source: tags/arb_5.0/EDIT/edit_naligner.cxx

Last change on this file was 5901, checked in by westram, 17 years ago
  • AW_BOOL → bool
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 10.6 KB
Line 
1#include <stdio.h>
2#include <stdlib.h>     // system
3#include <arbdb.h>
4#include <arbdbt.h>
5#include <aw_root.hxx>
6#include <aw_device.hxx>
7#include <aw_window.hxx>
8#include <aw_awars.hxx>
9#include <awt.hxx>
10#include <awt_sel_boxes.hxx>
11#include <iostream>
12#include <string.h>
13
14extern GBDATA *GLOBAL_gb_main;
15
16void aed_start_naligning(AW_window *aw) {
17    AW_root *root = aw->get_root();
18    char    *buffer;
19    int      i,j;
20
21    GBS_strstruct *strstruct = GBS_stropen(1000);
22    GBS_strcat(strstruct,"xterm -sl 1000 -sb -e sh -c 'LD_LIBRARY_PATH=\"");
23    GBS_strcat(strstruct,GB_getenv("LD_LIBRARY_PATH"));
24    GBS_strcat(strstruct,"\";export LD_LIBRARY_PATH;for i in ");
25    if ( root->awar("naligner/what")->read_int() ) {
26        GB_transaction dummy(GLOBAL_gb_main);
27        for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL_gb_main);
28             gb_species;
29             gb_species = GBT_next_marked_species(gb_species))
30        {
31            GBS_chrcat(strstruct, '\"');
32            GBS_strcat(strstruct, GBT_read_name(gb_species));
33            GBS_strcat(strstruct, "\" ");
34        }
35    }else{
36        char *species_name = root->awar( AWAR_SPECIES_NAME )->read_string();
37        GBS_strcat(strstruct,"\"");
38        GBS_strcat(strstruct,species_name);
39        GBS_strcat(strstruct,"\" ");
40        delete species_name;
41    }
42
43
44    GBS_strcat(strstruct,"; do arb_naligner");
45
46
47    if ( root->awar("naligner/against")->read_int() ) {
48        GBS_strcat(strstruct," -PARB_PT_SERVER");
49        GBS_intcat(strstruct,   root->awar( "naligner/pt_server" )->read_int()  );
50    }else{
51        GBS_strcat(strstruct," \"-f");
52        char *family = root->awar("naligner/sagainst")->read_string();
53        GBS_strcat(strstruct,family);
54        delete family;
55        GBS_strcat(strstruct,"\"");
56    }
57    GBS_strcat(strstruct," \"-s$i\" ");
58
59    if (root->awar( "naligner/mark_profile" )->read_int() ) GBS_strcat(strstruct," -mf");
60    if (root->awar( "naligner/unmark_sequence" )->read_int() ) GBS_strcat(strstruct," -us");
61
62    GBS_strcat(strstruct," -minf");     GBS_intcat(strstruct,root->awar("naligner/minf")->read_int());
63    GBS_strcat(strstruct," -maxf");     GBS_intcat(strstruct,root->awar("naligner/maxf")->read_int());
64    GBS_strcat(strstruct," -minw");     GBS_floatcat(strstruct,root->awar("naligner/minw")->read_float());
65    GBS_strcat(strstruct," -maxew");    GBS_floatcat(strstruct,root->awar("naligner/maxew")->read_float());
66    GBS_strcat(strstruct," -ib");       GBS_intcat(strstruct,root->awar("naligner/det/ib")->read_int());
67    GBS_strcat(strstruct," -ic");       GBS_intcat(strstruct,root->awar("naligner/det/ic")->read_int());
68
69    GBS_strcat(strstruct," -cl");       GBS_floatcat(strstruct, root->awar("naligner/det/cl")->read_float());
70
71
72
73
74    GBS_strcat(strstruct," -cm");       GBS_floatcat(strstruct,root->awar("naligner/det/cm")->read_float());
75    GBS_strcat(strstruct," -ch");       GBS_floatcat(strstruct,root->awar("naligner/det/ch")->read_float());
76    GBS_strcat(strstruct," -mgf");      GBS_floatcat(strstruct,root->awar("naligner/igap_panelty")->read_float());
77    GBS_strcat(strstruct," -mma1");
78    GBS_strcat(strstruct," -msub");
79    for (i=0;i<5;i++){
80        for (j=0;j<5;j++) {
81            char var[100];
82            if ( i==4 || j==4 ) {               /* gap panelty */
83                if (i==4 && j==4) {
84                    GBS_floatcat(strstruct,0.0);
85                }else{
86                    GBS_floatcat(strstruct,root->awar("naligner/gap_panelty")->read_float());
87                    GBS_chrcat(strstruct,',');
88                }
89            }else{
