| 1 | // ================================================================= // |
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| 2 | // // |
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| 3 | // File : consensus.h // |
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| 4 | // Purpose : interface for consensus calculation // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in September 2015 // |
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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 | #ifndef CONSENSUS_H |
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| 12 | #define CONSENSUS_H |
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| 13 | |
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| 14 | #ifndef AW_BASE_HXX |
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| 15 | #include <aw_base.hxx> |
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| 16 | #endif |
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| 17 | #ifndef _GLIBCXX_ALGORITHM |
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| 18 | #include <algorithm> |
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| 19 | #endif |
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| 20 | |
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| 21 | #define CAS_INTERNAL -1 |
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| 22 | #define CAS_NTREE 1 |
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| 23 | #define CAS_EDIT4 2 |
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| 24 | |
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| 25 | #ifndef CONSENSUS_AWAR_SOURCE |
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| 26 | # error you need to define CONSENSUS_AWAR_SOURCE before including consensus.h (allowed values: CAS_NTREE, CAS_EDIT4) |
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| 27 | #endif |
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| 28 | |
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| 29 | struct ConsensusBuildParams { |
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| 30 | bool countgaps; // count gaps? (otherwise they are completely ignored) |
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| 31 | int gapbound; // limit in % for gaps. If more gaps occur -> '-' |
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| 32 | bool group; // whether to group characters (NUC: using ambiguous IUPAC codes; AMINO: using amino groups) |
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| 33 | int considbound; // limit in %. Bases occurring that often are used to create ambiguity codes (other bases are ignored). gaps are ignored when checking this limit. |
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| 34 | int upper; // limit in %. If explicit base (or ambiguity code) occurs that often -> use upper case character |
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| 35 | int lower; // limit in %. If explicit base (or ambiguity code) occurs that often -> use lower case character. Otherwise use '.' |
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| 36 | |
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| 37 | static void force_in_range(int low, int& val, int high) { |
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| 38 | val = std::min(std::max(low, val), high); |
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| 39 | } |
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| 40 | |
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| 41 | void make_valid() { |
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| 42 | force_in_range(0, gapbound, 100); |
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| 43 | force_in_range(0, considbound, 100); |
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| 44 | force_in_range(0, upper, 100); |
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| 45 | force_in_range(0, lower, 100); |
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| 46 | } |
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| 47 | |
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| 48 | #if (CONSENSUS_AWAR_SOURCE == CAS_NTREE) |
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| 49 | ConsensusBuildParams(AW_root *awr) |
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| 50 | : countgaps (awr->awar(AWAR_CONSENSUS_COUNTGAPS)->read_int()), |
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| 51 | gapbound (awr->awar(AWAR_CONSENSUS_GAPBOUND)->read_int()), |
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| 52 | group (awr->awar(AWAR_CONSENSUS_GROUP)->read_int()), |
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| 53 | considbound(awr->awar(AWAR_CONSENSUS_CONSIDBOUND)->read_int()), |
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| 54 | upper (awr->awar(AWAR_CONSENSUS_UPPER)->read_int()), |
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| 55 | lower (awr->awar(AWAR_CONSENSUS_LOWER)->read_int()) |
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| 56 | { |
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| 57 | make_valid(); |
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| 58 | } |
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| 59 | #else |
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| 60 | # if (CONSENSUS_AWAR_SOURCE == CAS_EDIT4) |
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| 61 | ConsensusBuildParams(AW_root *awr) |
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| 62 | : countgaps (awr->awar(ED4_AWAR_CONSENSUS_COUNTGAPS)->read_int()), |
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| 63 | gapbound (awr->awar(ED4_AWAR_CONSENSUS_GAPBOUND)->read_int()), |
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| 64 | group (awr->awar(ED4_AWAR_CONSENSUS_GROUP)->read_int()), |
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| 65 | considbound(awr->awar(ED4_AWAR_CONSENSUS_CONSIDBOUND)->read_int()), |
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| 66 | upper (awr->awar(ED4_AWAR_CONSENSUS_UPPER)->read_int()), |
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| 67 | lower (awr->awar(ED4_AWAR_CONSENSUS_LOWER)->read_int()) |
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| 68 | { |
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| 69 | make_valid(); |
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| 70 | } |
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| 71 | # else |
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| 72 | # if (CONSENSUS_AWAR_SOURCE == CAS_INTERNAL) |
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| 73 | ConsensusBuildParams(AW_root *awr); // produce link error if used |
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| 74 | # else |
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| 75 | # error CONSENSUS_AWAR_SOURCE has invalid value |
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| 76 | # endif |
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| 77 | # endif |
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| 78 | #endif |
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| 79 | |
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| 80 | #if defined(UNIT_TESTS) // UT_DIFF |
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| 81 | ConsensusBuildParams() // uses defaults of EDIT4 awars |
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| 82 | : countgaps(true), |
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| 83 | gapbound(60), |
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| 84 | group(1), |
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| 85 | considbound(30), |
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| 86 | upper(95), |
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| 87 | lower(70) |
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| 88 | { |
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| 89 | make_valid(); |
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| 90 | } |
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| 91 | #endif |
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| 92 | }; |
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| 93 | |
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| 94 | #else |
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| 95 | #error consensus.h included twice |
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| 96 | #endif // CONSENSUS_H |
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