1 | // ============================================================= // |
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2 | // // |
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3 | // File : ED4_main.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 | |
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12 | #include "ed4_class.hxx" |
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13 | #include "ed4_awars.hxx" |
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14 | #include "ed4_edit_string.hxx" |
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15 | #include "ed4_nds.hxx" |
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16 | #include "ed4_visualizeSAI.hxx" |
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17 | #include "ed4_ProteinViewer.hxx" |
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18 | #include "ed4_protein_2nd_structure.hxx" |
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19 | #include "ed4_dots.hxx" |
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20 | #include "ed4_naligner.hxx" |
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21 | #include "ed4_seq_colors.hxx" |
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22 | #include "graph_aligner_gui.hxx" |
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23 | #include <ed4_extern.hxx> |
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24 | |
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25 | #include <st_window.hxx> |
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26 | #include <gde.hxx> |
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27 | #include <AW_helix.hxx> |
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28 | #include <AP_pro_a_nucs.hxx> |
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29 | #include <ad_config.h> |
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30 | #include <awt_map_key.hxx> |
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31 | #include <awt.hxx> |
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32 | |
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33 | #include <aw_preset.hxx> |
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34 | #include <aw_awars.hxx> |
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35 | #include <aw_msg.hxx> |
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36 | #include <aw_root.hxx> |
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37 | #include <aw_advice.hxx> |
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38 | |
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39 | #include <arbdbt.h> |
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40 | |
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41 | #include <arb_defs.h> |
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42 | #include <arb_global_defs.h> |
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43 | #include <macros.hxx> |
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44 | #include <aw_question.hxx> |
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45 | |
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46 | AW_HEADER_MAIN |
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47 | |
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48 | ED4_root *ED4_ROOT = NULp; |
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49 | |
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50 | int TERMINAL_HEIGHT; |
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51 | |
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52 | int INFO_TERM_TEXT_YOFFSET; |
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53 | int SEQ_TERM_TEXT_YOFFSET; |
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54 | |
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55 | int MAXSEQUENCECHARACTERLENGTH; // greatest # of characters in a sequence string terminal |
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56 | int MAXNAME_WIDTH; |
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57 | int MAXINFO_WIDTH; |
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58 | int FLAG_WIDTH; |
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59 | |
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60 | long ED4_counter = 0; |
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61 | |
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62 | size_t not_found_counter; // nr of species which haven't been found |
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63 | GBS_strstruct *not_found_message; |
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64 | |
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65 | long max_seq_terminal_length; // global maximum of sequence terminal length |
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66 | ED4_EDITMODE awar_edit_mode; |
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67 | long awar_edit_rightward; |
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68 | bool move_cursor; // only needed for editing in consensus |
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69 | bool DRAW; |
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70 | |
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71 | inline void replaceChars(char *s, char o, char n) { |
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72 | while (1) { |
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73 | char c = *s++; |
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74 | if (!c) { |
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75 | break; |
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76 | } |
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77 | if (c==o) { |
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78 | s[-1] = n; |
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79 | } |
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80 | } |
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81 | } |
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82 | |
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83 | inline void set_and_realloc_gde_array(uchar **&the_names, uchar **&the_sequences, long &allocated, long &numberspecies, long &maxalign, |
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84 | const char *name, int name_len, const char *seq, int seq_len) |
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85 | { |
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86 | if (allocated==numberspecies) { |
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87 | long new_allocated = (allocated*3)/2; |
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88 | |
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89 | ARB_recalloc(the_names, allocated, new_allocated); |
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90 | ARB_recalloc(the_sequences, allocated, new_allocated); |
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91 | allocated = new_allocated; |
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92 | } |
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93 | |
