1 | // =============================================================== // |
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2 | // // |
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3 | // File : MP_noclass.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 "MultiProbe.hxx" |
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12 | #include "mp_proto.hxx" |
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13 | #include "MP_externs.hxx" |
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14 | #include "MP_probe.hxx" |
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15 | |
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16 | #include <aw_select.hxx> |
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17 | #include <aw_msg.hxx> |
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18 | #include <arb_progress.h> |
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19 | #include <aw_root.hxx> |
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20 | #include <TreeCallbacks.hxx> |
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21 | #include <client.h> |
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22 | #include <servercntrl.h> |
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23 | |
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24 | #include <ctime> |
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25 | |
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26 | int get_random(int min, int max); // gibt eine Zufallszahl x mit der Eigenschaft : min <= x <= max |
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27 | |
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28 | int **system3_tab = NULL; |
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29 | static int system3_tab_size = 0; |
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30 | |
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31 | unsigned char **hamming_tab = NULL; |
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32 | bool new_pt_server = true; |
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33 | |
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34 | long k_aus_n(int k, int n) { |
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35 | int a = n, b = 1, i; |
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36 | |
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37 | if (k > (n / 2)) k = n - k; |
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38 | if (k <= 0) return (k == 0); |
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39 | for (i = 2; i <= k; n--, a *= n, b *= i, i++) ; |
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40 | return a / b; |
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41 | } |
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42 | |
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43 | int get_random(int min, int max) { |
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44 | mp_assert(min <= max); |
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45 | return GB_random(max-min+1)+min; |
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46 | } |
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47 | |
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48 | void MP_close_main(AW_window *aww) |
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49 | { |
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50 | AWT_canvas *scr = mp_main->get_canvas(); |
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51 | |
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52 | if (mp_main->get_mp_window()->get_result_window()) |
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53 | mp_main->get_mp_window()->get_result_window()->hide(); |
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54 | |
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55 | GB_transaction ta(scr->gb_main); |
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56 | |
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57 | AP_tree *ap_tree = AWT_TREE(scr)->get_root_node(); |
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58 | if (ap_tree) ap_tree->uncolorize(); |
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59 | |
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60 | if (scr->gb_main) |
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61 | scr->gfx->update(scr->gb_main); |
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62 | |
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63 | scr->refresh(); |
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64 | |
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65 | AW_POPDOWN(aww); |
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66 | delete mp_main->get_p_eval(); |
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67 | mp_main->set_p_eval(NULL); |
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68 | delete mp_main->get_stc(); |
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69 | mp_main->set_stc(NULL); |
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70 | |
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71 | new_pt_server = true; |
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72 | } |
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73 | |
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74 | static char *MP_get_probes(const char *str) { |
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75 | const char *result = strrchr(str, '#'); |
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76 | |
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77 | if (!result) { |
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78 | result = str; |
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79 | } |
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80 | else { |
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81 | ++result; |
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82 | result += strspn(result, " \t"); // skip over whitespace |
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83 | } |
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84 | return strdup(result); |
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85 | } |
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86 | |
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87 | void MP_gen_quality(AW_root *awr) { |
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88 | bool firsttime = true; // @@@ was this static in the past? |
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89 | |
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90 | if (firsttime) |
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91 | { |
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92 | firsttime = false; // @@@ unused |
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93 | return; |
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94 | } |
