1 | // =============================================================== // |
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2 | // // |
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3 | // File : GEN_map.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in 2001 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // =============================================================== // |
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11 | |
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12 | #include "GEN_local.hxx" |
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13 | #include "GEN_gene.hxx" |
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14 | #include "GEN_graphic.hxx" |
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15 | #include "GEN_nds.hxx" |
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16 | #include "EXP_local.hxx" |
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17 | |
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18 | #include <dbui.h> |
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19 | #include <db_query.h> |
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20 | |
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21 | #include <awt.hxx> |
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22 | #include <awt_prompt.hxx> |
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23 | #include <awt_input_mask.hxx> |
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24 | |
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25 | #include <aw_preset.hxx> |
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26 | #include <aw_awars.hxx> |
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27 | #include <aw_question.hxx> |
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28 | #include <AW_rename.hxx> |
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29 | #include <aw_msg.hxx> |
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30 | #include <aw_root.hxx> |
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31 | |
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32 | #include <adGene.h> |
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33 | #include <ad_cb.h> |
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34 | |
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35 | #include <arb_progress.h> |
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36 | #include <rootAsWin.h> |
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37 | #include <mode_text.h> |
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38 | |
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39 | #include <map> |
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40 | |
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41 | using namespace std; |
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42 | |
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43 | // ----------------------- |
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44 | // GEN_map_window |
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45 | |
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46 | class GEN_map_window : public AW_window_menu_modes { // derived from a Noncopyable |
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47 | int window_nr; |
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48 | GEN_graphic *gen_graphic; |
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49 | AWT_canvas *gen_canvas; |
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50 | |
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51 | public: |
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52 | GEN_map_window(int window_nr_) : |
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53 | AW_window_menu_modes(), |
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54 | window_nr(window_nr_), |
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55 | gen_graphic(NULp), |
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56 | gen_canvas(NULp) |
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57 | {} |
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58 | |
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59 | void init(AW_root *root, GBDATA *gb_main); |
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60 | |
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61 | GEN_graphic *get_graphic() const { gen_assert(gen_graphic); return gen_graphic; } |
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62 | AWT_canvas *get_canvas() const { gen_assert(gen_canvas); return gen_canvas; } |
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63 | int get_nr() const { return window_nr; } |
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64 | |
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65 | GBDATA *get_gb_main() const { return get_canvas()->gb_main; } |
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66 | }; |
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67 | |
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68 | // ------------------------ |
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69 | // GEN_map_manager |
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70 | |
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71 | DECLARE_CBTYPE_FVV_AND_BUILDERS(GenmapWindowCallback, void, GEN_map_window*); // generates makeGenmapWindowCallback |
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72 | |
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73 | class GEN_map_manager : virtual Noncopyable { |
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74 | static AW_root *aw_root; |
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75 | static GBDATA *gb_main; |
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76 | static GEN_map_manager *the_manager; // there can be only one! |
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77 | |
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78 | int window_counter; |
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79 | GEN_map_window **windows; // array of managed windows |
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80 | int windows_size; // size of 'windows' array |
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81 | |
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82 | public: |
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83 | |
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84 | GEN_map_manager(); |
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85 | |
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86 | static bool initialized() { return aw_root; } |
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87 | static void initialize(AW_root *aw_root_, GBDATA *gb_main_) { aw_root = aw_root_; gb_main = gb_main_; } |
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88 | |
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89 | static GEN_map_manager *get_map_manager(); |
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90 | |
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91 | GEN_map_window *get_map_window(int nr); |
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92 | |
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93 | int no_of_managed_windows() { return window_counter; } |
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94 | |
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95 | static void with_all_mapped_windows(const GenmapWindowCallback& gwcb); |
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96 | static void with_all_mapped_windows(void (*cb)(GEN_map_window*)) { with_all_mapped_windows(makeGenmapWindowCallback(cb)); } |
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97 | }; |
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98 | |
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99 | // ____________________________________________________________ |
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100 | // start of implementation of class GEN_map_manager: |
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101 | |
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102 | AW_root *GEN_map_manager::aw_root = NULp; |
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103 | GBDATA *GEN_map_manager::gb_main = NULp; |
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104 | GEN_map_manager *GEN_map_manager::the_manager = NULp; |
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105 | |
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106 | GEN_map_manager::GEN_map_manager() : |
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107 | window_counter(0), |
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108 | windows(new GEN_map_window *[5]), |
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109 | windows_size(5) |
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110 | { |
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111 | gen_assert(!the_manager); // only one instance allowed |
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112 | the_manager = this; |
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113 | } |
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114 | |
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115 | GEN_map_manager *GEN_map_manager::get_map_manager() { |
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116 | if (!the_manager) { |
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117 | gen_assert(aw_root); // call initialize() before! |
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118 | new GEN_map_manager; // sets the manager |
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119 | gen_assert(the_manager); |
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120 | } |
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121 | return the_manager; |
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122 | } |
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123 | |
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124 | void GEN_map_manager::with_all_mapped_windows(const GenmapWindowCallback& gwcb) { |
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125 | if (aw_root) { // no genemap opened yet |
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126 | GEN_map_manager *mm = get_map_manager(); |
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127 | int winCount = mm->no_of_managed_windows(); |
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128 | for (int nr = 0; nr<winCount; ++nr) { |
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129 | gwcb(mm->get_map_window(nr)); |
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130 | } |
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131 | } |
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132 | } |
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133 | |
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134 | GEN_map_window *GEN_map_manager::get_map_window(int nr) { |
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135 | gen_assert(aw_root); |
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136 | gen_assert(nr >= 0); |
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137 | if (nr<window_counter) { |
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138 | return windows[nr]; // window has already been created before |
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139 | } |
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140 | |
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141 | gen_assert(nr == window_counter); // increase nr sequentially! |
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142 | |
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143 | window_counter++; |
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144 | if (window_counter>windows_size) { |
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145 | int new_windows_size = windows_size+5; |
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146 | GEN_map_window **new_windows = new GEN_map_window*[new_windows_size]; |
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147 | |
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148 | for (int i = 0; i<windows_size; ++i) new_windows[i] = windows[i]; |
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149 | |
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150 | delete [] windows; |
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151 | windows = new_windows; |
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152 | windows_size = new_windows_size; |
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153 | } |
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154 | |
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155 | gen_assert(nr<windows_size); |
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156 | |
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157 | windows[nr] = new GEN_map_window(nr); |
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158 | windows[nr]->init(aw_root, gb_main); |
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159 | |
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160 | return windows[nr]; |
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161 | } |
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162 | |
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163 | // -end- of implementation of class GEN_map_manager. |
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164 | |
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165 | |
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166 | |
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167 | const char *GEN_window_local_awar_name(const char *awar_name, int window_nr) { |
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168 | return GBS_global_string("%s_%i", awar_name, window_nr); |
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169 | } |
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170 | |
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171 | static void reinit_NDS_4_window(GEN_map_window *win) { |
