1 | // =============================================================== // |
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2 | // // |
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3 | // File : EDB_root_bact.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // =============================================================== // |
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10 | |
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11 | #include <ed4_extern.hxx> |
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12 | #include "ed4_class.hxx" |
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13 | |
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14 | #include <aw_msg.hxx> |
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15 | #include <arb_progress.h> |
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16 | #include <arbdbt.h> |
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17 | #include <arb_strbuf.h> |
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18 | #include <ad_config.h> |
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19 | |
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20 | #define NAME_BUFFERSIZE 100 |
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21 | |
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22 | void EDB_root_bact::calc_no_of_all(const char *string_to_scan, long *group, long *species) { |
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23 | *group = 0; |
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24 | *species = 0; |
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25 | |
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26 | if (string_to_scan) { |
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27 | long i = 0; |
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28 | while (string_to_scan[i]) { |
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29 | if (string_to_scan[i] == 1) { |
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30 | if (string_to_scan[i+1] == 'L' || string_to_scan[i+1] == 'S') { |
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31 | (*species)++; |
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32 | i++; |
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33 | } |
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34 | else if (string_to_scan[i+1] == 'F' || string_to_scan[i+1] == 'G') { |
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35 | (*group)++; |
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36 | i++; |
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37 | } |
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38 | } |
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39 | i++; |
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40 | } |
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41 | } |
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42 | } |
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43 | |
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44 | ED4_returncode EDB_root_bact::fill_data(ED4_multi_species_manager *multi_species_manager, |
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45 | ED4_sequence_info_terminal *ref_sequence_info_terminal, |
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46 | ED4_sequence_terminal *ref_sequence_terminal, |
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47 | char *str, |
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48 | ED4_index *y, |
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49 | ED4_index curr_local_position, |
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50 | ED4_index *length_of_terminals, |
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51 | int group_depth, |
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52 | ED4_datamode datamode) |
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53 | { |
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54 | GBDATA *gb_datamode = NULL; |
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55 | switch (datamode) { |
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56 | case ED4_D_EXTENDED: gb_datamode = GBT_find_SAI(GLOBAL_gb_main, str); break; |
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57 | case ED4_D_SPECIES: gb_datamode = GBT_find_species(GLOBAL_gb_main, str); break; |
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58 | } |
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59 | |
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60 | if (!gb_datamode) { // didn't find this species |
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61 | not_found_counter++; |
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62 | if (not_found_counter <= MAX_SHOWN_MISSING_SPECIES) { |
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63 | char dummy[150]; |
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64 | sprintf(dummy, "%zu. %s\n", not_found_counter, str); |
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65 | e4_assert(not_found_message); |
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66 | GBS_strcat(not_found_message, dummy); |
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67 | } |
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68 | return ED4_R_BREAK; |
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69 | } |
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70 | |
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71 | // check whether sequence has data in desired alignment |
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72 | bool has_alignment = 0 != GB_entry(gb_datamode, ED4_ROOT->alignment_name); |
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73 | if (!has_alignment) { |
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74 | if (datamode == ED4_D_SPECIES) { // only warn about species w/o data (SAIs are skipped silently) |
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75 | not_found_counter++; |
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76 | if (not_found_counter <= MAX_SHOWN_MISSING_SPECIES) { |
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77 | char dummy[150]; |
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78 | sprintf(dummy, "%zu. %s (no data in alignment)\n", not_found_counter, str); |
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79 | GBS_strcat(not_found_message, dummy); |
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80 | } |
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81 | } |
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82 | return ED4_R_BREAK; |
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83 | } |
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84 | |
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85 | const ED4_index terminal_height = TERMINALHEIGHT; |
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86 | ED4_index local_count_position = curr_local_position; |
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87 | ED4_species_type spec_type = (datamode == ED4_D_EXTENDED) ? ED4_SP_SAI : ED4_SP_SPECIES; |
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88 | |
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89 | |
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90 | { |