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95 | |
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96 | char *probe, *new_qual, *ecol_pos; |
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97 | char *selected = awr->awar(MP_AWAR_SELECTEDPROBES)->read_string(); |
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98 | |
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99 | if (!selected || !selected[0]) |
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100 | return; |
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101 | |
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102 | probe = MP_get_probes(selected); |
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103 | if (!probe || !probe[0]) |
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104 | return; |
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105 | |
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106 | ecol_pos = MP_get_comment(3, selected); |
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107 | |
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108 | selected_list->delete_value(selected); |
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109 | |
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110 | new_qual = new char[5 + 7 + strlen(probe)]; // 5 = Zahl und Separator und Zahl und Separator und Nullzeichen |
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111 | sprintf(new_qual, "%1ld#%1ld#%6d#%s", mp_gl_awars.probe_quality, mp_gl_awars.singlemismatches, atoi(ecol_pos), probe); |
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112 | delete probe; |
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113 | |
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114 | selected_list->insert(new_qual, new_qual); |
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115 | selected_list->insert_default("", ""); |
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116 | selected_list->sort(false, true); |
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117 | selected_list->update(); |
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118 | awr->awar(MP_AWAR_SELECTEDPROBES)->write_string(new_qual); |
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119 | delete new_qual; |
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120 | delete ecol_pos; |
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121 | } |
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122 | |
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123 | void MP_modify_selected(AW_root *awr) { |
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124 | // setzt den 2.Parameter in selected_list |
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125 | char *com1, *com2, *com3, *probes, temp[120]; |
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126 | List<char> *l = new List<char>; |
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127 | |
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128 | AW_selection_list_iterator selentry(selected_list); |
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129 | |
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130 | const char *ptr2; |
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131 | while ((ptr2 = selentry.get_value())) { |
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132 | ++selentry; |
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133 | |
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134 | com1 = MP_get_comment(1, ptr2); |
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135 | com2 = MP_get_comment(2, ptr2); |
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136 | com3 = MP_get_comment(3, ptr2); |
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137 | probes = MP_get_probes(ptr2); |
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138 | |
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139 | if (!probes || !probes[0]) |
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140 | break; |
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141 | |
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142 | sprintf(temp, "%1d#%1ld#%6d#%s", atoi(com1), mp_gl_awars.no_of_mismatches, atoi(com3), probes); |
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143 | |
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144 | l->insert_as_last(strdup(temp)); |
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145 | |
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146 | delete probes; |
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147 | delete com1; |
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148 | delete com2; |
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149 | delete com3; |
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150 | } |
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151 | |
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152 | selected_list->clear(); |
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153 | |
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154 | ptr2 = l->get_first(); |
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155 | while (ptr2) |
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156 | { |
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157 | l->remove_first(); |
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158 | selected_list->insert(ptr2, ptr2); |
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159 | delete ptr2; |
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160 | ptr2 = l->get_first(); |
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161 | } |
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162 | |
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163 | selected_list->insert_default("", ""); |
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164 | selected_list->sort(false, true); |
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165 | selected_list->update(); |
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166 | awr->awar(MP_AWAR_SELECTEDPROBES)->write_string(""); |
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167 | |
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168 | remembered_mismatches = mp_gl_awars.no_of_mismatches; |
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169 | delete l; |
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170 | } |
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171 | |
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172 | void MP_gen_singleprobe(AW_root *awr) { |
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173 | char *probe, *new_sing; |
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174 | char *selected = awr->awar(MP_AWAR_SELECTEDPROBES)->read_string(); |
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175 | |
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176 | if (!selected || !selected[0]) |