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94 | the_names[numberspecies] = (uchar*)ARB_strndup(name, name_len); |
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95 | the_sequences[numberspecies] = (uchar*)ARB_strndup(seq, seq_len); |
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96 | |
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97 | replaceChars((char*)the_names[numberspecies], ' ', '_'); |
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98 | |
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99 | if (seq_len>maxalign) { |
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100 | maxalign = seq_len; |
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101 | } |
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102 | |
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103 | numberspecies++; |
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104 | } |
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105 | |
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106 | static char *add_area_for_gde(ED4_area_manager *area_man, uchar **&the_names, uchar **&the_sequences, |
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107 | long &allocated, long &numberspecies, long &maxalign, |
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108 | int show_sequence, int show_SAI, int show_helix, int show_consensus, int show_remark) |
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109 | { |
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110 | ED4_terminal *terminal = area_man->get_first_terminal(); |
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111 | ED4_terminal *last = area_man->get_last_terminal(); |
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112 | |
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113 | for (; terminal;) { |
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114 | if (terminal->is_species_name_terminal()) { |
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115 | ED4_species_manager *species_manager = terminal->get_parent(LEV_SPECIES)->to_species_manager(); |
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116 | ED4_species_name_terminal *species_name = species_manager->search_spec_child_rek(LEV_SPECIES_NAME)->to_species_name_terminal(); |
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117 | int name_len; |
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118 | char *name = species_name->resolve_pointer_to_string_copy(&name_len); |
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119 | ED4_sequence_terminal *sequence_terminal; |
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120 | |
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121 | { |
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122 | ED4_base *sequence_term = species_manager->search_spec_child_rek(LEV_SEQUENCE_STRING); |
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123 | if (!sequence_term) goto end_of_loop; |
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124 | sequence_terminal = sequence_term->to_sequence_terminal(); |
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125 | } |
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126 | |
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127 | int show = -1; |
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128 | |
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129 | bool is_consensus = false; |
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130 | bool is_SAI = false; |
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131 | |
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132 | if (sequence_terminal->is_consensus_terminal()) { |
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133 | is_consensus = true; |
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134 | show = show_consensus; |
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135 | } |
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136 | else if (sequence_terminal->is_SAI_terminal()) { |
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137 | is_SAI = true; |
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138 | show = show_SAI; |
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139 | } |
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140 | else { |
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141 | show = show_sequence; |
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142 | } |
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143 | |
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144 | e4_assert(show!=-1); |
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145 | |
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146 | if (show) { |
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147 | int seq_len; |
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148 | char *seq = NULp; |
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149 | |
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150 | if (is_consensus) { |
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151 | ED4_group_manager *group_manager = sequence_terminal->get_parent(LEV_GROUP)->to_group_manager(); |
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152 | |
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153 | seq = group_manager->build_consensus_string(&seq_len); |
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154 | e4_assert(seq && strlen(seq) == size_t(seq_len)); |
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155 | |
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156 | ED4_group_manager *folded_group_man = sequence_terminal->is_in_folded_group(); |
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157 | |
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158 | if (folded_group_man) { // we are in a folded group |
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159 | if (folded_group_man==group_manager) { // we are the consensus of the folded group |
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160 | if (folded_group_man->is_in_folded_group()) { // a folded group inside a folded group -> do not show |
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161 | freenull(seq); |
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162 | } |
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163 | else { // group folded but consensus shown -> add '-' before name |
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164 | char *new_name = ARB_alloc<char>(name_len+2); |
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165 | |
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166 | sprintf(new_name, "-%s", name); |
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167 | freeset(name, new_name); |
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168 | name_len++; |
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169 | } |
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170 | } |