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172 | AWT_auto_refresh allowed_on(win->get_canvas()); |
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173 | win->get_graphic()->get_gen_root()->reinit_NDS(); |
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174 | win->get_canvas()->request_refresh(); |
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175 | } |
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176 | |
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177 | static void GEN_NDS_changed(GBDATA *gb_viewkey) { |
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178 | GBDATA *gb_main = GB_get_root(gb_viewkey); |
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179 | GEN_make_node_text_init(gb_main); |
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180 | GEN_map_manager::with_all_mapped_windows(reinit_NDS_4_window); |
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181 | } |
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182 | |
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183 | struct gene_container_changed_cb_data { |
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184 | AWT_canvas *canvas; |
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185 | GEN_graphic *graphic; |
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186 | GBDATA *gb_gene_data; // callback was installed for this gene_data |
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187 | |
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188 | gene_container_changed_cb_data() : canvas(NULp), graphic(NULp), gb_gene_data(NULp) {} |
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189 | gene_container_changed_cb_data(AWT_canvas *canvas_, GEN_graphic *graphic_, GBDATA *gb_gene_data_) : |
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190 | canvas(canvas_), |
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191 | graphic(graphic_), |
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192 | gb_gene_data(gb_gene_data_) |
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193 | {} |
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194 | }; |
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195 | |
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196 | static void GEN_gene_container_changed_cb(GBDATA*, gene_container_changed_cb_data *cb_data) { |
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197 | AWT_auto_refresh allowed_on(cb_data->canvas); |
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198 | cb_data->graphic->reinit_gen_root(cb_data->canvas, true); |
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199 | cb_data->canvas->request_refresh(); |
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200 | } |
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201 | |
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202 | int GEN_find_windowNr_for(GEN_graphic *wanted_graphic) { |
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203 | // returns window_nr of GEN_map_window using 'wanted_graphic' (or -1) |
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204 | if (GEN_map_manager::initialized()) { |
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205 | GEN_map_manager *mapman = GEN_map_manager::get_map_manager(); |
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206 | for (int window_nr = 0; window_nr<mapman->no_of_managed_windows(); ++window_nr) { |
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207 | GEN_map_window *mapwin = mapman->get_map_window(window_nr); |
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208 | if (mapwin && mapwin->get_graphic() == wanted_graphic) { |
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209 | return window_nr; |
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210 | } |
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211 | } |
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212 | } |
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213 | return -1; |
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214 | } |
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215 | |
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216 | inline GBDATA *GEN_get_local_gene_data(GEN_graphic *gg) { |
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217 | int window_nr = GEN_find_windowNr_for(gg); |
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218 | gen_assert(window_nr>=0); |
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219 | |
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220 | GBDATA *gb_gene_data = NULp; |
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221 | if (window_nr>=0) { |
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222 | const char *organism = gg->get_aw_root()->awar(AWAR_LOCAL_ORGANISM_NAME(window_nr))->read_char_pntr(); |
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223 | if (organism) { |
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224 | GBDATA *gb_main = gg->get_gb_main(); |
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225 | GBDATA *gb_species = GBT_find_species(gb_main, organism); |
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226 | if (gb_species) gb_gene_data = GEN_expect_gene_data(gb_species); |
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227 | } |
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228 | } |
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229 | |
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230 | return gb_gene_data; |
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231 | } |
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232 | |
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233 | |
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234 | static void GEN_gene_container_cb_installer(CbInstallMode install, AWT_canvas *gmw, GEN_graphic *gg) { |
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235 | typedef map<GEN_graphic*, gene_container_changed_cb_data> callback_dict; |
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236 | static callback_dict installed_callbacks; |
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237 | |
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238 | callback_dict::iterator found = installed_callbacks.find(gg); |
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239 | if (found == installed_callbacks.end()) { |
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240 | gen_assert(install == INSTALL_CBS); // if not installing -> entry has to exist! |
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241 | installed_callbacks[gg] = gene_container_changed_cb_data(gmw, gg, NULp); |
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242 | found = installed_callbacks.find(gg); |
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243 | gen_assert(found != installed_callbacks.end()); |
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244 | } |
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245 | |
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246 | gene_container_changed_cb_data *curr_cb_data = &(found->second); |
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247 | |
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248 | switch (install) { |
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249 | case INSTALL_CBS: { |
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250 | gen_assert(!curr_cb_data->gb_gene_data); // NULp means : no callback installed |
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251 | |
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252 | GBDATA *gb_main = gg->get_gb_main(); |
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253 | GB_transaction ta(gb_main); |
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254 | |
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255 | curr_cb_data->gb_gene_data = GEN_get_local_gene_data(gg); |
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256 | |
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257 | if (curr_cb_data->gb_gene_data) { |
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258 | GB_add_callback(curr_cb_data->gb_gene_data, GB_CB_CHANGED_OR_DELETED, makeDatabaseCallback(GEN_gene_container_changed_cb, curr_cb_data)); |
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259 | } |
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260 | break; |
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261 | } |
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262 | case REMOVE_CBS: { |
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263 | if (curr_cb_data->gb_gene_data) { // if callback is installed |
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264 | GB_remove_callback(curr_cb_data->gb_gene_data, GB_CB_CHANGED_OR_DELETED, makeDatabaseCallback(GEN_gene_container_changed_cb, curr_cb_data)); |
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265 | curr_cb_data->gb_gene_data = NULp; |
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266 | } |
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267 | break; |
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268 | } |
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269 | case FORGET_CBS: { |
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270 | curr_cb_data->gb_gene_data = NULp; |
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271 | break; |
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272 | } |
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273 | } |
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274 | } |
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275 | |
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276 | static void GEN_jump_cb(AW_window *aww, bool force_center_if_fits) { |
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277 | // force_center_if_fits==true => center gene if it fits into display |
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278 | GEN_map_window *win = DOWNCAST(GEN_map_window*, aww); |
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279 | |
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280 | AW_device *device = win->get_graphic()->get_device(); |
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281 | const AW_screen_area& screen = device->get_area_size(); |
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282 | #if defined(DEBUG) |
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283 | printf("Window %i: screen is: %i/%i -> %i/%i\n", win->get_nr(), screen.l, screen.t, screen.r, screen.b); |
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284 | #endif // DEBUG |
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285 | |
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286 | AWT_canvas *canvas = win->get_canvas(); |
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287 | AWT_auto_refresh allowed_on(canvas); |
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288 | const GEN_root *gen_root = win->get_graphic()->get_gen_root(); |
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289 | if (gen_root) { |
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290 | const AW::Rectangle& wrange = gen_root->get_selected_range(); |
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291 | |
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292 | if (wrange.valid()) { |
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293 | #if defined(DEBUG) |
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294 | printf("Window %i: Draw world range of selected gene is: %f/%f -> %f/%f\n", |
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295 | win->get_nr(), wrange.left(), wrange.top(), wrange.right(), wrange.bottom()); |
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296 | #endif // DEBUG |
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297 | |
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298 | AW::Rectangle srange = device->transform(wrange); |
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299 | #if defined(DEBUG) |
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300 | printf("Window %i: Draw screen range of selected gene is: %f/%f -> %f/%f\n", |
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301 | win->get_nr(), srange.left(), srange.top(), srange.right(), srange.bottom()); |
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302 | #endif // DEBUG |
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303 | |
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304 | int scrollx = 0; |
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305 | int scrolly = 0; |
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306 | |
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307 | if (srange.top() < 0) { |
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308 | scrolly = AW_INT(srange.top())-2; |
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309 | } |
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310 | else if (srange.bottom() > screen.b) { |
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311 | scrolly = AW_INT(srange.bottom())-screen.b+2; |
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312 | } |
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313 | if (srange.left() < 0) { |
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314 | scrollx = AW_INT(srange.left())-2; |
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315 | } |
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316 | else if (srange.right() > screen.r) { |
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317 | scrollx = AW_INT(srange.right())-screen.r+2; |
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318 | } |
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319 | |
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320 | if (force_center_if_fits) { |
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321 | if (!scrollx) { // no scrolling needed, i.e. gene fits onto display horizontally |
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322 | int gene_center_x = AW_INT((srange.left()+srange.right())/2); |