90                if (i<j) sprintf(var,"naligner/%c%c","acgt-"[i],"acgt-"[j]);
91                else    sprintf(var,"naligner/%c%c","acgt-"[j],"acgt-"[i]);
92                GBS_floatcat(strstruct,root->awar(var)->read_float());
93                if (i<4 || j<4) GBS_chrcat(strstruct,',');
94            }
95        }
96    }
97    GBS_strcat(strstruct," || echo \"Aligner failed\";done;");
98
99
100    GBS_strcat(strstruct,"echo press \"(return)\" to close window;read a' &");
101    buffer = GBS_strclose(strstruct);
102    system(buffer);
103    printf("%s\n",buffer);
104    delete buffer;
105}
106
107
108void create_naligner_variables(AW_root *root,AW_default db1)
109{
110    root->awar_int(     "naligner/what", 0 ,    db1);
111
112    root->awar_int(     "naligner/against", 0 ,    db1);
113    root->awar_string(  "naligner/sagainst", "" ,    db1);
114    root->awar_int(     "naligner/pt_server", -1 ,    db1);
115
116    root->awar_int(     "naligner/mark_profile", 1 ,       db1);
117    root->awar_int(     "naligner/unmark_sequence", 0 ,       db1);
118
119
120    root->awar_float(   "naligner/aa", 0.0 ,    db1);
121    root->awar_float(   "naligner/ac", 3.0 ,    db1);
122    root->awar_float(   "naligner/ag", 1.0 ,    db1);
123    root->awar_float(   "naligner/at", 3.0 ,    db1);
124    root->awar_float(   "naligner/cc", 0.0 ,    db1);
125    root->awar_float(   "naligner/cg", 3.0 ,    db1);
126    root->awar_float(   "naligner/ct", 1.0 ,    db1);
127    root->awar_float(   "naligner/gg", 0.0 ,    db1);
128    root->awar_float(   "naligner/gt", 3.0 ,    db1);
129    root->awar_float(   "naligner/tt", 0.0 ,    db1);
130    root->awar_float(   "naligner/gap_panelty", 5.0      ,    db1);
131    root->awar_float(   "naligner/igap_panelty", 0.2 ,    db1);
132    root->awar_int(     "naligner/minf", 3 ,    db1);
133    root->awar_int(     "naligner/maxf", 30 ,    db1);
134
135
136    root->awar_float(   "naligner/minw", .7 ,    db1);
137    root->awar_float(   "naligner/maxew", .2 ,    db1);
138
139    root->awar_float(   "naligner/det/cl", .25 ,    db1);
140    root->awar_float(   "naligner/det/cm", .5 ,    db1);
141    root->awar_float(   "naligner/det/ch", .8 ,    db1);
142    root->awar_int(     "naligner/det/ib", 5 ,    db1);
143    root->awar_int(     "naligner/det/ic", 5 ,    db1);
144
145}
146
147void ed_nalign_save(AW_window *aww)
148{
149    AW_root *root = aww->get_root();
150    root->save_default("naligner/aa");
151}
152
153AW_window *create_expert_naligner_window(AW_root *root)
154{
155    const       int     mwidth = 5;
156    AW_window_simple *aws = new AW_window_simple;
157    aws->init( root, "ALIGNER_V2_EXPERT2", "ALIGNER V2.0 EXPERT 2");
158    aws->load_xfig("ed_al_ex.fig");
159
160    aws->at("close");
161    aws->callback     ( (AW_CB0)AW_POPDOWN  );
162    aws->create_button( "CLOSE", "CLOSE", "C" );
163
164    aws->at("save");
165    aws->callback(ed_nalign_save);
166    aws->create_button("SAVE", "SAVE","S");
167
168    aws->at("minw");
169    aws->create_input_field("naligner/minw",mwidth);
170
171    aws->at("maxew");
172    aws->create_input_field("naligner/maxew",mwidth);
173
174    aws->at("ib");
175    aws->create_input_field("naligner/det/ib",mwidth);
176
177    aws->at("ic");
178    aws->create_input_field("naligner/det/ic",mwidth);
179
180    aws->at("cl");
181    aws->create_input_field("naligner/det/cl",mwidth);
182
183    aws->at("cm");
184    aws->create_input_field("naligner/det/cm",mwidth);
185
186    aws->at("ch");
187    aws->create_input_field("naligner/det/ch",mwidth);
188
189    return (AW_window *)aws;
190}
191
192AW_window *create_special_naligner_window(AW_root *root, AW_CL cd2)
193{
194    AW_window_simple *aws = new AW_window_simple;
195    const       int     mwidth = 3;
196    aws->init( root, "ALIGNER_V2_EXPERT", "ALIGNER V2.0 EXPERT");
197    aws->load_xfig("ed_al_sp.fig");
198
199    AWUSE(cd2);
200    aws->label_length(22);
201
202    aws->at("close");
203    aws->callback     ( (AW_CB0)AW_POPDOWN  );