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171 | else { // we are really inside a folded group -> don't show |
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172 | freenull(seq); |
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173 | } |
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174 | } |
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175 | } |
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176 | else { // sequence |
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177 | if (!sequence_terminal->is_in_folded_group()) { |
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178 | seq = sequence_terminal->resolve_pointer_to_string_copy(&seq_len); |
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179 | } |
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180 | } |
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181 | |
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182 | if (seq) { |
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183 | set_and_realloc_gde_array(the_names, the_sequences, allocated, numberspecies, maxalign, name, name_len, seq, seq_len); |
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184 | if (show_helix && !is_SAI && ED4_ROOT->helix->size()) { |
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185 | char *helix = ED4_ROOT->helix->seq_2_helix(seq, '.'); |
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186 | set_and_realloc_gde_array(the_names, the_sequences, allocated, numberspecies, maxalign, name, name_len, helix, seq_len); |
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187 | free(helix); |
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188 | } |
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189 | if (show_remark && !is_consensus) { |
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190 | ED4_manager *ms_man = sequence_terminal->get_parent(LEV_MULTI_SEQUENCE); |
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191 | if (ms_man) { |
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192 | ED4_base *remark_name_term = ms_man->search_ID("remark"); |
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193 | if (remark_name_term) { |
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194 | ED4_base *remark_term = remark_name_term->get_next_terminal(); |
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195 | e4_assert(remark_term); |
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196 | |
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197 | int remark_len; |
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198 | char *remark = remark_term->resolve_pointer_to_string_copy(&remark_len); |
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199 | |
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200 | replaceChars(remark, ' ', '_'); |
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201 | set_and_realloc_gde_array(the_names, the_sequences, allocated, numberspecies, maxalign, name, name_len, remark, remark_len); |
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202 | free(remark); |
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203 | } |
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204 | } |
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205 | } |
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206 | free(seq); |
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207 | } |
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208 | } |
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209 | free(name); |
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210 | } |
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211 | end_of_loop : |
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212 | if (terminal==last) break; |
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213 | terminal = terminal->get_next_terminal(); |
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214 | } |
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215 | |
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216 | return NULp; |
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217 | } |
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218 | |
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219 | static char *ED4_create_sequences_for_gde(GBDATA **&the_species, uchar **&the_names, uchar **&the_sequences, long &numberspecies, long &maxalign) { |
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220 | int top = ED4_ROOT->aw_root->awar("gde/top_area")->read_int(); |
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221 | int tops = ED4_ROOT->aw_root->awar("gde/top_area_sai")->read_int(); |
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222 | int toph = ED4_ROOT->aw_root->awar("gde/top_area_helix")->read_int(); |
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223 | int topk = ED4_ROOT->aw_root->awar("gde/top_area_kons")->read_int(); |
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224 | int topr = ED4_ROOT->aw_root->awar("gde/top_area_remark")->read_int(); |
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225 | int middle = ED4_ROOT->aw_root->awar("gde/middle_area")->read_int(); |
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226 | int middles = ED4_ROOT->aw_root->awar("gde/middle_area_sai")->read_int(); |
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227 | int middleh = ED4_ROOT->aw_root->awar("gde/middle_area_helix")->read_int(); |
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228 | int middlek = ED4_ROOT->aw_root->awar("gde/middle_area_kons")->read_int(); |
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229 | int middler = ED4_ROOT->aw_root->awar("gde/middle_area_remark")->read_int(); |
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230 | |
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231 | numberspecies = 0; |
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232 | maxalign = 0; |
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233 | |
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234 | long allocated = 100; |
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235 | the_species = NULp; |
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236 | |
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237 | ARB_calloc(the_names, allocated); |
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238 | ARB_calloc(the_sequences, allocated); |
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239 | |
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240 | char *err = add_area_for_gde(ED4_ROOT->top_area_man, the_names, the_sequences, allocated, numberspecies, maxalign, top, tops, toph, topk, topr); |
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241 | if (!err) { |
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242 | err = add_area_for_gde(ED4_ROOT->middle_area_man, the_names, the_sequences, allocated, numberspecies, maxalign, middle, middles, middleh, middlek, middler); |
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243 | } |
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244 | |
