Context Navigation

source: branches/tree/SEQ_QUALITY/SQ_main.cxx

Visit:

Last change on this file was 18717, checked in by westram, 4 years ago
split `GBT_link_tree` into 2 flavors. also split `ARB_seqtree_root::linkToDB` into 2 flavors.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 11.8 KB

Line
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	inline size_t count_nodes(TreeNode *node) {
67	// calculate number of nodes in tree
68	return GBT_count_leafs(node)*2-1;
69	}
70
71	static void sq_calc_seq_quality_cb(AW_window * aww, adfiltercbstruct acbs, GBDATA gb_main) {
72	AW_root *aw_root = aww->get_root();
73	GB_ERROR error = NULp;
74	TreeNode *tree = NULp;
75	bool marked_only = (aw_root->awar(AWAR_SQ_MARK_ONLY_FLAG)->read_int() > 0);
76
77	arb_progress main_progress("Calculating sequence quality");
78
79	{
80	char *treename = aw_root->awar(AWAR_TREE)->read_string();
81
82	if (treename && strcmp(treename, NO_TREE_SELECTED) != 0) {
83	error = GB_push_transaction(gb_main);
84
85	if (!error) {
86	tree = GBT_read_tree(gb_main, treename, new SimpleRoot);
87	if (!tree) error = GB_await_error();
88	else {
89	error = GBT_link_tree(tree, gb_main, false);
90	if (!error) {
91	GBT_TreeRemoveType mode = marked_only ? GBT_KEEP_MARKED : GBT_REMOVE_ZOMBIES;
92	tree = GBT_remove_leafs(tree, mode, NULp, NULp, NULp);
93	if (!tree \|\| tree->is_leaf()) {
94	error = GBS_global_string("Tree contains less than 2 species after removing zombies%s",
95	marked_only ? " and non-marked" : "");
96	}
97	}
98	}
99	}
100
101	error = GB_end_transaction(gb_main, error);
102	}
103	free(treename);
104	}
105
106	// if tree == 0 -> do basic quality calculations that are possible without tree information
107	// otherwise -> use all groups found in tree and compare sequences against the groups they are contained in
108
109	if (!error) {
110	struct SQ_weights weights;
111
112	weights.bases = aw_root->awar(AWAR_SQ_WEIGHT_BASES)->read_int();
113	weights.diff_from_average = aw_root->awar(AWAR_SQ_WEIGHT_DEVIATION)->read_int();
114	weights.helix = aw_root->awar(AWAR_SQ_WEIGHT_HELIX)->read_int();
115	weights.consensus = aw_root->awar(AWAR_SQ_WEIGHT_CONSENSUS)->read_int();
116	weights.iupac = aw_root->awar(AWAR_SQ_WEIGHT_IUPAC)->read_int();
117	weights.gc = aw_root->awar(AWAR_SQ_WEIGHT_GC)->read_int();
118
119	int mark_flag = aw_root->awar(AWAR_SQ_MARK_FLAG)->read_int();
120	int mark_below = aw_root->awar(AWAR_SQ_MARK_BELOW)->read_int();
121	int reevaluate = aw_root->awar(AWAR_SQ_REEVALUATE)->read_int();
122
123	// Load and use Sequence-Filter
124	AP_filter *filter = awt_get_filter(acbs);
125	error = awt_invalid_filter(filter);
126
127	/*
128	SQ_evaluate() generates the final estimation for the quality of an alignment.
129	It takes the values from the different containers, which are generated by the other functions, weights them
130	and calculates a final value. The final value is stored in "value_of_evaluation" (see options).
131	With the values stored in "weights" one can customize how important a value stored in a container becomes
132	for the final result.
133	*/
134
135	if (!error) {
136	if (!tree) {
137	if (reevaluate) {
138	SQ_mark_species(gb_main, mark_below, marked_only);
139	}
140	else {
141	arb_progress progress(GBT_get_species_count(gb_main)*2);
142	SQ_GroupData *globalData = new SQ_GroupData_RNA;
143
144	progress.subtitle("pass1");
145	error = SQ_pass1_no_tree(globalData, gb_main, filter, progress);
146	if (!error) {
147	progress.subtitle("pass2");
148	error = SQ_pass2_no_tree(globalData, gb_main, filter, progress);
149	if (!error) {
150	error = SQ_evaluate(gb_main, weights, marked_only);
151	if (mark_flag && !error) {
152	SQ_mark_species(gb_main, mark_below, marked_only);
153	}
154	}
155	}
156	if (error) progress.done();
157	delete globalData;
158	}
159	}
160	else {
161	SQ_TREE_ERROR check = SQ_check_tree_structure(tree);
162	if (check != NONE) {
163	switch (check) {
164	case ZOMBIE:
165	error = "Found one or more zombies in the tree.\n"
166	"Please remove them or use another tree before running the quality check tool.";
