1 | // ==================================================================== // |
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2 | // // |
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3 | // File : SQ_physical_layout.h // |
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4 | // Purpose : Class used for calculation of the phys. layout of seq. // |
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5 | // // |
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6 | // // |
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7 | // Coded by Juergen Huber in July 2003 - February 2004 // |
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8 | // Coded by Kai Bader (baderk@in.tum.de) in 2007 - 2008 // |
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9 | // Copyright Department of Microbiology (Technical University Munich) // |
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10 | // // |
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11 | // Visit our web site at: http://www.arb-home.de/ // |
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12 | // // |
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13 | // ==================================================================== // |
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14 | |
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15 | |
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16 | #ifndef ARB_ASSERT_H |
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17 | #include <arb_assert.h> |
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18 | #endif |
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19 | #define seq_assert(bed) arb_assert(bed) |
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20 | |
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21 | class SQ_physical_layout { |
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22 | public: |
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23 | SQ_physical_layout(); |
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24 | void SQ_calc_physical_layout(const char *sequence, int size, |
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25 | GBDATA * gb_quality_ali); |
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26 | int SQ_get_number_of_bases() const; |
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27 | double SQ_get_gc_proportion() const; |
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28 | private: |
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29 | int roundme(double value); |
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30 | double temp; |
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31 | double count_bases; |
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32 | double count_scores; |
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33 | double count_dots; |
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34 | double GC; |
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35 | double GC_proportion; |
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36 | int percent_bases; |
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37 | int count_bases2; |
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38 | }; |
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39 | |
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40 | SQ_physical_layout::SQ_physical_layout() { |
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41 | temp = 0; |
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42 | count_bases = 0; |
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43 | count_scores = 0; |
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44 | count_dots = 0; |
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45 | percent_bases = 0; |
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46 | GC = 0; |
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47 | GC_proportion = 0; |
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48 | count_bases2 = 0; |
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49 | } |
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50 | |
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51 | int SQ_physical_layout::roundme(double value) { |
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52 | int x; |
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53 | value += 0.5; |
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54 | x = (int) floor(value); |
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55 | return x; |
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56 | } |
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57 | |
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58 | void SQ_physical_layout::SQ_calc_physical_layout(const char *sequence, |
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59 | int size, GBDATA * gb_quality_ali) { |
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60 | count_bases = size; |
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61 | |
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62 | for (int i = 0; i < size; i++) { |
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63 | switch (sequence[i]) { |
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64 | case '-': /*calculate number of dots and spaces */ |
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65 | count_bases--; |
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66 | count_scores++; |
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67 | break; |
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68 | case '.': |
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69 | count_bases--; |
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70 | count_dots++; |
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71 | break; |
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72 | case 'G': /*calculate GC layout of sequence */ |
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73 | case 'g': |
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74 | GC++; |
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75 | break; |
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76 | case 'C': |
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77 | case 'c': |
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78 | GC++; |
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79 | break; |
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80 | } |
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81 | } |
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82 | |
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83 | /*calculate layout in percent */ |
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84 | if (GC != 0) { |
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85 | GC_proportion = GC / count_bases; |
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86 | } |
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87 | temp = 100 - (100 * ((count_scores + count_dots) / size)); |
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88 | percent_bases = roundme(temp); |
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89 | count_bases2 = roundme(count_bases); |
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90 | |
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91 | GBDATA *gb_result1 = GB_search(gb_quality_ali, "number_of_bases", GB_INT); |
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92 | seq_assert(gb_result1); |
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93 | GB_write_int(gb_result1, count_bases2); |
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94 | |
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95 | GBDATA *gb_result2 = GB_search(gb_quality_ali, "percent_of_bases", GB_INT); |
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96 | seq_assert(gb_result2); |
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97 | GB_write_int(gb_result2, percent_bases); |
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98 | |
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99 | GBDATA *gb_result3 = GB_search(gb_quality_ali, "GC_proportion", GB_FLOAT); |
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100 | seq_assert(gb_result3); |
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101 | GB_write_float(gb_result3, GC_proportion); |
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102 | } |
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103 | |
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104 | inline int SQ_physical_layout::SQ_get_number_of_bases() const { |
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105 | int i; |
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106 | i = count_bases2; |
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107 | return i; |
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108 | } |
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109 | |
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110 | inline double SQ_physical_layout::SQ_get_gc_proportion() const { |
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111 | double i; |
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112 | i = GC_proportion; |
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113 | return i; |
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114 | } |
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