source: branches/profile/SEQ_QUALITY/SQ_main.cxx

Last change on this file was 12757, checked in by westram, 5 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
50void 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
70static 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
204static 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
209AW_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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