1 | #ifndef PRD_DESIGN_HXX |
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2 | #define PRD_DESIGN_HXX |
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3 | |
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4 | #ifndef PRD_GLOBALS_HXX |
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5 | #include "PRD_Globals.hxx" |
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6 | #endif |
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7 | #include "PRD_Range.hxx" |
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8 | #include "PRD_Node.hxx" |
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9 | #include "PRD_Item.hxx" |
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10 | #include "PRD_Pair.hxx" |
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11 | |
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12 | #include <deque> |
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13 | |
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14 | #ifndef ARBDB_H |
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15 | #include <arbdb.h> |
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16 | #endif |
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17 | |
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18 | class PrimerDesign { |
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19 | private: |
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20 | |
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21 | // zu untersuchendes Genom |
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22 | // sequence of bases/spaces to be examined |
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23 | |
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24 | const char* sequence; |
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25 | long int seqLength; |
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26 | |
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27 | // Laenge der Primer (Anzahl der enthaltenen Basen) |
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28 | // count of bases of primers (min/max) |
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29 | Range primer_length; |
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30 | |
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31 | // Position der Primer ( [min,max) ) |
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32 | // left/right position of primers |
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33 | |
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34 | Range primer1; |
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35 | Range primer2; |
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36 | |
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37 | // Abstand der Primer (bzgl. der Basen dazwischen, <=0 = ignorieren) |
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38 | // min/max distance of primers (regading number of bases between, <=0 = ignore) |
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39 | |
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40 | Range primer_distance; |
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41 | |
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42 | // maximale Anzahl zurueckzuliefernder Primerpaare |
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43 | // max. count of returned primer pairs |
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44 | |
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45 | int max_count_primerpairs; |
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46 | |
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47 | // GC-Verhaeltniss der Primer in Prozent <=0 = ignorieren |
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48 | // GC-ratio of primers in percent <=0 = ignore |
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49 | // [ ratio = (G+C)/Basen ] |
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50 | |
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51 | Range GC_ratio; |
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52 | |
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53 | // Temperatur der Primer <=0 = ignorieren |
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54 | // temperature of primers <=0 = ignore |
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55 | // [ temperature = 4*(G+C) + 2*(A+T) ] |
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56 | |
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57 | Range temperature; |
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58 | |
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59 | // Faktoren zur Gewichtung von CG-Verhaeltniss und Temperatur bei der Bewertung von Primerpaaren |
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60 | // factors to assess the GC-ratio and temperature at the evaluation of primerpairs |
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61 | // [ 0.0 .. 1.0 ] |
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62 | |
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63 | double GC_factor; |
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64 | double temperature_factor; |
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65 | |
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66 | // wird ein Primer ausserhalb dieser Distanz nocheinmal gefunden wird das Vorkommen ignoriert ( <= 0 = eindeutig ) |
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67 | // is a primer found again out of this range its occurence is ignored ( <=0 = explict match ) |
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68 | |
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69 | int min_distance_to_next_match; |
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70 | |
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71 | // erweitern der IUPAC-Codes beim matching der sequence gegen die primerbaeume ? |
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72 | // expand IUPAC-Codes while matching sequence vs. primertrees ? |
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73 | |
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74 | bool expand_IUPAC_Codes; |
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75 | |
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76 | |
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77 | // |
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78 | // INTERNAL STUFF |
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79 | // |
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80 | static const int FORWARD = 1; |
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81 | static const int BACKWARD = -1; |
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82 | |
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83 | // primertrees |
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84 | Node* root1; |
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85 | Node* root2; |
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86 | |
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87 | // primerlists |
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88 | Item* list1; |
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89 | Item* list2; |
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90 | |
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91 | // primerpairs |
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92 | Pair* pairs; |
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93 | |
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94 | GB_ERROR error; |
