Java Codons.getStateCount方法代码示例

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
public void testCodonSimulation() {
    Parameter kappa = new Parameter.Default(1, 2.0);
    Parameter omega = new Parameter.Default(1, 5.0); // Expect many more non-syn changes

    Codons codons = Codons.UNIVERSAL;
    int stateCount = codons.getStateCount();
    double[] p = new double[stateCount];
    for (int i = 0; i < stateCount; i++) {
        p[i] = 1.0 / (double) stateCount;
    }
    Parameter pi = new Parameter.Default(p);
    FrequencyModel f = new FrequencyModel(codons, pi);
    GY94CodonModel codonModel = new GY94CodonModel(codons, omega, kappa, f);

    Parameter mu = new Parameter.Default(1, 0.5);
    Parameter alpha = new Parameter.Default(1, 0.5);
    GammaSiteRateModel siteModel = new GammaSiteRateModel("gammaModel", mu, alpha, 4, null);
    siteModel.setSubstitutionModel(codonModel);
    BranchRateModel branchRateModel = new DefaultBranchRateModel();

    double analyticResult = TreeUtils.getTreeLength(tree, tree.getRoot()) * mu.getParameterValue(0);
    int nSites = 100;

    double[] synRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.SYN, codons, false); // use base 61
    double[] nonSynRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.NON_SYN, codons, false); // use base 61

    runSimulation(tree, siteModel, branchRateModel, nSites,
            new double[][] {synRegMatrix, nonSynRegMatrix}, analyticResult);

}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
private byte[] expandToBase64(Codons codonDataType, byte[] in) {
    final int stateCount = codonDataType.getStateCount();
    byte[] intermediateOut = new byte[64 * 64];
    int index = 0;
    for (int i = 0; i < stateCount; i++) {
        for (int j = i + 1; j < stateCount; j++) {
            intermediateOut[codonDataType.getCanonicalState(i) * 64
                    + codonDataType.getCanonicalState(j)] = in[index];
            index++;
        }
    }

    byte[] out = new byte[(64 * 63) / 2];
    index = 0;
    for (int i = 0; i < 64; i++) {
        for (int j = i + 1; j < 64; j++) {
            out[index] = intermediateOut[i * 64 + j];
            index++;
        }
    }
    return out;
}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
public MG94CodonModel(Codons codonDataType, Parameter alphaParameter, Parameter betaParameter,
                      FrequencyModel freqModel) {
    this(codonDataType, alphaParameter, betaParameter, freqModel,
            new DefaultEigenSystem(codonDataType.getStateCount()));
}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
public void testCodonSimulation() {
    Parameter kappa = new Parameter.Default(1, 2.0);
    Parameter omega = new Parameter.Default(1, 5.0); // Expect many more non-syn changes

    Codons codons = Codons.UNIVERSAL;
    int stateCount = codons.getStateCount();
    double[] p = new double[stateCount];
    for (int i = 0; i < stateCount; i++) {
        p[i] = 1.0 / (double) stateCount;
    }
    Parameter pi = new Parameter.Default(p);
    FrequencyModel f = new FrequencyModel(codons, pi);
    GY94CodonModel codonModel = new GY94CodonModel(codons, omega, kappa, f);

    Parameter mu = new Parameter.Default(1, 0.5);
    Parameter alpha = new Parameter.Default(1, 0.5);
    GammaSiteRateModel siteModel = new GammaSiteRateModel("gammaModel", mu, alpha, 4, null);
    siteModel.setSubstitutionModel(codonModel);
    BranchRateModel branchRateModel = new DefaultBranchRateModel();

    double analyticResult = Tree.Utils.getTreeLength(tree, tree.getRoot()) * mu.getParameterValue(0);
    int nSites = 100;

    double[] synRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.SYN, codons, false); // use base 61
    double[] nonSynRegMatrix = CodonLabeling.getRegisterMatrix(CodonLabeling.NON_SYN, codons, false); // use base 61

    runSimulation(tree, siteModel, branchRateModel, nSites,
            new double[][] {synRegMatrix, nonSynRegMatrix}, analyticResult);

}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
public MG94HKYCodonModel(Codons codonDataType, Parameter alphaParameter, Parameter betaParameter, Parameter kappaParameter,
                         FrequencyModel freqModel) {
    this(codonDataType, alphaParameter, betaParameter, kappaParameter, freqModel,
            new DefaultEigenSystem(codonDataType.getStateCount()));
}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
public GY94CodonModel(Codons codonDataType, Parameter omegaParameter, Parameter kappaParameter,
                      FrequencyModel freqModel) {
    this(codonDataType, omegaParameter, kappaParameter, freqModel,
            new DefaultEigenSystem(codonDataType.getStateCount()));
}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
/**
    * constructors
    *
    * @param codonDataType				Data type as Codons.UNIVERSAL
    * @param omegaParam				Parameter: Omega
    * @param kappaParam				Parameter: Kappa (multidimensional)
    * @param mntParam					Parameter: Multi-nt
    * @param rMat						Initial rate matrix and frequencies
    * @param freqModel					Frequency model
    */
public EmpiricalCodonModel(Codons codonDataType,
	    Parameter omegaParam,
	    Parameter kappaParam,
	    Parameter mntParam,
	    EmpiricalRateMatrixReader rMat,
	    FrequencyModel freqModel) {
	this(codonDataType, omegaParam, kappaParam, mntParam, rMat, freqModel,
			new DefaultEigenSystem(codonDataType.getStateCount()));
}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
/**
    * constructors
    *
    * @param codonDataType				Data type as Codons.UNIVERSAL
    * @param omegaParam				Parameter: Omega
    * @param kappaParam				Parameter: Kappa (multidimensional)
    * @param mntParam					Parameter: Multi-nt
    * @param rMat						Initial rate matrix and frequencies
    * @param freqModel					Frequency model
    */
public EmpiricalCodonModel(Codons codonDataType,
	    Parameter omegaParam,
	    Parameter kappaParam,
	    Parameter mntParam,
	    EmpiricalRateMatrix rMat,
	    FrequencyModel freqModel) {
	this(codonDataType, omegaParam, kappaParam, mntParam, rMat, freqModel,
			new DefaultEigenSystem(codonDataType.getStateCount()));
}
 

import dr.evolution.datatype.Codons; //导入方法依赖的package包/类
/**
    * constructors
    *
    * @param codonDataType				Data type as Codons.UNIVERSAL
    * @param pcaType           		Rate matrix with PCs, means, scale factors
    * @param pcaDimensionParameter		Scalars for PCs
    * @param freqModel					Frequency model
    */
public PCACodonModel(Codons codonDataType, AbstractPCARateMatrix pcaType, Parameter pcaDimensionParameter,
           FrequencyModel freqModel) {
	this(codonDataType, pcaType, pcaDimensionParameter, freqModel,
			new DefaultEigenSystem(codonDataType.getStateCount()));
}