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source: tags/ms_r16q2/SEQ_QUALITY/SQ_main.cxx

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Last change on this file was 14453, checked in by westram, 7 years ago
do not cast AW_POPDOWN
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 11.6 KB

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1	// ==================================================================== //
2	// //
3	// File : SQ_main.cxx //
4	// Purpose : Entrypoint to Seq. Quality analysis; calls functions //
5	// //
6	// //
7	// Coded by Juergen Huber in July 2003 - February 2004 //
8	// Coded by Kai Bader (baderk@in.tum.de) in 2007 - 2008 //
9	// Copyright Department of Microbiology (Technical University Munich) //
10	// //
11	// Visit our web site at: http://www.arb-home.de/ //
12	// //
13	// ==================================================================== //
14
15	#include "seq_quality.h"
16	#include "SQ_functions.h"
17
18	#include <awt_filter.hxx>
19	#include <awt_sel_boxes.hxx>
20
21	#include <aw_awars.hxx>
22	#include <aw_msg.hxx>
23	#include <aw_root.hxx>
24
25	#include <arb_progress.h>
26	#include <TreeNode.h>
27	#include <arb_global_defs.h>
28	#include <awt_config_manager.hxx>
29
30	// --------------------------------------------------------------------------------
31
32	#define AWAR_SQ_PERM "seq_quality/" // saved in properties
33	#define AWAR_SQ_TEMP "tmp/seq_quality/" // not saved in properties
34
35	#define AWAR_SQ_WEIGHT_BASES AWAR_SQ_PERM "weight_bases"
36	#define AWAR_SQ_WEIGHT_DEVIATION AWAR_SQ_PERM "weight_deviation"
37	#define AWAR_SQ_WEIGHT_HELIX AWAR_SQ_PERM "weight_helix"
38	#define AWAR_SQ_WEIGHT_CONSENSUS AWAR_SQ_PERM "weight_consensus"
39	#define AWAR_SQ_WEIGHT_IUPAC AWAR_SQ_PERM "weight_iupac"
40	#define AWAR_SQ_WEIGHT_GC AWAR_SQ_PERM "weight_gc"
41
42	#define AWAR_SQ_MARK_ONLY_FLAG AWAR_SQ_PERM "mark_only_flag"
43	#define AWAR_SQ_MARK_FLAG AWAR_SQ_PERM "mark_flag"
44	#define AWAR_SQ_MARK_BELOW AWAR_SQ_PERM "mark_below"
45	#define AWAR_SQ_REEVALUATE AWAR_SQ_PERM "reevaluate"
46	#define AWAR_SQ_FILTER_NAME AWAR_SQ_TEMP "filter/name"
47
48	void SQ_create_awars(AW_root *aw_root, AW_default aw_def) {
49	aw_root->awar_int(AWAR_SQ_WEIGHT_BASES, 5, aw_def);
50	aw_root->awar_int(AWAR_SQ_WEIGHT_DEVIATION, 15, aw_def);
51	aw_root->awar_int(AWAR_SQ_WEIGHT_HELIX, 15, aw_def);
52	aw_root->awar_int(AWAR_SQ_WEIGHT_CONSENSUS, 50, aw_def);
53	aw_root->awar_int(AWAR_SQ_WEIGHT_IUPAC, 5, aw_def);
54	aw_root->awar_int(AWAR_SQ_WEIGHT_GC, 10, aw_def);
55	aw_root->awar_int(AWAR_SQ_MARK_ONLY_FLAG, 0, aw_def);
56	aw_root->awar_int(AWAR_SQ_MARK_FLAG, 1, aw_def);
57	aw_root->awar_int(AWAR_SQ_MARK_BELOW, 40, aw_def);
58	aw_root->awar_int(AWAR_SQ_REEVALUATE, 0, aw_def);
59
60	awt_create_filter_awars(aw_root, aw_def, AWAR_SQ_FILTER_NAME, AWAR_DEFAULT_ALIGNMENT);
61	}
62
63	// --------------------------------------------------------------------------------
64
65
66	static void sq_calc_seq_quality_cb(AW_window * aww, adfiltercbstruct acbs, GBDATA gb_main) {
67	AW_root *aw_root = aww->get_root();
68	GB_ERROR error = 0;
69	TreeNode *tree = 0;
70	bool marked_only = (aw_root->awar(AWAR_SQ_MARK_ONLY_FLAG)->read_int() > 0);
71
72	arb_progress main_progress("Calculating sequence quality");
73
74	{
75	char *treename = aw_root->awar(AWAR_TREE)->read_string();
76
77	if (treename && strcmp(treename, NO_TREE_SELECTED) != 0) {
78	error = GB_push_transaction(gb_main);
79
80	if (!error) {
81	tree = GBT_read_tree(gb_main, treename, new SimpleRoot);