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245 | if (allocated!=(numberspecies+1)) { |
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246 | ARB_recalloc(the_names, allocated, numberspecies+1); |
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247 | ARB_recalloc(the_sequences, allocated, numberspecies+1); |
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248 | } |
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249 | |
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250 | return err; |
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251 | } |
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252 | |
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253 | void ED4_setup_gaps_and_alitype(const char *gap_chars, GB_alignment_type alitype) { |
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254 | BaseFrequencies::setup(gap_chars, alitype); |
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255 | } |
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256 | |
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257 | static void ED4_gap_chars_changed(AW_root *root) { |
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258 | char *gap_chars = root->awar_string(ED4_AWAR_GAP_CHARS)->read_string(); |
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259 | ED4_setup_gaps_and_alitype(gap_chars, ED4_ROOT->alignment_type); |
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260 | free(gap_chars); |
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261 | } |
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262 | |
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263 | void ED4_with_all_edit_windows(void (*cb)(ED4_window *)) { |
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264 | for (ED4_window *win = ED4_ROOT->first_window; win; win = win->next) { |
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265 | ED4_LocalWinContext uses(win); |
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266 | cb(win); |
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267 | } |
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268 | } |
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269 | |
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270 | static void redraw_cursor(ED4_window *win) { win->cursor.redraw(); } |
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271 | static void ED4_edit_direction_changed(AW_root * /* awr */) { |
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272 | ED4_with_all_edit_windows(redraw_cursor); |
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273 | } |
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274 | |
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275 | static void ed4_bind_mainDB_awar_callbacks(AW_root *root) { |
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276 | // callbacks to main DB awars are bound later |
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277 | // (otherwise its easy to crash the editor by clicking around in ARB_NTREE during editor startup) |
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278 | |
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279 | root->awar(AWAR_SET_CURSOR_POSITION)->add_callback(ED4_remote_set_cursor_cb); |
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280 | root->awar(AWAR_SPECIES_NAME)->add_callback(ED4_selected_species_changed_cb); |
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281 | root->awar(AWAR_SAI_NAME)->add_callback(ED4_selected_SAI_changed_cb); |
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282 | } |
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283 | |
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284 | static void ed4_create_mainDB_awars(AW_root *root) { |
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285 | // WARNING: do not bind callbacks here -> do it in ed4_bind_mainDB_awar_callbacks() |
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286 | |
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287 | GBDATA *gb_main = ED4_ROOT->get_gb_main(); |
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288 | |
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289 | root->awar_int(AWAR_CURSOR_POSITION, info2bio(0), gb_main); |
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290 | root->awar_int(AWAR_CURSOR_POSITION_LOCAL, 0, gb_main); |
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291 | root->awar_int(AWAR_SET_CURSOR_POSITION, 1, gb_main); |
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292 | |
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293 | root->awar_string(AWAR_FIELD_CHOSEN, NO_FIELD_SELECTED, gb_main); |
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294 | |
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295 | root->awar_string(AWAR_SPECIES_NAME, "", gb_main); |
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296 | root->awar_string(AWAR_SAI_NAME, "", gb_main); |
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297 | root->awar_string(AWAR_SAI_GLOBAL, "", gb_main); |
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298 | } |
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299 | |
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300 | static void ed4_create_all_awars(AW_root *root, const char *config_name) { |
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301 | // Note: cursor awars are created in window constructor |
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302 | |
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303 | root->awar_string(AWAR_EDIT_CONFIGURATION, config_name, AW_ROOT_DEFAULT); |
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304 | |
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305 | ed4_create_mainDB_awars(root); |
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306 | ED4_create_search_awars(root); |
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307 | |
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308 | #if defined(DEBUG) |
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309 | AWT_create_db_browser_awars(root, AW_ROOT_DEFAULT); |
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310 | #endif // DEBUG |
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311 | |
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312 | create_naligner_variables(root, AW_ROOT_DEFAULT); |
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313 | create_sina_variables(root, AW_ROOT_DEFAULT); |
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314 | |
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315 | awar_edit_mode = AD_ALIGN; |
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316 | |
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317 | int def_sec_level = 0; |
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318 | #ifdef DEBUG |
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319 | def_sec_level = 6; // don't nag developers |
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320 | #endif |