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177 | return; |
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178 | |
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179 | probe = MP_get_probes(selected); |
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180 | selected_list->delete_value(selected); |
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181 | |
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182 | new_sing = new char[5 + 7 + strlen(probe)]; // 5 = Zahl und Separator und Zahl und Separator und Nullzeichen |
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183 | sprintf(new_sing, "%1ld#%1ld#%6ld#%s", mp_gl_awars.probe_quality, mp_gl_awars.singlemismatches, mp_gl_awars.ecolipos, probe); |
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184 | delete probe; |
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185 | |
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186 | selected_list->insert(new_sing, new_sing); |
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187 | selected_list->insert_default("", ""); |
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188 | selected_list->sort(false, true); |
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189 | selected_list->update(); |
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190 | awr->awar(MP_AWAR_SELECTEDPROBES)->write_string(new_sing); |
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191 | delete new_sing; |
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192 | } |
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193 | |
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194 | static void init_system3_tab() |
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195 | { |
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196 | int i, j, k, |
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197 | size_hamming_tab, |
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198 | hamm_dist; |
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199 | int **dummy_int; |
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200 | int counter, wert; |
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201 | |
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202 | if (system3_tab) { |
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203 | for (j=0; j< system3_tab_size; j++) |
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204 | delete [] system3_tab[j]; |
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205 | |
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206 | delete [] system3_tab; |
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207 | } |
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208 | system3_tab = new int*[mp_gl_awars.no_of_probes]; |
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209 | system3_tab_size = mp_gl_awars.no_of_probes; |
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210 | for (j=0; j<mp_gl_awars.no_of_probes; j++) |
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211 | { |
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212 | system3_tab[j] = new int[3]; |
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213 | memset(system3_tab[j], 0, sizeof(int) * 3); |
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214 | } |
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215 | |
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216 | for (j=0; j< mp_gl_awars.no_of_probes; j++) |
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217 | { |
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218 | for (k=0; k<3; k++) |
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219 | { |
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220 | if (!j) system3_tab[j][k] = k; |
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221 | else system3_tab[j][k] = system3_tab[j-1][k] * 3; |
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222 | } |
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223 | } |
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224 | |
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225 | |
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226 | // ** hamming_tab |
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227 | if (hamming_tab) |
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228 | delete [] hamming_tab; |
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229 | |
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230 | size_hamming_tab = (int)pow(3.0, (double) mp_gl_awars.no_of_probes); |
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231 | hamming_tab = new unsigned char*[size_hamming_tab]; |
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232 | dummy_int = new int*[size_hamming_tab]; |
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233 | |
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234 | for (i=0; i<size_hamming_tab; i++) |
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235 | { |
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236 | hamming_tab[i] = new unsigned char[size_hamming_tab]; |
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237 | memset(hamming_tab[i], 0, sizeof(unsigned char) * size_hamming_tab); |
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238 | |
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239 | dummy_int[i] = new int[mp_gl_awars.no_of_probes]; |
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240 | memset(dummy_int[i], 0, sizeof(int) * mp_gl_awars.no_of_probes); |
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241 | } |
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242 | |
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243 | counter = 1; |
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244 | for (i=0; i< mp_gl_awars.no_of_probes; i++) |
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245 | { |
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246 | for (j=0; j<size_hamming_tab; j++) |
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247 | { |
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248 | for (wert = 0; wert < 3; wert++) |
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249 | { |
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250 | for (k=0; k<counter; k++) |
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251 | { |
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252 | dummy_int[j++][i] = wert; |
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253 | } |
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254 | } |
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255 | j--; |
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256 | } |
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257 | counter *= 3; |
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258 | } |
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259 | |
