Examples with FrequencyModel dr.evomodel.substmodel.FrequencyModel used on opensource projects

Example 11 with FrequencyModel

use of dr.evomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class PartitionData method createBranchModel.

public BranchModel createBranchModel() {
    BranchModel branchModel = null;
    if (this.substitutionModelIndex == 0) {
        // HKY
        Parameter kappa = new Parameter.Default(1, substitutionParameterValues[0]);
        FrequencyModel frequencyModel = this.createFrequencyModel();
        HKY hky = new HKY(kappa, frequencyModel);
        branchModel = new HomogeneousBranchModel(hky);
    } else if (this.substitutionModelIndex == 1) {
        // GTR
        Parameter ac = new Parameter.Default(1, substitutionParameterValues[1]);
        Parameter ag = new Parameter.Default(1, substitutionParameterValues[2]);
        Parameter at = new Parameter.Default(1, substitutionParameterValues[3]);
        Parameter cg = new Parameter.Default(1, substitutionParameterValues[4]);
        Parameter ct = new Parameter.Default(1, substitutionParameterValues[5]);
        Parameter gt = new Parameter.Default(1, substitutionParameterValues[6]);
        FrequencyModel frequencyModel = this.createFrequencyModel();
        GTR gtr = new GTR(ac, ag, at, cg, ct, gt, frequencyModel);
        branchModel = new HomogeneousBranchModel(gtr);
    } else if (this.substitutionModelIndex == 2) {
        // TN93
        Parameter kappa1 = new Parameter.Default(1, substitutionParameterValues[7]);
        Parameter kappa2 = new Parameter.Default(1, substitutionParameterValues[8]);
        FrequencyModel frequencyModel = this.createFrequencyModel();
        TN93 tn93 = new TN93(kappa1, kappa2, frequencyModel);
        branchModel = new HomogeneousBranchModel(tn93);
    } else if (this.substitutionModelIndex == 3) {
        // Yang Codon Model
        FrequencyModel frequencyModel = this.createFrequencyModel();
        Parameter kappa = new Parameter.Default(1, substitutionParameterValues[9]);
        Parameter omega = new Parameter.Default(1, substitutionParameterValues[10]);
        GY94CodonModel yangCodonModel = new GY94CodonModel(Codons.UNIVERSAL, omega, kappa, frequencyModel);
        branchModel = new HomogeneousBranchModel(yangCodonModel);
    } else if (this.substitutionModelIndex == 4) {
        // MG94CodonModel
        FrequencyModel frequencyModel = this.createFrequencyModel();
        Parameter alpha = new Parameter.Default(1, substitutionParameterValues[11]);
        Parameter beta = new Parameter.Default(1, substitutionParameterValues[12]);
        Parameter kappa = new Parameter.Default(1, substitutionParameterValues[13]);
        MG94HKYCodonModel mg94 = new MG94HKYCodonModel(Codons.UNIVERSAL, alpha, beta, kappa, frequencyModel);
        branchModel = new HomogeneousBranchModel(mg94);
    } else if (this.substitutionModelIndex == 5) {
        // Blosum62
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = Blosum62.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else if (this.substitutionModelIndex == 6) {
        // CPREV
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = CPREV.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else if (this.substitutionModelIndex == 7) {
        // Dayhoff
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = Dayhoff.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else if (this.substitutionModelIndex == 8) {
        // JTT
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = JTT.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else if (this.substitutionModelIndex == 9) {
        // LG
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = LG.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else if (this.substitutionModelIndex == 10) {
        // MTREV
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = MTREV.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else if (this.substitutionModelIndex == 11) {
        // WAG
        FrequencyModel frequencyModel = this.createFrequencyModel();
        EmpiricalRateMatrix rateMatrix = WAG.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, frequencyModel);
        branchModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
    } else {
        System.out.println("Not yet implemented");
    }
    return branchModel;
}

Example 12 with FrequencyModel

use of dr.evomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class PartitionData method createFrequencyModel.

