/usr/include/libphylo/codon.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 | // $Id: codon.h 5975 2009-03-17 08:00:37Z rubi $
#ifndef ____CODON
#define ____CODON
#include <cassert>
#include "definitions.h"
#include "errorMsg.h"
#include "someUtil.h"
#include "alphabet.h"
#include "geneticCodeHolder.h"
#include <map>
class codon;
class sequenceContainer;
class codonUtility {
public:
enum diffType {equal =0, tr, tv, twoTrs, twoTvs ,trtv, threesub};
static diffType codonDiff(const int c1, const int c2, const codon &cod);
static diffType codonDiff(const int c1, const int c2) {return _trtvDiff[c1][c2];}
enum replacementType {sameCodon=0, synonymous, non_synonymous};
static replacementType codonReplacement(const int c1, const int c2, const codon &cod);
static replacementType codonReplacement(const int c1, const int c2) {return _synNonsynDiff[c1][c2];}
enum nucDiffPlaceType {A1=0, A2, A3,C1, C2, C3, G1,G2,G3,T1,T2,T3, EQUAL, MUL_SUB};
static nucDiffPlaceType nucDiffPlace(const int fromCodon, const int targetCodon, const codon &cod);
static nucDiffPlaceType nucDiffPlace(const int fromCodon, const int targetCodon) {return _nucDiffPlace[fromCodon][targetCodon];}
enum nucsDiffType {AC=0, AG, AT, CG, CT, GT, SAME, DIFF}; //The difference between two codons: For exampe nucsDiff(ACT, ACG) returns GT. DIFF = more than one change.
static nucsDiffType nucsDiff(const int fromCodon, const int targetCodon, const codon &cod);
static nucsDiffType nucsDiff(const int fromCodon, const int targetCodon) {return _nucsDiff[fromCodon][targetCodon];}
static int aaOf(const int c1, const codon &cod);
static void initSubMatrices(const codon& cod);
//returns the number (codonCounter) and frequency (codonUsage) of each codon in the sequnece container
static void getCodonUsage(const sequenceContainer& sc, Vint& codonCounter, Vdouble& codonUsage);
static void readCodonUsage(const string& codonUsageFileName, Vdouble& codonUsage,const codon &inCodonAlpa);
//calculates the CAI for the whole MSA and for each position.
//The calculation is based on a pre-calculated codonUsage vector.
static MDOUBLE calcCodonAdaptationIndex(const sequenceContainer& sc, const Vdouble& codonUsage, Vdouble& cai4site);
private:
static vector<vector<diffType> > _trtvDiff;
static vector<vector<replacementType> > _synNonsynDiff;
static vector<vector<nucDiffPlaceType> > _nucDiffPlace;
static vector<vector<nucsDiffType> > _nucsDiff;
};
class codon : public alphabet {
public:
explicit codon(); //default constructor: reads "nuclearCode.txt"
explicit codon(const geneticCodeString& matrixFileString);
virtual ~codon() {}
// explicit codon( codon& other);
codon& operator=(const codon& other);
virtual alphabet* clone() const { return new codon(*this); }
void readMatrixFromFile(const string& matrixFileName);
const map <string,string> & geneticCode()const {return _geneticCode;}
int unknown() const {return 64;}
int gap() const {return -1;}
int size() const {return _alphabetSize;} // 3 stop codon excluded
int stringSize() const {return 3;} // 3 letter code.
vector<int> fromString(const string& str) const;
bool isStopCodon(const int in_id) const;
bool isStopCodon(const string& str) const {return isStopCodon(fromChar(str));};
bool isInitiationCodon(const int in_id) const;
bool isInitiationCodon(const string& str) const {return isInitiationCodon(fromChar(str));};
int fromChar(const string& s, const int pos=0) const;
string fromInt(const int in_id) const;
// "specific" here is not unknown, nor ambiguity, nor gap (for example, for nucleotides it will true for A,C,G, or T).
bool isSpecific(const int id) const {return (id>=0 && id < size());}
int relations(const int charInSeq, const int charToCheck) const{
if (charInSeq == -1) {
errorMsg::reportError("gaps in the sequences. Either change gaps to ? or remove gap positions");
}
else if (charInSeq == unknown()) return 1;
else if (charInSeq == charToCheck) return 1;
if (charInSeq >= _alphabetSize)
{
string err= "";
err+="charInSeq = ";
err += int2string(charInSeq);
err+= " _alphabetSize = ";
err+=int2string(_alphabetSize);
errorMsg::reportError(err);
}
assert(charInSeq < _alphabetSize);
return 0;
}
private:
void init(const geneticCodeString& matrixFileString);
private:
map <string,string> _geneticCode; //key - codon, value - amino acid
map <string,int> _codon2Int;//key string of codon int= integer value of codon
map <int,string> _initiationIndex2codon;//key: integer value of codon; value: string of initiation codon. the keys is an integer so that the value of the init codon can be found
int _alphabetSize;
};
#endif
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