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260 | for (i=0; i<size_hamming_tab; i++) |
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261 | { |
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262 | for (j=0; j<size_hamming_tab; j++) |
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263 | { |
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264 | hamm_dist = 0; |
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265 | for (k=0; k<mp_gl_awars.no_of_probes; k++) |
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266 | { |
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267 | if ((dummy_int[i][k] == 2 && dummy_int[j][k] == 0) || |
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268 | (dummy_int[i][k] == 0 && dummy_int[j][k] == 2)) |
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269 | hamm_dist++; |
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270 | } |
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271 | hamming_tab[i][j] = hamm_dist; |
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272 | } |
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273 | } |
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274 | |
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275 | for (i=0; i<size_hamming_tab; i++) |
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276 | { |
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277 | delete [] dummy_int[i]; |
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278 | } |
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279 | delete [] dummy_int; |
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280 | |
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281 | |
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282 | |
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283 | } |
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284 | |
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285 | void MP_popup_result_window(AW_window */*aww*/) { |
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286 | mp_main->get_mp_window()->create_result_window(mp_main->get_aw_root())->activate(); |
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287 | init_system3_tab(); |
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288 | } |
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289 | |
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290 | bool MP_aborted(int gen_cnt, double avg_fit, double min_fit, double max_fit, arb_progress& progress) { |
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291 | char view_text[150]; |
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292 | |
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293 | if (gen_cnt == 0) |
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294 | sprintf(view_text, "Evaluating first generation"); |
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295 | else |
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296 | sprintf(view_text, "Gen:%d Avg:%5i Min:%5i Max:%5i", gen_cnt, int(avg_fit), int(min_fit), int(max_fit)); |
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297 | |
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298 | progress.subtitle(view_text); |
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299 | return progress.aborted(); |
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300 | } |
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301 | |
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302 | |
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303 | void MP_compute(AW_window *, AW_CL cl_gb_main) { |
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304 | AW_root *aw_root = mp_main->get_aw_root(); |
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305 | AW_window *aww2; |
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306 | int i = 0; |
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307 | int *bew_array; |
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308 | char *ptr, *qual; |
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309 | char **probe_field; |
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310 | int *single_mismatch; |
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311 | ProbeValuation *p_eval = NULL; |
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312 | GBDATA *gb_main = (GBDATA*)cl_gb_main; |
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313 | |
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314 | MO_Liste::set_gb_main(gb_main); |
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315 | |
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316 | size_t selected_probes_count = selected_list->size(); |
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317 | if ((int)selected_probes_count < mp_gl_awars.no_of_probes) { |
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318 | aw_message("Not enough probes selected for computation !!!"); |
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319 | return; |
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320 | } |
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321 | |
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322 | if (mp_main->get_stc()) |
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323 | { |
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324 | delete mp_main->get_stc(); |
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325 | mp_main->set_stc(NULL); |
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326 | new_pt_server = true; |
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327 | } |
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328 | |
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329 | init_system3_tab(); |
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330 | |
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331 | aww2 = mp_main->get_mp_window()->create_result_window(aw_root); |
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332 | |
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333 | result_probes_list->clear(); |
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334 | result_probes_list->insert_default("", ""); |
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335 | result_probes_list->update(); |
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336 | |
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337 | AW_selection_list_iterator selentry(selected_list); |
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338 | probe_field = new char*[selected_probes_count]; |
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339 | bew_array = new int[selected_probes_count]; |
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340 | single_mismatch = new int[selected_probes_count]; |
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341 | |