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323 | int screen_center_x = (screen.l+screen.r)/2; |
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324 | scrollx = gene_center_x-screen_center_x; |
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325 | #if defined(DEBUG) |
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326 | printf("center x\n"); |
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327 | #endif // DEBUG |
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328 | } |
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329 | if (!scrolly) { // no scrolling needed, i.e. gene fits onto display vertically |
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330 | int gene_center_y = AW_INT((srange.top()+srange.bottom())/2); |
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331 | int screen_center_y = (screen.t+screen.b)/2; |
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332 | scrolly = gene_center_y-screen_center_y; |
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333 | #if defined(DEBUG) |
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334 | printf("center y\n"); |
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335 | #endif // DEBUG |
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336 | } |
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337 | } |
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338 | |
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339 | #if defined(DEBUG) |
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340 | printf("scroll %i/%i\n", scrollx, scrolly); |
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341 | #endif // DEBUG |
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342 | |
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343 | canvas->scroll(scrollx, scrolly); |
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344 | } |
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345 | } |
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346 | canvas->request_refresh(); |
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347 | } |
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348 | |
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349 | static void GEN_jump_cb_auto(AW_root *root, GEN_map_window *win, bool force_refresh, bool force_zoom_reset) { |
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350 | AWT_canvas *ntw = win->get_canvas(); |
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351 | assert_no_auto_refresh_for(ntw); // otherwise jump doesn't work! |
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352 | |
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353 | int jump = root->awar(AWAR_GENMAP_AUTO_JUMP)->read_int(); |
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354 | if (jump || force_refresh || force_zoom_reset) { |
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355 | AWT_auto_refresh allowed_on(ntw); |
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356 | if (force_zoom_reset) ntw->request_zoom_reset(); |
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357 | ntw->request_refresh(); |
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358 | } |
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359 | if (jump) { |
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360 | GEN_jump_cb(win, false); |
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361 | } |
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362 | } |
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363 | |
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364 | static void GEN_local_organism_or_gene_name_changed_cb(AW_root *awr, GEN_map_window *win) { |
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365 | { |
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366 | AWT_auto_refresh allowed_on(win->get_canvas()); |
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367 | win->get_graphic()->reinit_gen_root(win->get_canvas(), false); |
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368 | } |
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369 | GEN_jump_cb_auto(awr, win, true, false); |
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370 | } |
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371 | |
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372 | #define DISPLAY_TYPE_BIT(disp_type) (1<<(disp_type)) |
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373 | #define ALL_DISPLAY_TYPES (DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLES)-1) |
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374 | |
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375 | static void GEN_map_window_refresh(GEN_map_window *win) { |
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376 | AWT_auto_refresh allowed_on(win->get_canvas()); |
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377 | win->get_canvas()->request_refresh(); |
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378 | } |
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379 | void GEN_refresh_all_windows() { |
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380 | GEN_map_manager::with_all_mapped_windows(GEN_map_window_refresh); |
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381 | } |
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382 | |
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383 | static void GEN_map_window_refresh_if_display_type(GEN_map_window *win, bool zoom_reset, int display_type_mask) { |
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384 | int my_display_type = win->get_graphic()->get_display_style(); |
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385 | if (display_type_mask & DISPLAY_TYPE_BIT(my_display_type)) { |
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386 | if (zoom_reset) { |
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387 | GEN_jump_cb_auto(AW_root::SINGLETON, win, true, true); |
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388 | } |
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389 | else { |
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390 | GEN_map_window_refresh(win); |
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391 | } |
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392 | } |
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393 | } |
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394 | |
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395 | static void GEN_update_unlocked_organism_and_gene_awars(GEN_map_window *win, const char *organismName, const char *geneName) { |
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396 | AW_root *aw_root = win->get_graphic()->get_aw_root(); |
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397 | int window_nr = win->get_nr(); |
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398 | if (!aw_root->awar(AWAR_LOCAL_ORGANISM_LOCK(window_nr))->read_int()) { |
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399 | aw_root->awar(AWAR_LOCAL_ORGANISM_NAME(window_nr))->write_string(organismName); |
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400 | } |
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401 | if (!aw_root->awar(AWAR_LOCAL_GENE_LOCK(window_nr))->read_int()) { |
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402 | aw_root->awar(AWAR_LOCAL_GENE_NAME(window_nr))->write_string(geneName); |
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403 | } |
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404 | } |
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405 | |
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406 | static void GEN_organism_or_gene_changed_cb(AW_root *awr) { |
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407 | char *organism = awr->awar(AWAR_ORGANISM_NAME)->read_string(); |
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408 | char *gene = awr->awar(AWAR_GENE_NAME)->read_string(); |
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409 | |
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410 | GEN_map_manager::with_all_mapped_windows(makeGenmapWindowCallback(GEN_update_unlocked_organism_and_gene_awars, organism, gene)); |
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411 | |
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412 | free(gene); |
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413 | free(organism); |
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414 | } |
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415 | |
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416 | |
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417 | static void GEN_local_lock_changed_cb(AW_root *awr, GEN_map_window *win, bool gene_lock) { |
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418 | int window_nr = win->get_nr(); |
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419 | |
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420 | const char *local_awar_name = NULp; |
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421 | const char *local_lock_awar_name = NULp; |
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422 | const char *global_awar_name = NULp; |
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423 | |
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424 | if (gene_lock) { |
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425 | local_awar_name = AWAR_LOCAL_GENE_NAME(window_nr); |
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426 | local_lock_awar_name = AWAR_LOCAL_GENE_LOCK(window_nr); |
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427 | global_awar_name = AWAR_GENE_NAME; |
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428 | } |
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429 | else { // otherwise organism |
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430 | local_awar_name = AWAR_LOCAL_ORGANISM_NAME(window_nr); |
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431 | local_lock_awar_name = AWAR_LOCAL_ORGANISM_LOCK(window_nr); |
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432 | global_awar_name = AWAR_ORGANISM_NAME; |
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433 | } |
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434 | |
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435 | AW_awar *local_awar = awr->awar(local_awar_name); |
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436 | AW_awar *global_awar = awr->awar(global_awar_name); |
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437 | |
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438 | int lock_value = awr->awar(local_lock_awar_name)->read_int(); |
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439 | if (lock_value == 0) { // lock has been removed -> map to global awar |
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440 | local_awar->map(global_awar); |
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441 | } |
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442 | else { // lock has been installed -> unmap from global awar |
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443 | local_awar->unmap(); |
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444 | char *content = global_awar->read_string(); |
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445 | local_awar->write_string(content); |
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446 | free(content); |
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447 | } |
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448 | } |
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449 | |
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450 | // ------------------------------------- |
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451 | // display parameter change cb |
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452 | |
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453 | static void GEN_display_param_changed_cb(AW_root*, bool zoom_reset, int display_type_mask) { |
---|
454 | GEN_map_manager::with_all_mapped_windows(makeGenmapWindowCallback(GEN_map_window_refresh_if_display_type, zoom_reset, display_type_mask)); |
---|
455 | } |
---|
456 | inline void set_display_update_callback(AW_root *awr, const char *awar_name, bool zoom_reset, int display_type_mask) { |
---|
457 | awr->awar(awar_name)->add_callback(makeRootCallback(GEN_display_param_changed_cb, zoom_reset, display_type_mask)); |
---|
458 | } |
---|
459 | |
---|
460 | // -------------------------- |
---|
461 | // View-local AWARS |
---|
462 | |
---|
463 | static void GEN_create_genemap_local_awars(AW_root *aw_root, AW_default /* def */, int window_nr) { |
---|
464 | // awars local to each view |
---|
465 | |
---|
466 | aw_root->awar_int(AWAR_GENMAP_DISPLAY_TYPE(window_nr), GEN_DISPLAY_STYLE_RADIAL); // @@@ FIXME: make local |
---|
467 | |
---|
468 | aw_root->awar_string(AWAR_LOCAL_ORGANISM_NAME(window_nr), ""); |
---|
469 | aw_root->awar_string(AWAR_LOCAL_GENE_NAME(window_nr), ""); |
---|
470 | |
---|
471 | aw_root->awar_int(AWAR_LOCAL_ORGANISM_LOCK(window_nr), 0); |
---|
472 | aw_root->awar_int(AWAR_LOCAL_GENE_LOCK(window_nr), 0); |
---|
473 | } |
---|
474 | |
---|
475 | static void GEN_add_local_awar_callbacks(AW_root *awr, AW_default /* def */, GEN_map_window *win) { |
---|
476 | int window_nr = win->get_nr(); |
---|
477 | |
---|
478 | RootCallback nameChangedCb = makeRootCallback(GEN_local_organism_or_gene_name_changed_cb, win); |
---|
479 | awr->awar(AWAR_LOCAL_ORGANISM_NAME(window_nr))->add_callback(nameChangedCb); |
---|
480 | awr->awar(AWAR_LOCAL_GENE_NAME(window_nr)) ->add_callback(nameChangedCb); |
---|
481 | |
---|
482 | AW_awar *awar_lock_orga = awr->awar(AWAR_LOCAL_ORGANISM_LOCK(window_nr)); |
---|
483 | AW_awar *awar_lock_gene = awr->awar(AWAR_LOCAL_GENE_LOCK(window_nr)); |
---|
484 | |
---|
485 | awar_lock_orga->add_callback(makeRootCallback(GEN_local_lock_changed_cb, win, false)); |
---|
486 | awar_lock_gene->add_callback(makeRootCallback(GEN_local_lock_changed_cb, win, true)); |