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95 | unsigned long int total_node_counter_left; |
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96 | unsigned long int total_node_counter_right; |
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97 | unsigned long int primer_node_counter_left; |
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98 | unsigned long int primer_node_counter_right; |
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99 | |
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100 | public: |
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101 | PrimerDesign( const char *sequence_, long int seqLength_, |
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102 | Range pos1_, Range pos2_, Range length_, Range distance_, |
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103 | Range ratio_, Range temperature_, int min_dist_to_next_, bool expand_IUPAC_Codes_, |
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104 | int max_count_primerpairs_, double GC_factor_, double temp_factor_ ); |
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105 | PrimerDesign( const char *sequence_, long int seqLength_, |
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106 | Range pos1_, Range pos2_, Range length_, Range distance_, |
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107 | int max_count_primerpairs_, double GC_factor_, double temp_factor_ ); |
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108 | |
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109 | PrimerDesign( const char *sequence_, long int seqLength_); |
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110 | ~PrimerDesign(); |
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111 | |
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112 | void setPositionalParameters ( Range pos1_, Range pos2_, Range length_, Range distance_ ); |
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113 | void setConditionalParameters( Range ratio_, Range temperature_, int min_dist_to_next_, bool expand_IUPAC_Codes_, int max_count_primerpairs_, double GC_factor_, double temp_factor_ ); |
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114 | |
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115 | void buildPrimerTrees (); |
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116 | void printPrimerTrees (); |
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117 | |
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118 | void matchSequenceAgainstPrimerTrees (); |
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119 | |
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120 | void convertTreesToLists (); |
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121 | void printPrimerLists (); |
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122 | |
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123 | void evaluatePrimerPairs (); |
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124 | void printPrimerPairs (); |
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125 | |
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126 | void run ( int print_stages_ ); |
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127 | |
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128 | GB_ERROR get_error() const { return error; } |
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129 | |
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130 | PRD_Sequence_Pos get_max_primer_length() const { return primer_length.max(); } |
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131 | PRD_Sequence_Pos get_max_primer_pos() const { return primer2.max(); } |
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132 | const char *get_result( int num, const char *&primers, int max_primer_length, int max_position_length, int max_length_length ) const; // return 0 if no more results (primers is set to "leftPrimer,rightPrimer") |
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133 | |
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134 | public: |
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135 | static const int PRINT_RAW_TREES = 1; |
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136 | static const int PRINT_MATCHED_TREES = 2; |
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137 | static const int PRINT_PRIMER_LISTS = 4; |
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138 | static const int PRINT_PRIMER_PAIRS = 8; |
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139 | |
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140 | private: |
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141 | void init ( const char *sequence_, long int seqLength_, Range pos1_, Range pos2_, Range length_, Range distance_, Range ratio_, Range temperature_, int min_dist_to_next_, bool expand_IUPAC_Codes_, int max_count_primerpairs_, double GC_factor_, double temp_factor_ ); |
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142 | PRD_Sequence_Pos followUp ( Node *node_, std::deque<char> *primer_, int direction_ ); |
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143 | void findNextPrimer ( Node *start_at_, int depth_, int *counter_, int delivered_ ); |
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144 | int insertNode ( Node *current_, unsigned char base_, PRD_Sequence_Pos pos_, int delivered_, int offset_, int left_, int right_ ); |
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145 | void clearTree ( Node *start, int left_, int right_ ); |
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146 | bool treeContainsPrimer ( Node *start ); |
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147 | void calcGCandAT ( int &GC_, int &AT_, Node *start_at_ ); |
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148 | double evaluatePair ( Item *one_, Item *two_ ); |
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149 | void insertPair ( double rating_, Item *one_, Item *two_ ); |
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150 | |
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151 | int (*show_status_txt)(const char *msg); |
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152 | int (*show_status_double)(double gauge); |
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153 | |
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154 | inline int show_status(const char *msg) { return show_status_txt ? show_status_txt(msg) : 0; } |
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155 | inline int show_status(double gauge) { return show_status_double ? show_status_double(gauge) : 0; } |
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156 | |
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157 | public: |
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158 | void set_status_callbacks(int (*show_txt)(const char*), int (*show_double)(double)) { |
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159 | show_status_txt = show_txt; |
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160 | show_status_double = show_double; |
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161 | } |
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162 | }; |
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163 | |
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164 | |
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165 | #else |
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166 | #error PRD_Design.hxx included twice |
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167 | #endif // PRD_DESIGN_HXX |
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