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342 | arb_progress progress("Computing multiprobes"); |
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343 | |
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344 | const char *ptr2; |
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345 | while ((ptr2 = selentry.get_value())) { |
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346 | ++selentry; |
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347 | ptr = MP_get_probes(ptr2); // hier sind es einfachsonden |
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348 | if (ptr && ptr[0] != ' ' && ptr[0] != '\t' && ptr[0] != '\0') { |
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349 | qual = MP_get_comment(1, ptr2); |
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350 | bew_array[i] = atoi(qual); |
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351 | free(qual); |
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352 | |
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353 | qual = MP_get_comment(2, ptr2); |
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354 | single_mismatch[i] = atoi(qual); // single mismatch kann zwar eingestellt werden, aber wird noch nicht uebergeben |
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355 | free(qual); |
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356 | |
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357 | probe_field[i++] = ptr; |
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358 | } |
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359 | } |
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360 | |
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361 | p_eval = mp_main->new_probe_eval(probe_field, i, bew_array, single_mismatch); |
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362 | p_eval->init_valuation(); |
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363 | |
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364 | if (pt_server_different) |
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365 | { |
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366 | pt_server_different = false; |
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367 | aw_message("There are species in the tree which are\nnot included in the PT-Server"); |
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368 | } |
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369 | |
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370 | mp_main->destroy_probe_eval(); |
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371 | |
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372 | aww2->activate(); |
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373 | } |
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374 | |
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375 | static bool MP_is_probe(char *seq) { |
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376 | bool result=true; |
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377 | char *s, |
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378 | *seq2; |
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379 | |
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380 | if (! seq) |
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381 | return false; |
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382 | |
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383 | seq2 = MP_get_probes(seq); |
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384 | if (!seq2 || ! seq2[0]) |
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385 | return false; |
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386 | |
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387 | s = seq2; |
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388 | while (*s && result) |
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389 | { |
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390 | result = result && MP_probe_tab[(unsigned char)*s]; |
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391 | s++; |
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392 | } |
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393 | free(seq2); |
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394 | return result; |
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395 | } |
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396 | |
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397 | void MP_new_sequence(AW_window *aww) { |
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398 | AW_root *aw_root = aww->get_root(); |
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399 | char *seq = aw_root->awar(MP_AWAR_SEQIN)->read_string(); |
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400 | |
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401 | if (MP_is_probe(seq)) { |
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402 | char *new_seq = GBS_global_string_copy("%1ld#%1ld#%6d#%s", mp_gl_awars.probe_quality, mp_gl_awars.singlemismatches, 0, seq); |
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403 | |
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404 | selected_list->insert(new_seq, new_seq); |
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405 | selected_list->sort(false, true); |
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406 | selected_list->update(); |
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407 | |
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408 | aw_root->awar(MP_AWAR_SELECTEDPROBES)->write_string(new_seq); |
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409 | free(new_seq); |
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410 | } |
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411 | else { |
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412 | aw_message(GBS_global_string("'%s' is no valid probe", seq)); |
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413 | } |
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414 | free(seq); |
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415 | } |
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416 | |
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417 | void MP_cache_sonden(AW_window *) { new_pt_server = true; } |
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418 | void MP_cache_sonden2(AW_root *) { new_pt_server = true; } |
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419 | |
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420 | void MP_show_probes_in_tree_move(AW_window *aww, AW_CL cl_backward, AW_CL cl_result_probes_list) { |
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421 | bool backward = bool(cl_backward); |
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422 | AW_selection_list *resultProbesList = (AW_selection_list*)cl_result_probes_list; |