204    aws->create_button( "CLOSE", "CLOSE", "C" );
205
206    aws->at("minr");
207    aws->create_input_field( "naligner/minf", 6);
208
209    aws->at("maxr");
210    aws->create_input_field( "naligner/maxf", 6);
211
212    aws->at("aa");
213    aws->create_input_field("naligner/aa",mwidth);
214    aws->at("ac");
215    aws->create_input_field("naligner/ac",mwidth);
216    aws->at("ag");
217    aws->create_input_field("naligner/ag",mwidth);
218    aws->at("at");
219    aws->create_input_field("naligner/at",mwidth);
220
221    aws->at("ca");
222    aws->create_input_field("naligner/ac",mwidth);
223    aws->at("cc");
224    aws->create_input_field("naligner/cc",mwidth);
225    aws->at("cg");
226    aws->create_input_field("naligner/cg",mwidth);
227    aws->at("ct");
228    aws->create_input_field("naligner/ct",mwidth);
229
230    aws->at("ga");
231    aws->create_input_field("naligner/ag",mwidth);
232    aws->at("gc");
233    aws->create_input_field("naligner/cg",mwidth);
234    aws->at("gg");
235    aws->create_input_field("naligner/gg",mwidth);
236    aws->at("gt");
237    aws->create_input_field("naligner/gt",mwidth);
238
239    aws->at("ta");
240    aws->create_input_field("naligner/at",mwidth);
241    aws->at("tc");
242    aws->create_input_field("naligner/ct",mwidth);
243    aws->at("tg");
244    aws->create_input_field("naligner/gt",mwidth);
245    aws->at("tt");
246    aws->create_input_field("naligner/tt",mwidth);
247
248    aws->at("gap");
249    aws->create_input_field("naligner/gap_panelty",4);
250
251    aws->at("igap");
252    aws->create_input_field("naligner/igap_panelty",4);
253
254    aws->at("expert");
255    aws->callback((AW_CB1)AW_POPUP,(AW_CL)create_expert_naligner_window);
256    aws->create_button("EXPERT_OPTIONS", "EXPERT2","E");
257
258    aws->at("save");
259    aws->callback(ed_nalign_save);
260    aws->create_button("SAAVE", "SAVE","S");
261
262    return (AW_window *)aws;
263}
264
265AW_window *create_naligner_window( AW_root *root, AW_CL cd2 ) {
266
267    AW_window_simple *aws = new AW_window_simple;
268    aws->init( root, "ALIGNER_V2","ALIGNER V2.0");
269    aws->load_xfig("awt/align.fig");
270
271    AWUSE(cd2);
272
273    aws->label_length( 10 );
274    aws->button_length( 10 );
275
276    aws->at( "close" );
277    aws->callback     ( (AW_CB0)AW_POPDOWN  );
278    aws->create_button( "CLOSE", "CLOSE", "O" );
279
280    aws->at( "help" );
281    aws->callback     ( AW_POPUP_HELP, (AW_CL) "ne_align_seq.hlp"  );
282    aws->create_button( "HELP", "HELP" );
283
284    aws->at( "align" );
285    aws->callback     ( aed_start_naligning );
286    aws->highlight();
287    aws->create_button( "GO", "GO", "G");
288
289    aws->at( "expert" );
290    aws->callback     ( (AW_CB1)AW_POPUP,(AW_CL)create_special_naligner_window );
291    aws->create_button( "OPTIONS", "PARAMETERS", "E");
292
293    aws->at("what");
294    aws->create_toggle_field("naligner/what","Align","A");
295    aws->insert_toggle("Selected Species:","S",0);
296    aws->insert_default_toggle("Marked Species","M",1);
297    aws->update_toggle_field();
298
299    aws->at( "swhat" );
300    aws->create_input_field( AWAR_SPECIES_NAME, 2);
301
302    aws->at("against");
303    aws->create_toggle_field("naligner/against","Reference","g");
304    aws->insert_toggle("Species by name","S",0);
305    aws->insert_default_toggle("Auto search by pt_server","S",1);
306    aws->update_toggle_field();
307
308    aws->at( "sagainst" );
309    aws->create_input_field( "naligner/sagainst", 2);
310
311    aws->label_length( 25 );
312
313    aws->at( "pt_server" );
314    aws->label("PT_SERVER:");
315    awt_create_selection_list_on_pt_servers(aws, "naligner/pt_server", true);
316
317    aws->at( "mark" );
318    aws->label_length(40);
319    aws->label("Mark sequences found by the pt_server");
320    aws->create_toggle( "naligner/mark_profile");
321
322    return (AW_window *)aws;
323}
Note: See TracBrowser for help on using the repository browser.