1 | // =============================================================== // |
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2 | // // |
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3 | // File : ad_ali.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 "NT_local.h" |
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12 | #include <insdel.h> |
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13 | #include <awt_sel_boxes.hxx> |
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14 | #include <aw_root.hxx> |
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15 | #include <aw_question.hxx> |
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16 | #include <aw_awar.hxx> |
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17 | #include <aw_msg.hxx> |
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18 | #include <aw_awar_defs.hxx> |
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19 | #include <arbdbt.h> |
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20 | |
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21 | |
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22 | static void alignment_vars_callback(AW_root *aw_root) |
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23 | { |
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24 | GB_push_transaction(GLOBAL.gb_main); |
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25 | char *use = aw_root->awar(AWAR_DEFAULT_ALIGNMENT)->read_string(); |
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26 | GBDATA *ali_cont = GBT_get_alignment(GLOBAL.gb_main, use); |
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27 | if (!ali_cont) { |
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28 | GB_clear_error(); |
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29 | aw_root->awar("presets/alignment_name")->unmap(); |
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30 | aw_root->awar("presets/alignment_type")->unmap(); |
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31 | aw_root->awar("presets/alignment_len")->unmap(); |
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32 | aw_root->awar("presets/alignment_rem")->unmap(); |
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33 | aw_root->awar("presets/aligned")->unmap(); |
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34 | aw_root->awar("presets/auto_format")->unmap(); |
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35 | aw_root->awar("presets/security")->unmap(); |
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36 | } |
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37 | else { |
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38 | GBDATA *ali_name = GB_search(ali_cont, "alignment_name", GB_STRING); |
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39 | GBDATA *ali_len = GB_search(ali_cont, "alignment_len", GB_INT); |
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40 | GBDATA *ali_aligned = GB_search(ali_cont, "aligned", GB_INT); |
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41 | GBDATA *ali_auto_format = GB_search(ali_cont, "auto_format", GB_INT); |
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42 | GBDATA *ali_type = GB_search(ali_cont, "alignment_type", GB_STRING); |
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43 | GBDATA *ali_security = GB_search(ali_cont, "alignment_write_security", GB_INT); |
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44 | GBDATA *ali_rem = GB_search(ali_cont, "alignment_rem", GB_STRING); |
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45 | |
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46 | aw_root->awar("presets/alignment_name")->map(ali_name); |
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47 | aw_root->awar("presets/alignment_type")->map(ali_type); |
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48 | aw_root->awar("presets/alignment_len") ->map(ali_len); |
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49 | aw_root->awar("presets/alignment_rem") ->map(ali_rem); |
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50 | aw_root->awar("presets/aligned") ->map(ali_aligned); |
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51 | aw_root->awar("presets/auto_format") ->map(ali_auto_format); |
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52 | aw_root->awar("presets/security") ->map(ali_security); |
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53 | } |
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54 | GB_pop_transaction(GLOBAL.gb_main); |
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55 | free(use); |
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56 | } |
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57 | |
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58 | void NT_create_alignment_vars(AW_root *aw_root, AW_default aw_def) { |
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59 | AW_awar *awar_def_ali = aw_root->awar_string(AWAR_DEFAULT_ALIGNMENT, "", aw_def); |
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60 | GB_push_transaction(GLOBAL.gb_main); |
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61 | |
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62 | GBDATA *use = GB_search(GLOBAL.gb_main, AWAR_DEFAULT_ALIGNMENT, GB_STRING); |
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63 | awar_def_ali->map(use); |
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64 | |
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65 | aw_root->awar_string("presets/alignment_name", "", aw_def) ->set_srt(GBT_ALI_AWAR_SRT); |
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66 | aw_root->awar_string("presets/alignment_dest", "", aw_def) ->set_srt(GBT_ALI_AWAR_SRT); |
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67 | |
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68 | aw_root->awar_string("presets/alignment_type", "", aw_def); |
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69 | aw_root->awar_string("presets/alignment_rem"); |
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70 | aw_root->awar_int("presets/alignment_len", 0, aw_def); |
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71 | aw_root->awar_int("presets/aligned", 0, aw_def); |
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72 | aw_root->awar_int("presets/auto_format", 0, aw_def); |
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73 | aw_root->awar_int("presets/security", 0, aw_def); |
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74 | |
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75 | awar_def_ali->add_callback(alignment_vars_callback); |
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76 | alignment_vars_callback(aw_root); |
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77 | GB_pop_transaction(GLOBAL.gb_main); |
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78 | } |
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79 | |
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80 | static void ad_al_delete_cb(AW_window *aww) { |
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81 | if (aw_ask_sure("delete_ali_data", "Are you sure to delete all data belonging to this alignment")) { |
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82 | char *source = aww->get_root()->awar(AWAR_DEFAULT_ALIGNMENT)->read_string(); |
