAND:
538	break;
539
540	case COMPLEMENTARY_STRAND: {
541	// convert sequence to the complementary sequence
542	GB_ERROR compl_err = PV_ComplementarySequence(str_SeqData);
543	if (compl_err) error = GBS_global_string("Failed to calc complementary strand for '%s' (Reason: %s)", speciesName, compl_err);
544	break;
545	}
546	case DB_FIELD_STRAND: {
547	// for use database field options - fetch codon start and translation table from the respective species data
548	GBDATA *gb_translTable = GB_entry(gb_species, "transl_table");
549	if (gb_translTable) {
550	int sp_embl_table = atoi(GB_read_char_pntr(gb_translTable));
551	translationTable = TTIT_embl2arb(sp_embl_table);
552	}
553	else { // use selected translation table as default (if 'transl_table' field is missing)
554	gMissingTransTable++;
555	}
556	GBDATA *gb_codonStart = GB_entry(gb_species, "codon_start");
557	if (gb_codonStart) {
558	startPos4Translation = atoi(GB_read_char_pntr(gb_codonStart))-1;
559	if (startPos4Translation<0 \|\| startPos4Translation>2) {
560	error = GB_export_errorf("'%s' has invalid codon_start entry %i (allowed: 1..3)", speciesName, startPos4Translation+1);
561	}
562	}
563	else {
564	gMissingCodonStart++;
565	startPos4Translation = 0;
566	}
567	break;
568	}
569	}
570
571	if (!error) {
572	translate_nuc2aa(translationTable, str_SeqData, len, startPos4Translation, false, true, false, NULp); // translate
573
574	char *s = new char[len+1];
575	int iDisplayMode = ED4_ROOT->aw_root->awar(AWAR_PROTVIEW_DISPLAY_OPTIONS)->read_int();
576	int i, j;
577
578	if (iDisplayMode == PV_AA_NAME) {
579	char *gc = new char[len+1];
580
581	for (i=0, j=0; i<len && j<len;) {
582	// start from the start pos of aa sequence
583	for (; i<startPos4Translation; ++i) {
584	s[i] = ' ';
585	gc[i] = ' ';
586	}
587
588	char base = str_SeqData[j++];
589	const char *AAname = getAminoAcidAbbr(base);
590	if (!AAname) AAname = ED4_is_gap_character(base) ? "---" : "<?>";
591
592	e4_assert(AAname && strlen(AAname) == 3);
593	for (int n = 0; n<3 && i<len; ++n,++i) {
594	s[i] = AAname[n];
595	gc[i] = base;
596	}
597	}
598
599	gc[i] = '\0';
600	seqTerm->SET_aaColor(gc);
601	delete [] gc;
602	}
603	else {
604	int k = startPos4Translation+1;
605	for (i=0, j=0; i<len; i++) {
606	if ((k==i) && (j<len)) {
607	s[i] = str_SeqData[j++];
608	k += 3;
609	}
610	else s[i] = ' ';
611	}
612	seqTerm->SET_aaColor(NULp);
613	}
614	s[i] = '\0';
615
616	seqTerm->SET_aaSequence(s);
617	delete [] s;
618	}
619	free(str_SeqData);
620	}
621	}
622	}
623	free(defaultAlignment);
624	}
625
626	if (error) aw_message(GBS_global_string("Error: %s", error));
627	}
628
629	static void PV_PrintMissingDBentryInformation() {
630	GBDATA *gb_main = ED4_ROOT->get_gb_main();
631	if (gMissingCodonStart>0) {
632	aw_message(GBS_global_string("WARNING: 'codon start' entry not found in %d of %d species! Using 1st base as codon start...",
633	gMissingCodonStart,
634	(int)GBT_count_marked_species(gb_main)));
635	gMissingCodonStart = 0;
636	}
637	if (gMissingTransTable>0) {
638	aw_message(GBS_global_string("WARNING: 'translation table' entry not found in %d of %d species! Using selected translation table as a default table...",
