|
Last change
on this file was
6490,
checked in by westram, 14 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
|
|
File size:
2.2 KB
|
| Line | |
|---|
| 1 | // ============================================================= // |
|---|
| 2 | // // |
|---|
| 3 | // File : SQ_ambiguities.cxx // |
|---|
| 4 | // Purpose : // |
|---|
| 5 | // // |
|---|
| 6 | // Institute of Microbiology (Technical University Munich) // |
|---|
| 7 | // http://www.arb-home.de/ // |
|---|
| 8 | // // |
|---|
| 9 | // ============================================================= // |
|---|
| 10 | |
|---|
| 11 | #include "SQ_ambiguities.h" |
|---|
| 12 | #include <arbdb.h> |
|---|
| 13 | |
|---|
| 14 | using namespace std; |
|---|
| 15 | |
|---|
| 16 | void SQ_ambiguities::SQ_count_ambiguities(const char *iupac, int length, |
|---|
| 17 | GBDATA * gb_quality) { |
|---|
| 18 | char c; |
|---|
| 19 | |
|---|
| 20 | for (int i = 0; i < length; i++) { |
|---|
| 21 | c = iupac[i]; |
|---|
| 22 | switch (c) { |
|---|
| 23 | case 'R': |
|---|
| 24 | number++; |
|---|
| 25 | iupac_value = iupac_value + 2; |
|---|
| 26 | break; |
|---|
| 27 | case 'Y': |
|---|
| 28 | number++; |
|---|
| 29 | iupac_value = iupac_value + 3; |
|---|
| 30 | break; |
|---|
| 31 | case 'M': |
|---|
| 32 | number++; |
|---|
| 33 | iupac_value = iupac_value + 2; |
|---|
| 34 | break; |
|---|
| 35 | case 'K': |
|---|
| 36 | number++; |
|---|
| 37 | iupac_value = iupac_value + 3; |
|---|
| 38 | break; |
|---|
| 39 | case 'W': |
|---|
| 40 | number++; |
|---|
| 41 | iupac_value = iupac_value + 3; |
|---|
| 42 | break; |
|---|
| 43 | case 'S': |
|---|
| 44 | number++; |
|---|
| 45 | iupac_value = iupac_value + 2; |
|---|
| 46 | break; |
|---|
| 47 | case 'B': |
|---|
| 48 | number++; |
|---|
| 49 | iupac_value = iupac_value + 4; |
|---|
| 50 | break; |
|---|
| 51 | case 'D': |
|---|
| 52 | number++; |
|---|
| 53 | iupac_value = iupac_value + 4; |
|---|
| 54 | break; |
|---|
| 55 | case 'H': |
|---|
| 56 | number++; |
|---|
| 57 | iupac_value = iupac_value + 4; |
|---|
| 58 | break; |
|---|
| 59 | case 'V': |
|---|
| 60 | number++; |
|---|
| 61 | iupac_value = iupac_value + 3; |
|---|
| 62 | break; |
|---|
| 63 | case 'N': |
|---|
| 64 | number++; |
|---|
| 65 | iupac_value = iupac_value + 5; |
|---|
| 66 | break; |
|---|
| 67 | } |
|---|
| 68 | } |
|---|
| 69 | percent = (100 * number) / length; |
|---|
| 70 | |
|---|
| 71 | GBDATA *gb_result1 = GB_search(gb_quality, "iupac_value", GB_INT); |
|---|
| 72 | seq_assert(gb_result1); |
|---|
| 73 | GB_write_int(gb_result1, iupac_value); |
|---|
| 74 | } |
|---|
| 75 | |
|---|
Note: See
TracBrowser
for help on using the repository browser.
