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source: branches/profile/SEQ_QUALITY/SQ_main.cxx

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Last change on this file was 12757, checked in by westram, 11 years ago
unify selectionlist creator names awt_create_selection_list_on_pt_servers remove param 'popup', instead split into two function (button and list) as done for SAIs
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 11.3 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 <arbdbt.h>
27	#include <arb_global_defs.h>
28
29	// --------------------------------------------------------------------------------
30
31	#define AWAR_SQ_PERM "seq_quality/" // saved in properties
32	#define AWAR_SQ_TEMP "tmp/seq_quality/" // not saved in properties
33	#define AWAR_SQ_WEIGHT_BASES AWAR_SQ_PERM "weight_bases"
34	#define AWAR_SQ_WEIGHT_DEVIATION AWAR_SQ_PERM "weight_deviation"
35	#define AWAR_SQ_WEIGHT_HELIX AWAR_SQ_PERM "weight_helix"
36	#define AWAR_SQ_WEIGHT_CONSENSUS AWAR_SQ_PERM "weight_consensus"
37	#define AWAR_SQ_WEIGHT_IUPAC AWAR_SQ_PERM "weight_iupac"
38	#define AWAR_SQ_WEIGHT_GC AWAR_SQ_PERM "weight_gc"
39
40	#define AWAR_SQ_MARK_ONLY_FLAG AWAR_SQ_PERM "mark_only_flag"
41	#define AWAR_SQ_MARK_FLAG AWAR_SQ_PERM "mark_flag"
42	#define AWAR_SQ_MARK_BELOW AWAR_SQ_PERM "mark_below"
43	#define AWAR_SQ_REEVALUATE AWAR_SQ_PERM "reevaluate"
44
45	#define AWAR_FILTER_PREFIX AWAR_SQ_TEMP "filter/"
46	#define AWAR_FILTER_NAME AWAR_FILTER_PREFIX "name"
47	#define AWAR_FILTER_FILTER AWAR_FILTER_PREFIX "filter"
48	#define AWAR_FILTER_ALI AWAR_FILTER_PREFIX "alignment"
49
50	void SQ_create_awars(AW_root * aw_root, AW_default aw_def) {
51	aw_root->awar_int(AWAR_SQ_WEIGHT_BASES, 5, aw_def);
52	aw_root->awar_int(AWAR_SQ_WEIGHT_DEVIATION, 15, aw_def);
53	aw_root->awar_int(AWAR_SQ_WEIGHT_HELIX, 15, aw_def);
54	aw_root->awar_int(AWAR_SQ_WEIGHT_CONSENSUS, 50, aw_def);
55	aw_root->awar_int(AWAR_SQ_WEIGHT_IUPAC, 5, aw_def);
56	aw_root->awar_int(AWAR_SQ_WEIGHT_GC, 10, aw_def);
57	aw_root->awar_int(AWAR_SQ_MARK_ONLY_FLAG, 0, aw_def);
58	aw_root->awar_int(AWAR_SQ_MARK_FLAG, 1, aw_def);
59	aw_root->awar_int(AWAR_SQ_MARK_BELOW, 40, aw_def);
60	aw_root->awar_int(AWAR_SQ_REEVALUATE, 0, aw_def);
61	aw_root->awar_string(AWAR_FILTER_NAME, "none", aw_def);
62	aw_root->awar_string(AWAR_FILTER_FILTER, "", aw_def);
63	AW_awar *awar_ali = aw_root->awar_string(AWAR_FILTER_ALI, "", aw_def);
64	awar_ali->map(AWAR_DEFAULT_ALIGNMENT);
65	}
66
67	// --------------------------------------------------------------------------------
68
69
70	static void sq_calc_seq_quality_cb(AW_window * aww, AW_CL res_from_awt_create_select_filter, AW_CL cl_gb_main) {
71	GBDATA gb_main = (GBDATA)cl_gb_main;
72	AW_root *aw_root = aww->get_root();
73	GB_ERROR error = 0;
74	GBT_TREE *tree = 0;
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, GBT_TREE_NodeFactory());
87	if (!tree) error = GB_await_error();
88	else {
89	error = GBT_link_tree(tree, gb_main, false, NULL, NULL);
90	if (!error) {
91	GBT_TreeRemoveType mode = marked_only ? GBT_KEEP_MARKED : GBT_REMOVE_ZOMBIES;
92	tree = GBT_remove_leafs(tree, mode, NULL, NULL, NULL);
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((adfiltercbstruct)res_from_awt_create_select_filter);
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 == 0) {
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(SQ_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	delete tree;
202	}
203
204	static void sq_remove_quality_entries_cb(AW_window *, AW_CL cl_gb_main) {
205	GBDATA gb_main = (GBDATA)cl_gb_main;
206	SQ_remove_quality_entries(gb_main);
207	}
208
209	AW_window SQ_create_seq_quality_window(AW_root aw_root, GBDATA *gb_main) {
210	// create window for sequence quality calculation (called only once)
211
212	AW_window_simple *aws = new AW_window_simple;
213
214	aws->init(aw_root, "CALC_SEQ_QUALITY", "CALCULATE SEQUENCE QUALITY");
215	aws->load_xfig("seq_quality.fig");
216
217	aws->at("close");
218	aws->callback((AW_CB0) AW_POPDOWN);
219	aws->create_button("CLOSE", "CLOSE", "C");
220
221	aws->at("help");
222	aws->callback(makeHelpCallback("seq_quality.hlp"));
223	aws->create_button("HELP", "HELP", "H");
224
225	aws->at("base");
226	aws->create_input_field(AWAR_SQ_WEIGHT_BASES, 3);
227
228	aws->at("deviation");
229	aws->create_input_field(AWAR_SQ_WEIGHT_DEVIATION, 3);
230
231	aws->at("no_helices");
232	aws->create_input_field(AWAR_SQ_WEIGHT_HELIX, 3);
233
234	aws->at("consensus");
235	aws->create_input_field(AWAR_SQ_WEIGHT_CONSENSUS, 3);
236
237	aws->at("iupac");
238	aws->create_input_field(AWAR_SQ_WEIGHT_IUPAC, 3);
239
240	aws->at("gc_proportion");
241	aws->create_input_field(AWAR_SQ_WEIGHT_GC, 3);
242
243	aws->at("monly");
244	aws->create_toggle(AWAR_SQ_MARK_ONLY_FLAG);
245
246	aws->at("mark");
247	aws->create_toggle(AWAR_SQ_MARK_FLAG);
248
249	aws->at("mark_below");
250	aws->create_input_field(AWAR_SQ_MARK_BELOW, 3);
251
252	aws->at("tree");
253	awt_create_TREE_selection_list(gb_main, aws, AWAR_TREE, true);
254
255	aws->at("filter");
256	adfiltercbstruct *adfilter = awt_create_select_filter(aws->get_root(), gb_main, AWAR_FILTER_NAME);
257	aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, adfilter));
258	aws->create_button("SELECT_FILTER", AWAR_FILTER_NAME);
259
260	aws->at("go");
261	aws->callback(sq_calc_seq_quality_cb, (AW_CL)adfilter, (AW_CL)gb_main);
262	aws->highlight();
263	aws->create_button("GO", "GO", "G");
264
265	aws->at("remove");
266	aws->callback(sq_remove_quality_entries_cb, (AW_CL)gb_main);
267	aws->create_button("Remove", "Remove", "R");
268
269	aws->at("reevaluate");
270	aws->label("Re-Evaluate only");
271	aws->create_toggle(AWAR_SQ_REEVALUATE);
272
273	return aws;
274	}

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