639	gMissingTransTable,
640	(int)GBT_count_marked_species(gb_main)));
641	gMissingTransTable = 0;
642	}
643	}
644
645	static void PV_DisplayAminoAcidNames(AW_root *root) {
646	GB_transaction ta(ED4_ROOT->get_gb_main());
647
648	for (ED4_terminal *terminal = ED4_ROOT->root_group_man->get_first_terminal();
649	terminal;
650	terminal = terminal->get_next_terminal())
651	{
652	if (terminal->is_species_seq_terminal()) {
653	const char *speciesName = terminal->to_sequence_terminal()->species_name;
654
655	// we are in the sequence terminal section of a species
656	// walk through all the corresponding ORF terminals for the species and
657	// hide or unhide the terminals based on the display options set by the user
658	for (int i=0; i<PV_AA_Terminals4Species; i++) {
659	// get the corresponding orf_terminal skipping sequence_info terminal
660	terminal = terminal->get_next_terminal()->get_next_terminal();
661	// Make sure it is ORF terminal
662	if (terminal->is_orf_terminal()) {
663	ED4_orf_terminal *orfTerm = terminal->to_orf_terminal();
664	// we are in ORF terminal
665	int aaStartPos = int(orfTerm->GET_aaStartPos());
666	int aaStrandType = int(orfTerm->GET_aaStrandType());
667	// retranslate the genesequence and store it to the orf_terminal
668	TranslateGeneToAminoAcidSequence(root, orfTerm, speciesName, aaStartPos-1, aaStrandType);
669	}
670	}
671	}
672	}
673	// Print missing DB entries
674	PV_PrintMissingDBentryInformation();
675	PV_RefreshWindow(root);
676	}
677
678	static void PV_RefreshDisplay(AW_root *root) {
679	PV_DisplayAminoAcidNames(root);
680	}
681
682	static void PV_RefreshProtViewDisplay(AW_window *aww) {
683	if (gTerminalsCreated) {
684	PV_RefreshDisplay(aww->get_root());
685	}
686	}
687
688	void PV_SequenceUpdate_CB(GB_CB_TYPE gbtype) {
689	if (gbtype==GB_CB_CHANGED &&
690	gTerminalsCreated &&
691	(ED4_ROOT->alignment_type == GB_AT_DNA) &&
692	!gbWritingData)
693	{
694	GB_transaction ta(ED4_ROOT->get_gb_main());
695
696	for (ED4_window *win = ED4_ROOT->first_window; win; win = win->next) {
697	ED4_cursor& cursor = win->cursor;
698	if (cursor.in_species_seq_terminal()) {
699	ED4_terminal *cursorTerminal = cursor.owner_of_cursor;
700	char *speciesName = cursorTerminal->to_sequence_terminal()->species_name;
701	for (int i=0; i<PV_AA_Terminals4Species; i++) {
702	// get the corresponding orf_terminal skipping sequence_info terminal
703	// $$$$$ sequence_terminal->sequence_info_terminal->aa_sequence_terminal $$$$$$
704	cursorTerminal = cursorTerminal->get_next_terminal()->get_next_terminal();
705	// Make sure it is ORF terminal
706	if (cursorTerminal->is_orf_terminal()) {
707	ED4_orf_terminal *orfTerm = cursorTerminal->to_orf_terminal();
708	// Get the AA sequence flag - says which strand we are in
709	int aaStartPos = int(orfTerm->GET_aaStartPos());
710	int aaStrandType = int(orfTerm->GET_aaStrandType());
711	// retranslate the genesequence and store it to the orf_terminal
712	TranslateGeneToAminoAcidSequence(ED4_ROOT->aw_root, orfTerm, speciesName, aaStartPos-1, aaStrandType);
713	}
714	}
715	// Print missing DB entries
716	PV_PrintMissingDBentryInformation();
