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Last change
on this file was
6490,
checked in by westram, 16 years ago
|
- moved a few types to arbdb_base.h
- only use arbdb_base.h or arbdb.h where possible
- global included cleanup
- added MBI headers to many files
- moved SQ_ambiguities.SQ_count_ambiguities() to separate object
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|
File size:
2.2 KB
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| Line | |
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| 1 | // ============================================================= // |
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| 2 | // // |
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| 3 | // File : SQ_ambiguities.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 "SQ_ambiguities.h" |
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| 12 | #include <arbdb.h> |
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| 13 | |
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| 14 | using namespace std; |
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| 15 | |
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| 16 | void SQ_ambiguities::SQ_count_ambiguities(const char *iupac, int length, |
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| 17 | GBDATA * gb_quality) { |
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| 18 | char c; |
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| 19 | |
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| 20 | for (int i = 0; i < length; i++) { |
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| 21 | c = iupac[i]; |
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| 22 | switch (c) { |
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| 23 | case 'R': |
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| 24 | number++; |
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| 25 | iupac_value = iupac_value + 2; |
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| 26 | break; |
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| 27 | case 'Y': |
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| 28 | number++; |
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| 29 | iupac_value = iupac_value + 3; |
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| 30 | break; |
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| 31 | case 'M': |
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| 32 | number++; |
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| 33 | iupac_value = iupac_value + 2; |
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| 34 | break; |
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| 35 | case 'K': |
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| 36 | number++; |
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| 37 | iupac_value = iupac_value + 3; |
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| 38 | break; |
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| 39 | case 'W': |
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| 40 | number++; |
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| 41 | iupac_value = iupac_value + 3; |
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| 42 | break; |
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| 43 | case 'S': |
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| 44 | number++; |
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| 45 | iupac_value = iupac_value + 2; |
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| 46 | break; |
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| 47 | case 'B': |
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| 48 | number++; |
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| 49 | iupac_value = iupac_value + 4; |
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| 50 | break; |
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| 51 | case 'D': |
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| 52 | number++; |
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| 53 | iupac_value = iupac_value + 4; |
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| 54 | break; |
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| 55 | case 'H': |
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| 56 | number++; |
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| 57 | iupac_value = iupac_value + 4; |
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| 58 | break; |
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| 59 | case 'V': |
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| 60 | number++; |
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| 61 | iupac_value = iupac_value + 3; |
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| 62 | break; |
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| 63 | case 'N': |
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| 64 | number++; |
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| 65 | iupac_value = iupac_value + 5; |
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| 66 | break; |
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| 67 | } |
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| 68 | } |
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| 69 | percent = (100 * number) / length; |
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| 70 | |
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| 71 | GBDATA *gb_result1 = GB_search(gb_quality, "iupac_value", GB_INT); |
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| 72 | seq_assert(gb_result1); |
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| 73 | GB_write_int(gb_result1, iupac_value); |
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| 74 | } |
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| 75 | |
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