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83 | GB_transaction ta(GLOBAL.gb_main); |
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84 | GB_ERROR error = GBT_rename_alignment(GLOBAL.gb_main, source, 0, 0, 1); |
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85 | |
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86 | if (error) { |
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87 | error = ta.close(error); |
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88 | aw_message(error); |
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89 | } |
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90 | free(source); |
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91 | } |
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92 | } |
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93 | |
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94 | |
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95 | static void ed_al_check_auto_format(AW_window *aww) { |
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96 | AW_root *awr = aww->get_root(); |
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97 | char *use = awr->awar(AWAR_DEFAULT_ALIGNMENT)->read_string(); |
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98 | if (strcmp(use, "ali_genom") == 0) { |
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99 | awr->awar("presets/auto_format")->write_int(2); // ali_genom is always forced to "skip" |
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100 | } |
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101 | } |
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102 | |
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103 | static void ed_al_check_len_cb(AW_window *aww) |
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104 | { |
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105 | char *error = 0; |
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106 | char *use = aww->get_root()->awar(AWAR_DEFAULT_ALIGNMENT)->read_string(); |
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107 | GB_begin_transaction(GLOBAL.gb_main); |
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108 | if (!error) error = (char *)GBT_check_data(GLOBAL.gb_main, use); |
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109 | GB_commit_transaction(GLOBAL.gb_main); |
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110 | if (error) aw_message(error); |
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111 | free(use); |
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112 | } |
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113 | |
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114 | static void ed_al_align_cb(AW_window *aww) { |
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115 | char *use = aww->get_root()->awar(AWAR_DEFAULT_ALIGNMENT)->read_string(); |
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116 | GB_begin_transaction(GLOBAL.gb_main); |
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117 | GB_ERROR err = ARB_format_alignment(GLOBAL.gb_main, use); |
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118 | GB_commit_transaction(GLOBAL.gb_main); |
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119 | if (err) aw_message(err); |
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120 | free(use); |
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121 | ed_al_check_len_cb(aww); |
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122 | } |
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123 | |
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124 | static void aa_copy_delete_rename(AW_window *aww, AW_CL copy, AW_CL dele) { |
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125 | char *source = aww->get_root()->awar(AWAR_DEFAULT_ALIGNMENT)->read_string(); |
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126 | char *dest = aww->get_root()->awar("presets/alignment_dest")->read_string(); |
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127 | |
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128 | GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main); |
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129 | if (!error) error = GBT_rename_alignment(GLOBAL.gb_main, source, dest, (int)copy, (int)dele); |
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130 | if (!error) { |
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131 | char *nfield = GBS_global_string_copy("%s/data", dest); |
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132 | error = GBT_add_new_changekey(GLOBAL.gb_main, nfield, GB_STRING); |
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133 | free(nfield); |
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134 | } |
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135 | |
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136 | error = GB_end_transaction(GLOBAL.gb_main, error); |
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137 | aww->hide_or_notify(error); |
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138 | |
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139 | free(source); |
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140 | free(dest); |
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141 | } |
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142 | |
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143 | static AW_window *create_alignment_copy_window(AW_root *root) |
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144 | { |
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145 | AW_window_simple *aws = new AW_window_simple; |
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146 | aws->init(root, "COPY_ALIGNMENT", "ALIGNMENT COPY"); |
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147 | aws->load_xfig("ad_al_si.fig"); |
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148 | |
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149 | aws->callback((AW_CB0)AW_POPDOWN); |
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150 | aws->at("close"); |
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151 | aws->create_button("CLOSE", "CLOSE", "C"); |
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152 | |
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153 | aws->at("label"); |
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154 | aws->create_autosize_button(0, "Please enter the new name\nof the alignment"); |
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155 | |
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156 | aws->at("input"); |
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157 | aws->create_input_field("presets/alignment_dest", 15); |
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158 | |
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159 | aws->at("ok"); |
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160 | aws->callback(aa_copy_delete_rename, 1, 0); |
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161 | aws->create_button("GO", "GO", "G"); |
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162 | |
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163 | return (AW_window *)aws; |
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164 | } |
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165 | static AW_window *create_alignment_rename_window(AW_root *root) |
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166 | { |
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167 | AW_window_simple *aws = new AW_window_simple; |
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168 | aws->init(root, "RENAME_ALIGNMENT", "ALIGNMENT RENAME"); |
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169 | aws->load_xfig("ad_al_si.fig"); |
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170 | |
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171 | aws->callback((AW_CB0)AW_POPDOWN); |
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172 | aws->at("close"); |
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173 | aws->create_button("CLOSE", "CLOSE", "C"); |
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174 | |
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175 | aws->at("label"); |
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176 | aws->create_autosize_button(0, "Please enter the name\nof the new alignment"); |
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177 | |
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178 | aws->at("input"); |
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179 | aws->create_input_field("presets/alignment_dest", 15); |
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180 | |
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181 | aws->at("ok"); |
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182 | aws->callback(aa_copy_delete_rename, 1, 1); |
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183 | aws->create_button("GO", "GO", "G"); |
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184 | |
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185 | return (AW_window *)aws; |
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186 | } |
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187 | |
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188 | static void aa_create_alignment(AW_window *aww) { |
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189 | GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main); |
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190 | if (!error) { |
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191 | char *name = aww->get_root()->awar("presets/alignment_dest")->read_string(); |
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192 | GBDATA *gb_alignment = GBT_create_alignment(GLOBAL.gb_main, name, 0, 0, 0, "dna"); |
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193 | if (!gb_alignment) error = GB_await_error(); |
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194 | else { |
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195 | char *nfield = GBS_global_string_copy("%s/data", name); |
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196 | error = GBT_add_new_changekey(GLOBAL.gb_main, nfield, GB_STRING); |
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197 | free(nfield); |
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198 | } |
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199 | free(name); |
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200 | } |
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201 | GB_end_transaction_show_error(GLOBAL.gb_main, error, aw_message); |
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202 | } |
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203 | |
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204 | static AW_window *create_alignment_create_window(AW_root *root) |
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205 | { |
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206 | AW_window_simple *aws = new AW_window_simple; |
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207 | aws->init(root, "CREATE_ALIGNMENT", "ALIGNMENT CREATE"); |
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208 | aws->load_xfig("ad_al_si.fig"); |
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209 | |
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210 | aws->callback((AW_CB0)AW_POPDOWN); |
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211 | aws->at("close"); |
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212 | aws->create_button("CLOSE", "CLOSE", "C"); |
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213 | |
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214 | aws->at("label"); |
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215 | aws->create_autosize_button(0, "Please enter the new name\nof the alignment"); |
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216 | |
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217 | aws->at("input"); |
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218 | aws->create_input_field("presets/alignment_dest", 15); |
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219 | |
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220 | aws->at("ok"); |
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221 | aws->callback(aa_create_alignment); |
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222 | aws->create_button("GO", "GO", "G"); |
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223 | |
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224 | return (AW_window *)aws; |
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225 | } |
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226 | |
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227 | AW_window *NT_create_alignment_window(AW_root *root, AW_window *aw_popmedown) { |
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228 | // if 'aw_popmedown' points to a window, that window is popped down |
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229 | |
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230 | static AW_window_simple *aws = 0; |
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231 | |
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232 | if (aw_popmedown) aw_popmedown->hide(); |
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233 | |
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234 | if (aws) return aws; // do not duplicate |
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235 | |
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236 | aws = new AW_window_simple; |
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237 | |
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238 | aws->init(root, "INFO_OF_ALIGNMENT", "ALIGNMENT INFORMATION"); |
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239 | aws->load_xfig("ad_align.fig"); |
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240 | |
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241 | aws->callback((AW_CB0)AW_POPDOWN); |
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242 | aws->at("close"); |
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243 | aws->create_button("CLOSE", "CLOSE", "C"); |
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244 | |
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245 | aws->callback(makeHelpCallback("ad_align.hlp")); |
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246 | aws->at("help"); |
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247 | aws->create_button("HELP", "HELP", "H"); |
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248 | |
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249 | aws->button_length(13); |
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250 | |
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251 | aws->at("delete"); |
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252 | aws->callback(ad_al_delete_cb); |
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253 | aws->create_button("DELETE", "DELETE", "D"); |
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254 | |
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255 | aws->at("rename"); |
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256 | aws->callback(AW_POPUP, (AW_CL)create_alignment_rename_window, 0); |
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257 | aws->create_button("RENAME", "RENAME", "R"); |
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258 | |
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259 | aws->at("create"); |
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260 | aws->callback(AW_POPUP, (AW_CL)create_alignment_create_window, 0); |
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261 | aws->create_button("CREATE", "CREATE", "N"); |
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262 | |
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263 | aws->at("copy"); |
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264 | aws->callback(AW_POPUP, (AW_CL)create_alignment_copy_window, 0); |
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265 | aws->create_button("COPY", "COPY", "C"); |
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266 | |
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267 | aws->at("check_len"); |
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268 | aws->callback(ed_al_check_len_cb); |
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269 | aws->create_button("CHECK_LEN", "CHECK LEN", "L"); |
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270 | |
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271 | aws->at("align"); |
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272 | aws->callback(ed_al_align_cb); |
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273 | aws->create_button("FORMAT", "FORMAT", "F"); |
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274 | |
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275 | aws->at("list"); |
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276 | awt_create_selection_list_on_alignments(GLOBAL.gb_main, aws, AWAR_DEFAULT_ALIGNMENT, "*="); |
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277 | |
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278 | aws->at("aligned"); |
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279 | aws->create_option_menu("presets/aligned", true); |
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280 | aws->callback(ed_al_check_len_cb); |
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281 | aws->insert_default_option("not formatted", "n", 0); |
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282 | aws->callback(ed_al_align_cb); |
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283 | aws->insert_option("formatted", "j", 1); |
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284 | aws->update_option_menu(); |
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285 | |
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286 | aws->at("auto_format"); |
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287 | aws->create_option_menu("presets/auto_format", true); |
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288 | aws->callback(ed_al_check_auto_format); |
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289 | aws->insert_default_option("ask", "a", 0); |
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290 | aws->callback(ed_al_check_auto_format); |
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291 | aws->insert_option("always", "", 1); |
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292 | aws->callback(ed_al_check_auto_format); |
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293 | aws->insert_option("never", "", 2); |
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294 | aws->update_option_menu(); |
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295 | |
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296 | aws->at("len"); |
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297 | aws->create_input_field("presets/alignment_len", 7); |
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298 | |
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299 | aws->at("type"); |
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300 | aws->create_option_menu("presets/alignment_type", true); |
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301 | aws->insert_option("dna", "d", "dna"); |
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302 | aws->insert_option("rna", "r", "rna"); |
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303 | aws->insert_option("pro", "p", "ami"); |
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304 | aws->insert_default_option("???", "?", "usr"); |
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305 | aws->update_option_menu(); |
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306 | |
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307 | aws->at("security"); |
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308 | aws->create_option_menu("presets/security", true); |
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309 | aws->callback(ed_al_check_len_cb); |
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310 | aws->insert_option("0", "0", 0); |
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311 | aws->callback(ed_al_check_len_cb); |
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312 | aws->insert_option("1", "1", 1); |
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313 | aws->callback(ed_al_check_len_cb); |
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314 | aws->insert_option("2", "2", 2); |
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315 | aws->callback(ed_al_check_len_cb); |
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316 | aws->insert_option("3", "3", 3); |
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317 | aws->callback(ed_al_check_len_cb); |
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318 | aws->insert_option("4", "4", 4); |
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319 | aws->callback(ed_al_check_len_cb); |
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320 | aws->insert_option("5", "5", 5); |
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321 | aws->callback(ed_al_check_len_cb); |
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322 | aws->insert_default_option("6", "6", 6); |
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323 | aws->update_option_menu(); |
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324 | |
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325 | aws->at("rem"); |
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326 | aws->create_text_field("presets/alignment_rem"); |
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327 | |
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328 | return aws; |
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329 | } |
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