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321 | root->awar_int(AWAR_EDIT_SECURITY_LEVEL, def_sec_level, AW_ROOT_DEFAULT); |
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322 | |
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323 | root->awar_int(AWAR_EDIT_SECURITY_LEVEL_ALIGN, def_sec_level, AW_ROOT_DEFAULT)->add_callback(ed4_changesecurity); |
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324 | root->awar_int(AWAR_EDIT_SECURITY_LEVEL_CHANGE, def_sec_level, AW_ROOT_DEFAULT)->add_callback(ed4_changesecurity); |
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325 | |
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326 | root->awar_int(AWAR_EDIT_MODE, 0)->add_callback(ed4_change_edit_mode); |
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327 | root->awar_int(AWAR_INSERT_MODE, 1)->add_callback(ed4_change_edit_mode); |
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328 | |
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329 | root->awar_int(AWAR_EDIT_RIGHTWARD, 1)->add_target_var(&awar_edit_rightward)->add_callback(ED4_edit_direction_changed); |
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330 | root->awar_int(AWAR_EDIT_TITLE_MODE, 0); |
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331 | |
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332 | root->awar_int(AWAR_EDIT_HELIX_SPACING, 0) ->set_minmax(-30, 30) ->add_target_var(&ED4_ROOT->helix_add_spacing) ->add_callback(makeRootCallback(ED4_request_relayout)); |
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333 | root->awar_int(AWAR_EDIT_TERMINAL_SPACING, 0) ->set_minmax(-30, 30) ->add_target_var(&ED4_ROOT->terminal_add_spacing) ->add_callback(makeRootCallback(ED4_request_relayout)); |
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334 | |
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335 | ed4_changesecurity(root); |
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336 | |
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337 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_GAPS, 0)->add_callback(makeRootCallback(ED4_compression_toggle_changed_cb, false)); |
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338 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_HIDE, 0)->add_callback(makeRootCallback(ED4_compression_toggle_changed_cb, true)); |
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339 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_TYPE, 0)->add_callback(ED4_compression_changed_cb); |
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340 | root->awar_int(ED4_AWAR_COMPRESS_SEQUENCE_PERCENT, 1)->add_callback(ED4_compression_changed_cb)->set_minmax(1, 99); |
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341 | |
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342 | root->awar_int(ED4_AWAR_DIGITS_AS_REPEAT, 0); |
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343 | root->awar_int(ED4_AWAR_FAST_CURSOR_JUMP, 0); |
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344 | root->awar_int(ED4_AWAR_CURSOR_TYPE, (int)ED4_RIGHT_ORIENTED_CURSOR); |
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345 | |
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346 | ED4_create_consensus_awars(root); |
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347 | ED4_create_NDS_awars(root); |
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348 | |
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349 | root->awar_string(ED4_AWAR_REP_SEARCH_PATTERN, "."); |
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350 | root->awar_string(ED4_AWAR_REP_REPLACE_PATTERN, "-"); |
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351 | |
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352 | root->awar_int(ED4_AWAR_SCROLL_SPEED_X, 40); |
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353 | root->awar_int(ED4_AWAR_SCROLL_SPEED_Y, 20); |
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354 | root->awar_int(ED4_AWAR_SCROLL_MARGIN, 5); |
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355 | |
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356 | root->awar_string(ED4_AWAR_SPECIES_TO_CREATE, ""); |
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357 | |
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358 | root->awar_string(ED4_AWAR_GAP_CHARS, GAP::anyGapChars())->add_callback(ED4_gap_chars_changed); |
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359 | ED4_gap_chars_changed(root); |
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360 | root->awar_int(ED4_AWAR_ANNOUNCE_CHECKSUM_CHANGES, 0); |
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361 | |
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362 | GBDATA *gb_main = ED4_ROOT->get_gb_main(); |
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363 | { |
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364 | GB_ERROR gde_err = GDE_init(ED4_ROOT->aw_root, ED4_ROOT->props_db, gb_main, ED4_create_sequences_for_gde, NULp, GDE_WINDOWTYPE_EDIT4); |
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365 | if (gde_err) GBK_terminatef("Fatal error: %s", gde_err); |
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366 | } |
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367 | |
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368 | root->awar_string(ED4_AWAR_CREATE_FROM_CONS_REPL_EQUAL, "-"); |
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369 | root->awar_string(ED4_AWAR_CREATE_FROM_CONS_REPL_POINT, "?"); |
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370 | root->awar_int(ED4_AWAR_CREATE_FROM_CONS_CREATE_POINTS, 1); |
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371 | root->awar_int(ED4_AWAR_CREATE_FROM_CONS_ALL_UPPER, 1); |
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372 | root->awar_int(ED4_AWAR_CREATE_FROM_CONS_DATA_SOURCE, 0); |
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373 | |
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374 | ED4_createVisualizeSAI_Awars(root, AW_ROOT_DEFAULT); |
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375 | ED4_create_dot_missing_bases_awars(root, AW_ROOT_DEFAULT); |
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376 | |
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377 | // Create Awars To Be Used In Protein Viewer |
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378 | if (ED4_ROOT->alignment_type == GB_AT_DNA) { |
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379 | PV_CreateAwars(root, AW_ROOT_DEFAULT); |
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380 | } |
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381 | |
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382 | // create awars to be used for protein secondary structure match |
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383 | if (ED4_ROOT->alignment_type == GB_AT_AA) { |
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384 | root->awar_int(PFOLD_AWAR_ENABLE, 1); |