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91 | char namebuffer[NAME_BUFFERSIZE]; |
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92 | int count_two = 0; |
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93 | |
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94 | sprintf(namebuffer, "Species_Manager.%ld.%d", ED4_counter, count_two); |
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95 | ED4_species_manager *species_manager = new ED4_species_manager(spec_type, namebuffer, 0, local_count_position, 0, 0, multi_species_manager); |
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96 | |
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97 | species_manager->set_property(ED4_P_MOVABLE); |
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98 | if (spec_type == ED4_SP_SAI) { |
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99 | ED4_abstract_group_manager *group_man = species_manager->get_parent(ED4_level(ED4_L_GROUP|ED4_L_ROOTGROUP))->to_abstract_group_manager(); |
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100 | group_man->table().ignore_me(); // ignore SAI tables (does not work - instead ignore SAIs when calculating consensus) |
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101 | } |
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102 | species_manager->set_species_pointer(gb_datamode); |
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103 | multi_species_manager->children->append_member(species_manager); |
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104 | |
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105 | sprintf(namebuffer, "MultiName_Manager.%ld.%d", ED4_counter, count_two); |
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106 | ED4_multi_name_manager *multi_name_manager = new ED4_multi_name_manager(namebuffer, 0, 0, 0, 0, species_manager); |
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107 | species_manager->children->append_member(multi_name_manager); |
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108 | |
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109 | sprintf(namebuffer, "MultiSeq_Manager.%ld.%d", ED4_counter, count_two++); |
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110 | ED4_multi_sequence_manager *multi_sequence_manager = new ED4_multi_sequence_manager(namebuffer, MAXSPECIESWIDTH-(group_depth*BRACKETWIDTH), 0, 0, 0, species_manager); |
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111 | species_manager->children->append_member(multi_sequence_manager); |
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112 | |
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113 | sprintf(namebuffer, "Name_Manager%ld.%d", ED4_counter, count_two++); // hier fehlt noch y |
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114 | ED4_name_manager *name_manager = new ED4_name_manager(namebuffer, 0, 0*terminal_height, 0, 0, multi_name_manager); // hier fehlt noch y |
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115 | name_manager->set_property(ED4_P_MOVABLE); // only Speciesname should be movable !!!! |
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116 | multi_name_manager->children->append_member(name_manager); |
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117 | |
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118 | { |
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119 | sprintf(namebuffer, "Species_Name_Term%ld.%d", ED4_counter, count_two++); |
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120 | ED4_species_name_terminal *species_name_terminal = new ED4_species_name_terminal(namebuffer, 0, 0, MAXSPECIESWIDTH-(group_depth*BRACKETWIDTH), terminal_height, name_manager); |
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121 | species_name_terminal->set_property((ED4_properties) (ED4_P_SELECTABLE | ED4_P_DRAGABLE | ED4_P_IS_HANDLE)); |
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122 | species_name_terminal->set_links(NULL, ref_sequence_terminal); |
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123 | species_name_terminal->set_species_pointer(GB_entry(gb_datamode, "name")); |
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124 | name_manager->children->append_member(species_name_terminal); |
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125 | } |
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126 | |
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127 | { |
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128 | ED4_index name_coords = terminal_height; |
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129 | ED4_index seq_coords = 0; |
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130 | |
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131 | search_sequence_data_rek(multi_sequence_manager, ref_sequence_info_terminal, ref_sequence_terminal, gb_datamode, |
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132 | count_two, &seq_coords, &max_seq_terminal_length, ED4_A_DEFAULT, datamode == ED4_D_EXTENDED); |
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133 | |
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134 | local_count_position += std::max(name_coords, seq_coords); |
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135 | } |
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136 | } |
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137 | |
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138 | if (!(multi_species_manager->flag.hidden)) { |
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139 | *length_of_terminals = local_count_position-curr_local_position; |
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140 | *y += *length_of_terminals; // needed for global coordinates of manager |
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141 | } |
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142 | |
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143 | return ED4_R_OK; |
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144 | } |
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145 | |
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146 | ED4_returncode EDB_root_bact::search_sequence_data_rek(ED4_multi_sequence_manager *multi_sequence_manager, |
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147 | ED4_sequence_info_terminal *ref_sequence_info_terminal, |
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148 | ED4_sequence_terminal *ref_sequence_terminal, |
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149 | GBDATA *gb_datamode, |
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150 | int count_too, |
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151 | ED4_index *seq_coords, |
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152 | ED4_index *max_sequence_terminal_length, |
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153 | ED4_alignment alignment_flag, |
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154 | bool isSAI) |
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155 | { |
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156 | AW_device *device; |
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157 | int j = 0; |
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158 | int pixel_length; |