717	PV_RefreshWindow(ED4_ROOT->aw_root);
718	}
719	}
720	}
721	}
722
723	static void PV_AddNewAAseqTerminals(ED4_sequence_terminal seqTerminal, ED4_species_manager speciesManager) {
724	int translationMode = 0;
725	char namebuffer[NAME_BUFFERSIZE];
726
727	for (int i = 0; i<PV_AA_Terminals4Species; i++) {
728	int count = 1;
729	int startPos = 0;
730
731	sprintf(namebuffer, "Sequence_Manager.%ld.%d", ED4_counter, count++);
732	ED4_multi_sequence_manager *multiSeqManager = speciesManager->search_spec_child_rek(LEV_MULTI_SEQUENCE)->to_multi_sequence_manager();
733	ED4_sequence_manager *new_SeqManager = new ED4_sequence_manager(namebuffer, 0, 0, multiSeqManager);
734	new_SeqManager->set_property(PROP_MOVABLE);
735	multiSeqManager->append_member(new_SeqManager);
736
737	if (i<FORWARD_STRANDS) sprintf(namebuffer, "F%d ProteinInfo_Term%ld.%d", i+1, ED4_counter, count++);
738	else if ((i-FORWARD_STRANDS)<COMPLEMENTARY_STRANDS) sprintf(namebuffer, "C%dProteinInfo_Term%ld.%d", (i-FORWARD_STRANDS)+1, ED4_counter, count++);
739	else sprintf(namebuffer, "DBProteinInfo_Term%ld.%d", ED4_counter, count++);
740
741	{
742	ED4_sequence_info_terminal *new_SeqInfoTerminal = new ED4_sequence_info_terminal(namebuffer, SEQUENCE_INFO_WIDTH, TERMINAL_HEIGHT, new_SeqManager);
743	new_SeqInfoTerminal->set_property((ED4_properties) (PROP_SELECTABLE \| PROP_DRAGABLE \| PROP_IS_HANDLE));
744
745	ED4_sequence_info_terminal *seqInfoTerminal = speciesManager->search_spec_child_rek(LEV_SEQUENCE_INFO)->to_sequence_info_terminal();
746	new_SeqInfoTerminal->set_both_links(seqInfoTerminal);
747	new_SeqManager->append_member(new_SeqInfoTerminal);
748	}
749
750	{
751	sprintf(namebuffer, "AA_Sequence_Term%ld.%d", ED4_counter, count++);
752	ED4_orf_terminal *AA_SeqTerminal = new ED4_orf_terminal(namebuffer, 0, TERMINAL_HEIGHT, new_SeqManager);
753	AA_SeqTerminal->set_both_links(seqTerminal);
754
755	char *speciesName = seqTerminal->species_name;
756	if (i<FORWARD_STRANDS) {
757	startPos = i;
758	translationMode = FORWARD_STRAND;
759	}
760	else if ((i-FORWARD_STRANDS)<COMPLEMENTARY_STRANDS) {
761	startPos = i-FORWARD_STRANDS;
762	translationMode = COMPLEMENTARY_STRAND;
763	}
764	else {
765	startPos = 0;
766	translationMode = DB_FIELD_STRAND;
767	}
768	TranslateGeneToAminoAcidSequence(ED4_ROOT->aw_root, AA_SeqTerminal, speciesName, startPos, translationMode);
769	AA_SeqTerminal->SET_aaSeqFlags(startPos+1, translationMode);
770	new_SeqManager->append_member(AA_SeqTerminal);
771	}
772
773	ED4_counter++;
774
775	new_SeqManager->request_resize();
776	}
777	}
778
779	void PV_AddCorrespondingOrfTerminals(ED4_species_name_terminal *spNameTerm) {
780	if (gTerminalsCreated && spNameTerm) {
781	ED4_sequence_terminal *seqTerminal = spNameTerm->corresponding_sequence_terminal();
782	ED4_species_manager *speciesManager = spNameTerm->get_parent(LEV_SPECIES)->to_species_manager();
783	PV_AddNewAAseqTerminals(seqTerminal, speciesManager);
784	PV_RefreshWindow(ED4_ROOT->aw_root);
785	}
786	}
787
788	void PV_AddOrfTerminalsToLoadedSpecies() {
789	if (gTerminalsCreated) {
790	GBDATA *gb_main = ED4_ROOT->get_gb_main();
791	GB_transaction ta(gb_main);