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385 | root->awar_string(PFOLD_AWAR_SELECTED_SAI, "PFOLD"); |
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386 | root->awar_int(PFOLD_AWAR_MATCH_METHOD, SECSTRUCT_SEQUENCE); |
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387 | int pt; |
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388 | char awar[256]; |
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389 | for (int i = 0; pfold_match_type_awars[i].name; i++) { |
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390 | e4_assert(i<PFOLD_PAIRS); |
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391 | pt = pfold_match_type_awars[i].value; |
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392 | sprintf(awar, PFOLD_AWAR_PAIR_TEMPLATE, pfold_match_type_awars[i].name); |
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393 | root->awar_string(awar, pfold_pairs[pt])->add_target_var(&pfold_pairs[pt]); |
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394 | sprintf(awar, PFOLD_AWAR_SYMBOL_TEMPLATE, pfold_match_type_awars[i].name); |
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395 | root->awar_string(awar, pfold_pair_chars[pt])->add_target_var(&pfold_pair_chars[pt]); |
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396 | } |
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397 | root->awar_string(PFOLD_AWAR_SYMBOL_TEMPLATE_2, PFOLD_PAIR_CHARS_2); |
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398 | root->awar_string(PFOLD_AWAR_SAI_FILTER, "pfold"); |
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399 | } |
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400 | |
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401 | GB_ERROR error = ARB_init_global_awars(root, AW_ROOT_DEFAULT, gb_main); |
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402 | if (error) aw_message(error); |
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403 | } |
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404 | |
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405 | static void ED4_postcbcb(AW_window *aww) { |
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406 | ED4_ROOT->announce_useraction_in(aww); |
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407 | ED4_trigger_instant_refresh(); |
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408 | } |
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409 | static void seq_colors_changed_cb() { |
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410 | ED4_ROOT->request_refresh_for_sequence_terminals(); |
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411 | } |
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412 | |
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413 | int ARB_main(int argc, char *argv[]) { |
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414 | const char *data_path = ":"; |
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415 | char *config_name = NULp; |
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416 | |
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417 | if (argc > 1 && ((strcmp(argv[1], "-h") == 0) || (strcmp(argv[1], "--help") == 0))) { |
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418 | fprintf(stderr, |
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419 | "Usage: arb_edit4 [options] database\n" |
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420 | " database name of database or ':' to connect to arb-database-server\n" |
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421 | "\n" |
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422 | " options:\n" |
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423 | " -c config loads configuration 'config' (default: '" DEFAULT_CONFIGURATION "')\n" |
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424 | ); |
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425 | return EXIT_SUCCESS; |
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426 | } |
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427 | |
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428 | if (argc > 1 && strcmp(argv[1], "-c") == 0) { |
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429 | config_name = new char[strlen(argv[2])+1]; |
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430 | strcpy(config_name, argv[2]); |
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431 | argc -= 2; argv += 2; |
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432 | } |
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433 | else { // load default configuration if no command line is given |
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434 | config_name = ARB_strdup(DEFAULT_CONFIGURATION); |
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435 | printf("Using '%s'\n", DEFAULT_CONFIGURATION); |
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436 | } |
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437 | |
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438 | if (argc>1) { |
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439 | data_path = argv[1]; |
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440 | argc--; argv++; |
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441 | } |
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442 | |
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443 | aw_initstatus(); |
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444 | |
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445 | GB_shell shell; |
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446 | ARB_ERROR error; |
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447 | GBDATA *gb_main = GB_open(data_path, "rwt"); |
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448 | |
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449 | if (!gb_main) { |
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450 | error = GB_await_error(); |
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451 | } |
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452 | else { |
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453 | #if defined(DEBUG) |
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454 | AWT_announce_db_to_browser(gb_main, GBS_global_string("ARB database (%s)", data_path)); |
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455 | #endif // DEBUG |
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456 | |
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457 | ED4_ROOT = new ED4_root(gb_main); |
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458 | |
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459 | error = configure_macro_recording(ED4_ROOT->aw_root, "ARB_EDIT4", gb_main); |
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460 | if (!error) error = ED4_ROOT->init_alignment(); |
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461 | if (!error) { |
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462 | ed4_create_all_awars(ED4_ROOT->aw_root, config_name); |
