source: tags/initial/PHYLO/PH_matr.cxx

Last change on this file was 2, checked in by oldcode, 23 years ago

Initial revision
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 6.5 KB
Line 
1#include "include.hxx"
2
3extern void ph_view_matrix_cb(AW_window *);
4
5
6#define CHECK_NAN(x) if ( (!(x>=0.0)) && (!(x<0.0))  ) *(int *)0=0;
7
8
9static AP_smatrix *global_ratematrix = 0;
10
11
12void set_globel_r_m_value(AW_root *aw_root, long i, long j) {
13        char buffer[256];
14        sprintf(buffer,"phyl/ratematrix/val_%li_%li",i,j);
15        global_ratematrix->set(i,j,aw_root->awar(buffer)->read_float());
16}
17
18void create_matrix_variables(AW_root *aw_root, AW_default def)
19{
20    aw_root->awar_string( "tmp/dummy_string","0",def);
21
22
23    aw_root->awar_string( "phyl/which_species","marked",def);
24    aw_root->awar_string( "phyl/alignment","",def);
25
26    aw_root->awar_string( "phyl/filter/alignment","none",def);
27    aw_root->awar_string( "phyl/filter/name","none",def);
28    aw_root->awar_string( "phyl/filter/filter","",def);
29
30    aw_root->awar_string( "phyl/weights/name","none",def);
31    aw_root->awar_string( "phyl/weights/alignment","none",def);
32
33    aw_root->awar_string( "phyl/rates/name","none",def);
34    aw_root->awar_string( "phyl/cancel/chars",".",def);
35    aw_root->awar_string( "phyl/correction/transformation","none",def);
36
37    aw_root->awar("phyl/filter/alignment")->map("phyl/alignment");
38    aw_root->awar("phyl/weights/alignment")->map("phyl/alignment");
39
40    aw_root->awar_string( "tmp/phyl/save_matrix/file_name", "infile", def);
41    aw_root->awar_string( "tmp/phyl/save_matrix/directory", ".", def);
42    aw_root->awar_string( "tmp/phyl/save_matrix/filter", "", def);
43
44    aw_root->awar_string( "phyl/tree/tree_name","tree_temp",def);
45
46    aw_root->awar_float( "phyl/alpha",1.0,def);
47
48    global_ratematrix = new AP_smatrix(AP_MAX);
49
50    long i,j;
51    for (i=0; i <AP_MAX; i++){
52        for (j=0; j <AP_MAX; j++){
53            if (i!=j) global_ratematrix->set(i,j,1.0);
54        }
55    }
56    for (i=AP_A; i <AP_MAX; i*=2){
57        for (j = AP_A; j < i; j*=2){
58            char buffer[256];
59            sprintf(buffer,"phyl/ratematrix/val_%li_%li",i,j);
60            aw_root->awar_float(buffer, 1.0, def);
61            aw_root->awar(buffer)->add_callback((AW_RCB)set_globel_r_m_value,(AW_CL)i,(AW_CL)j);
62        }
63    }
64}
65
66
67
68
69void ph_calculate_matrix_cb(AW_window *aww,AW_CL cb1,AW_CL cb2)
70{ AWUSE(cb1); AWUSE(cb2);
71  char *cancel,*transformation;
72
73  if(!PHDATA::ROOT) 
74   { aw_message("data_base not opened !!");
75     return;
76   }
77  AW_root *aw_root = aww->get_root();
78
79  PH_TRANSFORMATION trans = PH_TRANSFORMATION_NONE;
80// transformation = aw_root->awar("phyl/correction/transformation")->read_string();
81transformation=strdup(PH_TRANSFORMATION_JUKES_CANTOR_STRING);
82
83//  double alpha = aw_root->awar("phyl/alpha")->read_float();
84double alpha = 1.0;
85  cancel = aw_root->awar("phyl/cancel/chars")->read_string();
86 printf("\ntransformation: %s",transformation);
87 printf("\ncancel: %s\n",cancel);
88  if (!strcmp(transformation,PH_TRANSFORMATION_JUKES_CANTOR_STRING))
89              trans = PH_TRANSFORMATION_JUKES_CANTOR;
90  else if (!strcmp(transformation,PH_TRANSFORMATION_KIMURA_STRING))
91              trans = PH_TRANSFORMATION_KIMURA;
92  else if (!strcmp(transformation,PH_TRANSFORMATION_TAJIMA_NEI_STRING))
93              trans = PH_TRANSFORMATION_TAJIMA_NEI;
94  else if (!strcmp(transformation,PH_TRANSFORMATION_TAJIMA_NEI_PAIRWISE_STRING))
95              trans = PH_TRANSFORMATION_TAJIMA_NEI_PAIRWISE;
96  else if (!strcmp(transformation,PH_TRANSFORMATION_BANDELT_STRING))
97              trans = PH_TRANSFORMATION_BANDELT;
98  else if (!strcmp(transformation,PH_TRANSFORMATION_BANDELT_JC_STRING))