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423 | |
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424 | resultProbesList->move_selection(backward ? -1 : 1); |
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425 | MP_show_probes_in_tree(aww); |
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426 | } |
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427 | |
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428 | void MP_show_probes_in_tree(AW_window */*aww*/) { |
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429 | AWT_canvas *scr = mp_main->get_canvas(); |
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430 | char *mism, *mism_temp; |
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431 | char *a_probe, *another_probe, *the_probe, *mism_temp2; |
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432 | int i, how_many_probes = 0; |
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433 | |
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434 | { |
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435 | char *sel = mp_main->get_aw_root()->awar(MP_AWAR_RESULTPROBES)->read_string(); |
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436 | a_probe = MP_get_probes(sel); // haelt jetzt Sondenstring |
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437 | if (! a_probe || ! a_probe[0]) { |
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438 | free(a_probe); |
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439 | free(sel); |
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440 | return; |
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441 | } |
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442 | |
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443 | mism_temp2 = MP_get_comment(2, sel); |
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444 | mism_temp = mism_temp2; |
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445 | free(sel); |
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446 | } |
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447 | |
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448 | char **probe_field = new char*[MAXMISMATCHES]; |
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449 | int *mismatches = new int[MAXMISMATCHES]; |
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450 | |
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451 | for (i=0; i<MAXMISMATCHES; i++) |
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452 | { |
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453 | probe_field[i] = NULL; |
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454 | mismatches[i] = 0; |
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455 | } |
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456 | |
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457 | another_probe = a_probe; |
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458 | for (i=0; i< MAXPROBECOMBIS; i++) // generiert probe_field und mismatches array |
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459 | { |
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460 | mism = strchr(mism_temp, ' '); |
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461 | if (mism) |
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462 | *(mism++) = 0; |
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463 | |
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464 | mismatches[i] = atoi(mism_temp); |
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465 | mism_temp = mism; |
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466 | |
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467 | |
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468 | probe_field[i] = NULL; |
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469 | the_probe = another_probe; |
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470 | another_probe = strchr(another_probe, ' '); |
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471 | if (another_probe) |
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472 | { |
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473 | *(another_probe++) = 0; |
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474 | while (*another_probe == ' ' || *another_probe == '\t') |
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475 | another_probe++; |
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476 | } |
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477 | else |
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478 | { |
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479 | probe_field[i] = strdup(the_probe); |
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480 | how_many_probes ++; |
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481 | break; |
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482 | } |
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483 | |
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484 | if (the_probe && the_probe[0]) |
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485 | { |
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486 | probe_field[i] = strdup(the_probe); |
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487 | how_many_probes ++; |
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488 | } |
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489 | } |
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490 | |
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491 | free(a_probe); |
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492 | free(mism_temp2); |
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493 | |
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494 | if (new_pt_server) |
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495 | { |
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496 | new_pt_server = false; |
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497 | |
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498 | if (mp_main->get_stc()) |
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499 | delete mp_main->get_stc(); |
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500 | |
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501 | mp_main->set_stc(new ST_Container(MAXSONDENHASHSIZE)); |
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502 | if (pt_server_different) |
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503 | { |
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504 | mp_main->set_stc(NULL); |
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505 | new_pt_server = true; |
---|
506 | aw_message("There are species in the tree which are\nnot included in the PT-Server"); |
---|
507 | pt_server_different = false; |
---|
508 | return; |
---|
509 | } |
---|
510 | } |
---|
511 | |
---|
512 | delete mp_main->get_stc()->sondentopf; |
---|