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159 | GBDATA *gb_ali_xxx = NULL; |
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160 | GBDATA *gb_alignment; |
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161 | long string_length; |
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162 | char namebuffer[NAME_BUFFERSIZE]; |
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163 | |
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164 | device = ED4_ROOT->first_window->get_device(); |
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165 | |
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166 | if (alignment_flag == ED4_A_DEFAULT) { |
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167 | gb_ali_xxx = GB_entry(gb_datamode, ED4_ROOT->alignment_name); |
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168 | } |
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169 | else if (alignment_flag == ED4_A_CONTAINER) { |
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170 | gb_ali_xxx = gb_datamode; |
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171 | } |
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172 | if (!gb_ali_xxx) return ED4_R_OK; |
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173 | |
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174 | j=0; |
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175 | for (gb_alignment = GB_child(gb_ali_xxx); gb_alignment; gb_alignment = GB_nextChild(gb_alignment)) { |
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176 | GB_TYPES type = GB_read_type(gb_alignment); |
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177 | |
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178 | if (type == GB_INTS || type == GB_FLOATS) { |
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179 | continue; |
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180 | } |
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181 | |
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182 | if (type == GB_DB) { // we have to unpack container |
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183 | search_sequence_data_rek(multi_sequence_manager, ref_sequence_info_terminal, ref_sequence_terminal, |
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184 | gb_alignment, count_too, seq_coords, max_sequence_terminal_length, ED4_A_CONTAINER, isSAI); |
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185 | } |
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186 | else { // otherwise we enter the data |
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187 | char *key_string = GB_read_key(gb_alignment); |
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188 | if (key_string[0] != '_') { // don't show sequences starting with an underscore |
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189 | sprintf(namebuffer, "Sequence_Manager.%ld.%d", ED4_counter, count_too++); |
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190 | ED4_sequence_manager *seq_manager = new ED4_sequence_manager(namebuffer, 0, j*TERMINALHEIGHT, 0, 0, multi_sequence_manager); |
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191 | seq_manager->set_property(ED4_P_MOVABLE); |
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192 | multi_sequence_manager->children->append_member(seq_manager); |
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193 | |
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194 | ED4_sequence_info_terminal *sequence_info_terminal = |
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195 | new ED4_sequence_info_terminal(key_string, 0, 0, SEQUENCEINFOSIZE, TERMINALHEIGHT, seq_manager); |
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196 | sequence_info_terminal->set_property((ED4_properties) (ED4_P_SELECTABLE | ED4_P_DRAGABLE | ED4_P_IS_HANDLE)); |
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197 | sequence_info_terminal->set_links(ref_sequence_info_terminal, ref_sequence_info_terminal); |
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198 | sequence_info_terminal->set_species_pointer(gb_alignment); |
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199 | seq_manager->children->append_member(sequence_info_terminal); |
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200 | |
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201 | ED4_text_terminal *text_terminal = 0; |
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202 | |
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203 | bool is_data = false; |
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204 | bool is_data2 = false; |
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205 | bool is_bits = false; |
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206 | bool is_quality = false; |
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207 | |
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208 | if (strcmp(key_string, "data") == 0) is_data = true; // SAI or species |
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209 | else if (strcmp(key_string, "data2") == 0) is_data2 = true; // used by SAIs with two entries (e.g. first and second digit of 2-digit-numbers) |
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210 | else if (strcmp(key_string, "bits") == 0) is_bits = true; // used by binary SAIs (e.g. MARKERLINE) |
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211 | else if (strcmp(key_string, "quality") == 0) is_quality = true; // used by "quality" entry written by chimera check; see ../STAT/ST_quality.cxx@chimera_check_quality_string |
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212 | |
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213 | bool is_aligned = is_data || is_data2 || is_bits || is_quality; |
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214 | |
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215 | if (is_aligned) { |
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216 | bool shall_display_secinfo = is_data; |
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217 | |
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218 | if (isSAI) { |
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219 | GBDATA *gb_sai = GB_get_grandfather(gb_alignment); |
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220 | GBDATA *gb_disp_sec = GB_searchOrCreate_int(gb_sai, "showsec", 0); |
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221 | shall_display_secinfo = GB_read_int(gb_disp_sec); |
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222 | } |
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223 | |
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224 | sprintf(namebuffer, "Sequence_Term%ld.%d", ED4_counter, count_too++); |
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225 | ED4_sequence_terminal *seq_term = new ED4_sequence_terminal(namebuffer, SEQUENCEINFOSIZE, 0, 0, TERMINALHEIGHT, seq_manager, shall_display_secinfo); |
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226 | seq_term->species_name = seq_term->get_name_of_species(); |
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227 | |
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228 | if (is_data) seq_term->set_property(ED4_P_CONSENSUS_RELEVANT); |