---|
487 | |
---|
488 | awar_lock_orga->touch(); |
---|
489 | awar_lock_gene->touch(); |
---|
490 | } |
---|
491 | |
---|
492 | // ---------------------- |
---|
493 | // global AWARS |
---|
494 | |
---|
495 | static void GEN_create_genemap_global_awars(AW_root *aw_root, AW_default def, GBDATA *gb_main) { |
---|
496 | // layout options: |
---|
497 | |
---|
498 | aw_root->awar_int(AWAR_GENMAP_ARROW_SIZE, 150)->set_minmax(0, 500); |
---|
499 | aw_root->awar_int(AWAR_GENMAP_SHOW_HIDDEN, 0); |
---|
500 | aw_root->awar_int(AWAR_GENMAP_SHOW_ALL_NDS, 0); |
---|
501 | |
---|
502 | aw_root->awar_int(AWAR_GENMAP_BOOK_BASES_PER_LINE, 15000)->set_minmax(1, 100000); |
---|
503 | aw_root->awar_float(AWAR_GENMAP_BOOK_WIDTH_FACTOR, 0.1)->set_minmax(0, 1); |
---|
504 | aw_root->awar_int(AWAR_GENMAP_BOOK_LINE_HEIGHT, 20)->set_minmax(0, 100); |
---|
505 | aw_root->awar_int(AWAR_GENMAP_BOOK_LINE_SPACE, 5)->set_minmax(-20, 20); |
---|
506 | |
---|
507 | aw_root->awar_float(AWAR_GENMAP_VERTICAL_FACTOR_X, 1.0)->set_minmax(0, 10); |
---|
508 | aw_root->awar_float(AWAR_GENMAP_VERTICAL_FACTOR_Y, 0.3)->set_minmax(0, 10); |
---|
509 | |
---|
510 | aw_root->awar_float(AWAR_GENMAP_RADIAL_INSIDE, 50)->set_minmax(0, 100); |
---|
511 | aw_root->awar_float(AWAR_GENMAP_RADIAL_OUTSIDE, 4)->set_minmax(0, 100); |
---|
512 | |
---|
513 | // other options: |
---|
514 | |
---|
515 | aw_root->awar_int(AWAR_GENMAP_AUTO_JUMP, 1); |
---|
516 | |
---|
517 | GEN_create_nds_vars(aw_root, def, gb_main, makeDatabaseCallback(GEN_NDS_changed)); |
---|
518 | } |
---|
519 | |
---|
520 | static void GEN_add_global_awar_callbacks(AW_root *awr) { |
---|
521 | enum { REFRESH_ONLY = 0, ZOOM_RESET = 1 }; |
---|
522 | |
---|
523 | set_display_update_callback(awr, AWAR_GENMAP_ARROW_SIZE, REFRESH_ONLY, ALL_DISPLAY_TYPES^DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_BOOK)); |
---|
524 | set_display_update_callback(awr, AWAR_GENMAP_SHOW_HIDDEN, REFRESH_ONLY, ALL_DISPLAY_TYPES); |
---|
525 | set_display_update_callback(awr, AWAR_GENMAP_SHOW_ALL_NDS, REFRESH_ONLY, ALL_DISPLAY_TYPES); |
---|
526 | |
---|
527 | set_display_update_callback(awr, AWAR_GENMAP_BOOK_BASES_PER_LINE, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_BOOK)); |
---|
528 | set_display_update_callback(awr, AWAR_GENMAP_BOOK_WIDTH_FACTOR, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_BOOK)); |
---|
529 | set_display_update_callback(awr, AWAR_GENMAP_BOOK_LINE_HEIGHT, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_BOOK)); |
---|
530 | set_display_update_callback(awr, AWAR_GENMAP_BOOK_LINE_SPACE, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_BOOK)); |
---|
531 | |
---|
532 | set_display_update_callback(awr, AWAR_GENMAP_VERTICAL_FACTOR_X, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_VERTICAL)); |
---|
533 | set_display_update_callback(awr, AWAR_GENMAP_VERTICAL_FACTOR_Y, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_VERTICAL)); |
---|
534 | |
---|
535 | set_display_update_callback(awr, AWAR_GENMAP_RADIAL_INSIDE, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_RADIAL)); |
---|
536 | set_display_update_callback(awr, AWAR_GENMAP_RADIAL_OUTSIDE, ZOOM_RESET, DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLE_RADIAL)); |
---|
537 | |
---|
538 | awr->awar(AWAR_ORGANISM_NAME)->add_callback(GEN_organism_or_gene_changed_cb); |
---|
539 | awr->awar(AWAR_GENE_NAME)->add_callback(GEN_organism_or_gene_changed_cb); |
---|
540 | } |
---|
541 | |
---|
542 | |
---|
543 | // -------------------------------------------------------------------------------- |
---|
544 | |
---|
545 | static void GEN_mode_event(AW_window *aws, GEN_map_window *win, AWT_COMMAND_MODE mode) { |
---|
546 | const char *text = NULp; |
---|
547 | switch (mode) { |
---|
548 | case AWT_MODE_SELECT: text = MODE_TEXT_1BUTTON("SELECT", "click to select a gene"); break; |
---|
549 | case AWT_MODE_INFO: text = MODE_TEXT_1BUTTON("INFO", "click for info"); break; |
---|
550 | |
---|
551 | case AWT_MODE_ZOOM: text = MODE_TEXT_STANDARD_ZOOMMODE(); break; |
---|
552 | |
---|
553 | default: text = no_mode_text_defined(); break; |
---|
554 | } |
---|
555 | |
---|
556 | gen_assert(strlen(text) < AWAR_FOOTER_MAX_LEN); // text too long! |
---|
557 | |
---|
558 | aws->get_root()->awar(AWAR_FOOTER)->write_string(text); |
---|
559 | |
---|
560 | AWT_canvas *canvas = win->get_canvas(); |
---|
561 | AWT_auto_refresh allowed_on(canvas); |
---|
562 | |
---|
563 | canvas->set_mode(mode); |
---|
564 | canvas->request_refresh(); |
---|
565 | } |
---|
566 | |
---|
567 | static void GEN_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, GBDATA *gb_main) { |
---|
568 | GB_ERROR error = GB_undo(gb_main, undo_type); |
---|
569 | if (error) { |
---|
570 | aw_message(error); |
---|
571 | } |
---|
572 | else { |
---|
573 | GB_begin_transaction(gb_main); |
---|
574 | GB_commit_transaction(gb_main); |
---|
575 | } |
---|
576 | } |
---|
577 | |
---|
578 | static AW_window *GEN_create_options_window(AW_root *awr) { |
---|
579 | static AW_window_simple *aws = NULp; |
---|
580 | |
---|
581 | if (!aws) { |
---|
582 | aws = new AW_window_simple; |
---|
583 | |
---|
584 | aws->init(awr, "GEN_OPTS", "Genemap options"); |
---|
585 | aws->load_xfig("gen_options.fig"); |
---|
586 | |
---|
587 | aws->at("close"); |
---|
588 | aws->callback(AW_POPDOWN); |
---|
589 | aws->create_button("CLOSE", "CLOSE", "C"); |
---|
590 | |
---|
591 | aws->callback(makeHelpCallback("gen_options.hlp")); |
---|
592 | aws->at("help"); |
---|
593 | aws->create_button("HELP", "HELP", "H"); |
---|
594 | |
---|
595 | aws->auto_space(5, 5); |
---|
596 | aws->label_length(26); |
---|
597 | |
---|
598 | const int FIELDWIDTH = 12; |
---|
599 | const int SCALERWIDTH = 300; |
---|
600 | |
---|
601 | // all displays: |
---|
602 | aws->at("arrow_size"); aws->create_input_field_with_scaler(AWAR_GENMAP_ARROW_SIZE, FIELDWIDTH, SCALERWIDTH); |
---|
603 | |
---|
604 | aws->at("show_hidden"); |
---|
605 | aws->label("Show hidden genes"); |
---|
606 | aws->create_toggle(AWAR_GENMAP_SHOW_HIDDEN); |
---|
607 | |
---|
608 | aws->at("show_all"); |
---|
609 | aws->label("Show NDS for all genes"); |
---|
610 | aws->create_toggle(AWAR_GENMAP_SHOW_ALL_NDS); |
---|
611 | |
---|
612 | aws->at("autojump"); |
---|
613 | aws->label("Auto jump to selected gene"); |
---|
614 | aws->create_toggle(AWAR_GENMAP_AUTO_JUMP); |
---|
615 | |
---|
616 | // book-style: |
---|
617 | aws->at("base_pos"); aws->create_input_field_with_scaler(AWAR_GENMAP_BOOK_BASES_PER_LINE, FIELDWIDTH, SCALERWIDTH); |
---|
618 | aws->at("width_factor"); aws->create_input_field_with_scaler(AWAR_GENMAP_BOOK_WIDTH_FACTOR, FIELDWIDTH, SCALERWIDTH, AW_SCALER_EXP_LOWER); |
---|
619 | aws->at("line_height"); aws->create_input_field_with_scaler(AWAR_GENMAP_BOOK_LINE_HEIGHT, FIELDWIDTH, SCALERWIDTH, AW_SCALER_EXP_LOWER); |
---|
620 | aws->at("line_space"); aws->create_input_field_with_scaler(AWAR_GENMAP_BOOK_LINE_SPACE, FIELDWIDTH, SCALERWIDTH); |
---|
621 | |
---|
622 | // vertical-style: |
---|
623 | aws->at("factor_x"); aws->create_input_field_with_scaler(AWAR_GENMAP_VERTICAL_FACTOR_X, FIELDWIDTH, SCALERWIDTH, AW_SCALER_EXP_LOWER); |
---|
624 | aws->at("factor_y"); aws->create_input_field_with_scaler(AWAR_GENMAP_VERTICAL_FACTOR_Y, FIELDWIDTH, SCALERWIDTH, AW_SCALER_EXP_LOWER); |
---|
625 | |
---|
626 | // radial style: |
---|
627 | aws->at("inside"); aws->create_input_field_with_scaler(AWAR_GENMAP_RADIAL_INSIDE, FIELDWIDTH, SCALERWIDTH, AW_SCALER_EXP_LOWER); |
---|
628 | aws->at("outside"); aws->create_input_field_with_scaler(AWAR_GENMAP_RADIAL_OUTSIDE, FIELDWIDTH, SCALERWIDTH, AW_SCALER_EXP_LOWER); |
---|
629 | } |
---|
630 | return aws; |
---|
631 | } |
---|
632 | |
---|
633 | static AW_window *GEN_create_gc_window(AW_root *awr, AW_gc_manager *gcman) { |
---|
634 | // only create one gc window for all genemap views |
---|
635 | static AW_window *awgc = NULp; |
---|
636 | if (!awgc) awgc = AW_create_gc_window_named(awr, gcman, "GENMAP_COLOR_DEF2", "Genemap colors and fonts"); // use named gc window (otherwise clashes with ARB_NTREE gc window) |
---|
637 | return awgc; |
---|
638 | } |
---|
639 | |
---|
640 | enum GEN_PERFORM_MODE { |
---|
641 | GEN_PERFORM_ALL_ORGANISMS, |
---|
642 | GEN_PERFORM_CURRENT_ORGANISM, |
---|
643 | GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, |
---|
644 | GEN_PERFORM_MARKED_ORGANISMS, |
---|
645 | |
---|
646 | GEN_PERFORM_MODES, // counter |
---|
647 | }; |
---|
648 | |
---|
649 | static const char *GEN_PERFORM_MODE_id[GEN_PERFORM_MODES] = { |
---|
650 | "org_all", |
---|
651 | "org_current", |
---|
652 | "org_butcur", |
---|
653 | "org_marked", |
---|
654 | }; |
---|
655 | |
---|
656 | inline string performmode_relative_id(const char *id, GEN_PERFORM_MODE pmode) { |
---|
657 | return GBS_global_string("%s_%s", GEN_PERFORM_MODE_id[pmode], id); |
---|
658 | } |
---|
659 | |
---|
660 | enum GEN_MARK_MODE { |
---|
661 | GEN_MARK, |
---|
662 | GEN_UNMARK, |
---|
663 | GEN_INVERT_MARKED, |
---|
664 | GEN_COUNT_MARKED, |
---|
665 | |
---|
666 | // GEN_MARK_COLORED, done by awt_colorize_marked now |
---|
667 | // GEN_UNMARK_COLORED, |
---|
668 | // GEN_INVERT_COLORED, |
---|
669 | // GEN_COLORIZE_MARKED, |
---|
670 | |
---|
671 | GEN_EXTRACT_MARKED, |
---|
672 | |
---|
673 | GEN_MARK_HIDDEN, |
---|
674 | GEN_MARK_VISIBLE, |
---|
675 | GEN_UNMARK_HIDDEN, |
---|
676 | GEN_UNMARK_VISIBLE |
---|
677 | }; |
---|
678 | |
---|
679 | enum GEN_HIDE_MODE { |
---|
680 | GEN_HIDE_ALL, |
---|
681 | GEN_UNHIDE_ALL, |
---|
682 | GEN_INVERT_HIDE_ALL, |
---|
683 | |
---|
684 | GEN_HIDE_MARKED, |
---|
685 | GEN_UNHIDE_MARKED, |
---|
686 | GEN_INVERT_HIDE_MARKED |
---|
687 | }; |
---|
688 | |
---|
689 | // -------------------------------------------------------------------------------- |
---|
690 | |
---|
691 | inline bool nameIsUnique(const char *short_name, GBDATA *gb_species_data) { |
---|
692 | return !GBT_find_species_rel_species_data(gb_species_data, short_name); |
---|
693 | } |
---|
694 | |
---|
695 | static GB_ERROR GEN_species_add_entry(GBDATA *gb_pseudo, const char *key, const char *value) { |
---|
696 | GB_ERROR error = NULp; |
---|
697 | GB_clear_error(); |
---|
698 | GBDATA *gbd = GB_entry(gb_pseudo, key); |
---|
699 | |
---|
700 | if (!gbd) { // key does not exist yet -> create |
---|
701 | gbd = GB_create(gb_pseudo, key, GB_STRING); |
---|
702 | if (!gbd) error = GB_await_error(); |
---|
703 | } |
---|
704 | else { // key exists |
---|
705 | if (GB_read_type(gbd) != GB_STRING) { // test correct key type |
---|
706 | error = GB_export_errorf("field '%s' exists and has wrong type", key); |
---|
707 | } |
---|
708 | } |
---|
709 | |
---|
710 | if (!error) error = GB_write_string(gbd, value); |
---|
711 | |
---|
712 | return error; |
---|
713 | } |
---|
714 | |
---|
715 | static AW_repeated_question *ask_about_existing_gene_species = NULp; |
---|
716 | static AW_repeated_question *ask_to_overwrite_alignment = NULp; |
---|
717 | |
---|
718 | struct EG2PS_data : virtual Noncopyable { |
---|
719 | arb_progress progress; |
---|
720 | GBDATA *gb_species_data; |
---|
721 | char *ali; |
---|
722 | UniqueNameDetector existing; |
---|
723 | GB_HASH *pseudo_hash; |
---|
724 | int duplicateSpecies; // counts created gene-species with identical ACC |
---|
725 | bool nameProblem; // nameserver and DB disagree about names |
---|
726 | |
---|
727 | EG2PS_data(const char *ali_, GBDATA *gb_species_data_, long marked_genes_) |
---|
728 | : progress(marked_genes_), |
---|
729 | gb_species_data(gb_species_data_), |
---|
730 | ali(ARB_strdup(ali_)), |
---|
731 | existing(gb_species_data, marked_genes_), |
---|
732 | duplicateSpecies(0), |
---|
733 | nameProblem(false) |
---|
734 | { |
---|
735 | pseudo_hash = GEN_create_pseudo_species_hash(GB_get_root(gb_species_data), marked_genes_); |
---|
736 | } |
---|
737 | |
---|
738 | ~EG2PS_data() { |
---|
739 | if (duplicateSpecies>0) { |
---|
740 | aw_message(GBS_global_string("There are %i duplicated gene-species (with identical sequence and accession number)\n" |
---|
741 | "Duplicated gene-species got names with numerical postfixes ('.1', '.2', ...)" |
---|
742 | , duplicateSpecies)); |
---|
743 | } |
---|
744 | if (nameProblem) { |
---|
745 | aw_message("Naming problems occurred.\nYou have to call 'Species/Synchronize IDs'!"); |
---|
746 | } |
---|
747 | GBS_free_hash(pseudo_hash); |
---|
748 | free(ali); |
---|
749 | } |
---|
750 | }; |
---|
751 | |
---|
752 | static const char* readACC(GBDATA *gb_species_data, const char *name) { |
---|
753 | const char *other_acc = NULp; |
---|
754 | GBDATA *gb_other_species = GBT_find_species_rel_species_data(gb_species_data, name); |
---|
755 | if (gb_other_species) { |
---|
756 | GBDATA *gb_other_acc = GB_entry(gb_other_species, "acc"); |
---|
757 | if (gb_other_acc) other_acc = GB_read_char_pntr(gb_other_acc); |
---|
758 | } |
---|
759 | return other_acc; |
---|
760 | } |
---|
761 | |
---|
762 | static void gen_extract_gene_2_pseudoSpecies(GBDATA *gb_species, GBDATA *gb_gene, EG2PS_data *eg2ps) { |
---|
763 | char *gene_name = ARB_strdup(GBT_get_name_or_description(gb_gene)); |
---|
764 | char *species_name = ARB_strdup(GBT_get_name_or_description(gb_species)); |
---|
765 | |
---|
766 | const char *full_species_name = GBT_read_char_pntr(gb_species, "full_name"); |
---|
767 | if (!full_species_name) full_species_name = species_name; |
---|
768 | |
---|
769 | char *full_name = GBS_global_string_copy("%s [%s]", full_species_name, gene_name); |
---|
770 | char *sequence = GBT_read_gene_sequence(gb_gene, true, 0); |
---|
771 | GB_ERROR error = NULp; |
---|
772 | |
---|
773 | if (!sequence) error = GB_await_error(); |
---|
774 | else { |
---|
775 | const char *ali = eg2ps->ali; |
---|
776 | long id = GBS_checksum(sequence, 1, ".-"); |
---|
777 | char acc[100]; |
---|
778 | |
---|
779 | sprintf(acc, "ARB_GENE_%lX", id); |
---|
780 | |
---|
781 | // test if this gene has been already extracted to a gene-species |
---|
782 | |
---|
783 | GBDATA *gb_main = GB_get_root(gb_species); |
---|
