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#ifndef CODON_UTILS_H
#define CODON_UTILS_H
#include <iostream>
#include "nucleotide.h"
#include "codon.h"
#include "amino.h"
#include "logFile.h"
#include "fastaFormat.h"
#include "clustalFormat.h"
#include "recognizeFormat.h"
#include "someUtil.h"
#include "definitions.h"
#include "sequenceContainer.h"
#include "stochasticProcess.h"
#include "wYangModel.h"
#include "evaluateCharacterFreq.h"
#include "geneticCodeHolder.h"
#include "codon.h"
using namespace std;
void checkInputSeqLength(string codonFile);
sequenceContainer convertCodonToAmino(sequenceContainer &codonSc,codon *codonAlph);
vector<vector<int> > create7ColorValues();
void outToRasmolFile(string fileName,vector<int>& color4Site);
MDOUBLE getMatricesNormalizationFactor(vector<stochasticProcess> & spVec,const distribution * forceDistr);
void normalizeMatrices(vector<stochasticProcess> & spVec,const distribution * forceDistr);
Vdouble freqCodonF3x4(const sequenceContainer &nucSc,codon *coAlph);
void kaks2Color(const Vdouble & kaksVec,const Vdouble &lowerBoundV,
const sequence & refSeq, string fileName,codon *co);
#endif
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