513 | mp_main->get_stc()->sondentopf = new Sondentopf(mp_main->get_stc()->Bakterienliste, mp_main->get_stc()->Auswahlliste); |
---|
514 | |
---|
515 | for (i=0; i<MAXMISMATCHES; i++) { |
---|
516 | if (probe_field[i]) { |
---|
517 | mp_main->get_stc()->sondentopf->put_Sonde(probe_field[i], mismatches[i], mismatches[i] + mp_gl_awars.outside_mismatches_difference); |
---|
518 | } |
---|
519 | } |
---|
520 | |
---|
521 | mp_main->get_stc()->sondentopf->gen_color_hash(mp_gl_awars.no_of_probes); |
---|
522 | |
---|
523 | GB_transaction ta(scr->gb_main); |
---|
524 | AWT_TREE(scr)->get_root_node()->colorize(mp_main->get_stc()->sondentopf->get_color_hash()); |
---|
525 | |
---|
526 | if (scr->gb_main) |
---|
527 | scr->gfx->update(scr->gb_main); |
---|
528 | |
---|
529 | scr->refresh(); |
---|
530 | |
---|
531 | for (i=0; i<MAXMISMATCHES; i++) |
---|
532 | free(probe_field[i]); |
---|
533 | |
---|
534 | delete [] probe_field; |
---|
535 | delete [] mismatches; |
---|
536 | } |
---|
537 | |
---|
538 | void MP_mark_probes_in_tree(AW_window *aww) { |
---|
539 | AWT_canvas *scr = mp_main->get_canvas(); |
---|
540 | char *mism, *mism_temp; |
---|
541 | char *a_probe, *another_probe, *the_probe, *mism_temp2; |
---|
542 | int i, how_many_probes = 0; |
---|
543 | GBDATA *gb_species; |
---|
544 | |
---|
545 | { |
---|
546 | char *sel = mp_main->get_aw_root()->awar(MP_AWAR_RESULTPROBES)->read_string(); |
---|
547 | a_probe = MP_get_probes(sel); // haelt jetzt Sondenstring |
---|
548 | |
---|
549 | if (! a_probe || ! a_probe[0]) { |
---|
550 | free(a_probe); |
---|
551 | free(sel); |
---|
552 | return; |
---|
553 | } |
---|
554 | |
---|
555 | mism_temp2 = MP_get_comment(2, sel); |
---|
556 | mism_temp = mism_temp2; |
---|
557 | free(sel); |
---|
558 | } |
---|
559 | |
---|
560 | char **probe_field = new char*[MAXMISMATCHES]; |
---|
561 | int *mismatches = new int[MAXMISMATCHES]; |
---|
562 | |
---|
563 | for (i=0; i<MAXMISMATCHES; i++) |
---|
564 | { |
---|
565 | probe_field[i] = NULL; |
---|
566 | mismatches[i] = 0; |
---|
567 | } |
---|
568 | |
---|
569 | another_probe = a_probe; |
---|
570 | for (i=0; i< MAXPROBECOMBIS; i++) // generiert probe_field und mismatches array |
---|
571 | { |
---|
572 | mism = strchr(mism_temp, ' '); |
---|
573 | if (mism) |
---|
574 | *(mism++) = 0; |
---|
575 | |
---|
576 | mismatches[i] = atoi(mism_temp); |
---|
577 | mism_temp = mism; |
---|
578 | |
---|
579 | probe_field[i] = NULL; |
---|
580 | the_probe = another_probe; |
---|
581 | another_probe = strchr(another_probe, ' '); |
---|
582 | if (another_probe) { |
---|
583 | *(another_probe++) = 0; |
---|
584 | while (*another_probe == ' ' || *another_probe == '\t') |
---|
585 | another_probe++; |
---|
586 | } |
---|
587 | else { |
---|
588 | probe_field[i] = strdup(the_probe); |
---|
589 | how_many_probes ++; |
---|
590 | break; |
---|
591 | } |
---|
592 | |
---|
593 | if (the_probe && the_probe[0]) { |
---|
594 | probe_field[i] = strdup(the_probe); |
---|
595 | how_many_probes ++; |
---|
596 | } |
---|
597 | } |
---|
598 | |
---|
599 | free(a_probe); |
---|
600 | free(mism_temp2); |
---|
601 | |
---|
602 | if (new_pt_server) { |
---|
603 | new_pt_server = false; |
---|
604 | |
---|
605 | if (mp_main->get_stc()) |
---|
606 | delete mp_main->get_stc(); |
---|
607 | |
---|
608 | mp_main->set_stc(new ST_Container(MAXSONDENHASHSIZE)); |
---|
609 | if (pt_server_different) |
---|
610 | { |
---|
611 | mp_main->set_stc(NULL); |
---|
612 | new_pt_server = true; |
---|
613 | aw_message("There are species in the tree which are\nnot included in the PT-Server"); |
---|
614 | pt_server_different = false; |
---|
615 | return; |
---|
616 | } |
---|
617 | } |
---|
618 | |
---|
619 | delete mp_main->get_stc()->sondentopf; |
---|
620 | mp_main->get_stc()->sondentopf = new Sondentopf(mp_main->get_stc()->Bakterienliste, mp_main->get_stc()->Auswahlliste); |
---|
621 | |
---|
622 | for (i=0; i<MAXMISMATCHES; i++) { |
---|
623 | if (probe_field[i]) { |
---|
624 | mp_main->get_stc()->sondentopf->put_Sonde(probe_field[i], mismatches[i], mismatches[i] + mp_gl_awars.outside_mismatches_difference); |
---|
625 | } |
---|
626 | } |
---|
627 | mp_main->get_stc()->sondentopf->gen_color_hash(mp_gl_awars.no_of_probes); |
---|
628 | |
---|
629 | { |
---|
630 | GB_push_transaction(scr->gb_main); |
---|
631 | GB_HASH *col_hash = mp_main->get_stc()->sondentopf->get_color_hash(); |
---|
632 | for (gb_species = GBT_first_species(scr->gb_main); gb_species; gb_species = GBT_next_species(gb_species)) { |
---|
633 | GB_write_flag(gb_species, GBS_read_hash(col_hash, GBT_read_name(gb_species)) > AWT_GC_BLACK); |
---|
634 | } |
---|
635 | } |
---|
636 | GB_pop_transaction(scr->gb_main); |
---|
637 | |
---|
638 | GB_transaction ta(scr->gb_main); |
---|
639 | |
---|
640 | if (scr->gb_main) |
---|
641 | scr->gfx->update(scr->gb_main); |
---|
642 | |
---|
643 | scr->refresh(); |
---|
644 | |
---|
645 | for (i=0; i<MAXMISMATCHES; i++) |
---|
646 | free(probe_field[i]); |
---|
647 | |
---|
648 | delete [] probe_field; |
---|
649 | delete [] mismatches; |
---|
650 | |
---|
651 | MP_normal_colors_in_tree(aww); |
---|
652 | } |
---|
653 | |
---|
654 | void MP_Comment(AW_window *, AW_CL cl_com) { |
---|
655 | // Comment fuer Auswahl eintragen |
---|
656 | |
---|
657 | AW_root *awr = mp_main->get_aw_root(); |
---|
658 | char *selprobes = awr->awar(MP_AWAR_RESULTPROBES)->read_string(); |
---|
659 | char *new_val = MP_get_probes(selprobes); |
---|
660 | |
---|
661 | if (new_val && new_val[0]) { |
---|
662 | char *new_list_string; |
---|
663 | { |
---|
664 | char *edited_comment = NULL; |
---|
665 | const char *comment = NULL; |
---|
666 | |
---|
667 | if (cl_com) { |
---|
668 | comment = (char*)cl_com; |
---|
669 | } |
---|
670 | else { |
---|
671 | edited_comment = awr->awar(MP_AWAR_RESULTPROBESCOMMENT)->read_string(); |
---|
672 | for (int i = 0; edited_comment[i]; ++i) { // remove all '#' from new comment |
---|
673 | if (edited_comment[i] == SEPARATOR[0]) { |
---|
674 | edited_comment[i] = '|'; |
---|
675 | } |
---|
676 | } |
---|
677 | } |
---|
678 | |
---|
679 | char *misms = MP_get_comment(2, selprobes); |
---|
680 | char *ecol = MP_get_comment(3, selprobes); |
---|
681 | |
---|
682 | new_list_string = GBS_global_string_copy("%-20s" SEPARATOR "%s" SEPARATOR "%s" SEPARATOR "%s", |
---|
683 | comment, misms, ecol, new_val); |
---|
684 | free(ecol); |
---|
685 | free(misms); |
---|
686 | free(edited_comment); |
---|
687 | } |
---|
688 | |
---|
689 | { |
---|
690 | bool autoadvance = awr->awar(MP_AWAR_AUTOADVANCE)->read_int(); |
---|
691 | |
---|
692 | if (autoadvance) result_probes_list->move_selection(1); |
---|
693 | |
---|
694 | result_probes_list->delete_value(selprobes); |
---|
695 | result_probes_list->insert(new_list_string, new_list_string); |
---|
696 | result_probes_list->update(); |
---|
697 | |
---|
698 | if (!autoadvance) awr->awar(MP_AWAR_RESULTPROBES)->write_string(new_list_string); |