82	if (!tree) error = GB_await_error();
83	else {
84	error = GBT_link_tree(tree, gb_main, false, NULL, NULL);
85	if (!error) {
86	GBT_TreeRemoveType mode = marked_only ? GBT_KEEP_MARKED : GBT_REMOVE_ZOMBIES;
87	tree = GBT_remove_leafs(tree, mode, NULL, NULL, NULL);
88	if (!tree \|\| tree->is_leaf) {
89	error = GBS_global_string("Tree contains less than 2 species after removing zombies%s",
90	marked_only ? " and non-marked" : "");
91	}
92	}
93	}
94	}
95
96	error = GB_end_transaction(gb_main, error);
97	}
98	free(treename);
99	}
100
101	// if tree == 0 -> do basic quality calculations that are possible without tree information
102	// otherwise -> use all groups found in tree and compare sequences against the groups they are contained in
103
104	if (!error) {
105	struct SQ_weights weights;
106
107	weights.bases = aw_root->awar(AWAR_SQ_WEIGHT_BASES)->read_int();
108	weights.diff_from_average = aw_root->awar(AWAR_SQ_WEIGHT_DEVIATION)->read_int();
109	weights.helix = aw_root->awar(AWAR_SQ_WEIGHT_HELIX)->read_int();
110	weights.consensus = aw_root->awar(AWAR_SQ_WEIGHT_CONSENSUS)->read_int();
111	weights.iupac = aw_root->awar(AWAR_SQ_WEIGHT_IUPAC)->read_int();
112	weights.gc = aw_root->awar(AWAR_SQ_WEIGHT_GC)->read_int();
113
114	int mark_flag = aw_root->awar(AWAR_SQ_MARK_FLAG)->read_int();
115	int mark_below = aw_root->awar(AWAR_SQ_MARK_BELOW)->read_int();
116	int reevaluate = aw_root->awar(AWAR_SQ_REEVALUATE)->read_int();
117
118	// Load and use Sequence-Filter
119	AP_filter *filter = awt_get_filter(acbs);
120	error = awt_invalid_filter(filter);
121
122	/*
123	SQ_evaluate() generates the final estimation for the quality of an alignment.
124	It takes the values from the different containers, which are generated by the other functions, weights them
125	and calculates a final value. The final value is stored in "value_of_evaluation" (see options).
126	With the values stored in "weights" one can customize how important a value stored in a container becomes
127	for the final result.
128	*/
129
130	if (!error) {
131	if (tree == 0) {
132	if (reevaluate) {
133	SQ_mark_species(gb_main, mark_below, marked_only);
134	}
135	else {
136	arb_progress progress(GBT_get_species_count(gb_main)*2);
137	SQ_GroupData *globalData = new SQ_GroupData_RNA;
138
139	progress.subtitle("pass1");
140	error = SQ_pass1_no_tree(globalData, gb_main, filter, progress);
141	if (!error) {
142	progress.subtitle("pass2");
143	error = SQ_pass2_no_tree(globalData, gb_main, filter, progress);
144	if (!error) {
145	error = SQ_evaluate(gb_main, weights, marked_only);
146	if (mark_flag && !error) {
147	SQ_mark_species(gb_main, mark_below, marked_only);
148	}
149	}
150	}
151	if (error) progress.done();
152	delete globalData;
153	}
154	}
155	else {
156	SQ_TREE_ERROR check = SQ_check_tree_structure(tree);
157	if (check != NONE) {
158	switch (check) {
159	case ZOMBIE:
160	error = "Found one or more zombies in the tree.\n"
161	"Please remove them or use another tree before running the quality check tool.";
162	break;
163	case MISSING_NODE:
164	error = "Missing node(s) or unusable tree structure.\n"
165	"Please fix the tree before running the quality check tool.";
166	break;
167	default:
168	error = "An error occurred while traversing the tree.\n"
169	"Please fix the tree before running the quality check tool.";
170	break;
171	}
172	}
173	else if (reevaluate) {
174	SQ_mark_species(gb_main, mark_below, marked_only);
175	}
176	else {
177	arb_progress progress(SQ_count_nodes(tree)*2);
178	SQ_GroupData *globalData = new SQ_GroupData_RNA;
