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

Example 36 with FrequencyModel

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

the class GeneralSubstitutionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter ratesParameter = null;
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FREQUENCIES)) {
        XMLObject cxo = xo.getChild(FREQUENCIES);
        freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    }
    DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null)
        dataType = (DataType) xo.getChild(DataType.class);
    if (dataType == null)
        dataType = freqModel.getDataType();
    if (dataType != freqModel.getDataType()) {
        throw new XMLParseException("Data type of " + getParserName() + " element does not match that of its frequencyModel.");
    }
    XMLObject cxo = xo.getChild(RATES);
    ratesParameter = (Parameter) cxo.getChild(Parameter.class);
    int states = dataType.getStateCount();
    Logger.getLogger("dr.evomodel").info("  General Substitution Model (stateCount=" + states + ")");
    boolean hasRelativeRates = cxo.hasChildNamed(RELATIVE_TO) || (cxo.hasAttribute(RELATIVE_TO) && cxo.getIntegerAttribute(RELATIVE_TO) > 0);
    int nonReversibleRateCount = ((dataType.getStateCount() - 1) * dataType.getStateCount());
    int reversibleRateCount = (nonReversibleRateCount / 2);
    boolean isNonReversible = ratesParameter.getDimension() == nonReversibleRateCount;
    boolean hasIndicator = xo.hasChildNamed(INDICATOR);
    if (!hasRelativeRates) {
        Parameter indicatorParameter = null;
        if (ratesParameter.getDimension() != reversibleRateCount && ratesParameter.getDimension() != nonReversibleRateCount) {
            throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + (reversibleRateCount) + " dimensions for reversible model or " + nonReversibleRateCount + " dimensions for non-reversible. " + "However parameter dimension is " + ratesParameter.getDimension());
        }
        if (hasIndicator) {
            // this is using BSSVS
            cxo = xo.getChild(INDICATOR);
            indicatorParameter = (Parameter) cxo.getChild(Parameter.class);
            if (indicatorParameter.getDimension() != ratesParameter.getDimension()) {
                throw new XMLParseException("Rates and indicator parameters in " + getParserName() + " element must be the same dimension.");
            }
            boolean randomize = xo.getAttribute(ComplexSubstitutionModelParser.RANDOMIZE, false);
            if (randomize) {
                BayesianStochasticSearchVariableSelection.Utils.randomize(indicatorParameter, dataType.getStateCount(), !isNonReversible);
            }
        }
        if (isNonReversible) {
            Logger.getLogger("dr.evomodel").info("  Using BSSVS Complex Substitution Model");
            return new SVSComplexSubstitutionModel(getParserName(), dataType, freqModel, ratesParameter, indicatorParameter);
        } else {
            Logger.getLogger("dr.evomodel").info("  Using BSSVS General Substitution Model");
            return new SVSGeneralSubstitutionModel(dataType, freqModel, ratesParameter, indicatorParameter);
        }
    } else {
        if (ratesParameter.getDimension() != reversibleRateCount - 1) {
            throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + (reversibleRateCount - 1) + " dimensions. However parameter dimension is " + ratesParameter.getDimension());
        }
        int relativeTo = 0;
        if (hasRelativeRates) {
            relativeTo = cxo.getIntegerAttribute(RELATIVE_TO) - 1;
        }
        if (relativeTo < 0 || relativeTo >= reversibleRateCount) {
            throw new XMLParseException(RELATIVE_TO + " must be 1 or greater");
        } else {
            int t = relativeTo;
            int s = states - 1;
            int row = 0;
            while (t >= s) {
                t -= s;
                s -= 1;
                row += 1;
            }
            int col = t + row + 1;
            Logger.getLogger("dr.evomodel").info("  Rates relative to " + dataType.getCode(row) + "<->" + dataType.getCode(col));
        }
        if (ratesParameter == null) {
            if (reversibleRateCount == 1) {
            // simplest model for binary traits...
            } else {
                throw new XMLParseException("No rates parameter found in " + getParserName());
            }
        }
        return new GeneralSubstitutionModel(dataType, freqModel, ratesParameter, relativeTo);
    }
}