---|
699 | } |
---|
700 | free(new_list_string); |
---|
701 | } |
---|
702 | |
---|
703 | free(new_val); |
---|
704 | free(selprobes); |
---|
705 | } |
---|
706 | |
---|
707 | void MP_selected_chosen(AW_window */*aww*/) { |
---|
708 | AW_root *aw_root = mp_main->get_aw_root(); |
---|
709 | char *selected = aw_root->awar(MP_AWAR_SELECTEDPROBES)->read_string(); |
---|
710 | if (selected && selected[0]) { |
---|
711 | char *probe = MP_get_comment(3, selected); |
---|
712 | if (probe) { |
---|
713 | aw_root->awar(MP_AWAR_ECOLIPOS)->write_int(atoi(probe)); |
---|
714 | free(probe); |
---|
715 | |
---|
716 | if (probe) { |
---|
717 | probe = MP_get_comment(1, selected); |
---|
718 | aw_root->awar(MP_AWAR_QUALITY)->write_int(atoi(probe)); |
---|
719 | free(probe); |
---|
720 | |
---|
721 | if (probe) { |
---|
722 | probe = MP_get_comment(2, selected); |
---|
723 | aw_root->awar(MP_AWAR_SINGLEMISMATCHES)->write_int(atoi(probe)); |
---|
724 | free(probe); |
---|
725 | |
---|
726 | if (probe) { |
---|
727 | probe = MP_get_probes(selected); |
---|
728 | aw_root->awar_string(MP_AWAR_SEQIN)->write_string(MP_get_probes(probe)); |
---|
729 | free(probe); |
---|
730 | return; |
---|
731 | } |
---|
732 | } |
---|
733 | } |
---|
734 | } |
---|
735 | aw_message("can't parse entry"); |
---|
736 | } |
---|
737 | } |
---|
738 | |
---|
739 | void MP_group_all_except_marked(AW_window * /* aww */) { |
---|
740 | AWT_canvas *scr = mp_main->get_canvas(); |
---|
741 | NT_group_not_marked_cb(0, scr); |
---|
742 | } |
---|
743 | |
---|
744 | void MP_normal_colors_in_tree(AW_window */*aww*/) { |
---|
745 | AWT_canvas *scr = mp_main->get_canvas(); |
---|
746 | GB_transaction ta(scr->gb_main); |
---|
747 | |
---|
748 | AWT_graphic_tree *tree = AWT_TREE(scr); |
---|
749 | if (tree) { |
---|
750 | AP_tree *root = tree->get_root_node(); |
---|
751 | if (root) { |
---|
752 | root->uncolorize(); |
---|
753 | if (scr->gb_main) scr->gfx->update(scr->gb_main); |
---|
754 | scr->refresh(); |
---|
755 | } |
---|
756 | } |
---|
757 | } |
---|
758 | |
---|
759 | void MP_delete_selected(UNFIXED, AW_selection_list *sellist) { |
---|
760 | if (!sellist->default_is_selected()) { |
---|
761 | int idx = sellist->get_index_of_selected(); |
---|
762 | sellist->delete_element_at(idx); |
---|
763 | sellist->select_element_at(idx); |
---|
764 | sellist->update(); |
---|
765 | } |
---|
766 | } |
---|
767 | |
---|
768 | |
---|
769 | char *MP_get_comment(int which, const char *str) { |
---|
770 | // Parses information from strings like "val1#val2#val3#probes". |
---|
771 | // 'which' == 1 -> 'val1' |
---|
772 | // 'which' == 2 -> 'val2' |
---|
773 | // ... |
---|
774 | // Values may be present or not (i.e. 'probes', 'val1#probes', ... are also valid as 'str') |
---|
775 | |
---|
776 | char *result = NULL; |
---|
777 | const char *numsign = strchr(str, '#'); |
---|
778 | |
---|
779 | mp_assert(which >= 1); |
---|
780 | |
---|
781 | if (numsign) { |
---|
782 | if (which == 1) { |
---|
783 | result = GB_strpartdup(str, numsign-1); |
---|
784 | } |
---|
785 | else { |
---|
786 | result = MP_get_comment(which-1, numsign+1); |
---|
787 | } |
---|
788 | } |
---|
789 | |
---|
790 | return result; |
---|
791 | } |
---|
792 | |
---|
793 | void MP_result_chosen(AW_window */*aww*/) { |
---|
794 | AW_root *aw_root = mp_main->get_aw_root(); |
---|
795 | char *str = aw_root->awar(MP_AWAR_RESULTPROBES)->read_as_string(); |
---|
796 | char *new_str; |
---|
797 | |
---|
798 | new_str = MP_get_comment(1, str); |
---|
799 | |
---|
800 | aw_root->awar(MP_AWAR_RESULTPROBESCOMMENT)->write_string(new_str); |
---|
801 | free(str); |
---|
802 | free(new_str); |
---|
803 | } |
---|
804 | |
---|
805 | |
---|
806 | |
---|
807 | // |
---|
808 | // functions concerning the server |
---|
809 | // |
---|
810 | |
---|
811 | int MP_init_local_com_struct() |
---|
812 | { |
---|
813 | const char *user = GB_getenvUSER(); |
---|
814 | |
---|
815 | if (aisc_create(mp_pd_gl.link, PT_MAIN, mp_pd_gl.com, |
---|
816 | MAIN_LOCS, PT_LOCS, mp_pd_gl.locs, |
---|
817 | LOCS_USER, user, |
---|
818 | NULL)) { |
---|
819 | return 1; |
---|
820 | } |
---|
821 | return 0; |
---|
822 | } |
---|
823 | |
---|
824 | const char *MP_probe_pt_look_for_server() { |
---|
825 | const char *server_tag = GBS_ptserver_tag(mp_gl_awars.ptserver); |
---|
826 | GB_ERROR error = arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag); |
---|
827 | |
---|
828 | if (error) { |
---|
829 | aw_message(error); |
---|
830 | return 0; |
---|
831 | } |
---|
832 | return GBS_read_arb_tcp(server_tag); |
---|
833 | } |
---|
834 | |
---|
835 | // -------------------------------------------------------------------------------- |
---|
836 | |
---|
837 | #ifdef UNIT_TESTS |
---|
838 | |
---|
839 | #include <test_unit.h> |
---|
840 | |
---|
841 | #define MP_GET_COMMENT_EQUAL(which, str, expect) \ |
---|
842 | do { \ |
---|
843 | char *got = MP_get_comment(which, str); \ |
---|
844 | TEST_EXPECT_EQUAL(got, expect); \ |
---|
845 | free(got); \ |
---|
846 | } while(0) \ |
---|
847 | |
---|
848 | #define MP_GET_PROBES_EQUAL(str, expect) \ |
---|
849 | do { \ |
---|
850 | char *got = MP_get_probes(str); \ |
---|
851 | TEST_EXPECT_EQUAL(got, expect); \ |
---|
852 | free(got); \ |
---|
853 | } while(0) \ |
---|
854 | |
---|
855 | void TEST_MP_get_comment_and_probes() { |
---|
856 | char *probes_only = strdup("ACGT TGCA ATCG"); |
---|
857 | char *probes_comment = strdup("val1#val2#val3#ACGT TGCA ATCG"); |
---|
858 | char *probes_1 = strdup("one# \t ACGT TGCA ATCG"); |
---|
859 | char *probes_2 = strdup("one#two#\tACGT TGCA ATCG"); |
---|
860 | |
---|
861 | MP_GET_PROBES_EQUAL(probes_only, "ACGT TGCA ATCG"); |
---|
862 | MP_GET_PROBES_EQUAL(probes_comment, "ACGT TGCA ATCG"); |
---|
863 | MP_GET_PROBES_EQUAL(probes_1, "ACGT TGCA ATCG"); |
---|
864 | MP_GET_PROBES_EQUAL(probes_2, "ACGT TGCA ATCG"); |
---|
865 | |
---|
866 | MP_GET_COMMENT_EQUAL(1, probes_comment, "val1"); |
---|
867 | MP_GET_COMMENT_EQUAL(2, probes_comment, "val2"); |
---|
868 | MP_GET_COMMENT_EQUAL(3, probes_comment, "val3"); |
---|
869 | |
---|
870 | MP_GET_COMMENT_EQUAL(1, probes_only, (const char *)NULL); |
---|
871 | MP_GET_COMMENT_EQUAL(2, probes_only, (const char *)NULL); |
---|
872 | MP_GET_COMMENT_EQUAL(3, probes_only, (const char *)NULL); |
---|
873 | |
---|
874 | MP_GET_COMMENT_EQUAL(1, probes_1, "one"); |
---|
875 | MP_GET_COMMENT_EQUAL(2, probes_1, (const char *)NULL); |
---|
876 | MP_GET_COMMENT_EQUAL(3, probes_1, (const char *)NULL); |
---|
877 | |
---|
878 | MP_GET_COMMENT_EQUAL(1, probes_2, "one"); |
---|
879 | MP_GET_COMMENT_EQUAL(2, probes_2, "two"); |
---|
880 | MP_GET_COMMENT_EQUAL(3, probes_2, (const char *)NULL); |
---|
881 | |
---|
882 | free(probes_2); |
---|
883 | free(probes_1); |
---|
884 | free(probes_comment); |
---|
885 | free(probes_only); |
---|
886 | } |
---|
887 | |
---|
888 | #endif // UNIT_TESTS |
---|