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