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229 | seq_term->set_property(ED4_P_ALIGNMENT_DATA); |
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230 | |
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231 | text_terminal = seq_term; |
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232 | } |
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233 | else { |
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234 | sprintf(namebuffer, "PureText_Term%ld.%d", ED4_counter, count_too++); |
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235 | text_terminal = new ED4_pure_text_terminal(namebuffer, SEQUENCEINFOSIZE, 0, 0, TERMINALHEIGHT, seq_manager); |
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236 | } |
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237 | |
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238 | text_terminal->set_property(ED4_P_CURSOR_ALLOWED); |
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239 | text_terminal->set_links(ref_sequence_terminal, ref_sequence_terminal); |
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240 | seq_manager->children->append_member(text_terminal); |
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241 | #if defined(DEBUG) |
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242 | // ensure only 1 terminal is consensus-relevant! |
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243 | if (is_data) { |
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244 | seq_manager->get_consensus_relevant_terminal(); // does an error otherwise! |
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245 | } |
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246 | #endif // DEBUG |
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247 | text_terminal->set_species_pointer(gb_alignment); |
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248 | |
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249 | if (gb_alignment) { |
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250 | string_length = GB_read_count(gb_alignment); |
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251 | } |
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252 | else { |
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253 | string_length = 100; |
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254 | } |
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255 | |
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256 | pixel_length = device->get_string_size(ED4_G_SEQUENCES, NULL, string_length) + 100; |
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257 | |
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258 | *max_sequence_terminal_length = std::max(*max_sequence_terminal_length, long(pixel_length)); |
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259 | text_terminal->extension.size[WIDTH] = pixel_length; |
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260 | |
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261 | if (MAXSEQUENCECHARACTERLENGTH < string_length) { |
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262 | MAXSEQUENCECHARACTERLENGTH = string_length; |
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263 | ref_sequence_terminal->extension.size[WIDTH] = pixel_length; |
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264 | } |
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265 | |
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266 | if (!ED4_ROOT->scroll_links.link_for_hor_slider) { |
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267 | ED4_ROOT->scroll_links.link_for_hor_slider = text_terminal; |
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268 | } |
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269 | else if (*max_sequence_terminal_length > ED4_ROOT->scroll_links.link_for_hor_slider->extension.size[WIDTH]) { |
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270 | ED4_ROOT->scroll_links.link_for_hor_slider = text_terminal; |
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271 | } |
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272 | |
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273 | *seq_coords += TERMINALHEIGHT; |
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274 | j++; |
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275 | } |
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276 | free(key_string); |
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277 | } |
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278 | } |
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279 | |
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280 | return ED4_R_OK; |
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281 | } |
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282 | |
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283 | |
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284 | char* EDB_root_bact::make_string() |
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285 | { |
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286 | const char *sep_name = "\1"; // Trennzeichen |
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287 | char* configstring = new char[500]; |
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288 | |
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289 | strcpy(configstring, sep_name); |
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290 | |
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291 | strcat(configstring, "FGruppe1lang"); |
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292 | strcat(configstring, sep_name); |
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293 | strcat(configstring, "SHELIX_PAIRS"); |
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294 | strcat(configstring, sep_name); |
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295 | strcat(configstring, "SHELIX_LINE"); |
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296 | strcat(configstring, sep_name); |
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297 | strcat(configstring, "E"); |
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298 | strcat(configstring, sep_name); |
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299 | strcat(configstring, "GFltDorot"); // Speciesmark L |
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300 | strcat(configstring, sep_name); |
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301 | strcat(configstring, "LCasElega"); |
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302 | strcat(configstring, sep_name); |
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303 | strcat(configstring, "E"); |
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304 | strcat(configstring, sep_name); |
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305 | strcat(configstring, "LBaeFrag3"); |
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306 | strcat(configstring, sep_name); |
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307 | strcat(configstring, "LFlaFerr2"); |
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308 | strcat(configstring, sep_name); |
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309 | strcat(configstring, "LCytLyti3"); |