792	int marked = GBT_count_marked_species(gb_main);
793	if (marked) {
794	GBDATA *gbSpecies;
795	for (gbSpecies = GBT_first_marked_species(gb_main);
796	gbSpecies;
797	gbSpecies = GBT_next_marked_species(gbSpecies))
798	{
799	const char *spName = GBT_get_name_or_description(gbSpecies);
800	cout<<marked--<<". "<<spName<<endl;
801	ED4_species_name_terminal *spNameTerm = ED4_find_species_name_terminal(spName);
802	if (spNameTerm) {
803	ED4_terminal *terminal = spNameTerm->corresponding_sequence_terminal();
804	// $$$ If next terminal is species_name terminal => corresponding AA seq terminal doesn't exist ==> create one $$$
805	terminal = terminal->get_next_terminal();
806	if (terminal->is_species_name_terminal() \|\| terminal->is_spacer_terminal()) {
807	ED4_sequence_terminal *seqTerminal = spNameTerm->corresponding_sequence_terminal();
808	ED4_species_manager *speciesManager = spNameTerm->get_parent(LEV_SPECIES)->to_species_manager();
809	PV_AddNewAAseqTerminals(seqTerminal, speciesManager);
810	}
811	}
812	}
813	PV_RefreshWindow(ED4_ROOT->aw_root);
814	}
815	}
816	}
817
818	static void PV_CreateAllTerminals(AW_root *root) {
819	// 1. Get the species terminal pointer
820	// 2. Append the second terminal
821	// 3. resize the multi-species manager
822	// 4. refresh all the terminals including new appended terminals
823
824	// Look for already created terminals, if found do nothing, otherwise, create
825	// new terminals and set gTerminalsCreated to true
826	bool bTerminalsFound = PV_LookForNewTerminals(root);
827	// if terminals are already created then do nothing exit the function
828	if (bTerminalsFound) return;
829
830	GB_transaction ta(ED4_ROOT->get_gb_main());
831
832	// Number of ORF terminals to be created = 3 forward strands + 3 complementary strands + 1 DB field strand
833	// totally 7 strands has to be created
834	int aaTerminalsToBeCreated = FORWARD_STRANDS + COMPLEMENTARY_STRANDS + DB_FIELD_STRANDS;
835	PV_AA_Terminals4Species = aaTerminalsToBeCreated;
836
837	ED4_terminal *terminal = NULp;
838	for (terminal = ED4_ROOT->root_group_man->get_first_terminal();
839	terminal;
840	terminal = terminal->get_next_terminal())
841	{
842	if (terminal->is_sequence_terminal()) {
843	ED4_sequence_terminal *seqTerminal = terminal->to_sequence_terminal();
844	if (seqTerminal->species_name) {
845	ED4_species_manager *speciesManager = terminal->get_parent(LEV_SPECIES)->to_species_manager();
846	if (speciesManager->is_species_seq_manager()) {
847	PV_AddNewAAseqTerminals(seqTerminal, speciesManager);
848	}
849	}
850	}
851	}
852	ED4_ROOT->main_manager->request_resize(); // @@@ instead needs to be called whenever adding or deleting PV-terminals
853
854	gTerminalsCreated = true;
855
856	// Print missing DB entries
857	PV_PrintMissingDBentryInformation();
858	}
859
860	void PV_CallBackFunction(AW_root *root) {
861	// Create New Terminals If Aminoacid Sequence Terminals Are Not Created
862	if (!gTerminalsCreated) {
863	// AWAR_PROTEIN_TYPE is not initialized (if called from ED4_main before creating proteinViewer window)
864	// so, initialize it here
865	root->awar_int(AWAR_PROTEIN_TYPE, AWAR_PROTEIN_TYPE_bacterial_code_index, ED4_ROOT->get_gb_main());