179
180	progress.subtitle("pass1");
181	SQ_calc_and_apply_group_data(tree, gb_main, globalData, filter, progress);
182	progress.subtitle("pass2");
183	SQ_calc_and_apply_group_data2(tree, gb_main, globalData, filter, progress);
184	SQ_evaluate(gb_main, weights, marked_only);
185	if (mark_flag) SQ_mark_species(gb_main, mark_below, marked_only);
186	delete globalData;
187	}
188	}
189	}
190	awt_destroy_filter(filter);
191	}
192
193	if (error) aw_message(error);
194
195	SQ_clear_group_dictionary();
196	UNCOVERED();
197	destroy(tree);
198	}
199
200	static void sq_remove_quality_entries_cb(AW_window, GBDATA gb_main) {
201	GB_ERROR error = SQ_remove_quality_entries(gb_main);
202	aw_message_if(error);
203	}
204
205	static AWT_config_mapping_def seq_quality_config_mapping[] = {
206	{ AWAR_SQ_WEIGHT_BASES, "wbases" },
207	{ AWAR_SQ_WEIGHT_DEVIATION, "wdeviation" },
208	{ AWAR_SQ_WEIGHT_HELIX, "whelix" },
209	{ AWAR_SQ_WEIGHT_CONSENSUS, "wconsens" },
210	{ AWAR_SQ_WEIGHT_IUPAC, "wiupac" },
211	{ AWAR_SQ_WEIGHT_GC, "wgc" },
212	{ AWAR_SQ_MARK_ONLY_FLAG, "onlymarked" },
213	{ AWAR_SQ_MARK_FLAG, "markbad" },
214	{ AWAR_SQ_MARK_BELOW, "markbelow" },
215	{ AWAR_SQ_REEVALUATE, "reeval" },
216
217	{ 0, 0 }
218	};
219
220	AW_window SQ_create_seq_quality_window(AW_root aw_root, GBDATA *gb_main) {
221	// create window for sequence quality calculation (called only once)
222
223	AW_window_simple *aws = new AW_window_simple;
224
225	aws->init(aw_root, "CALC_SEQ_QUALITY", "CALCULATE SEQUENCE QUALITY");
226	aws->load_xfig("seq_quality.fig");
227
228	aws->at("close");
229	aws->callback(AW_POPDOWN);
230	aws->create_button("CLOSE", "CLOSE", "C");
231
232	aws->at("help");
233	aws->callback(makeHelpCallback("seq_quality.hlp"));
234	aws->create_button("HELP", "HELP", "H");
235
236	aws->at("base");
237	aws->create_input_field(AWAR_SQ_WEIGHT_BASES, 3);
238
239	aws->at("deviation");
240	aws->create_input_field(AWAR_SQ_WEIGHT_DEVIATION, 3);
241
242	aws->at("no_helices");
243	aws->create_input_field(AWAR_SQ_WEIGHT_HELIX, 3);
244
245	aws->at("consensus");
246	aws->create_input_field(AWAR_SQ_WEIGHT_CONSENSUS, 3);
247
248	aws->at("iupac");
249	aws->create_input_field(AWAR_SQ_WEIGHT_IUPAC, 3);
250
251	aws->at("gc_proportion");
252	aws->create_input_field(AWAR_SQ_WEIGHT_GC, 3);
253
254	aws->at("monly");
255	aws->create_toggle(AWAR_SQ_MARK_ONLY_FLAG);
256
257	aws->at("mark");
258	aws->create_toggle(AWAR_SQ_MARK_FLAG);
259
260	aws->at("mark_below");
261	aws->create_input_field(AWAR_SQ_MARK_BELOW, 3);
262
263	aws->at("tree");
264	awt_create_TREE_selection_list(gb_main, aws, AWAR_TREE, true);
265
266	aws->at("filter");
267	adfiltercbstruct *adfilter = awt_create_select_filter(aws->get_root(), gb_main, AWAR_SQ_FILTER_NAME);
268	aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, adfilter));
269	aws->create_button("SELECT_FILTER", AWAR_SQ_FILTER_NAME);
270
271	aws->at("go");
272	aws->callback(makeWindowCallback(sq_calc_seq_quality_cb, adfilter, gb_main));
273	aws->highlight();
274	aws->create_button("GO", "GO", "G");
275
276	aws->at("config");
277	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "seq_quality", seq_quality_config_mapping);
278
279	aws->at("reevaluate");
280	aws->label("Re-Evaluate only");
281	aws->create_toggle(AWAR_SQ_REEVALUATE);
282
283	aws->at("remove");
284	aws->callback(makeWindowCallback(sq_remove_quality_entries_cb, gb_main));
285	aws->create_button("Remove", "Remove", "R");
286
287	return aws;
288	}

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