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310 | strcat(configstring, "\0"); |
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311 | |
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312 | return configstring; |
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313 | } |
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314 | |
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315 | char* EDB_root_bact::make_top_bot_string() // is only called when started manually |
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316 | { |
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317 | char* configstring; |
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318 | configstring = new char[400]; |
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319 | sprintf(configstring, "%cFSAI's%cSHELIX_PAIRS%cSHELIX_LINE%cSALI_ERR%cSALI_CON%cSALI_INT%cSALI_BIND%cSantibiot%cSmodnuc%cSelong%cStRNA%cSALI_BOR%cSALI_PRE_I%cSALI_PRE%cSALI_INSERTS%cSinseuca2%cSregaps%cSallr5%cSbacr5%cSarcr5%cSeucr5%cSgplr5%cSinsEuca%cSprimer1%cSprimer2%cSbetar5%cSprimer3%cE", 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1); |
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320 | |
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321 | strcat(configstring, "\0"); |
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322 | |
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323 | return configstring; |
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324 | } |
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325 | |
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326 | |
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327 | ED4_returncode EDB_root_bact::fill_species(ED4_multi_species_manager *multi_species_manager, |
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328 | ED4_sequence_info_terminal *ref_sequence_info_terminal, |
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329 | ED4_sequence_terminal *ref_sequence_terminal, |
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330 | const char *str, |
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331 | int *index, |
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332 | ED4_index *y, |
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333 | ED4_index curr_local_position, |
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334 | ED4_index *length_of_terminals, // height of terminals is meant |
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335 | int group_depth, |
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336 | arb_progress *progress) |
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337 | { |
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338 | #define SHIPSIZE 1024 |
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339 | |
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340 | int lauf = 0; |
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341 | bool word = 0; |
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342 | |
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343 | ED4_index height_of_created_terminals = 0; |
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344 | |
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345 | ED4_datamode datamode = ED4_D_SPECIES; |
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346 | ED4_returncode retCode = ED4_R_OK; |
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347 | |
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348 | char *ship = (char*)GB_calloc(SHIPSIZE, sizeof(*ship)); |
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349 | ED4_index local_count_position = curr_local_position; |
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350 | |
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351 | do { |
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352 | if (word == 0) { // word is needed for jump over separator |
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353 | if (str[(*index)+1] == 'L') { |
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354 | datamode = ED4_D_SPECIES; |
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355 | } |
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356 | else if (str[(*index)+1] == 'S') { |
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357 | datamode = ED4_D_EXTENDED; |
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358 | } |
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359 | else { |
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360 | |
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361 | const char *entry = str+*index+1; |
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362 | char tag = entry[0]; |
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363 | const char *sep = strchr(entry, 1); |
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364 | |
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365 | if (sep) { |
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366 | int len = sep-entry+1; |
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367 | char *content = (char*)GB_calloc(len+1, 1); |
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368 | memcpy(content, entry+1, len); |
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369 | |
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370 | char *message = GBS_global_string_copy("Unknown or misplaced tag-id '%c' (with content '%s'). Error in configuration-data!\nTrying to continue..", tag, content); |
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371 | fprintf(stderr, "ARB_EDIT4: %s\n", message); |
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372 | aw_message(message); |
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373 | |
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374 | free(message); |
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375 | free(content); |
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376 | retCode = ED4_R_WARNING; |
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377 | |
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378 | (*index) += sep-entry+1; // set index to next separator |
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379 | continue; |
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380 | } |
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381 | else { |
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382 | fprintf(stderr, "Error reading configuration: Unexpected end of data (at '%s')\n", str+*index); |
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383 | |
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384 | e4_assert(0); |
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385 | retCode = ED4_R_ERROR; |
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386 | break; |
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387 | } |
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388 | e4_assert(0); // never reached! |
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389 | } |
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390 | |
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391 | (*index) += 2; |
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392 | } |
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393 | |