866	PV_CreateAllTerminals(root);
867	}
868
869	PV_RefreshWindow(root);
870	}
871
872	// --------------------------------------------------------------------------------
873	// Binding callback function to the AWARS
874
875	static void PV_AddCallBacks(AW_root *awr) {
876
877	awr->awar(AWAR_PV_DISPLAY_ALL)->add_callback(PV_CallBackFunction);
878	awr->awar(AWAR_PROTVIEW_FORWARD_STRAND_1)->add_callback(PV_CallBackFunction);
879	awr->awar(AWAR_PROTVIEW_FORWARD_STRAND_2)->add_callback(PV_CallBackFunction);
880	awr->awar(AWAR_PROTVIEW_FORWARD_STRAND_3)->add_callback(PV_CallBackFunction);
881	awr->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1)->add_callback(PV_CallBackFunction);
882	awr->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2)->add_callback(PV_CallBackFunction);
883	awr->awar(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3)->add_callback(PV_CallBackFunction);
884	awr->awar(AWAR_PROTVIEW_DEFINED_FIELDS)->add_callback(PV_CallBackFunction);
885
886	awr->awar(AWAR_PROTVIEW_DISPLAY_OPTIONS)->add_callback(PV_RefreshDisplay);
887	awr->awar(AWAR_SPECIES_NAME)->add_callback(PV_CallBackFunction);
888
889	awr->awar(AWAR_PV_SELECTED)->add_callback(PV_CallBackFunction);
890	awr->awar(AWAR_PV_SELECTED_DB)->add_callback(PV_CallBackFunction);
891	awr->awar(AWAR_PV_SELECTED_FS_1)->add_callback(PV_CallBackFunction);
892	awr->awar(AWAR_PV_SELECTED_FS_2)->add_callback(PV_CallBackFunction);
893	awr->awar(AWAR_PV_SELECTED_FS_3)->add_callback(PV_CallBackFunction);
894	awr->awar(AWAR_PV_SELECTED_CS_1)->add_callback(PV_CallBackFunction);
895	awr->awar(AWAR_PV_SELECTED_CS_2)->add_callback(PV_CallBackFunction);
896	awr->awar(AWAR_PV_SELECTED_CS_3)->add_callback(PV_CallBackFunction);
897
898	awr->awar(AWAR_PV_MARKED)->add_callback(PV_CallBackFunction);
899	awr->awar(AWAR_PV_MARKED_DB)->add_callback(PV_CallBackFunction);
900	awr->awar(AWAR_PV_MARKED_FS_1)->add_callback(PV_CallBackFunction);
901	awr->awar(AWAR_PV_MARKED_FS_2)->add_callback(PV_CallBackFunction);
902	awr->awar(AWAR_PV_MARKED_FS_3)->add_callback(PV_CallBackFunction);
903	awr->awar(AWAR_PV_MARKED_CS_1)->add_callback(PV_CallBackFunction);
904	awr->awar(AWAR_PV_MARKED_CS_2)->add_callback(PV_CallBackFunction);
905	awr->awar(AWAR_PV_MARKED_CS_3)->add_callback(PV_CallBackFunction);
906
907	awr->awar(AWAR_PV_CURSOR)->add_callback(PV_CallBackFunction);
908	awr->awar(AWAR_PV_CURSOR_DB)->add_callback(PV_CallBackFunction);
909	awr->awar(AWAR_PV_CURSOR_FS_1)->add_callback(PV_CallBackFunction);
910	awr->awar(AWAR_PV_CURSOR_FS_2)->add_callback(PV_CallBackFunction);
911	awr->awar(AWAR_PV_CURSOR_FS_3)->add_callback(PV_CallBackFunction);
912	awr->awar(AWAR_PV_CURSOR_CS_1)->add_callback(PV_CallBackFunction);
913	awr->awar(AWAR_PV_CURSOR_CS_2)->add_callback(PV_CallBackFunction);
914	awr->awar(AWAR_PV_CURSOR_CS_3)->add_callback(PV_CallBackFunction);
915	}
916
917	// --------------------------------------------------------------------------------
918	// Creating AWARS to be used by the PROTVIEW module
919
920	void PV_CreateAwars(AW_root *root, AW_default aw_def) {
921
922	root->awar_int(AWAR_PV_DISPLAY_ALL, 0, aw_def);
923