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463 | |
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464 | ED4_ROOT->st_ml = STAT_create_ST_ML(gb_main); |
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465 | ED4_ROOT->sequence_colors = new ED4_seq_colors(ED4_G_SEQUENCES, seq_colors_changed_cb); |
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466 | |
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467 | ED4_ROOT->edk = new ed_key; |
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468 | ED4_ROOT->edk->create_awars(ED4_ROOT->aw_root); |
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469 | |
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470 | ED4_ROOT->helix = new AW_helix(ED4_ROOT->aw_root); |
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471 | |
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472 | { |
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473 | GB_ERROR warning = NULp; |
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474 | switch (ED4_ROOT->alignment_type) { |
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475 | case GB_AT_RNA: |
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476 | case GB_AT_DNA: |
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477 | warning = ED4_ROOT->helix->init(gb_main); |
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478 | break; |
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479 | |
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480 | case GB_AT_AA: |
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481 | warning = ED4_pfold_set_SAI(&ED4_ROOT->protstruct, gb_main, ED4_ROOT->alignment_name, &ED4_ROOT->protstruct_len); |
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482 | break; |
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483 | |
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484 | default: |
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485 | e4_assert(0); |
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486 | break; |
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487 | } |
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488 | |
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489 | if (warning) aw_message(warning); // write to console |
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490 | ED4_ROOT->create_first_window(); |
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491 | if (warning) { aw_message(warning); warning = NULp; } // write again to status window |
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492 | } |
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493 | |
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494 | ED4_objspec::init_object_specs(); |
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495 | { |
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496 | bool found_config = false; |
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497 | ED4_LocalWinContext uses(ED4_ROOT->first_window); |
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498 | |
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499 | if (config_name) { |
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500 | GB_transaction ta(gb_main); |
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501 | GB_ERROR cfg_error; |
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502 | GBT_config cfg(gb_main, config_name, cfg_error); |
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503 | |
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504 | if (cfg.exists()) { |
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505 | ED4_ROOT->create_hierarchy(cfg.get_definition(GBT_config::MIDDLE_AREA), cfg.get_definition(GBT_config::TOP_AREA)); // create internal hierarchy |
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506 | found_config = true; |
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507 | } |
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508 | else { |
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509 | aw_message(GBS_global_string("Could not find configuration '%s'", config_name)); |
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510 | } |
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511 | } |
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512 | |
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513 | if (!found_config) { |
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514 | aw_popup_ok("The editor needs a configuration stored in database.\n" |
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515 | "Cannot continue and will terminate now."); |
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516 | ED4_exit(); |
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517 | } |
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518 | } |
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519 | |
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520 | // now bind DB depending callbacks |
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521 | ed4_bind_mainDB_awar_callbacks(ED4_ROOT->aw_root); |
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522 | |
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523 | // Create Additional sequence (aminoacid) terminals to be used in Protein Viewer |
---|
524 | if (ED4_ROOT->alignment_type == GB_AT_DNA) { |
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525 | PV_CallBackFunction(ED4_ROOT->aw_root); |
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526 | } |
---|
527 | |
---|
528 | AWT_install_postcb_cb(ED4_postcbcb); |
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529 | AWT_install_cb_guards(); |
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530 | e4_assert(!ED4_WinContext::have_context()); // no global context shall be active |
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531 | ED4_ROOT->aw_root->main_loop(); // enter main-loop |
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532 | } |
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533 | |
---|
534 | shutdown_macro_recording(ED4_ROOT->aw_root); |
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535 | GB_close(gb_main); |
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536 | } |
---|
537 | |
---|
538 | bool have_aw_root = ED4_ROOT && ED4_ROOT->aw_root; |
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539 | if (error) { |
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540 | if (have_aw_root) aw_popup_ok(error.deliver()); |
---|
541 | else fprintf(stderr, "arb_edit4: Error: %s\n", error.deliver()); |
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542 | } |
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543 | if (have_aw_root) delete ED4_ROOT->aw_root; |
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544 | |
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545 | return EXIT_SUCCESS; |
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546 | } |
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547 | |
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