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394 | if (str[*index] != 1) { |
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395 | ship[lauf++] = str[*index]; |
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396 | word = 1; |
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397 | (*index)++; |
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398 | } |
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399 | |
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400 | if (str[*index] == 1 || str[*index] == '\0') { |
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401 | ship[lauf] = '\0'; // speciesname-generation is finished |
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402 | lauf = 0; |
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403 | |
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404 | if (progress) { |
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405 | progress->inc(); |
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406 | if (progress->aborted()) ED4_exit(); |
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407 | } |
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408 | |
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409 | fill_data(multi_species_manager, ref_sequence_info_terminal, ref_sequence_terminal, ship /* species name */, |
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410 | y, local_count_position, &height_of_created_terminals, group_depth, datamode); |
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411 | |
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412 | ED4_counter++; |
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413 | local_count_position += height_of_created_terminals; |
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414 | *length_of_terminals += height_of_created_terminals; |
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415 | word = 0; |
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416 | } |
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417 | } while (!((str[(*index)] == 1) && (str[(*index)+1] == 'G' || str[(*index)+1]=='E' || str[(*index)+1]=='F')) |
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418 | && (str[*index] != '\0')); |
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419 | |
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420 | free(ship); |
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421 | return retCode; |
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422 | #undef SHIPSIZE |
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423 | } |
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424 | |
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425 | ED4_index EDB_root_bact::scan_string(ED4_multi_species_manager *parent, |
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426 | ED4_sequence_info_terminal *ref_sequence_info_terminal, |
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427 | ED4_sequence_terminal *ref_sequence_terminal, |
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428 | const char *str, |
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429 | int *index, |
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430 | ED4_index *y, |
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431 | arb_progress& progress) |
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432 | { |
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433 | ED4_multi_species_manager *multi_species_manager = NULL; |
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434 | ED4_bracket_terminal *bracket_terminal = NULL; |
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435 | ED4_spacer_terminal *group_spacer_terminal = NULL; |
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436 | char namebuffer[NAME_BUFFERSIZE]; |
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437 | char groupname[GB_GROUP_NAME_MAX]; |
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438 | ED4_index y_old = 0; |
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439 | ED4_index lauf = 0; |
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440 | ED4_index local_count_position = 0; |
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441 | ED4_index length_of_terminals = 0; |
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442 | static int group_depth = 0; |
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443 | |
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444 | if (!parent->parent->is_area_manager()) { // add 25 if group is not child of; not the first time! |
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445 | local_count_position = TERMINALHEIGHT + SPACERHEIGHT; // a folded group |
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446 | } |
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447 | |
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448 | while (str[(*index)] != '\0' && str[(*index)+1] != 'E') { // E = |
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449 | if (str[(*index)+1] == 'L' || str[(*index)+1] == 'S') { // L = species, S = SAI |
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450 | length_of_terminals = 0; |
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451 | |
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452 | fill_species(parent, ref_sequence_info_terminal, ref_sequence_terminal, str, index, |
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453 | y, local_count_position, &length_of_terminals, group_depth, &progress); |
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454 | |
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455 | local_count_position += length_of_terminals; |
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456 | ED4_counter ++; // counter is only needed to generate |
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457 | } |
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458 | |
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459 | if (str[(*index)] && (str[(*index)+1] == 'G' || str[(*index)+1] == 'F')) { // Group or folded group |
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460 | group_depth++; |
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461 | bool is_folded = str[(*index)+1]=='F'; |
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462 | |
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463 | for (*index += 2, lauf = 0; str[*index] != 1; (*index)++) { // Jump over 'G' and Blank to get Groupname |
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464 | groupname[lauf++] = str[*index]; |
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465 | } |
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466 | groupname[lauf] = '\0'; |
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467 | |
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468 | create_group_header(parent, ref_sequence_info_terminal, ref_sequence_terminal, &multi_species_manager, &bracket_terminal, |
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469 | y, groupname, group_depth, is_folded, local_count_position); |
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470 | |
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471 | y_old = local_count_position; |
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472 | ED4_counter++; |