924	root->awar_int(AWAR_PROTVIEW_FORWARD_STRAND_1, 0, aw_def);
925	root->awar_int(AWAR_PROTVIEW_FORWARD_STRAND_2, 0, aw_def);
926	root->awar_int(AWAR_PROTVIEW_FORWARD_STRAND_3, 0, aw_def);
927
928	root->awar_int(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1, 0, aw_def);
929	root->awar_int(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2, 0, aw_def);
930	root->awar_int(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3, 0, aw_def);
931
932	root->awar_int(AWAR_PROTVIEW_DEFINED_FIELDS, 0, aw_def);
933	root->awar_int(AWAR_PROTVIEW_DISPLAY_OPTIONS, 0, aw_def);
934
935	root->awar_int(AWAR_PV_SELECTED, 0, aw_def);
936	root->awar_int(AWAR_PV_SELECTED_DB, 0, aw_def);
937	root->awar_int(AWAR_PV_SELECTED_FS_1, 0, aw_def);
938	root->awar_int(AWAR_PV_SELECTED_FS_2, 0, aw_def);
939	root->awar_int(AWAR_PV_SELECTED_FS_3, 0, aw_def);
940	root->awar_int(AWAR_PV_SELECTED_CS_1, 0, aw_def);
941	root->awar_int(AWAR_PV_SELECTED_CS_2, 0, aw_def);
942	root->awar_int(AWAR_PV_SELECTED_CS_3, 0, aw_def);
943
944	root->awar_int(AWAR_PV_MARKED, 0, aw_def);
945	root->awar_int(AWAR_PV_MARKED_DB, 0, aw_def);
946	root->awar_int(AWAR_PV_MARKED_FS_1, 0, aw_def);
947	root->awar_int(AWAR_PV_MARKED_FS_2, 0, aw_def);
948	root->awar_int(AWAR_PV_MARKED_FS_3, 0, aw_def);
949	root->awar_int(AWAR_PV_MARKED_CS_1, 0, aw_def);
950	root->awar_int(AWAR_PV_MARKED_CS_2, 0, aw_def);
951	root->awar_int(AWAR_PV_MARKED_CS_3, 0, aw_def);
952
953	root->awar_int(AWAR_PV_CURSOR, 0, aw_def);
954	root->awar_int(AWAR_PV_CURSOR_DB, 0, aw_def);
955	root->awar_int(AWAR_PV_CURSOR_FS_1, 0, aw_def);
956	root->awar_int(AWAR_PV_CURSOR_FS_2, 0, aw_def);
957	root->awar_int(AWAR_PV_CURSOR_FS_3, 0, aw_def);
958	root->awar_int(AWAR_PV_CURSOR_CS_1, 0, aw_def);
959	root->awar_int(AWAR_PV_CURSOR_CS_2, 0, aw_def);
960	root->awar_int(AWAR_PV_CURSOR_CS_3, 0, aw_def);
961	}
962
963	AW_window ED4_CreateProteinViewer_window(AW_root aw_root) {
964	GBDATA *gb_main = ED4_ROOT->get_gb_main();
965	GB_transaction ta(gb_main);
966
967	static AW_window_simple *aws = NULp;
968	if (aws) return aws;
969
970	aws = new AW_window_simple;
971
972	aws->init(aw_root, "PROTEIN_VIEWER", "Protein Viewer");
973	aws->load_xfig("proteinViewer.fig");
974
975	aws->at("refresh");
976	aws->callback(PV_RefreshProtViewDisplay);
977	aws->button_length(0);
978	aws->create_button("REFRESH", "#refresh_text.xpm");
979
980	aws->callback(makeHelpCallback("proteinViewer.hlp"));
981	aws->at("help");
982	aws->button_length(0);
983	aws->create_button("HELP", "#help_text.xpm");
984
985	aws->at("close");
986	aws->callback(AW_POPDOWN);
987	aws->button_length(0);
988	aws->create_button("CLOSE", "#close_text.xpm");
989
990	{
991	aw_root->awar_int(AWAR_PROTEIN_TYPE, AWAR_PROTEIN_TYPE_bacterial_code_index, gb_main);
992	aws->at("table");
993	aws->create_option_menu(AWAR_PROTEIN_TYPE, true);
994	for (int code_nr=0; code_nr<AWT_CODON_TABLES; code_nr++) {
995	aws->insert_option(AWT_get_codon_code_name(code_nr), "", code_nr);
996	}
997	aws->update_option_menu();
998
999	aws->at("all");
1000	aws->create_toggle(AWAR_PV_DISPLAY_ALL);
1001
1002	aws->at("f1");
1003	aws->create_toggle(AWAR_PROTVIEW_FORWARD_STRAND_1);
1004