784 | GBDATA *gb_exist_geneSpec = GEN_find_pseudo_species(gb_main, species_name, gene_name, eg2ps->pseudo_hash); |
---|
785 | bool create_new_gene_species = true; |
---|
786 | char *short_name = NULp; |
---|
787 | |
---|
788 | if (gb_exist_geneSpec) { |
---|
789 | char *existing_name = ARB_strdup(GBT_get_name_or_description(gb_exist_geneSpec)); |
---|
790 | |
---|
791 | gen_assert(ask_about_existing_gene_species); |
---|
792 | gen_assert(ask_to_overwrite_alignment); |
---|
793 | |
---|
794 | char *question = GBS_global_string_copy("Already have a gene-species for %s/%s ('%s')", species_name, gene_name, existing_name); |
---|
795 | int answer = ask_about_existing_gene_species->get_answer("existing_pseudo_species", question, "Overwrite species,Insert new alignment,Skip,Create new", "all", true); |
---|
796 | |
---|
797 | create_new_gene_species = false; |
---|
798 | |
---|
799 | switch (answer) { |
---|
800 | case 0: { // Overwrite species |
---|
801 | // @@@ FIXME: delete species needed here |
---|
802 | create_new_gene_species = true; |
---|
803 | short_name = ARB_strdup(existing_name); |
---|
804 | break; |
---|
805 | } |
---|
806 | case 1: { // Insert new alignment or overwrite alignment |
---|
807 | GBDATA *gb_ali = GB_entry(gb_exist_geneSpec, ali); |
---|
808 | if (gb_ali) { // the alignment already exists |
---|
809 | char *question2 = GBS_global_string_copy("Gene-species '%s' already has data in '%s'", existing_name, ali); |
---|
810 | int overwrite_answer = ask_to_overwrite_alignment->get_answer("overwrite_gene_data", question2, "Overwrite data,Skip", "all", true); |
---|
811 | |
---|
812 | if (overwrite_answer == 1) error = GBS_global_string("Skipped gene-species '%s' (already had data in alignment)", existing_name); // Skip |
---|
813 | else if (overwrite_answer == 2) error = "Aborted."; // Abort |
---|
814 | // @@@ FIXME: overwrite data is missing |
---|
815 | |
---|
816 | free(question2); |
---|
817 | } |
---|
818 | break; |
---|
819 | } |
---|
820 | case 2: { // Skip existing ones |
---|
821 | error = GBS_global_string("Skipped gene-species '%s'", existing_name); |
---|
822 | break; |
---|
823 | } |
---|
824 | case 3: { // Create with new name |
---|
825 | create_new_gene_species = true; |
---|
826 | break; |
---|
827 | } |
---|
828 | case 4: { // Abort |
---|
829 | error = "Aborted."; |
---|
830 | break; |
---|
831 | } |
---|
832 | default: gen_assert(0); |
---|
833 | } |
---|
834 | free(question); |
---|
835 | free(existing_name); |
---|
836 | } |
---|
837 | |
---|
838 | if (!error) { |
---|
839 | if (create_new_gene_species) { |
---|
840 | if (!short_name) { // create a new name |
---|
841 | error = AWTC_generate_one_name(gb_main, full_name, acc, NULp, short_name); |
---|
842 | if (!error) { // name has been created |
---|
843 | if (eg2ps->existing.name_known(short_name)) { // nameserver-generated name is already in use |
---|
844 | const char *other_acc = readACC(eg2ps->gb_species_data, short_name); |
---|
845 | if (other_acc) { |
---|
846 | if (strcmp(acc, other_acc) == 0) { // duplicate (gene-)species -> generate postfixed name |
---|
847 | char *newName = NULp; |
---|
848 | for (int postfix = 1; ; ++postfix) { |
---|
849 | newName = GBS_global_string_copy("%s.%i", short_name, postfix); |
---|
850 | if (!eg2ps->existing.name_known(newName)) { |
---|
851 | eg2ps->duplicateSpecies++; |
---|
852 | break; |
---|
853 | } |
---|
854 | |
---|
855 | other_acc = readACC(eg2ps->gb_species_data, newName); |
---|
856 | if (!other_acc || strcmp(acc, other_acc) != 0) { |
---|
857 | eg2ps->nameProblem = true; |
---|
858 | error = GBS_global_string("Unexpected acc-mismatch for '%s'", newName); |
---|
859 | break; |
---|
860 | } |
---|
861 | } |
---|
862 | |
---|
863 | if (!error) freeset(short_name, newName); |
---|
864 | else free(newName); |
---|
865 | } |
---|
866 | else { // different acc, but uses name generated by nameserver |
---|
867 | eg2ps->nameProblem = true; |
---|
868 | error = GBS_global_string("acc of '%s' differs from acc stored in nameserver", short_name); |
---|
869 | } |
---|
870 | } |
---|
871 | else { // can't detect acc of existing species |
---|
872 | eg2ps->nameProblem = true; |
---|
873 | error = GBS_global_string("can't detect acc of species '%s'", short_name); |
---|
874 | } |
---|
875 | } |
---|
876 | } |
---|
877 | if (error) { // try to make a random name |
---|
878 | const char *msg = GBS_global_string("%s\nGenerating a random name instead.", error); |
---|
879 | aw_message(msg); |
---|
880 | error = NULp; |
---|
881 | |
---|
882 | short_name = AWTC_generate_random_name(eg2ps->existing); |
---|
883 | if (!short_name) error = GBS_global_string("Failed to create a new name for pseudo gene-species '%s'", full_name); |
---|
884 | } |
---|
885 | } |
---|
886 | |
---|
887 | if (!error) { // create the species |
---|
888 | gen_assert(short_name); |
---|
889 | gb_exist_geneSpec = GBT_find_or_create_species(gb_main, short_name, true); |
---|
890 | if (!gb_exist_geneSpec) error = GB_export_errorf("Failed to create pseudo-species '%s'", short_name); |
---|
891 | else eg2ps->existing.add_name(short_name); |
---|
892 | } |
---|
893 | } |
---|
894 | else { |
---|
895 | gen_assert(gb_exist_geneSpec); // do not generate new or skip -> should only occur when gene-species already existed |
---|
896 | } |
---|
897 | |
---|
898 | if (!error) { // write sequence data |
---|
899 | GBDATA *gb_data = GBT_add_data(gb_exist_geneSpec, ali, "data", GB_STRING); |
---|
900 | if (!gb_data) error = GB_await_error(); |
---|
901 | else error = GB_write_string(gb_data, sequence); |
---|
902 | } |
---|
903 | |
---|
904 | // write other entries: |
---|
905 | if (!error) error = GEN_species_add_entry(gb_exist_geneSpec, "full_name", full_name); |
---|
906 | if (!error) error = GEN_species_add_entry(gb_exist_geneSpec, "ARB_origin_species", species_name); |
---|
907 | if (!error) error = GEN_species_add_entry(gb_exist_geneSpec, "ARB_origin_gene", gene_name); |
---|
908 | if (!error) GEN_add_pseudo_species_to_hash(gb_exist_geneSpec, eg2ps->pseudo_hash); |
---|
909 | if (!error) error = GEN_species_add_entry(gb_exist_geneSpec, "acc", acc); |
---|
910 | |
---|
911 | // copy codon_start and transl_table : |
---|
912 | const char *codon_start = NULp; |
---|
913 | const char *transl_table = NULp; |
---|
914 | { |
---|
915 | GBDATA *gb_codon_start = GB_entry(gb_gene, "codon_start"); |
---|
916 | GBDATA *gb_transl_table = GB_entry(gb_gene, "transl_table"); |
---|
917 | |
---|
918 | if (gb_codon_start) codon_start = GB_read_char_pntr(gb_codon_start); |
---|
919 | if (gb_transl_table) transl_table = GB_read_char_pntr(gb_transl_table); |
---|
920 | } |
---|
921 | |
---|
922 | if (!error && codon_start) error = GEN_species_add_entry(gb_exist_geneSpec, "codon_start", codon_start); |
---|
923 | if (!error && transl_table) error = GEN_species_add_entry(gb_exist_geneSpec, "transl_table", transl_table); |
---|
924 | } |
---|
925 | |
---|
926 | free(short_name); |
---|
927 | free(sequence); |
---|
928 | } |
---|
929 | if (error) aw_message(error); |
---|
930 | |
---|
931 | free(full_name); |
---|
932 | free(species_name); |
---|
933 | free(gene_name); |
---|
934 | } |
---|
935 | |
---|
936 | static long gen_count_marked_genes = 0; // used to count marked genes |
---|
937 | |
---|
938 | static void do_mark_command_for_one_species(int imode, GBDATA *gb_species, AW_CL cl_user) { |
---|
939 | GEN_MARK_MODE mode = (GEN_MARK_MODE)imode; |
---|
940 | |
---|
941 | for (GBDATA *gb_gene = GEN_first_gene(gb_species); |
---|
942 | gb_gene; |
---|
943 | gb_gene = GEN_next_gene(gb_gene)) |
---|
944 | { |
---|
945 | bool mark_flag = GB_read_flag(gb_gene) != 0; |
---|
946 | bool org_mark_flag = mark_flag; |
---|
947 | |
---|
948 | switch (mode) { |
---|
949 | case GEN_MARK: mark_flag = 1; break; |
---|
950 | case GEN_UNMARK: mark_flag = 0; break; |
---|
951 | case GEN_INVERT_MARKED: mark_flag = !mark_flag; break; |
---|
952 | |
---|
953 | case GEN_COUNT_MARKED: { |
---|
954 | if (mark_flag) ++gen_count_marked_genes; |
---|
955 | break; |
---|
956 | } |
---|
957 | case GEN_EXTRACT_MARKED: { |
---|
958 | if (mark_flag) { |
---|
959 | EG2PS_data *eg2ps = (EG2PS_data*)cl_user; |
---|
960 | gen_extract_gene_2_pseudoSpecies(gb_species, gb_gene, eg2ps); |
---|
961 | eg2ps->progress.inc(); |
---|
962 | } |
---|
963 | break; |
---|
964 | } |
---|
965 | default: { |
---|
966 | GBDATA *gb_hidden = GB_entry(gb_gene, ARB_HIDDEN); |
---|
967 | bool hidden = gb_hidden ? GB_read_byte(gb_hidden) != 0 : false; |
---|
968 | |
---|
969 | switch (mode) { |
---|
970 | case GEN_MARK_HIDDEN: if (hidden) mark_flag = 1; break; |
---|
971 | case GEN_UNMARK_HIDDEN: if (hidden) mark_flag = 0; break; |
---|
972 | case GEN_MARK_VISIBLE: if (!hidden) mark_flag = 1; break; |
---|
973 | case GEN_UNMARK_VISIBLE: if (!hidden) mark_flag = 0; break; |
---|
974 | default: gen_assert(0); break; |
---|
975 | } |
---|
976 | } |
---|
977 | } |
---|
978 | |
---|
979 | if (mark_flag != org_mark_flag) GB_write_flag(gb_gene, mark_flag ? 1 : 0); |
---|
980 | } |
---|
981 | } |
---|
982 | |
---|
983 | static void do_hide_command_for_one_species(int imode, GBDATA *gb_species, AW_CL /* cl_user */) { |
---|
984 | GEN_HIDE_MODE mode = (GEN_HIDE_MODE)imode; |
---|
985 | |
---|
986 | for (GBDATA *gb_gene = GEN_first_gene(gb_species); |
---|
987 | gb_gene; |
---|
988 | gb_gene = GEN_next_gene(gb_gene)) |
---|
989 | { |
---|
990 | bool marked = GB_read_flag(gb_gene) != 0; |
---|
991 | |
---|
992 | GBDATA *gb_hidden = GB_entry(gb_gene, ARB_HIDDEN); |
---|
993 | bool hidden = gb_hidden ? (GB_read_byte(gb_hidden) != 0) : false; |
---|
994 | bool org_hidden = hidden; |
---|
995 | |
---|
996 | switch (mode) { |
---|
997 | case GEN_HIDE_ALL: hidden = true; break; |
---|
998 | case GEN_UNHIDE_ALL: hidden = false; break; |
---|
999 | case GEN_INVERT_HIDE_ALL: hidden = !hidden; break; |
---|
1000 | case GEN_HIDE_MARKED: if (marked) hidden = true; break; |
---|
1001 | case GEN_UNHIDE_MARKED: if (marked) hidden = false; break; |
---|
1002 | case GEN_INVERT_HIDE_MARKED: if (marked) hidden = !hidden; break; |
---|
1003 | default: gen_assert(0); break; |
---|
1004 | } |
---|
1005 | |
---|
1006 | if (hidden != org_hidden) { |
---|
1007 | if (!gb_hidden) gb_hidden = GB_create(gb_gene, ARB_HIDDEN, GB_BYTE); |
---|
1008 | GB_write_byte(gb_hidden, hidden ? 1 : 0); // change gene visibility |
---|
1009 | } |
---|
1010 | } |
---|
1011 | } |
---|
1012 | |
---|
1013 | static void GEN_perform_command(GBDATA *gb_main, GEN_PERFORM_MODE pmode, |
---|
1014 | void (*do_command)(int cmode, GBDATA *gb_species, AW_CL cl_user), int mode, AW_CL cl_user) { |
---|
1015 | GB_ERROR error = NULp; |
---|
1016 | |
---|
1017 | GB_begin_transaction(gb_main); |
---|
1018 | |
---|
1019 | switch (pmode) { |
---|
1020 | case GEN_PERFORM_ALL_ORGANISMS: { |
---|
1021 | for (GBDATA *gb_organism = GEN_first_organism(gb_main); |
---|
1022 | gb_organism; |
---|
1023 | gb_organism = GEN_next_organism(gb_organism)) |
---|
1024 | { |
---|
1025 | do_command(mode, gb_organism, cl_user); |
---|
1026 | } |
---|
1027 | break; |
---|
1028 | } |
---|
1029 | case GEN_PERFORM_MARKED_ORGANISMS: { |
---|
1030 | for (GBDATA *gb_organism = GEN_first_marked_organism(gb_main); |
---|
1031 | gb_organism; |
---|
1032 | gb_organism = GEN_next_marked_organism(gb_organism)) |
---|
1033 | { |
---|
1034 | do_command(mode, gb_organism, cl_user); |
---|
1035 | } |
---|
1036 | break; |
---|
1037 | } |
---|
1038 | case GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM: { |
---|
1039 | GBDATA *gb_curr_organism = GEN_get_current_organism(gb_main); |
---|
1040 | for (GBDATA *gb_organism = GEN_first_organism(gb_main); |
---|
1041 | gb_organism; |
---|
1042 | gb_organism = GEN_next_organism(gb_organism)) |
---|
1043 | { |
---|
1044 | if (gb_organism != gb_curr_organism) do_command(mode, gb_organism, cl_user); |
---|
1045 | } |
---|
1046 | break; |
---|
1047 | } |
---|
1048 | case GEN_PERFORM_CURRENT_ORGANISM: { |
---|
1049 | GBDATA *gb_organism = GEN_get_current_organism(gb_main); |
---|
1050 | if (!gb_organism) { |
---|
1051 | error = "First you have to select a species."; |
---|
1052 | } |
---|
1053 | else { |
---|
1054 | do_command(mode, gb_organism, cl_user); |
---|
1055 | } |
---|
1056 | break; |
---|
1057 | } |
---|
1058 | default: { |
---|
1059 | gen_assert(0); |
---|
1060 | break; |
---|
1061 | } |
---|
1062 | } |
---|
1063 | |
---|
1064 | GB_end_transaction_show_error(gb_main, error, aw_message); |
---|
1065 | } |
---|
1066 | |
---|
1067 | class GEN_unique_param { |
---|
1068 | GEN_unique_param(GBDATA *gb_main_, AW_CL unique_) : |
---|
1069 | unique(unique_), |
---|
1070 | gb_main(gb_main_) |
---|
1071 | {} |
---|
1072 | |
---|
1073 | typedef map<AW_CL, GEN_unique_param> ExistingParams; |
---|
1074 | static ExistingParams existing_params; // to ensure exactly one instance per 'command_mode' |
---|
1075 | |
---|
1076 | AW_CL unique; |
---|
1077 | public: |
---|
1078 | GBDATA *gb_main; |
---|
1079 | |
---|
1080 | AW_CL get_unique() { return unique; } |
---|
1081 | |
---|
1082 | static GEN_unique_param *get(GBDATA *gb_main_, AW_CL unique_) { // get unique instance for each 'unique_' |
---|
1083 | pair<ExistingParams::iterator, bool> created = existing_params.insert(ExistingParams::value_type(unique_, GEN_unique_param(gb_main_, unique_))); |
---|
1084 | ExistingParams::iterator wanted = created.first; |
---|
1085 | GEN_unique_param& param = wanted->second; |
---|
1086 | return ¶m; |
---|
1087 | } |
---|
1088 | }; |
---|
1089 | GEN_unique_param::ExistingParams GEN_unique_param::existing_params; |
---|
1090 | |
---|
1091 | |
---|
1092 | struct GEN_command_mode_param : public GEN_unique_param { |
---|
1093 | static GEN_command_mode_param *get(GBDATA *gb_main_, AW_CL command_mode_) { return (GEN_command_mode_param*)GEN_unique_param::get(gb_main_, command_mode_); } |
---|
1094 | AW_CL get_command_mode() { return get_unique(); } |
---|
1095 | }; |
---|
1096 | |
---|
1097 | |
---|
1098 | static void GEN_hide_command(AW_window*, GEN_PERFORM_MODE perform_mode, GEN_command_mode_param *param) { |
---|