99              trans = PH_TRANSFORMATION_BANDELT_JC;
100  else if (!strcmp(transformation,PH_TRANSFORMATION_BANDELT2_STRING))
101              trans = PH_TRANSFORMATION_BANDELT2;
102  else if (!strcmp(transformation,PH_TRANSFORMATION_BANDELT2_JC_STRING))
103              trans = PH_TRANSFORMATION_BANDELT2_JC;
104
105  GB_ERROR error = PHDATA::ROOT->calculate_matrix(".-",alpha,trans);
106
107  if (error) aw_message(error);
108  delete transformation;
109  delete cancel;
110  if(!error) ph_view_matrix_cb(aww);  // call callback directly to see what you did
111}
112
113void ph_save_matrix_cb(AW_window *aww)
114        {                       // save the matrix
115        if (!PHDATA::ROOT) return;
116        PHDATA::ROOT->print();
117        char *filename = aww->get_root()->awar("tmp/phyl/save_matrix/file_name")->read_string();
118        GB_ERROR error = PHDATA::ROOT->save(filename);
119        delete filename;
120        if (error) aw_message(error);
121        aww->hide();
122}
123
124AW_window *create_save_matrix_window(AW_root *aw_root, char *base_name)
125        {
126        AW_window_simple *aws = new AW_window_simple;
127        aws->init( aw_root, "SAVE_MATRIX", "SAVE MATRIX TO DISC", 10, 10 );
128        aws->load_xfig("sel_box.fig");
129
130        aws->at("close");aws->callback((AW_CB0)AW_POPDOWN);
131        aws->create_button("CLOSE","CLOSE","C");                           
132
133        aws->at("save");aws->callback(ph_save_matrix_cb);
134        aws->create_button("SAVE","SAVE","S");                     
135
136        aws->callback( (AW_CB0)AW_POPDOWN);
137        aws->at("cancel");
138        aws->create_button("CANCEL","CANCEL","C");                         
139
140        awt_create_selection_box((AW_window *)aws,base_name);
141
142        return (AW_window *)aws;
143}
144
145
146AW_window *awt_create_select_cancel_window(AW_root *aw_root)
147        {
148        AW_window_simple *aws = new AW_window_simple;
149        aws->init( aw_root, "CANCEL_SELECT", "CANCEL SELECT", 10, 10 );
150        aws->load_xfig("phylo/cancel.fig");
151
152        aws->at("close");aws->callback((AW_CB0)AW_POPDOWN);
153        aws->create_button("CLOSE","CLOSE","C");                           
154
155        aws->at("cancel");
156        aws->create_input_field("phyl/cancel/chars",12);
157
158        return (AW_window *)aws;
159}
160
161
162
163
164AW_window *create_matrix_window(AW_root *aw_root)
165{ AW_window_simple *aws = new AW_window_simple;
166  aws->init( aw_root, "DISTANCE_TABLE", "DistanceTable", 10, 10 );
167  aws->load_xfig("phylo/matrix.fig");
168  aws->button_length( 10 );
169 
170  aws->at("close");aws->callback((AW_CB0)AW_POPDOWN);
171  aws->create_button("CLOSE","CLOSE","C");                   
172 
173  aws->at("point_opts");
174  aws->create_option_menu("phyl/matrix/point","'.' in column      ","0");  // "0": no shortcut
175    aws->insert_option("forget pair for distancematrix","0",0);
176    aws->insert_option("use distancetable","0",1);
177  aws->update_option_menu();
178
179  aws->at("minus_opts");
180  aws->create_option_menu("phyl/matrix/minus","'-' in column      ","0");
181    aws->insert_option("forget pair for distancematrix","0",0);
182    aws->insert_option("use distancetable","0",1);
183  aws->update_option_menu();
184
185  aws->at("rest_opts");
186  aws->create_option_menu("phyl/matrix/rest","rest in column     ","0");
187    aws->insert_option("forget pair for distancematrix","0",0);
188    aws->insert_option("use distancetable","0",1);
189  aws->update_option_menu();
190
191  aws->at("lower_opts");
192  aws->create_option_menu("phyl/matrix/lower","'acgtu' in column  ","0");
193    aws->insert_option("forget pair for distancematrix","0",0);
194    aws->insert_option("use distancetable","0",1);
195  aws->update_option_menu();
196
197  return (AW_window *)aws;
198}
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