1005	aws->at("f2");
1006	aws->create_toggle(AWAR_PROTVIEW_FORWARD_STRAND_2);
1007
1008	aws->at("f3");
1009	aws->create_toggle(AWAR_PROTVIEW_FORWARD_STRAND_3);
1010
1011	aws->at("c1");
1012	aws->create_toggle(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_1);
1013
1014	aws->at("c2");
1015	aws->create_toggle(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_2);
1016
1017	aws->at("c3");
1018	aws->create_toggle(AWAR_PROTVIEW_COMPLEMENTARY_STRAND_3);
1019
1020	aws->at("defined");
1021	aws->create_toggle(AWAR_PROTVIEW_DEFINED_FIELDS);
1022
1023	aws->at("dispOption");
1024	aws->create_toggle_field(AWAR_PROTVIEW_DISPLAY_OPTIONS, 0);
1025	aws->insert_toggle("Single Letter Code", "S", 0);
1026	aws->insert_toggle("Triple Letter Code", "T", 1);
1027	aws->insert_toggle("Colored Box", "B", 2);
1028	aws->update_toggle_field();
1029
1030	aws->at("colMaps");
1031	aws->callback(makeCreateWindowCallback(ED4_create_seq_colors_window, ED4_ROOT->sequence_colors));
1032	aws->button_length(0);
1033	aws->create_button("COLORMAPS", "#colorMaps.xpm");
1034
1035	aws->at("colors");
1036	aws->callback(makeWindowCallback(ED4_popup_gc_window, ED4_ROOT->gc_manager));
1037	aws->button_length(0);
1038	aws->create_button("COLORS", "#colors.xpm");
1039
1040	{
1041	aws->at("sel"); aws->create_toggle(AWAR_PV_SELECTED);
1042	aws->at("sf1"); aws->create_toggle(AWAR_PV_SELECTED_FS_1);
1043	aws->at("sf2"); aws->create_toggle(AWAR_PV_SELECTED_FS_2);
1044	aws->at("sf3"); aws->create_toggle(AWAR_PV_SELECTED_FS_3);
1045	aws->at("sc1"); aws->create_toggle(AWAR_PV_SELECTED_CS_1);
1046	aws->at("sc2"); aws->create_toggle(AWAR_PV_SELECTED_CS_2);
1047	aws->at("sc3"); aws->create_toggle(AWAR_PV_SELECTED_CS_3);
1048	aws->at("sdb"); aws->create_toggle(AWAR_PV_SELECTED_DB);
1049
1050	aws->at("mrk"); aws->create_toggle(AWAR_PV_MARKED);
1051	aws->at("mf1"); aws->create_toggle(AWAR_PV_MARKED_FS_1);
1052	aws->at("mf2"); aws->create_toggle(AWAR_PV_MARKED_FS_2);
1053	aws->at("mf3"); aws->create_toggle(AWAR_PV_MARKED_FS_3);
1054	aws->at("mc1"); aws->create_toggle(AWAR_PV_MARKED_CS_1);
1055	aws->at("mc2"); aws->create_toggle(AWAR_PV_MARKED_CS_2);
1056	aws->at("mc3"); aws->create_toggle(AWAR_PV_MARKED_CS_3);
1057	aws->at("mdb"); aws->create_toggle(AWAR_PV_MARKED_DB);
1058
1059	aws->at("cur"); aws->create_toggle(AWAR_PV_CURSOR);
1060	aws->at("cf1"); aws->create_toggle(AWAR_PV_CURSOR_FS_1);
1061	aws->at("cf2"); aws->create_toggle(AWAR_PV_CURSOR_FS_2);
1062	aws->at("cf3"); aws->create_toggle(AWAR_PV_CURSOR_FS_3);
1063	aws->at("cc1"); aws->create_toggle(AWAR_PV_CURSOR_CS_1);
1064	aws->at("cc2"); aws->create_toggle(AWAR_PV_CURSOR_CS_2);
1065	aws->at("cc3"); aws->create_toggle(AWAR_PV_CURSOR_CS_3);
1066	aws->at("cdb"); aws->create_toggle(AWAR_PV_CURSOR_DB);
1067	}
1068
1069	aws->at("save");
1070	aws->callback(PV_SaveData);
1071	aws->button_length(5);
1072	aws->create_button("SAVE", "#save.xpm");
1073	}
1074
1075	// binding callback function to the AWARS
1076	PV_AddCallBacks(aw_root);
1077
1078	// Create All Terminals
1079	PV_CreateAllTerminals(aw_root);
1080
1081	aws->show();
1082
1083	return aws;
1084	}
1085

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