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473 | |
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474 | local_count_position += scan_string(multi_species_manager, ref_sequence_info_terminal, ref_sequence_terminal, str, index, y, progress); |
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475 | sprintf(namebuffer, "Group_Spacer_Terminal_End.%ld", ED4_counter); |
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476 | |
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477 | local_count_position += SPACERHEIGHT; |
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478 | |
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479 | bracket_terminal->extension.size[HEIGHT] = local_count_position - y_old; |
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480 | group_spacer_terminal = new ED4_spacer_terminal(namebuffer, false, 0, local_count_position - y_old + SPACERHEIGHT, 10, SPACERHEIGHT, multi_species_manager); |
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481 | bracket_terminal->set_links(NULL, multi_species_manager); |
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482 | |
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483 | (*y) += SPACERHEIGHT; |
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484 | |
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485 | multi_species_manager->children->append_member(group_spacer_terminal); |
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486 | |
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487 | if (is_folded) multi_species_manager->hide_children(); |
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488 | } |
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489 | } |
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490 | |
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491 | if (str[(*index)] && str[(*index)+1] == 'E') { |
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492 | (*index)+=2; |
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493 | group_depth--; |
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494 | } |
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495 | |
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496 | return local_count_position; |
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497 | } |
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498 | |
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499 | ED4_returncode EDB_root_bact::create_group_header(ED4_multi_species_manager *parent, |
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500 | ED4_sequence_info_terminal *ref_sequence_info_terminal, |
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501 | ED4_sequence_terminal *ref_sequence_terminal, |
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502 | ED4_multi_species_manager **multi_species_manager, |
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503 | ED4_bracket_terminal **bracket_terminal, |
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504 | ED4_index *y, |
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505 | char *groupname, |
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506 | int group_depth, |
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507 | bool is_folded, |
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508 | ED4_index local_count_position) |
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509 | { |
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510 | const int height_terminal = TERMINALHEIGHT; |
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511 | const int height_spacer = SPACERHEIGHT; |
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512 | |
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513 | char namebuffer[NAME_BUFFERSIZE]; |
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514 | |
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515 | sprintf(namebuffer, "Group_Manager.%ld", ED4_counter); // create new group manager |
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516 | ED4_group_manager *group_manager = new ED4_group_manager(namebuffer, 0, local_count_position, 0, 0, parent); |
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517 | parent->children->append_member(group_manager); |
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518 | |
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519 | sprintf(namebuffer, "Bracket_Terminal.%ld", ED4_counter); |
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520 | *bracket_terminal = new ED4_bracket_terminal(namebuffer, 0, 0, BRACKETWIDTH, 0, group_manager); |
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521 | group_manager->children->append_member(*bracket_terminal); |
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522 | |
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523 | sprintf(namebuffer, "MultiSpecies_Manager.%ld", ED4_counter); // create new multi_species_manager |
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524 | *multi_species_manager = new ED4_multi_species_manager(namebuffer, BRACKETWIDTH, 0, 0, 0, group_manager); // Objekt Gruppen name_terminal noch |
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525 | group_manager->children->append_member(*multi_species_manager); // auszeichnen |
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526 | |
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527 | if (is_folded) { // only set FOLDED-flag if group is folded |
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528 | group_manager->set_property((ED4_properties) (ED4_P_IS_FOLDED | ED4_P_MOVABLE)); |
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529 | (*multi_species_manager)->set_property((ED4_properties) (ED4_P_IS_FOLDED | ED4_P_IS_HANDLE)); |
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530 | (*bracket_terminal)->set_property((ED4_properties) (ED4_P_IS_FOLDED | ED4_P_IS_HANDLE)); |
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531 | } |
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532 | else { |
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533 | group_manager->set_property(ED4_P_MOVABLE); |
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534 | (*multi_species_manager)->set_property(ED4_P_IS_HANDLE); |
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535 | (*bracket_terminal)->set_property(ED4_P_IS_HANDLE); |
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536 | } |
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537 | |
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538 | { |
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539 | sprintf(namebuffer, "Group_Spacer_Terminal_Beg.%ld", ED4_counter); // Spacer at beginning of group |
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540 | ED4_spacer_terminal *group_spacer_terminal = new ED4_spacer_terminal(namebuffer, false, 0, 0, 10, height_spacer, *multi_species_manager); // For better Overview |
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541 | (*multi_species_manager)->children->append_member(group_spacer_terminal); |
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542 | } |
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543 | |
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544 | { |
