1 | // =============================================================== // |
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2 | // // |
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3 | // File : phylo.hxx // |
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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 | #ifndef PHYLO_HXX |
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12 | #define PHYLO_HXX |
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13 | |
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14 | #ifndef PH_FILTER_HXX |
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15 | #include "PH_filter.hxx" |
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16 | #endif |
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17 | #ifndef AW_BASE_HXX |
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18 | #include <aw_base.hxx> |
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19 | #endif |
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20 | #ifndef ARB_ASSERT_H |
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21 | #include <arb_assert.h> |
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22 | #endif |
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23 | |
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24 | #define ph_assert(cond) arb_assert(cond) |
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25 | |
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26 | #define AWAR_PHYLO_ALIGNMENT "tmp/phyl/alignment" |
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27 | #define AWAR_PHYLO_FILTER_FILTER "phyl/filter/filter" |
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28 | |
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29 | #define AWAR_PHYLO_FILTER_STARTCOL "phyl/filter/startcol" |
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30 | #define AWAR_PHYLO_FILTER_STOPCOL "phyl/filter/stopcol" |
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31 | #define AWAR_PHYLO_FILTER_MINHOM "phyl/filter/minhom" |
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32 | #define AWAR_PHYLO_FILTER_MAXHOM "phyl/filter/maxhom" |
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33 | #define AWAR_PHYLO_FILTER_DOT "phyl/filter/point" |
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34 | #define AWAR_PHYLO_FILTER_MINUS "phyl/filter/minus" |
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35 | #define AWAR_PHYLO_FILTER_AMBIG "phyl/filter/rest" |
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36 | #define AWAR_PHYLO_FILTER_LOWER "phyl/filter/lower" |
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37 | #define AWAR_PHYLO_FILTER_AUTOCALC "phyl/filter/autocalc" |
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38 | |
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39 | #define AWAR_PHYLO_MARKERLINENAME "tmp/phylo/markerlinename" |
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40 | |
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41 | enum FilterMode { |
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42 | DONT_COUNT, |
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43 | SKIP_COLUMN_IF_MAX, |
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44 | SKIP_COLUMN_IF_OCCUR, |
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45 | COUNT_DONT_USE_MAX, |
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46 | TREAT_AS_UPPERCASE, |
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47 | TREAT_AS_REGULAR, |
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48 | |
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49 | // Note: enum values are saved in properties (do not modify w/o need!) |
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50 | // update on changes: PH_main.cxx@filter_text |
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51 | }; |
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52 | const int FILTER_MODES = TREAT_AS_REGULAR+1; |
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53 | |
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54 | |
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55 | #define PH_DB_CACHE_SIZE 2000000 |
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56 | |
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57 | enum { |
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58 | PH_GC_SEQUENCE, |
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59 | PH_GC_MARKER, |
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60 | PH_GC_NOT_MARKER, |
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61 | PH_GC_DRAG |
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62 | }; |
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63 | |
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64 | enum { |
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65 | PH_GC_BOTTOM_TEXT, |
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66 | PH_GC_BOTTOM_DRAG |
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67 | }; |
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68 | |
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69 | void PH_create_filter_variables(AW_root *aw_root, AW_default default_file, GBDATA *gb_main); |
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70 | AW_window *PH_create_filter_window(AW_root *aw_root); |
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71 | |
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72 | enum display_type { |
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73 | DISP_NONE, // initial |
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74 | DISP_SPECIES, // after startup, filter not calculated yet |
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75 | DISP_FILTER, // after filter has been calculated |
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76 | }; |
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77 | |
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78 | // --------------------------- |
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79 | // class definitions |
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80 | |
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81 | class PH_root : virtual Noncopyable { |
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82 | char *use; |
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83 | GBDATA *gb_main; |
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84 | |
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85 | static PH_root *SINGLETON; |
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86 | |
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87 | public: |
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88 | |
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89 | PH_root() |
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90 | : use(NULL), |
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91 | gb_main(NULL) |
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92 | { |
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93 | ph_assert(!SINGLETON); |
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94 | SINGLETON = this; |
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95 | } |
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96 | ~PH_root() { |
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97 | ph_assert(this == SINGLETON); |
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98 | SINGLETON = NULL; |
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99 | free(use); |
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100 | } |
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101 | |
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102 | GB_ERROR open(const char *db_server); |
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103 | GBDATA *get_gb_main() const { ph_assert(gb_main); return gb_main; } |
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104 | }; |
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105 | |
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106 | |
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107 | class PHDATA : virtual Noncopyable { |
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108 | // connection to database |
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109 | // pointers to all elements and important values of the database |
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110 | |
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111 | struct PHENTRY : virtual Noncopyable { |
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112 | unsigned int key; |
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113 | char *name; |
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114 | char *full_name; |
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115 | GBDATA *gb_species_data_ptr; |
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116 | PHENTRY *next; |
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117 | PHENTRY *prev; |
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118 | |
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119 | PHENTRY() |
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120 | : key(0), |
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121 | name(NULL), |
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122 | full_name(NULL), |
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123 | gb_species_data_ptr(NULL), |
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124 | next(NULL), |
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125 | prev(NULL) |
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126 | {} |
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127 | |
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128 | ~PHENTRY() { |
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129 | ph_assert(0); // @@@ why not called? |
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130 | } |
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131 | }; |
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132 | |
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133 | unsigned int last_key_number; |
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134 | long seq_len; |
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135 | |
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136 | AW_root *aw_root; // only link |
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137 | PH_root *ph_root; // only link |
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138 | |
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139 | PHENTRY *entries; |
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140 | |
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141 | char *unload(); |
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142 | |
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143 | public: |
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144 | GBDATA *get_gb_main() { return ph_root->get_gb_main(); } |
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145 | |
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146 | char *use; // @@@ elim (PH_root has same field) |
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147 | |
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148 | PHENTRY **hash_elements; |
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149 | unsigned int nentries; // total number of entries |
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150 | |
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151 | static PHDATA *ROOT; // 'global' pointer |
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152 | |
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153 | float *markerline; |
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154 | |
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155 | PHDATA(AW_root *aw_root_, PH_root *ph_root_) |
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156 | : last_key_number(0), |
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157 | seq_len(0), |
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158 | aw_root(aw_root_), |
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159 | ph_root(ph_root_), |
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160 | entries(NULL), |
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161 | use(NULL), |
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162 | hash_elements(NULL), |
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163 | nentries(0), |
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164 | markerline(NULL) |
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165 | {} |
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166 | ~PHDATA() { |
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167 | unload(); |
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168 | } |
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169 | |
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170 | char *load(char*& use); // open database and get pointers to it |
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171 | |
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172 | long get_seq_len() { return seq_len; } |
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173 | }; |
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174 | |
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175 | #else |
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176 | #error phylo.hxx included twice |
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177 | #endif // PHYLO_HXX |
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