| 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 | #ifndef _GLIBCXX_CMATH |
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| 16 | #include <cmath> |
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| 17 | #endif |
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| 18 | |
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| 19 | #ifndef ARB_ASSERT_H |
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| 20 | #include <arb_assert.h> |
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| 21 | #endif |
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| 22 | #define seq_assert(bed) arb_assert(bed) |
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| 23 | |
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| 24 | class SQ_physical_layout { |
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| 25 | double temp; |
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| 26 | double count_bases; |
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| 27 | double count_scores; |
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| 28 | double count_dots; |
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| 29 | double GC; |
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| 30 | double GC_proportion; |
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| 31 | int percent_bases; |
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| 32 | int count_bases2; |
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| 33 | |
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| 34 | int roundme(double value); |
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| 35 | |
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| 36 | public: |
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| 37 | SQ_physical_layout(); |
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| 38 | void SQ_calc_physical_layout(const char *sequence, int size, GBDATA *gb_quality_ali); |
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| 39 | int SQ_get_number_of_bases() const; |
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| 40 | double SQ_get_gc_proportion() const; |
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| 41 | }; |
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| 42 | |
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| 43 | SQ_physical_layout::SQ_physical_layout() { |
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| 44 | temp = 0; |
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| 45 | count_bases = 0; |
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| 46 | count_scores = 0; |
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| 47 | count_dots = 0; |
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| 48 | percent_bases = 0; |
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| 49 | GC = 0; |
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| 50 | GC_proportion = 0; |
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| 51 | count_bases2 = 0; |
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| 52 | } |
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| 53 | |
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| 54 | int SQ_physical_layout::roundme(double value) { |
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| 55 | int x; |
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| 56 | value += 0.5; |
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| 57 | x = (int) floor(value); |
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| 58 | return x; |
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| 59 | } |
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| 60 | |
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| 61 | void SQ_physical_layout::SQ_calc_physical_layout(const char *sequence, int size, GBDATA *gb_quality_ali) { |
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| 62 | count_bases = size; |
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| 63 | |
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| 64 | for (int i = 0; i < size; i++) { |
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| 65 | switch (sequence[i]) { |
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| 66 | case '-': // calculate number of dots and spaces |
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| 67 | count_bases--; |
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| 68 | count_scores++; |
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| 69 | break; |
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| 70 | case '.': |
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| 71 | count_bases--; |
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| 72 | count_dots++; |
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| 73 | break; |
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| 74 | case 'G': // calculate GC layout of sequence |
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| 75 | case 'g': |
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| 76 | GC++; |
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| 77 | break; |
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| 78 | case 'C': |
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| 79 | case 'c': |
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| 80 | GC++; |
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| 81 | break; |
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| 82 | } |
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| 83 | } |
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| 84 | |
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| 85 | // calculate layout in percent |
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| 86 | if (GC != 0) { |
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| 87 | GC_proportion = GC / count_bases; |
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| 88 | } |
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| 89 | temp = 100 - (100 * ((count_scores + count_dots) / size)); |
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| 90 | percent_bases = roundme(temp); |
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| 91 | count_bases2 = roundme(count_bases); |
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| 92 | |
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| 93 | GBDATA *gb_result1 = GB_search(gb_quality_ali, "number_of_bases", GB_INT); |
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| 94 | seq_assert(gb_result1); |
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| 95 | GB_write_int(gb_result1, count_bases2); |
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| 96 | |
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| 97 | GBDATA *gb_result2 = GB_search(gb_quality_ali, "percent_of_bases", GB_INT); |
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| 98 | seq_assert(gb_result2); |
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| 99 | GB_write_int(gb_result2, percent_bases); |
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| 100 | |
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| 101 | GBDATA *gb_result3 = GB_search(gb_quality_ali, "GC_proportion", GB_FLOAT); |
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| 102 | seq_assert(gb_result3); |
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| 103 | GB_write_float(gb_result3, GC_proportion); |
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| 104 | } |
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| 105 | |
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| 106 | inline int SQ_physical_layout::SQ_get_number_of_bases() const { |
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| 107 | int i; |
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| 108 | i = count_bases2; |
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| 109 | return i; |
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| 110 | } |
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| 111 | |
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| 112 | inline double SQ_physical_layout::SQ_get_gc_proportion() const { |
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| 113 | double i; |
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| 114 | i = GC_proportion; |
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| 115 | return i; |
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| 116 | } |
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