|
Last change
on this file was
19409,
checked in by westram, 20 months ago
|
- mostly cosmetic changes to SEQ_QUALITY:
- compact else-if cascades.
- avoid using abs() repeatedly in cascades
- unwrap lines.
- use GB_end_transaction.
- whitespace fixes.
|
|
File size:
2.1 KB
|
| 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, GBDATA *gb_quality) { |
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| 17 | char c; |
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| 18 | |
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| 19 | for (int i = 0; i < length; i++) { |
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| 20 | c = iupac[i]; |
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| 21 | switch (c) { |
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| 22 | case 'R': |
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| 23 | number++; |
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| 24 | iupac_value = iupac_value + 2; |
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| 25 | break; |
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| 26 | case 'Y': |
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| 27 | number++; |
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| 28 | iupac_value = iupac_value + 3; |
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| 29 | break; |
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| 30 | case 'M': |
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| 31 | number++; |
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| 32 | iupac_value = iupac_value + 2; |
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| 33 | break; |
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| 34 | case 'K': |
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| 35 | number++; |
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| 36 | iupac_value = iupac_value + 3; |
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| 37 | break; |
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| 38 | case 'W': |
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| 39 | number++; |
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| 40 | iupac_value = iupac_value + 3; |
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| 41 | break; |
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| 42 | case 'S': |
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| 43 | number++; |
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| 44 | iupac_value = iupac_value + 2; |
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| 45 | break; |
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| 46 | case 'B': |
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| 47 | number++; |
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| 48 | iupac_value = iupac_value + 4; |
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| 49 | break; |
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| 50 | case 'D': |
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| 51 | number++; |
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| 52 | iupac_value = iupac_value + 4; |
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| 53 | break; |
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| 54 | case 'H': |
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| 55 | number++; |
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| 56 | iupac_value = iupac_value + 4; |
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| 57 | break; |
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| 58 | case 'V': |
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| 59 | number++; |
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| 60 | iupac_value = iupac_value + 3; |
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| 61 | break; |
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| 62 | case 'N': |
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| 63 | number++; |
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| 64 | iupac_value = iupac_value + 5; |
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| 65 | break; |
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| 66 | } |
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| 67 | } |
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| 68 | percent = (100 * number) / length; |
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| 69 | |
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| 70 | GBDATA *gb_result1 = GB_search(gb_quality, "iupac_value", GB_INT); |
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| 71 | seq_assert(gb_result1); |
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| 72 | GB_write_int(gb_result1, iupac_value); |
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| 73 | } |
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| 74 | |
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