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545 | sprintf(namebuffer, "Consensus_Manager.%ld", ED4_counter); // Create competence terminal |
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546 | ED4_species_manager *species_manager = new ED4_species_manager(ED4_SP_CONSENSUS, namebuffer, 0, height_spacer, 0, 0, *multi_species_manager); |
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547 | species_manager->set_property(ED4_P_MOVABLE); |
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548 | (*multi_species_manager)->children->append_member(species_manager); |
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549 | |
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550 | ED4_species_name_terminal *species_name_terminal = new ED4_species_name_terminal(groupname, 0, 0, MAXSPECIESWIDTH-(group_depth*BRACKETWIDTH), height_terminal, species_manager); |
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551 | species_name_terminal->set_property((ED4_properties) (ED4_P_SELECTABLE | ED4_P_DRAGABLE | ED4_P_IS_HANDLE)); // only some terminals |
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552 | species_name_terminal->set_links(NULL, ref_sequence_terminal); |
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553 | species_manager->children->append_member(species_name_terminal); // properties |
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554 | |
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555 | { |
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556 | sprintf(namebuffer, "Consensus_Seq_Manager.%ld", ED4_counter); |
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557 | ED4_sequence_manager *sequence_manager = new ED4_sequence_manager(namebuffer, MAXSPECIESWIDTH-(group_depth*BRACKETWIDTH), 0, 0, 0, species_manager); |
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558 | sequence_manager->set_property(ED4_P_MOVABLE); |
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559 | species_manager->children->append_member(sequence_manager); |
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560 | |
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561 | ED4_sequence_info_terminal *sequence_info_terminal = new ED4_sequence_info_terminal("CONS", 0, 0, SEQUENCEINFOSIZE, height_terminal, sequence_manager); // Info fuer Gruppe |
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562 | sequence_info_terminal->set_links(ref_sequence_info_terminal, ref_sequence_info_terminal); |
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563 | sequence_info_terminal->set_property((ED4_properties) (ED4_P_SELECTABLE | ED4_P_DRAGABLE | ED4_P_IS_HANDLE)); |
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564 | sequence_manager->children->append_member(sequence_info_terminal); |
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565 | |
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566 | { |
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567 | AW_device *device = ED4_ROOT->first_window->get_device(); |
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568 | int pixel_length = device->get_string_size(ED4_G_SEQUENCES, "whatever", 0); |
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569 | |
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570 | sprintf(namebuffer, "Consensus_Seq_Terminal.%ld", ED4_counter); |
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571 | ED4_sequence_terminal *sequence_terminal = new ED4_consensus_sequence_terminal(namebuffer, SEQUENCEINFOSIZE, 0, pixel_length + 10, height_terminal, sequence_manager); |
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572 | |
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573 | sequence_terminal->set_property(ED4_P_CURSOR_ALLOWED); |
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574 | sequence_terminal->set_links(ref_sequence_terminal, ref_sequence_terminal); |
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575 | sequence_manager->children->append_member(sequence_terminal); |
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576 | } |
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577 | } |
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578 | } |
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579 | |
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580 | (*y) += height_terminal + height_spacer; |
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581 | |
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582 | return ED4_R_OK; |
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583 | } |
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584 | |
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585 | void EDB_root_bact::save_current_config(char *confname) { // and save it in database |
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586 | GB_ERROR error; |
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587 | GBT_config cfg(GLOBAL_gb_main, confname, error); |
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588 | error = NULL; // ignore not-found error |
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589 | |
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590 | int counter = 0; |
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591 | ED4_device_manager *device_manager = ED4_ROOT->get_device_manager(); |
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592 | ED4_members *children = device_manager->children; |
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593 | |
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594 | for (int i=0; i<children->members(); i++) { |
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595 | ED4_base *area = children->member(i); |
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596 | if (area->is_area_manager()) { |
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597 | GBS_strstruct area_config(10000); |
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598 | area->generate_configuration_string(area_config); |
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599 | cfg.set_definition(counter++, area_config.release()); |
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600 | } |
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601 | } |
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602 | |
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603 | // add/update comment |
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604 | { |
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605 | char *newComment = GBS_log_dated_action_to(cfg.get_comment(), "saved from ARB_EDIT4"); |
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606 | cfg.set_comment(newComment); |
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607 | free(newComment); |
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608 | } |
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609 | |
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610 | error = cfg.save(GLOBAL_gb_main, confname, true); |
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611 | aw_message_if(error); |
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612 | } |
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613 | |
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