public FrequencyModel createFrequencyModel() {
    FrequencyModel frequencyModel = null;
    if (this.frequencyModelIndex == 0) {
        // Nucleotidefrequencies
        Parameter freqs = new Parameter.Default(new double[] { frequencyParameterValues[0], frequencyParameterValues[1], frequencyParameterValues[2], frequencyParameterValues[3] });
        DataType dataType = this.createDataType();
        frequencyModel = new FrequencyModel(dataType, freqs);
    } else if (this.frequencyModelIndex == 1) {
        Parameter freqs = new Parameter.Default(new double[] { frequencyParameterValues[4], frequencyParameterValues[5], frequencyParameterValues[6], frequencyParameterValues[7], frequencyParameterValues[8], frequencyParameterValues[9], frequencyParameterValues[10], frequencyParameterValues[11], frequencyParameterValues[12], frequencyParameterValues[13], frequencyParameterValues[14], frequencyParameterValues[15], frequencyParameterValues[16], frequencyParameterValues[17], frequencyParameterValues[18], frequencyParameterValues[19], frequencyParameterValues[20], frequencyParameterValues[21], frequencyParameterValues[22], frequencyParameterValues[23], frequencyParameterValues[24], frequencyParameterValues[25], frequencyParameterValues[26], frequencyParameterValues[27], frequencyParameterValues[28], frequencyParameterValues[29], frequencyParameterValues[30], frequencyParameterValues[31], frequencyParameterValues[32], frequencyParameterValues[33], frequencyParameterValues[34], frequencyParameterValues[35], frequencyParameterValues[36], frequencyParameterValues[37], frequencyParameterValues[38], frequencyParameterValues[39], frequencyParameterValues[40], frequencyParameterValues[41], frequencyParameterValues[42], frequencyParameterValues[43], frequencyParameterValues[44], frequencyParameterValues[45], frequencyParameterValues[46], frequencyParameterValues[47], frequencyParameterValues[48], frequencyParameterValues[49], frequencyParameterValues[50], frequencyParameterValues[51], frequencyParameterValues[52], frequencyParameterValues[53], frequencyParameterValues[54], frequencyParameterValues[55], frequencyParameterValues[56], frequencyParameterValues[57], frequencyParameterValues[58], frequencyParameterValues[59], frequencyParameterValues[60], frequencyParameterValues[61], frequencyParameterValues[62], frequencyParameterValues[63], frequencyParameterValues[64] });
        DataType dataType = this.createDataType();
        frequencyModel = new FrequencyModel(dataType, freqs);
    } else if (this.frequencyModelIndex == 2) {
        Parameter freqs = new Parameter.Default(new double[] { frequencyParameterValues[65], frequencyParameterValues[66], frequencyParameterValues[67], frequencyParameterValues[68], frequencyParameterValues[69], frequencyParameterValues[70], frequencyParameterValues[71], frequencyParameterValues[72], frequencyParameterValues[73], frequencyParameterValues[74], frequencyParameterValues[75], frequencyParameterValues[76], frequencyParameterValues[77], frequencyParameterValues[78], frequencyParameterValues[79], frequencyParameterValues[80], frequencyParameterValues[81], frequencyParameterValues[82], frequencyParameterValues[83], frequencyParameterValues[84] });
        DataType dataType = this.createDataType();
        frequencyModel = new FrequencyModel(dataType, freqs);
    } else {
        System.out.println("Not yet implemented");
    }
    return frequencyModel;
}

Example 13 with FrequencyModel

use of dr.evomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class EmpiricalCodonModelParser method createNewFreqModel.

// creates new FrequencyModel from XML frequencies
private FrequencyModel createNewFreqModel(DataType codons, EmpiricalRateMatrixReader type) throws XMLParseException {
    double[] freqs = type.getFrequencies();
    double sum = 0;
    for (int j = 0; j < freqs.length; j++) {
        sum += freqs[j];
    }
    if (Math.abs(sum - 1.0) > 1e-8) {
        throw new XMLParseException("Frequencies do not sum to 1 (they sum to " + sum + ")");
    }
    FrequencyModel fm = new FrequencyModel(codons, freqs);
    Logger.getLogger("dr.evomodel").info("Using frequencies from data file");
    return fm;
}

Example 14 with FrequencyModel

use of dr.evomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class GLMSubstitutionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null)
        dataType = (DataType) xo.getChild(DataType.class);
    int rateCount = (dataType.getStateCount() - 1) * dataType.getStateCount();
    // Should be constructed as a log-linear model
    GeneralizedLinearModel glm = (GeneralizedLinearModel) xo.getChild(GeneralizedLinearModel.class);
    // LogLinearModel glm = (LogLinearModel) xo.getChild(GeneralizedLinearModel.class);
    int length = glm.getXBeta().length;
    if (length != rateCount) {
        throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + (rateCount) + " dimensions.  However GLM dimension is " + length);
    }
    XMLObject cxo = xo.getChild(ComplexSubstitutionModelParser.ROOT_FREQUENCIES);
    FrequencyModel rootFreq = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    if (dataType != rootFreq.getDataType()) {
        throw new XMLParseException("Data type of " + getParserName() + " element does not match that of its rootFrequencyModel.");
    }
    return new GLMSubstitutionModel(xo.getId(), dataType, rootFreq, glm);
}

Example 15 with FrequencyModel

use of dr.evomodel.substmodel.FrequencyModel in project beast-mcmc by beast-dev.

the class GY94CodonModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Codons codons = Codons.UNIVERSAL;
    if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
        String codeStr = xo.getStringAttribute(GeneticCode.GENETIC_CODE);
        codons = Codons.findByName(codeStr);
    }
    Parameter omegaParameter = (Parameter) xo.getElementFirstChild(OMEGA);
    int dim = omegaParameter.getDimension();
    double value = omegaParameter.getParameterValue(dim - 1);
    if (value < 0) {
        throw new RuntimeException("Negative Omega parameter value " + value);
    }
    //END: negative check
    Parameter kappaParameter = (Parameter) xo.getElementFirstChild(KAPPA);
    dim = kappaParameter.getDimension();
    value = kappaParameter.getParameterValue(dim - 1);
    if (value < 0) {
        throw new RuntimeException("Negative kappa parameter value value " + value);
    }
    //END: negative check
    FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    GY94CodonModel codonModel = new GY94CodonModel(codons, omegaParameter, kappaParameter, freqModel);
    return codonModel;
}