167	break;
168	case MISSING_NODE:
169	error = "Missing node(s) or unusable tree structure.\n"
170	"Please fix the tree before running the quality check tool.";
171	break;
172	default:
173	error = "An error occurred while traversing the tree.\n"
174	"Please fix the tree before running the quality check tool.";
175	break;
176	}
177	}
178	else if (reevaluate) {
179	SQ_mark_species(gb_main, mark_below, marked_only);
180	}
181	else {
182	arb_progress progress(count_nodes(tree)*2);
183	SQ_GroupData *globalData = new SQ_GroupData_RNA;
184
185	progress.subtitle("pass1");
186	SQ_calc_and_apply_group_data(tree, gb_main, globalData, filter, progress);
187	progress.subtitle("pass2");
188	SQ_calc_and_apply_group_data2(tree, gb_main, globalData, filter, progress);
189	SQ_evaluate(gb_main, weights, marked_only);
190	if (mark_flag) SQ_mark_species(gb_main, mark_below, marked_only);
191	delete globalData;
192	}
193	}
194	}
195	awt_destroy_filter(filter);
196	}
197
198	if (error) aw_message(error);
199
200	SQ_clear_group_dictionary();
201	UNCOVERED();
202	destroy(tree);
203	}
204
205	static void sq_remove_quality_entries_cb(AW_window, GBDATA gb_main) {
206	GB_ERROR error = SQ_remove_quality_entries(gb_main);
207	aw_message_if(error);
208	}
209
210	static AWT_config_mapping_def seq_quality_config_mapping[] = {
211	{ AWAR_SQ_WEIGHT_BASES, "wbases" },
212	{ AWAR_SQ_WEIGHT_DEVIATION, "wdeviation" },
213	{ AWAR_SQ_WEIGHT_HELIX, "whelix" },
214	{ AWAR_SQ_WEIGHT_CONSENSUS, "wconsens" },
215	{ AWAR_SQ_WEIGHT_IUPAC, "wiupac" },
216	{ AWAR_SQ_WEIGHT_GC, "wgc" },
217	{ AWAR_SQ_MARK_ONLY_FLAG, "onlymarked" },
218	{ AWAR_SQ_MARK_FLAG, "markbad" },
219	{ AWAR_SQ_MARK_BELOW, "markbelow" },
220	{ AWAR_SQ_REEVALUATE, "reeval" },
221
222	{ NULp, NULp }
223	};
224
225	AW_window SQ_create_seq_quality_window(AW_root aw_root, GBDATA *gb_main) {
226	// create window for sequence quality calculation (called only once)
227
228	AW_window_simple *aws = new AW_window_simple;
229
230	aws->init(aw_root, "CALC_SEQ_QUALITY", "CALCULATE SEQUENCE QUALITY");
231	aws->load_xfig("seq_quality.fig");
232
233	aws->at("close");
234	aws->callback(AW_POPDOWN);
235	aws->create_button("CLOSE", "CLOSE", "C");
236
237	aws->at("help");
238	aws->callback(makeHelpCallback("seq_quality.hlp"));
239	aws->create_button("HELP", "HELP", "H");
240
241	aws->at("base");
242	aws->create_input_field(AWAR_SQ_WEIGHT_BASES, 3);
243
244	aws->at("deviation");
245	aws->create_input_field(AWAR_SQ_WEIGHT_DEVIATION, 3);
246
247	aws->at("no_helices");
248	aws->create_input_field(AWAR_SQ_WEIGHT_HELIX, 3);
249
250	aws->at("consensus");
251	aws->create_input_field(AWAR_SQ_WEIGHT_CONSENSUS, 3);
252
253	aws->at("iupac");
254	aws->create_input_field(AWAR_SQ_WEIGHT_IUPAC, 3);
255
256	aws->at("gc_proportion");
257	aws->create_input_field(AWAR_SQ_WEIGHT_GC, 3);
258
259	aws->at("monly");
260	aws->create_toggle(AWAR_SQ_MARK_ONLY_FLAG);
261
262	aws->at("mark");
263	aws->create_toggle(AWAR_SQ_MARK_FLAG);
264
265	aws->at("mark_below");
266	aws->create_input_field(AWAR_SQ_MARK_BELOW, 3);
267
268	aws->at("tree");
269	awt_create_TREE_selection_list(gb_main, aws, AWAR_TREE, true);
270
271	aws->at("filter");
272	adfiltercbstruct *adfilter = awt_create_select_filter(aws->get_root(), gb_main, AWAR_SQ_FILTER_NAME);
273	aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, adfilter));
274	aws->create_button("SELECT_FILTER", AWAR_SQ_FILTER_NAME);
275
276	aws->at("go");
277	aws->callback(makeWindowCallback(sq_calc_seq_quality_cb, adfilter, gb_main));
278	aws->highlight();
279	aws->create_button("GO", "GO", "G");
280
281	aws->at("config");
282	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "seq_quality", seq_quality_config_mapping);
283
284	aws->at("reevaluate");
285	aws->label("Re-Evaluate only");
286	aws->create_toggle(AWAR_SQ_REEVALUATE);
287
288	aws->at("remove");
289	aws->callback(makeWindowCallback(sq_remove_quality_entries_cb, gb_main));
290	aws->create_button("Remove", "Remove", "R");
291
292	return aws;
293	}

Note: See TracBrowser for help on using the repository browser.

Download in other formats: