1 | // =============================================================== // |
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2 | // // |
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3 | // File : MG_alignment.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 "merge.hxx" |
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12 | |
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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 <arbdbt.h> |
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19 | #include <arb_strarray.h> |
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20 | |
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21 | #include <unistd.h> |
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22 | |
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23 | #define AWAR_ALI_NAME(db_nr) awar_name_tmp(db_nr, "alignment_name") |
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24 | #define AWAR_ALI_DEST(db_nr) awar_name_tmp(db_nr, "alignment_dest") |
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25 | #define AWAR_ALI_TYPE(db_nr) awar_name_tmp(db_nr, "alignment_type") |
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26 | #define AWAR_ALI_LEN(db_nr) awar_name_tmp(db_nr, "alignment_len") |
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27 | #define AWAR_ALIGNED(db_nr) awar_name_tmp(db_nr, "aligned") |
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28 | #define AWAR_SECURITY(db_nr) awar_name_tmp(db_nr, "security") |
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29 | |
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30 | #define AWAR_ALI_SRC AWAR_MERGE_TMP_SRC "alignment_name" |
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31 | #define AWAR_ALI_DST AWAR_MERGE_TMP_DST "alignment_name" |
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32 | |
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33 | static void MG_alignment_vars_callback(AW_root *aw_root, int db_nr) { |
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34 | GBDATA *gb_main = get_gb_main(db_nr); |
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35 | GB_transaction ta(gb_main); |
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36 | |
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37 | char *use = aw_root->awar(AWAR_ALI_NAME(db_nr))->read_string(); |
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38 | GBDATA *ali_cont = GBT_get_alignment(gb_main, use); |
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39 | |
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40 | if (!ali_cont) { |
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41 | aw_root->awar(AWAR_ALI_TYPE(db_nr))->unmap(); |
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42 | aw_root->awar(AWAR_ALI_LEN (db_nr))->unmap(); |
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43 | aw_root->awar(AWAR_ALIGNED (db_nr))->unmap(); |
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44 | aw_root->awar(AWAR_SECURITY(db_nr))->unmap(); |
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45 | } |
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46 | else { |
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47 | GBDATA *ali_len = GB_entry(ali_cont, "alignment_len"); |
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48 | GBDATA *ali_aligned = GB_entry(ali_cont, "aligned"); |
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49 | GBDATA *ali_type = GB_entry(ali_cont, "alignment_type"); |
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50 | GBDATA *ali_security = GB_entry(ali_cont, "alignment_write_security"); |
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51 | |
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52 | aw_root->awar(AWAR_ALI_TYPE(db_nr))->map(ali_type); |
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53 | aw_root->awar(AWAR_ALI_LEN (db_nr))->map(ali_len); |
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54 | aw_root->awar(AWAR_ALIGNED (db_nr))->map(ali_aligned); |
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55 | aw_root->awar(AWAR_SECURITY(db_nr))->map(ali_security); |
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56 | |
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57 | } |
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58 | free(use); |
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59 | } |
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60 | |
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61 | |
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62 | void MG_create_alignment_awars(AW_root *aw_root, AW_default aw_def) { |
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63 | for (int db_nr = 1; db_nr <= 2; ++db_nr) { |
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64 | aw_root->awar_string(AWAR_ALI_NAME(db_nr), "", aw_def); |
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65 | aw_root->awar_string(AWAR_ALI_DEST(db_nr), "", aw_def); |
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66 | aw_root->awar_string(AWAR_ALI_TYPE(db_nr), "", aw_def); |
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67 | aw_root->awar_int (AWAR_ALI_LEN (db_nr), 0, aw_def); |
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68 | aw_root->awar_int (AWAR_ALIGNED (db_nr), 0, aw_def); |
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69 | aw_root->awar_int (AWAR_SECURITY(db_nr), 0, aw_def); |
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70 | } |
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71 | } |
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72 | |
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73 | static void copy_and_check_alignments_ignoreResult() { MG_copy_and_check_alignments(); } |
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74 | int MG_copy_and_check_alignments() { |
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75 | // returns 0 if alignments are ok for merging. |
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76 | // otherwise an error message is shown in message box. |
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77 | // checks types and names. |
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78 | |
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79 | GB_ERROR error = NULL; |
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80 | |
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81 | GB_begin_transaction(GLOBAL_gb_dst); |
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82 | GB_begin_transaction(GLOBAL_gb_src); |
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83 | |
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84 | ConstStrArray names; |
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85 | GBT_get_alignment_names(names, GLOBAL_gb_src); |
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86 | |
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87 | GBDATA *gb_dst_presets = NULL; |
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88 | |
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89 | for (int i = 0; names[i] && !error; ++i) { |
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90 | const char *name = names[i]; |
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91 | GBDATA *gb_dst_ali = GBT_get_alignment(GLOBAL_gb_dst, name); |
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92 | |
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93 | if (!gb_dst_ali) { |
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94 | GB_clear_error(); // ignore "alignment not found" |
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95 | |
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96 | GBDATA *gb_src_ali = GBT_get_alignment(GLOBAL_gb_src, name); |
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97 | mg_assert(gb_src_ali); |
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98 | |
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99 | if (!gb_dst_presets) gb_dst_presets = GBT_get_presets(GLOBAL_gb_dst); |
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100 | |
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101 | gb_dst_ali = GB_create_container(gb_dst_presets, "alignment"); |
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102 | GB_copy(gb_dst_ali, gb_src_ali); |
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103 | GBT_add_new_changekey(GLOBAL_gb_dst, (char *)GBS_global_string("%s/data", name), GB_STRING); |
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104 | } |
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105 | |
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106 | char *src_type = GBT_get_alignment_type_string(GLOBAL_gb_src, name); |
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107 | char *dst_type = GBT_get_alignment_type_string(GLOBAL_gb_dst, name); |
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108 | |
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109 | if (strcmp(src_type, dst_type) != 0) { |
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110 | error = GBS_global_string("The alignments '%s' have different types (%s != %s)", name, src_type, dst_type); |
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111 | } |
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112 | free(dst_type); |
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113 | free(src_type); |
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114 | } |
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115 | |
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116 | GB_commit_transaction(GLOBAL_gb_dst); |
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117 | GB_commit_transaction(GLOBAL_gb_src); |
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118 | |
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119 | if (error) aw_message(error); |
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120 | |
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121 | return !!error; |
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122 | } |
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123 | |
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124 | static void MG_ad_al_delete_cb(AW_window *aww, int db_nr) { |
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125 | if (aw_ask_sure("merge_delete_ali", "Are you sure to delete all data belonging to this alignment?")) { |
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126 | GBDATA *gb_main = get_gb_main(db_nr); |
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127 | char *source = aww->get_root()->awar(AWAR_ALI_NAME(db_nr))->read_string(); |
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128 | { |
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129 | GB_transaction ta(gb_main); |
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130 | GB_ERROR error = GBT_rename_alignment(gb_main, source, 0, 0, 1); |
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131 | |
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132 | error = ta.close(error); |
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133 | if (error) aw_message(error); |
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134 | } |
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135 | free(source); |
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136 | } |
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137 | } |
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138 | |
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139 | |
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140 | static void MG_ed_al_check_len_cb(AW_window *aww, int db_nr) { |
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141 | GBDATA *gb_main = get_gb_main(db_nr); |
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142 | char *use = aww->get_root()->awar(AWAR_ALI_NAME(db_nr))->read_string(); |
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143 | |
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144 | GB_transaction ta(gb_main); |
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145 | |
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146 | GB_ERROR error = GBT_check_data(gb_main, use); |
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147 | error = ta.close(error); |
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148 | |
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149 | aw_message_if(error); |
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150 | free(use); |
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151 | } |
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152 | |
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153 | static void MG_copy_delete_rename(AW_window * aww, int db_nr, int dele) { |
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154 | GBDATA *gb_main = get_gb_main(db_nr); |
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155 | |
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156 | AW_root *awr = aww->get_root(); |
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157 | char *source = awr->awar(AWAR_ALI_NAME(db_nr))->read_string(); |
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158 | char *dest = awr->awar(AWAR_ALI_DEST(db_nr))->read_string(); |
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159 | |
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160 | GB_ERROR error = GB_begin_transaction(gb_main); |
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161 | |
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162 | if (!error) error = GBT_rename_alignment(gb_main, source, dest, (int)1, (int)dele); |
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163 | if (!error) error = GBT_add_new_changekey(gb_main, GBS_global_string("%s/data", dest), GB_STRING); |
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164 | |
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165 | error = GB_end_transaction(gb_main, error); |
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166 | aww->hide_or_notify(error); |
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167 | |
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168 | free(source); |
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169 | free(dest); |
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170 | } |
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171 | |
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172 | |
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173 | static AW_window *create_alignment_copy_window(AW_root *root, int db_nr) |
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174 | { |
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175 | AW_window_simple *aws = new AW_window_simple; |
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176 | char header[80]; |
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177 | sprintf(header, "ALIGNMENT COPY %i", db_nr); |
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178 | aws->init(root, header, header); |
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179 | aws->load_xfig("ad_al_si.fig"); |
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180 | |
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181 | aws->callback((AW_CB0)AW_POPDOWN); |
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182 | aws->at("close"); |
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183 | aws->create_button("CLOSE", "CLOSE", "C"); |
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184 | |
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185 | aws->at("label"); |
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186 | aws->create_autosize_button(0, "Please enter the new name\nof the alignment"); |
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187 | |
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188 | aws->at("input"); |
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189 | aws->create_input_field(AWAR_ALI_DEST(db_nr), 15); |
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190 | |
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191 | aws->at("ok"); |
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192 | aws->callback(makeWindowCallback(MG_copy_delete_rename, db_nr, 0)); |
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193 | aws->create_button("GO", "GO", "G"); |
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194 | |
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195 | return (AW_window *)aws; |
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196 | } |
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197 | static AW_window *MG_create_alignment_rename_window(AW_root *root, int db_nr) |
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198 | { |
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199 | AW_window_simple *aws = new AW_window_simple; |
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200 | char header[80]; |
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201 | sprintf(header, "ALIGNMENT RENAME %i", db_nr); |
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202 | aws->init(root, header, header); |
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203 | aws->load_xfig("ad_al_si.fig"); |
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204 | |
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205 | aws->callback((AW_CB0)AW_POPDOWN); |
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206 | aws->at("close"); |
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207 | aws->create_button("CLOSE", "CLOSE", "C"); |
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208 | |
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209 | aws->at("label"); |
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210 | aws->create_autosize_button(0, "Please enter the name\nof the new alignment"); |
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211 | |
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212 | aws->at("input"); |
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213 | aws->create_input_field(AWAR_ALI_DEST(db_nr), 15); |
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214 | |
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215 | aws->at("ok"); |
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216 | aws->callback(makeWindowCallback(MG_copy_delete_rename, db_nr, 1)); |
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217 | aws->create_button("GO", "GO", "G"); |
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218 | |
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219 | return (AW_window *)aws; |
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220 | } |
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221 | |
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222 | static void MG_aa_create_alignment(AW_window *aww, int db_nr) { |
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223 | GBDATA *gb_main = get_gb_main(db_nr); |
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224 | char *name = aww->get_root()->awar(AWAR_ALI_DEST(db_nr))->read_string(); |
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225 | GB_ERROR error = GB_begin_transaction(gb_main); |
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226 | GBDATA *gb_alignment = GBT_create_alignment(gb_main, name, 0, 0, 0, "dna"); |
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227 | |
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228 | if (!gb_alignment) error = GB_await_error(); |
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229 | GB_end_transaction_show_error(gb_main, error, aw_message); |
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230 | free(name); |
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231 | } |
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232 | |
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233 | static AW_window *MG_create_alignment_create_window(AW_root *root, int db_nr) { |
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234 | AW_window_simple *aws = new AW_window_simple; |
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235 | char header[80]; |
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236 | sprintf(header, "ALIGNMENT CREATE %i", db_nr); |
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237 | aws->init(root, header, header); |
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238 | aws->load_xfig("ad_al_si.fig"); |
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239 | |
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240 | aws->callback((AW_CB0)AW_POPDOWN); |
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241 | aws->at("close"); |
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242 | aws->create_button("CLOSE", "CLOSE", "C"); |
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243 | |
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244 | aws->at("label"); |
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245 | aws->create_autosize_button(0, "Please enter the new name\nof the alignment"); |
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246 | |
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247 | aws->at("input"); |
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248 | aws->create_input_field(AWAR_ALI_DEST(db_nr), 15); |
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249 | |
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250 | aws->at("ok"); |
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251 | aws->callback(makeWindowCallback(MG_aa_create_alignment, db_nr)); |
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252 | aws->create_button("GO", "GO", "G"); |
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253 | |
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254 | return (AW_window *)aws; |
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255 | } |
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256 | |
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257 | |
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258 | |
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259 | static AW_window *MG_create_alignment_window(AW_root *root, int db_nr) { |
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260 | GBDATA *gb_main = get_gb_main(db_nr); |
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261 | AW_window_simple *aws = new AW_window_simple; |
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262 | char header[80]; |
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263 | |
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264 | sprintf(header, "ALIGNMENT CONTROL %i", db_nr); |
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265 | aws->init(root, header, header); |
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266 | aws->load_xfig("merge/ad_align.fig"); |
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267 | |
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268 | aws->callback((AW_CB0)AW_POPDOWN); |
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269 | aws->at("close"); |
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270 | aws->create_button("CLOSE", "CLOSE", "C"); |
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271 | |
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272 | aws->callback(makeHelpCallback("ad_align.hlp")); |
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273 | aws->at("help"); |
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274 | aws->create_button("HELP", "HELP", "H"); |
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275 | |
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276 | aws->button_length(13); |
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277 | |
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278 | aws->at("list"); |
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279 | awt_create_selection_list_on_alignments(gb_main, aws, AWAR_ALI_NAME(db_nr), "*="); |
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280 | |
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281 | aws->at("delete"); |
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282 | aws->callback(makeWindowCallback(MG_ad_al_delete_cb, db_nr)); |
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283 | aws->create_button("DELETE", "DELETE", "D"); |
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284 | |
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285 | aws->at("rename"); |
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286 | aws->callback(makeCreateWindowCallback(MG_create_alignment_rename_window, db_nr)); |
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287 | aws->create_button("RENAME", "RENAME", "R"); |
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288 | |
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289 | aws->at("create"); |
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290 | aws->callback(makeCreateWindowCallback(MG_create_alignment_create_window, db_nr)); |
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291 | aws->create_button("CREATE", "CREATE", "N"); |
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292 | |
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293 | aws->at("copy"); |
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294 | aws->callback(makeCreateWindowCallback(create_alignment_copy_window, db_nr)); |
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295 | aws->create_button("COPY", "COPY", "C"); |
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296 | |
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297 | aws->at("aligned"); |
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298 | aws->create_option_menu(AWAR_ALIGNED(db_nr), true); |
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299 | aws->insert_option("justified", "j", 1); |
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300 | aws->insert_default_option("not justified", "n", 0); |
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301 | aws->update_option_menu(); |
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302 | |
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303 | aws->at("len"); |
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304 | aws->create_input_field(AWAR_ALI_LEN(db_nr), 8); |
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305 | |
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306 | aws->at("type"); |
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307 | aws->create_option_menu(AWAR_ALI_TYPE(db_nr), true); |
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308 | aws->insert_option("dna", "d", "dna"); |
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309 | aws->insert_option("rna", "r", "rna"); |
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310 | aws->insert_option("pro", "p", "ami"); |
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311 | aws->insert_default_option("???", "?", "usr"); |
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312 | aws->update_option_menu(); |
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313 | |
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314 | aws->at("security"); |
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315 | aws->callback(makeWindowCallback(MG_ed_al_check_len_cb, db_nr)); |
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316 | aws->create_option_menu(AWAR_SECURITY(db_nr), true); |
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317 | aws->insert_option("0", "0", 0); |
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318 | aws->insert_option("1", "1", 1); |
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319 | aws->insert_option("2", "2", 2); |
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320 | aws->insert_option("3", "3", 3); |
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321 | aws->insert_option("4", "4", 4); |
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322 | aws->insert_option("5", "5", 5); |
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323 | aws->insert_default_option("6", "6", 6); |
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324 | aws->update_option_menu(); |
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325 | |
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326 | return aws; |
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327 | } |
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328 | |
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329 | AW_window *MG_create_merge_alignment_window(AW_root *awr) { |
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330 | AW_window_simple *aws = new AW_window_simple; |
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331 | |
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332 | awr->awar(AWAR_ALI_SRC)->add_callback(makeRootCallback(MG_alignment_vars_callback, 1)); |
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333 | awr->awar(AWAR_ALI_DST)->add_callback(makeRootCallback(MG_alignment_vars_callback, 2)); |
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334 | |
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335 | aws->init(awr, "MERGE_ALIGNMENTS", "MERGE ALIGNMENTS"); |
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336 | aws->load_xfig("merge/alignment.fig"); |
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337 | |
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338 | aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN); |
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339 | aws->create_button("CLOSE", "CLOSE", "C"); |
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340 | |
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341 | aws->at("help"); |
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342 | aws->callback(makeHelpCallback("mg_alignment.hlp")); |
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343 | aws->create_button("HELP", "HELP", "H"); |
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344 | |
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345 | aws->at("check"); |
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346 | aws->callback(makeWindowCallback(copy_and_check_alignments_ignoreResult)); |
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347 | aws->create_button("CHECK", "Check"); |
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348 | |
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349 | aws->at("ali1"); |
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350 | awt_create_selection_list_on_alignments(GLOBAL_gb_src, aws, AWAR_ALI_SRC, "*="); |
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351 | |
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352 | aws->at("ali2"); |
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353 | awt_create_selection_list_on_alignments(GLOBAL_gb_dst, aws, AWAR_ALI_DST, "*="); |
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354 | |
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355 | aws->at("modify1"); |
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356 | aws->callback(makeCreateWindowCallback(MG_create_alignment_window, 1)); |
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357 | aws->create_button("MODIFY_DB1", "MODIFY"); |
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358 | |
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359 | aws->at("modify2"); |
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360 | aws->callback(makeCreateWindowCallback(MG_create_alignment_window, 2)); |
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361 | aws->create_button("MODIFY_DB2", "MODIFY"); |
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362 | |
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363 | |
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364 | aws->button_length(0); |
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365 | aws->shadow_width(1); |
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366 | aws->at("icon"); |
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367 | aws->callback(makeHelpCallback("mg_alignment.hlp")); |
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368 | aws->create_button("HELP_MERGE", "#merge/icon.xpm"); |
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369 | |
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370 | return aws; |
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371 | } |
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