1099 | GEN_perform_command(param->gb_main, perform_mode, do_hide_command_for_one_species, param->get_command_mode(), 0); |
---|
1100 | } |
---|
1101 | |
---|
1102 | static void GEN_mark_command(AW_window*, GEN_PERFORM_MODE perform_mode, GEN_command_mode_param *param) { |
---|
1103 | gen_count_marked_genes = 0; |
---|
1104 | GEN_perform_command(param->gb_main, perform_mode, do_mark_command_for_one_species, param->get_command_mode(), 0); |
---|
1105 | |
---|
1106 | if ((GEN_MARK_MODE)param->get_command_mode() == GEN_COUNT_MARKED) { |
---|
1107 | const char *where = NULp; |
---|
1108 | |
---|
1109 | switch (perform_mode) { |
---|
1110 | case GEN_PERFORM_CURRENT_ORGANISM: where = "the current species"; break; |
---|
1111 | case GEN_PERFORM_MARKED_ORGANISMS: where = "all marked species"; break; |
---|
1112 | case GEN_PERFORM_ALL_ORGANISMS: where = "all species"; break; |
---|
1113 | case GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM: where = "all but the current species"; break; |
---|
1114 | default: gen_assert(0); break; |
---|
1115 | } |
---|
1116 | aw_message(GBS_global_string("There are %li marked genes in %s", gen_count_marked_genes, where)); |
---|
1117 | } |
---|
1118 | } |
---|
1119 | |
---|
1120 | struct GEN_extract_mode_param : public GEN_unique_param { |
---|
1121 | static GEN_extract_mode_param *get(GBDATA *gb_main_, GEN_PERFORM_MODE perform_mode) { return (GEN_extract_mode_param*)GEN_unique_param::get(gb_main_, perform_mode); } |
---|
1122 | GEN_PERFORM_MODE get_perform_mode() { return (GEN_PERFORM_MODE)get_unique(); } |
---|
1123 | }; |
---|
1124 | |
---|
1125 | static GB_ERROR gene_extract_handler(const char *ali, GEN_extract_mode_param *param) { |
---|
1126 | GBDATA *gb_main = param->gb_main; |
---|
1127 | GB_ERROR error = GBT_check_alignment_name(ali); |
---|
1128 | |
---|
1129 | if (!error) { |
---|
1130 | GB_transaction ta(gb_main); |
---|
1131 | GBDATA *gb_ali = GBT_get_alignment(gb_main, ali); |
---|
1132 | |
---|
1133 | if (!gb_ali) { |
---|
1134 | GB_clear_error(); // ali not found |
---|
1135 | if (!GBT_create_alignment(gb_main, ali, 0, 0, 0, "dna")) { |
---|
1136 | error = GB_await_error(); |
---|
1137 | } |
---|
1138 | } |
---|
1139 | } |
---|
1140 | |
---|
1141 | if (!error) { |
---|
1142 | ask_about_existing_gene_species = new AW_repeated_question; |
---|
1143 | ask_to_overwrite_alignment = new AW_repeated_question; |
---|
1144 | |
---|
1145 | arb_progress progress("Extracting pseudo-species"); |
---|
1146 | { |
---|
1147 | EG2PS_data *eg2ps = NULp; |
---|
1148 | { |
---|
1149 | gen_count_marked_genes = 0; |
---|
1150 | GEN_perform_command(gb_main, param->get_perform_mode(), do_mark_command_for_one_species, GEN_COUNT_MARKED, 0); |
---|
1151 | |
---|
1152 | GB_transaction ta(gb_main); |
---|
1153 | GBDATA *gb_species_data = GBT_get_species_data(gb_main); |
---|
1154 | eg2ps = new EG2PS_data(ali, gb_species_data, gen_count_marked_genes); |
---|
1155 | } |
---|
1156 | |
---|
1157 | PersistentNameServerConnection stayAlive; |
---|
1158 | |
---|
1159 | GEN_perform_command(gb_main, param->get_perform_mode(), do_mark_command_for_one_species, GEN_EXTRACT_MARKED, (AW_CL)eg2ps); |
---|
1160 | delete eg2ps; |
---|
1161 | } |
---|
1162 | |
---|
1163 | delete ask_to_overwrite_alignment; |
---|
1164 | delete ask_about_existing_gene_species; |
---|
1165 | ask_to_overwrite_alignment = NULp; |
---|
1166 | ask_about_existing_gene_species = NULp; |
---|
1167 | } |
---|
1168 | return error; |
---|
1169 | } |
---|
1170 | static void gene_extract_cb(AW_window*, GEN_extract_mode_param *param) { |
---|
1171 | AWT_activate_prompt("Extract genes to alignment", "Enter the name of the alignment to extract to:", "ali_gene_", "Extract", makeResultHandler(gene_extract_handler, param), "", SRT_AUTOCORRECT_ALINAME); |
---|
1172 | } |
---|
1173 | |
---|
1174 | enum MarkCommand { |
---|
1175 | UNMARK, // UNMARK and MARK have to be 0 and 1! |
---|
1176 | MARK, |
---|
1177 | INVERT, |
---|
1178 | MARK_UNMARK_REST, |
---|
1179 | }; |
---|
1180 | |
---|
1181 | static void mark_organisms(AW_window*, MarkCommand mark, GBDATA *gb_main) { |
---|
1182 | GB_transaction ta(gb_main); |
---|
1183 | |
---|
1184 | if (mark == MARK_UNMARK_REST) { |
---|
1185 | GBT_mark_all(gb_main, 0); // unmark all species |
---|
1186 | mark = MARK; |
---|
1187 | } |
---|
1188 | |
---|
1189 | for (GBDATA *gb_org = GEN_first_organism(gb_main); |
---|
1190 | gb_org; |
---|
1191 | gb_org = GEN_next_organism(gb_org)) |
---|
1192 | { |
---|
1193 | if (mark == INVERT) { |
---|
1194 | GB_write_flag(gb_org, !GB_read_flag(gb_org)); // invert mark of organism |
---|
1195 | } |
---|
1196 | else { |
---|
1197 | GB_write_flag(gb_org, mark); // mark/unmark organism |
---|
1198 | } |
---|
1199 | } |
---|
1200 | } |
---|
1201 | |
---|
1202 | |
---|
1203 | static void mark_gene_species(AW_window*, MarkCommand mark, GBDATA *gb_main) { |
---|
1204 | GB_transaction ta(gb_main); |
---|
1205 | |
---|
1206 | if (mark == MARK_UNMARK_REST) { |
---|
1207 | GBT_mark_all(gb_main, 0); // unmark all species |
---|
1208 | mark = MARK; |
---|
1209 | } |
---|
1210 | |
---|
1211 | for (GBDATA *gb_pseudo = GEN_first_pseudo_species(gb_main); |
---|
1212 | gb_pseudo; |
---|
1213 | gb_pseudo = GEN_next_pseudo_species(gb_pseudo)) |
---|
1214 | { |
---|
1215 | if (mark == INVERT) { |
---|
1216 | GB_write_flag(gb_pseudo, !GB_read_flag(gb_pseudo)); // invert mark of pseudo-species |
---|
1217 | } |
---|
1218 | else { |
---|
1219 | GB_write_flag(gb_pseudo, mark); // mark/unmark gene-species |
---|
1220 | } |
---|
1221 | } |
---|
1222 | } |
---|
1223 | |
---|
1224 | static void mark_gene_species_of_marked_genes(AW_window*, GBDATA *gb_main) { |
---|
1225 | GB_transaction ta(gb_main); |
---|
1226 | GB_HASH *organism_hash = GBT_create_organism_hash(gb_main); |
---|
1227 | |
---|
1228 | for (GBDATA *gb_pseudo = GEN_first_pseudo_species(gb_main); |
---|
1229 | gb_pseudo; |
---|
1230 | gb_pseudo = GEN_next_pseudo_species(gb_pseudo)) |
---|
1231 | { |
---|
1232 | GBDATA *gb_gene = GEN_find_origin_gene(gb_pseudo, organism_hash); |
---|
1233 | if (GB_read_flag(gb_gene)) { |
---|
1234 | GB_write_flag(gb_pseudo, 1); // mark pseudo |
---|
1235 | } |
---|
1236 | } |
---|
1237 | |
---|
1238 | GBS_free_hash(organism_hash); |
---|
1239 | } |
---|
1240 | |
---|
1241 | |
---|
1242 | |
---|
1243 | static void mark_organisms_with_marked_genes(AW_window*, GBDATA *gb_main) { |
---|
1244 | GB_transaction ta(gb_main); |
---|
1245 | |
---|
1246 | for (GBDATA *gb_species = GEN_first_organism(gb_main); |
---|
1247 | gb_species; |
---|
1248 | gb_species = GEN_next_organism(gb_species)) |
---|
1249 | { |
---|
1250 | for (GBDATA *gb_gene = GEN_first_gene(gb_species); |
---|
1251 | gb_gene; |
---|
1252 | gb_gene = GEN_next_gene(gb_gene)) |
---|
1253 | { |
---|
1254 | if (GB_read_flag(gb_gene)) { |
---|
1255 | GB_write_flag(gb_species, 1); |
---|
1256 | break; // continue with next organism |
---|
1257 | } |
---|
1258 | } |
---|
1259 | } |
---|
1260 | } |
---|
1261 | static void mark_gene_species_using_current_alignment(AW_window*, GBDATA *gb_main) { |
---|
1262 | GB_transaction ta(gb_main); |
---|
1263 | char *ali = GBT_get_default_alignment(gb_main); |
---|
1264 | |
---|
1265 | for (GBDATA *gb_pseudo = GEN_first_pseudo_species(gb_main); |
---|
1266 | gb_pseudo; |
---|
1267 | gb_pseudo = GEN_next_pseudo_species(gb_pseudo)) |
---|
1268 | { |
---|
1269 | GBDATA *gb_ali = GB_entry(gb_pseudo, ali); |
---|
1270 | if (gb_ali) { |
---|
1271 | GBDATA *gb_data = GB_entry(gb_ali, "data"); |
---|
1272 | if (gb_data) { |
---|
1273 | GB_write_flag(gb_pseudo, 1); |
---|
1274 | } |
---|
1275 | } |
---|
1276 | } |
---|
1277 | } |
---|
1278 | static void mark_genes_of_marked_gene_species(AW_window*, GBDATA *gb_main) { |
---|
1279 | GB_transaction ta(gb_main); |
---|
1280 | GB_HASH *organism_hash = GBT_create_organism_hash(gb_main); |
---|
1281 | |
---|
1282 | for (GBDATA *gb_pseudo = GEN_first_pseudo_species(gb_main); |
---|
1283 | gb_pseudo; |
---|
1284 | gb_pseudo = GEN_next_pseudo_species(gb_pseudo)) |
---|
1285 | { |
---|
1286 | if (GB_read_flag(gb_pseudo)) { |
---|
1287 | GBDATA *gb_gene = GEN_find_origin_gene(gb_pseudo, organism_hash); |
---|
1288 | GB_write_flag(gb_gene, 1); // mark gene |
---|
1289 | } |
---|
1290 | } |
---|
1291 | |
---|
1292 | GBS_free_hash(organism_hash); |
---|
1293 | } |
---|
1294 | |
---|
1295 | static void GEN_insert_extract_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file) { |
---|
1296 | awm->insert_sub_menu(submenu_name, hot_key); |
---|
1297 | |
---|
1298 | char macro_name_buffer[50]; |
---|
1299 | |
---|
1300 | sprintf(macro_name_buffer, "%s_of_current", macro_prefix); |
---|
1301 | awm->insert_menu_topic(awm->local_id(macro_name_buffer), "of current species...", "c", help_file, AWM_ALL, makeWindowCallback(gene_extract_cb, GEN_extract_mode_param::get(gb_main, GEN_PERFORM_CURRENT_ORGANISM))); |
---|
1302 | |
---|
1303 | sprintf(macro_name_buffer, "%s_of_marked", macro_prefix); |
---|
1304 | awm->insert_menu_topic(awm->local_id(macro_name_buffer), "of marked species...", "m", help_file, AWM_ALL, makeWindowCallback(gene_extract_cb, GEN_extract_mode_param::get(gb_main, GEN_PERFORM_MARKED_ORGANISMS))); |
---|
1305 | |
---|
1306 | sprintf(macro_name_buffer, "%s_of_all", macro_prefix); |
---|
1307 | awm->insert_menu_topic(awm->local_id(macro_name_buffer), "of all species...", "a", help_file, AWM_ALL, makeWindowCallback(gene_extract_cb, GEN_extract_mode_param::get(gb_main, GEN_PERFORM_ALL_ORGANISMS))); |
---|
1308 | |
---|
1309 | awm->close_sub_menu(); |
---|
1310 | } |
---|
1311 | |
---|
1312 | static void GEN_insert_multi_submenu(AW_window_menu_modes *awm, const char *macro_prefix, const char *submenu_name, const char *hot_key, |
---|
1313 | const char *help_file, void (*command)(AW_window*, GEN_PERFORM_MODE, GEN_command_mode_param*), GEN_command_mode_param *command_mode) |
---|
1314 | { |
---|
1315 | awm->insert_sub_menu(submenu_name, hot_key); |
---|
1316 | |
---|
1317 | char macro_name_buffer[50]; |
---|
1318 | |
---|
1319 | sprintf(macro_name_buffer, "%s_of_current", macro_prefix); |
---|
1320 | awm->insert_menu_topic(macro_name_buffer, "of current species", "c", help_file, AWM_ALL, makeWindowCallback(command, GEN_PERFORM_CURRENT_ORGANISM, command_mode)); |
---|
1321 | |
---|
1322 | sprintf(macro_name_buffer, "%s_of_all_but_current", macro_prefix); |
---|
1323 | awm->insert_menu_topic(macro_name_buffer, "of all but current species", "b", help_file, AWM_ALL, makeWindowCallback(command, GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, command_mode)); |
---|
1324 | |
---|
1325 | sprintf(macro_name_buffer, "%s_of_marked", macro_prefix); |
---|
1326 | awm->insert_menu_topic(macro_name_buffer, "of marked species", "m", help_file, AWM_ALL, makeWindowCallback(command, GEN_PERFORM_MARKED_ORGANISMS, command_mode)); |
---|
1327 | |
---|
1328 | sprintf(macro_name_buffer, "%s_of_all", macro_prefix); |
---|
1329 | awm->insert_menu_topic(macro_name_buffer, "of all species", "a", help_file, AWM_ALL, makeWindowCallback(command, GEN_PERFORM_ALL_ORGANISMS, command_mode)); |
---|
1330 | |
---|
1331 | awm->close_sub_menu(); |
---|
1332 | } |
---|
1333 | |
---|
1334 | static void GEN_insert_mark_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file, GEN_MARK_MODE mark_mode) { |
---|
1335 | GEN_insert_multi_submenu(awm, macro_prefix, submenu_name, hot_key, help_file, GEN_mark_command, GEN_command_mode_param::get(gb_main, mark_mode)); |
---|
1336 | } |
---|
1337 | static void GEN_insert_hide_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file, GEN_HIDE_MODE hide_mode) { |
---|
1338 | GEN_insert_multi_submenu(awm, macro_prefix, submenu_name, hot_key, help_file, GEN_hide_command, GEN_command_mode_param::get(gb_main, hide_mode)); |
---|
1339 | } |
---|
1340 | |
---|
1341 | #if defined(DEBUG) |
---|
1342 | static AW_window *GEN_create_awar_debug_window(AW_root *aw_root) { |
---|
1343 | static AW_window_simple *aws = NULp; |
---|
1344 | if (!aws) { |
---|
1345 | aws = new AW_window_simple; |
---|
1346 | |
---|
1347 | aws->init(aw_root, "DEBUG_AWARS", "DEBUG AWARS"); |
---|
1348 | aws->at(10, 10); |
---|
1349 | aws->auto_space(10, 10); |
---|
1350 | |
---|
1351 | const int width = 50; |
---|
1352 | |
---|
1353 | ; aws->label("AWAR_SPECIES_NAME "); aws->create_input_field(AWAR_SPECIES_NAME, width); |
---|
1354 | aws->at_newline(); aws->label("AWAR_ORGANISM_NAME "); aws->create_input_field(AWAR_ORGANISM_NAME, width); |
---|
1355 | aws->at_newline(); aws->label("AWAR_GENE_NAME "); aws->create_input_field(AWAR_GENE_NAME, width); |
---|
1356 | aws->at_newline(); aws->label("AWAR_COMBINED_GENE_NAME "); aws->create_input_field(AWAR_COMBINED_GENE_NAME, width); |
---|
1357 | aws->at_newline(); aws->label("AWAR_EXPERIMENT_NAME "); aws->create_input_field(AWAR_EXPERIMENT_NAME, width); |
---|
1358 | aws->at_newline(); aws->label("AWAR_COMBINED_EXPERIMENT_NAME"); aws->create_input_field(AWAR_COMBINED_EXPERIMENT_NAME, width); |
---|
1359 | aws->at_newline(); aws->label("AWAR_PROTEOM_NAME "); aws->create_input_field(AWAR_PROTEOM_NAME, width); |
---|
1360 | aws->at_newline(); aws->label("AWAR_PROTEIN_NAME "); aws->create_input_field(AWAR_PROTEIN_NAME, width); |
---|
1361 | |
---|
1362 | aws->window_fit(); |
---|
1363 | } |
---|
1364 | return aws; |
---|
1365 | } |
---|
1366 | #endif // DEBUG |
---|
1367 | |
---|
1368 | // --------------------------- |
---|
1369 | // user mask section |
---|
1370 | |
---|
1371 | struct GEN_item_type_species_selector : public awt_item_type_selector { |
---|
1372 | GEN_item_type_species_selector() : awt_item_type_selector(AWT_IT_GENE) {} |
---|
1373 | ~GEN_item_type_species_selector() OVERRIDE {} |
---|
1374 | |
---|
1375 | const char *get_self_awar() const OVERRIDE { |
---|
1376 | return AWAR_COMBINED_GENE_NAME; |
---|
1377 | } |
---|
1378 | size_t get_self_awar_content_length() const OVERRIDE { |
---|
1379 | return 12 + 1 + 40; // species-name+'/'+gene_name |
---|
1380 | } |
---|
1381 | GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item |
---|
1382 | char *species_name = root->awar(AWAR_ORGANISM_NAME)->read_string(); |
---|
1383 | char *gene_name = root->awar(AWAR_GENE_NAME)->read_string(); |
---|
1384 | GBDATA *gb_gene = NULp; |
---|
1385 | |
---|
1386 | if (species_name[0] && gene_name[0]) { |
---|
1387 | GB_transaction ta(gb_main); |
---|
1388 | GBDATA *gb_species = GBT_find_species(gb_main, species_name); |
---|
1389 | if (gb_species) { |
---|
1390 | gb_gene = GEN_find_gene(gb_species, gene_name); |
---|
1391 | } |
---|
1392 | } |
---|
1393 | |
---|
1394 | free(gene_name); |
---|
1395 | free(species_name); |
---|
1396 | |
---|
1397 | return gb_gene; |
---|
1398 | } |
---|
1399 | const char *getKeyPath() const OVERRIDE { // give the keypath for items |
---|
1400 | return CHANGE_KEY_PATH_GENES; |
---|
1401 | } |
---|
1402 | }; |
---|
1403 | |
---|
1404 | static GEN_item_type_species_selector item_type_gene; |
---|
1405 | |
---|
1406 | static void GEN_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) { |
---|
1407 | const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id); |
---|
1408 | gen_assert(descriptor); |
---|
1409 | if (descriptor) { |
---|
1410 | AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_gene, descriptor->get_internal_maskname(), descriptor->is_local_mask()); |
---|
1411 | } |
---|
1412 | } |
---|
1413 | |
---|
1414 | static void GEN_create_mask_submenu(AW_window_menu_modes *awm, GBDATA *gb_main) { |
---|
1415 | AWT_create_mask_submenu(awm, AWT_IT_GENE, GEN_open_mask_window, gb_main); |
---|
1416 | } |
---|
1417 | |
---|
1418 | static AW_window *create_colorize_genes_window(AW_root *aw_root, GBDATA *gb_main) { |
---|
1419 | return QUERY::create_colorize_items_window(aw_root, gb_main, GEN_get_selector()); |
---|
1420 | } |
---|
1421 | |
---|
1422 | static AW_window *create_colorize_organisms_window(AW_root *aw_root, GBDATA *gb_main) { |
---|
1423 | return QUERY::create_colorize_items_window(aw_root, gb_main, ORGANISM_get_selector()); |
---|
1424 | } |
---|
1425 | |
---|
1426 | static void GEN_create_organism_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, bool submenu) { |
---|
1427 | const char *title = "Organisms"; |
---|
1428 | const char *hotkey = "O"; |
---|
1429 | |
---|
1430 | if (submenu) awm->insert_sub_menu(title, hotkey); |
---|
1431 | else awm->create_menu(title, hotkey, AWM_ALL); |
---|
1432 | |
---|
1433 | { |
---|
1434 | awm->insert_menu_topic("organism_info", "Organism information", "i", "sp_info.hlp", AWM_ALL, RootAsWindowCallback::simple(DBUI::popup_organism_info_window, gb_main)); |
---|
1435 | |
---|
1436 | awm->sep______________(); |
---|
1437 | |
---|
1438 | awm->insert_menu_topic("mark_organisms", "Mark All organisms", "A", "organism_mark.hlp", AWM_ALL, makeWindowCallback(mark_organisms, MARK, gb_main)); |
---|
1439 | awm->insert_menu_topic("mark_organisms_unmark_rest", "Mark all organisms, unmark Rest", "R", "organism_mark.hlp", AWM_ALL, makeWindowCallback(mark_organisms, MARK_UNMARK_REST, gb_main)); |
---|
1440 | awm->insert_menu_topic("unmark_organisms", "Unmark all organisms", "U", "organism_mark.hlp", AWM_ALL, makeWindowCallback(mark_organisms, UNMARK, gb_main)); |
---|
1441 | awm->insert_menu_topic("invmark_organisms", "Invert marks of all organisms", "v", "organism_mark.hlp", AWM_ALL, makeWindowCallback(mark_organisms, INVERT, gb_main)); |
---|
1442 | awm->sep______________(); |
---|
1443 | awm->insert_menu_topic("mark_organisms_with_marked_genes", "Mark organisms with marked Genes", "G", "organism_mark.hlp", AWM_ALL, makeWindowCallback(mark_organisms_with_marked_genes, gb_main)); |
---|
1444 | awm->sep______________(); |
---|
1445 | awm->insert_menu_topic(awm->local_id("organism_colors"), "Colors ...", "C", "colorize.hlp", AWM_ALL, makeCreateWindowCallback(create_colorize_organisms_window, gb_main)); |
---|
1446 | } |
---|
1447 | if (submenu) awm->close_sub_menu(); |
---|
1448 | } |
---|
1449 | |
---|
1450 | static void GEN_create_gene_species_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, bool submenu) { |
---|
1451 | const char *title = "Gene-Species"; |
---|
1452 | const char *hotkey = "S"; |
---|
1453 | |
---|
1454 | if (submenu) awm->insert_sub_menu(title, hotkey); |
---|
1455 | else awm->create_menu(title, hotkey, AWM_ALL); |
---|
1456 | |
---|
1457 | { |
---|
1458 | awm->insert_menu_topic("mark_gene_species", "Mark All gene-species", "A", "gene_species_mark.hlp", AWM_ALL, makeWindowCallback(mark_gene_species, MARK, gb_main)); |
---|
1459 | awm->insert_menu_topic("mark_gene_species_unmark_rest", "Mark all gene-species, unmark Rest", "R", "gene_species_mark.hlp", AWM_ALL, makeWindowCallback(mark_gene_species, MARK_UNMARK_REST, gb_main)); |
---|
1460 | awm->insert_menu_topic("unmark_gene_species", "Unmark all gene-species", "U", "gene_species_mark.hlp", AWM_ALL, makeWindowCallback(mark_gene_species, UNMARK, gb_main)); |
---|
1461 | awm->insert_menu_topic("invmark_gene_species", "Invert marks of all gene-species", "I", "gene_species_mark.hlp", AWM_ALL, makeWindowCallback(mark_gene_species, INVERT, gb_main)); |
---|
1462 | awm->sep______________(); |
---|
1463 | awm->insert_menu_topic("mark_gene_species_of_marked_genes", "Mark gene-species of marked genes", "M", "gene_species_mark.hlp", AWM_ALL, makeWindowCallback(mark_gene_species_of_marked_genes, gb_main)); |
---|
1464 | awm->insert_menu_topic("mark_gene_species_curr_ali", "Mark all gene-species using Current alignment", "C", "gene_species_mark.hlp", AWM_ALL, makeWindowCallback(mark_gene_species_using_current_alignment, gb_main)); |
---|
1465 | } |
---|
1466 | |
---|
1467 | if (submenu) awm->close_sub_menu(); |
---|
1468 | } |
---|
1469 | |
---|
1470 | struct GEN_update_info { |
---|
1471 | AWT_canvas *canvas1; // just canvasses of different windows (needed for updates) |
---|
1472 | AWT_canvas *canvas2; |
---|
1473 | }; |
---|
1474 | |
---|
1475 | void GEN_create_genes_submenu(AW_window_menu_modes *awm, GBDATA *gb_main, bool for_ARB_NTREE) { |
---|
1476 | awm->create_menu("Genome", "G", AWM_ALL); |
---|
1477 | { |
---|
1478 | #if defined(DEBUG) |
---|
1479 | awm->insert_menu_topic(awm->local_id("debug_awars"), "[DEBUG] Show main AWARs", "A", NULp, AWM_ALL, GEN_create_awar_debug_window); |
---|
1480 | awm->sep______________(); |
---|
1481 | #endif // DEBUG |
---|
1482 | |
---|
1483 | if (for_ARB_NTREE) { |
---|
1484 | awm->insert_menu_topic("gene_map", "Gene Map", "p", "gene_map.hlp", AWM_ALL, makeCreateWindowCallback(GEN_create_first_map, gb_main)); // initial gene map |
---|
1485 | awm->sep______________(); |
---|
1486 | |
---|
1487 | GEN_create_gene_species_submenu(awm, gb_main, true); // Gene-species |
---|
1488 | GEN_create_organism_submenu (awm, gb_main, true); // Organisms |
---|
1489 | EXP_create_experiments_submenu (awm, gb_main, true); // Experiments |
---|
1490 | awm->sep______________(); |
---|
1491 | } |
---|
1492 | |
---|
1493 | awm->insert_menu_topic("gene_info", "Gene information", "i", "gene_info.hlp", AWM_ALL, RootAsWindowCallback::simple(GEN_popup_gene_infowindow, gb_main)); |
---|
1494 | awm->insert_menu_topic(awm->local_id("gene_search"), "Search and Query", "Q", "gene_search.hlp", AWM_ALL, makeCreateWindowCallback (GEN_create_gene_query_window, gb_main)); |
---|
1495 | |
---|
1496 | GEN_create_mask_submenu(awm, gb_main); |
---|
1497 | |
---|
1498 | awm->sep______________(); |
---|
1499 | |
---|
1500 | GEN_insert_mark_submenu(awm, gb_main, "gene_mark_all", "Mark all genes", "M", "gene_mark.hlp", GEN_MARK); |
---|
1501 | GEN_insert_mark_submenu(awm, gb_main, "gene_unmark_all", "Unmark all genes", "U", "gene_mark.hlp", GEN_UNMARK); |
---|
1502 | GEN_insert_mark_submenu(awm, gb_main, "gene_invert_marked", "Invert marked genes", "v", "gene_mark.hlp", GEN_INVERT_MARKED); |
---|
1503 | GEN_insert_mark_submenu(awm, gb_main, "gene_count_marked", "Count marked genes", "C", "gene_mark.hlp", GEN_COUNT_MARKED); |
---|
1504 | |
---|
1505 | awm->insert_menu_topic(awm->local_id("gene_colors"), "Colors ...", "l", "colorize.hlp", AWM_ALL, makeCreateWindowCallback(create_colorize_genes_window, gb_main)); |
---|
1506 | |
---|
1507 | awm->sep______________(); |
---|
1508 | |
---|
1509 | awm->insert_menu_topic("mark_genes_of_marked_gene_species", "Mark genes of marked gene-species", "g", "gene_mark.hlp", AWM_ALL, makeWindowCallback(mark_genes_of_marked_gene_species, gb_main)); |
---|
1510 | |
---|
1511 | awm->sep______________(); |
---|
1512 | |
---|
1513 | GEN_insert_extract_submenu(awm, gb_main, "gene_extract_marked", "Extract marked genes", "E", "gene_extract.hlp"); |
---|
1514 | |
---|
1515 | if (!for_ARB_NTREE) { // only in ARB_GENE_MAP: |
---|
1516 | awm->sep______________(); |
---|
1517 | GEN_insert_mark_submenu(awm, gb_main, "gene_mark_hidden", "Mark hidden genes", "h", "gene_hide.hlp", GEN_MARK_HIDDEN); |
---|
1518 | GEN_insert_mark_submenu(awm, gb_main, "gene_mark_visible", "Mark visible genes", "s", "gene_hide.hlp", GEN_MARK_VISIBLE); |
---|
1519 | |
---|
1520 | awm->sep______________(); |
---|
1521 | GEN_insert_mark_submenu(awm, gb_main, "gene_unmark_hidden", "Unmark hidden genes", "d", "gene_hide.hlp", GEN_UNMARK_HIDDEN); |
---|
1522 | GEN_insert_mark_submenu(awm, gb_main, "gene_unmark_visible", "Unmark visible genes", "r", "gene_hide.hlp", GEN_UNMARK_VISIBLE); |
---|
1523 | } |
---|
1524 | } |
---|
1525 | } |
---|
1526 | |
---|
1527 | static void GEN_create_hide_submenu(AW_window_menu_modes *awm, GBDATA *gb_main) { |
---|
1528 | awm->create_menu("Hide", "H", AWM_ALL); |
---|
1529 | { |
---|
1530 | GEN_insert_hide_submenu(awm, gb_main, "gene_hide_marked", "Hide marked genes", "H", "gene_hide.hlp", GEN_HIDE_MARKED); |
---|
1531 | GEN_insert_hide_submenu(awm, gb_main, "gene_unhide_marked", "Unhide marked genes", "U", "gene_hide.hlp", GEN_UNHIDE_MARKED); |
---|
1532 | GEN_insert_hide_submenu(awm, gb_main, "gene_invhide_marked", "Invert-hide marked genes", "v", "gene_hide.hlp", GEN_INVERT_HIDE_MARKED); |
---|
1533 | |
---|
1534 | awm->sep______________(); |
---|
1535 | GEN_insert_hide_submenu(awm, gb_main, "gene_hide_all", "Hide all genes", "a", "gene_hide.hlp", GEN_HIDE_ALL); |
---|
1536 | GEN_insert_hide_submenu(awm, gb_main, "gene_unhide_all", "Unhide all genes", "l", "gene_hide.hlp", GEN_UNHIDE_ALL); |
---|
1537 | GEN_insert_hide_submenu(awm, gb_main, "gene_invhide_all", "Invert-hide all genes", "I", "gene_hide.hlp", GEN_INVERT_HIDE_ALL); |
---|
1538 | } |
---|
1539 | } |
---|
1540 | |
---|
1541 | static void GEN_set_display_style(AW_window *aww, GEN_DisplayStyle style) { |
---|
1542 | GEN_map_window *win = DOWNCAST(GEN_map_window*, aww); |
---|
1543 | AWT_auto_refresh allowed_on(win->get_canvas()); |
---|
1544 | |
---|
1545 | win->get_root()->awar(AWAR_GENMAP_DISPLAY_TYPE(win->get_nr()))->write_int(style); |
---|
1546 | win->get_graphic()->set_display_style(style); |
---|
1547 | } |
---|
1548 | |
---|
1549 | static AW_window *GEN_create_map(AW_root *aw_root, GEN_create_map_param *param) { |
---|
1550 | // param->window_nr shall be 0 for first window (called from ARB_NTREE) |
---|
1551 | // additional views are always created by the previous window created with GEN_map |
---|
1552 | GEN_map_manager *manager = NULp; |
---|
1553 | |
---|
1554 | if (!GEN_map_manager::initialized()) { // first call |
---|
1555 | gen_assert(param->window_nr == 0); // has to be 0 for first call |
---|
1556 | |
---|
1557 | GEN_map_manager::initialize(aw_root, param->gb_main); |
---|
1558 | manager = GEN_map_manager::get_map_manager(); // creates the manager |
---|
1559 | |
---|
1560 | // global initialization (AWARS etc.) done here : |
---|
1561 | |
---|
1562 | GEN_create_genemap_global_awars(aw_root, AW_ROOT_DEFAULT, param->gb_main); |
---|
1563 | GEN_add_global_awar_callbacks(aw_root); |
---|
1564 | { |
---|
1565 | GB_transaction ta(param->gb_main); |
---|
1566 | GEN_make_node_text_init(param->gb_main); |
---|
1567 | } |
---|
1568 | } |
---|
1569 | else { |
---|
1570 | manager = GEN_map_manager::get_map_manager(); |
---|
1571 | } |
---|
1572 | |
---|
1573 | GEN_map_window *gmw = manager->get_map_window(param->window_nr); |
---|
1574 | return gmw; |
---|
1575 | } |
---|
1576 | |
---|
1577 | AW_window *GEN_create_first_map(AW_root *aw_root, GBDATA *gb_main) { |
---|
1578 | return GEN_create_map(aw_root, new GEN_create_map_param(gb_main, 0)); |
---|
1579 | } |
---|
1580 | |
---|
1581 | // ------------------------ |
---|
1582 | // GEN_map_window |
---|
1583 | |
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1584 | void GEN_map_window::init(AW_root *awr, GBDATA *gb_main) { |
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1585 | { |
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1586 | char *windowName = (window_nr == 0) ? ARB_strdup("ARB Gene Map") : GBS_global_string_copy("ARB Gene Map %i", window_nr); |
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1587 | char *windowID = (window_nr == 0) ? ARB_strdup("ARB_GENE_MAP") : GBS_global_string_copy("ARB_GENE_MAP_%i", window_nr); |
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1588 | |
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1589 | AW_window_menu_modes::init(awr, windowID, windowName, 200, 200); |
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1590 | |
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1591 | free(windowID); |
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1592 | free(windowName); |
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1593 | } |
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1594 | |
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1595 | GEN_create_genemap_local_awars(awr, AW_ROOT_DEFAULT, window_nr); |
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1596 | |
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1597 | gen_graphic = new GEN_graphic(awr, gb_main, GEN_gene_container_cb_installer, window_nr); |
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1598 | gen_canvas = new AWT_canvas(gb_main, this, get_window_id(), gen_graphic); |
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1599 | |
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1600 | GEN_add_local_awar_callbacks(awr, AW_ROOT_DEFAULT, this); |
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1601 | |
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1602 | AWT_auto_refresh allowed_on(gen_canvas); |
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1603 | { |
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1604 | GB_transaction ta(gb_main); |
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1605 | gen_graphic->reinit_gen_root(gen_canvas, false); |
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1606 | } |
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1607 | gen_canvas->request_resize(); |
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1608 | gen_canvas->set_mode(AWT_MODE_SELECT); // Default-Mode |
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1609 | |
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1610 | // --------------- |
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1611 | // menus |
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1612 | |
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1613 | // File Menu |
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1614 | create_menu("File", "F", AWM_ALL); |
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1615 | insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN); |
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1616 | insert_menu_topic(local_id("new_view"), "New view", "v", "gen_new_view.hlp", AWM_ALL, makeCreateWindowCallback(GEN_create_map, new GEN_create_map_param(gb_main, window_nr+1))); |
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1617 | |
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1618 | GEN_create_genes_submenu (this, gb_main, false); // Genes |
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1619 | GEN_create_gene_species_submenu(this, gb_main, false); // Gene-species |
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1620 | GEN_create_organism_submenu (this, gb_main, false); // Organisms |
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1621 | EXP_create_experiments_submenu (this, gb_main, false); // Experiments |
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1622 | GEN_create_hide_submenu(this, gb_main); // Hide Menu |
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1623 | |
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1624 | // Properties Menu |
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1625 | create_menu("Properties", "r", AWM_ALL); |
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1626 | insert_menu_topic(local_id("gene_props_menu"), "Frame settings ...", "M", "props_frame.hlp", AWM_ALL, AW_preset_window); |
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1627 | insert_menu_topic(local_id("gene_props"), "GENEMAP: Colors and Fonts ...", "C", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(GEN_create_gc_window, gen_canvas->gc_manager)); |
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1628 | insert_menu_topic(local_id("gene_options"), "Options", "O", "gen_options.hlp", AWM_ALL, GEN_create_options_window); |
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1629 | insert_menu_topic(local_id("gene_nds"), "NDS ( Select Gene Information ) ...", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(GEN_open_nds_window, gb_main)); |
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1630 | sep______________(); |
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1631 | AW_insert_common_property_menu_entries(this); |
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1632 | sep______________(); |
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1633 | insert_menu_topic("gene_save_props", "Save Defaults (ntree.arb)", "D", "savedef.hlp", AWM_ALL, AW_save_properties); |
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1634 | |
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1635 | // ---------------------- |
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1636 | // mode buttons |
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1637 | |
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1638 | create_mode("mode_select.xpm", "gen_mode.hlp", AWM_ALL, makeWindowCallback(GEN_mode_event, this, AWT_MODE_SELECT)); |
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1639 | create_mode("mode_zoom.xpm", "gen_mode.hlp", AWM_ALL, makeWindowCallback(GEN_mode_event, this, AWT_MODE_ZOOM)); |
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1640 | create_mode("mode_info.xpm", "gen_mode.hlp", AWM_ALL, makeWindowCallback(GEN_mode_event, this, AWT_MODE_INFO)); |
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1641 | |
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1642 | // ------------------- |
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1643 | // info area |
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1644 | |
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1645 | set_info_area_height(250); |
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1646 | at(11, 2); |
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1647 | auto_space(2, -2); |
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1648 | shadow_width(1); |
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1649 | |
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1650 | // close + undo button, info area, define line y-positions: |
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1651 | |
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1652 | int cur_x, cur_y, start_x, first_line_y, second_line_y, third_line_y; |
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1653 | get_at_position(&start_x, &first_line_y); |
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1654 | button_length(6); |
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1655 | |
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1656 | at(start_x, first_line_y); |
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1657 | help_text("quit.hlp"); |
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1658 | callback(AW_POPDOWN); |
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1659 | create_button("Close", "Close"); |
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1660 | |
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1661 | get_at_position(&cur_x, &cur_y); |
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1662 | |
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1663 | int gene_x = cur_x; |
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1664 | at_newline(); |
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1665 | get_at_position(&cur_x, &second_line_y); |
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1666 | |
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1667 | at(start_x, second_line_y); |
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1668 | help_text("undo.hlp"); |
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1669 | callback(makeWindowCallback(GEN_undo_cb, GB_UNDO_UNDO, gb_main)); |
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1670 | create_button("Undo", "Undo"); |
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1671 | |
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1672 | at_newline(); |
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1673 | get_at_position(&cur_x, &third_line_y); |
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1674 | |
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1675 | button_length(AWAR_FOOTER_MAX_LEN); |
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1676 | create_button(NULp, AWAR_FOOTER); |
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1677 | |
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1678 | at_newline(); |
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1679 | get_at_position(&cur_x, &cur_y); |
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1680 | set_info_area_height(cur_y+6); |
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1681 | |
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1682 | // gene+species buttons: |
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1683 | button_length(20); |
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1684 | |
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1685 | at(gene_x, first_line_y); |
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1686 | help_text("sp_search.hlp"); |
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1687 | callback(makeCreateWindowCallback(DBUI::create_species_query_window, gb_main)); // @@@ should use an organism search (using ITEM_organism) |
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1688 | create_button("SEARCH_ORGANISM", AWAR_LOCAL_ORGANISM_NAME(window_nr)); |
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1689 | |
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1690 | at(gene_x, second_line_y); |
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1691 | help_text("gene_search.hlp"); |
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1692 | callback(makeCreateWindowCallback(GEN_create_gene_query_window, gb_main)); |
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1693 | create_button("SEARCH_GENE", AWAR_LOCAL_GENE_NAME(window_nr)); |
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1694 | |
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1695 | get_at_position(&cur_x, &cur_y); |
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1696 | int lock_x = cur_x; |
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1697 | |
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1698 | at(lock_x, first_line_y); |
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1699 | create_toggle(AWAR_LOCAL_ORGANISM_LOCK(window_nr)); |
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1700 | |
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1701 | at(lock_x, second_line_y); |
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1702 | create_toggle(AWAR_LOCAL_GENE_LOCK(window_nr)); |
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1703 | |
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1704 | get_at_position(&cur_x, &cur_y); |
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1705 | int dtype_x1 = cur_x; |
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1706 | |
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1707 | // display type buttons: |
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1708 | |
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1709 | button_length(4); |
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1710 | |
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1711 | at(dtype_x1, first_line_y); |
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1712 | help_text("gen_disp_style.hlp"); |
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1713 | callback(makeWindowCallback(GEN_set_display_style, GEN_DISPLAY_STYLE_RADIAL)); |
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1714 | create_button("RADIAL_DISPLAY_TYPE", "#gen_radial.xpm"); |
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1715 | |
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1716 | help_text("gen_disp_style.hlp"); |
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1717 | callback(makeWindowCallback(GEN_set_display_style, GEN_DISPLAY_STYLE_BOOK)); |
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1718 | create_button("BOOK_DISPLAY_TYPE", "#gen_book.xpm"); |
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1719 | |
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1720 | get_at_position(&cur_x, &cur_y); |
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1721 | int jump_x = cur_x; |
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1722 | |
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1723 | at(dtype_x1, second_line_y); |
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1724 | help_text("gen_disp_style.hlp"); |
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1725 | callback(makeWindowCallback(GEN_set_display_style, GEN_DISPLAY_STYLE_VERTICAL)); |
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1726 | create_button("VERTICAL_DISPLAY_TYPE", "#gen_vertical.xpm"); |
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1727 | |
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1728 | // jump button: |
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1729 | |
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1730 | button_length(0); |
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1731 | |
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1732 | at(jump_x, first_line_y); |
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1733 | help_text("gen_jump.hlp"); |
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1734 | callback(makeWindowCallback(GEN_jump_cb, true)); |
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1735 | create_button("Jump", "Jump"); |
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1736 | |
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1737 | // help buttons: |
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1738 | |
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1739 | get_at_position(&cur_x, &cur_y); |
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1740 | int help_x = cur_x; |
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1741 | |
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1742 | at(help_x, first_line_y); |
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1743 | help_text("help.hlp"); |
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1744 | callback(makeHelpCallback("gene_map.hlp")); |
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1745 | create_button("HELP", "HELP", "H"); |
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1746 | |
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1747 | at(help_x, second_line_y); |
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1748 | callback(AW_help_entry_pressed); |
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1749 | create_button(NULp, "?"); |
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1750 | } |
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