Example 37 with FrequencyModel

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

the class MutationDeathModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter dummyFreqParameter;
    Parameter delParam = (Parameter) xo.getChild(Parameter.class);
    Logger.getLogger("dr.evomodel").info("Creating MutationDeath substitution model.\n\tInitial death rate is " + delParam.getParameterValue(0));
    MutationDeathType dT = (MutationDeathType) xo.getChild(MutationDeathType.class);
    AbstractSubstitutionModel evoModel = (AbstractSubstitutionModel) xo.getChild(AbstractSubstitutionModel.class);
    if (evoModel == null) {
        // Assuming pure survival model
        Logger.getLogger("dr.evomodel").info("\tSubstitutionModel not provided assuming pure death/survival model.");
        dummyFreqParameter = new Parameter.Default(new double[] { 1.0, 0.0 });
    } else {
        dummyFreqParameter = new Parameter.Default(dT.getStateCount());
        double[] freqs = evoModel.getFrequencyModel().getFrequencies();
        for (int i = 0; i < freqs.length; ++i) {
            dummyFreqParameter.setParameterValueQuietly(i, freqs[i]);
        }
        dummyFreqParameter.setParameterValueQuietly(dT.getStateCount() - 1, 0.0);
    }
    FrequencyModel dummyFrequencies = new FrequencyModel(dT, dummyFreqParameter);
    Parameter mutationRate;
    if (xo.hasChildNamed(MUTATION_RATE)) {
        mutationRate = (Parameter) xo.getElementFirstChild(MUTATION_RATE);
    } else {
        mutationRate = new Parameter.Default(new double[] { 1.0 });
    }
    Logger.getLogger("dr.evomodel").info("\tInitial mutation rate is " + mutationRate.getParameterValue(0));
    return new MutationDeathModel(delParam, dT, evoModel, dummyFrequencies, mutationRate);
}

Example 38 with FrequencyModel

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

the class PCACodonModelParser 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);
        if (codeStr.equals(GeneticCode.UNIVERSAL.getName())) {
            codons = Codons.UNIVERSAL;
        } else if (codeStr.equals(GeneticCode.VERTEBRATE_MT.getName())) {
            codons = Codons.VERTEBRATE_MT;
        } else if (codeStr.equals(GeneticCode.YEAST.getName())) {
            codons = Codons.YEAST;
        } else if (codeStr.equals(GeneticCode.MOLD_PROTOZOAN_MT.getName())) {
            codons = Codons.MOLD_PROTOZOAN_MT;
        } else if (codeStr.equals(GeneticCode.INVERTEBRATE_MT.getName())) {
            codons = Codons.INVERTEBRATE_MT;
        } else if (codeStr.equals(GeneticCode.CILIATE.getName())) {
            codons = Codons.CILIATE;
        } else if (codeStr.equals(GeneticCode.ECHINODERM_MT.getName())) {
            codons = Codons.ECHINODERM_MT;
        } else if (codeStr.equals(GeneticCode.EUPLOTID_NUC.getName())) {
            codons = Codons.EUPLOTID_NUC;
        } else if (codeStr.equals(GeneticCode.BACTERIAL.getName())) {
            codons = Codons.BACTERIAL;
        } else if (codeStr.equals(GeneticCode.ALT_YEAST.getName())) {
            codons = Codons.ALT_YEAST;
        } else if (codeStr.equals(GeneticCode.ASCIDIAN_MT.getName())) {
            codons = Codons.ASCIDIAN_MT;
        } else if (codeStr.equals(GeneticCode.FLATWORM_MT.getName())) {
            codons = Codons.FLATWORM_MT;
        } else if (codeStr.equals(GeneticCode.BLEPHARISMA_NUC.getName())) {
            codons = Codons.BLEPHARISMA_NUC;
        } else if (codeStr.equals(GeneticCode.NO_STOPS.getName())) {
            codons = Codons.NO_STOPS;
        }
    }
    // get number of PCs
    Parameter pcaDimensionParameter = (Parameter) xo.getElementFirstChild(PCA_DIMENSION);
    // get directory with pca rate matrix files; fallback to default "pcadata"
    String dirString = "pcadata";
    if (xo.hasAttribute(PCA_DATA_DIR)) {
        dirString = xo.getStringAttribute(PCA_DATA_DIR);
    }
    // get type of rate matrix; fallback to mammalia pca
    AbstractPCARateMatrix pcaType = new PCARateMatrixMammalia(pcaDimensionParameter.getDimension(), dirString);
    // check for other type of pca
    if (xo.hasAttribute(PCATYPE)) {
        String pcaTypeString = xo.getStringAttribute(PCATYPE);
        if (pcaTypeString.equals(PCARateMatrixMammalia.getName())) {
            pcaType = new PCARateMatrixMammalia(pcaDimensionParameter.getDimension(), dirString);
        }
    }
    // decide if getting frequencies from csv or estimating from MSA
    FrequencyModel freqModel = null;
    if (xo.getChild(FrequencyModel.class) != null) {
        freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    } else {
        freqModel = createNewFreqModel(codons, pcaType);
    }
    return new PCACodonModel(codons, pcaType, pcaDimensionParameter, freqModel);
}

Example 39 with FrequencyModel

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

the class HKYParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Variable kappaParam = (Variable) xo.getElementFirstChild(KAPPA);
    FrequencyModel freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    Logger.getLogger("dr.evomodel").info("Creating HKY substitution model. Initial kappa = " + kappaParam.getValue(0));
    return new HKY(kappaParam, freqModel);
}

Example 40 with FrequencyModel

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

the class LinearBiasModelParser method parseXMLObject.

//AbstractXMLObjectParser implementation
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    OnePhaseModel subModel = (OnePhaseModel) xo.getElementFirstChild(SUBMODEL);
    Microsatellite dataType = (Microsatellite) subModel.getDataType();
    Parameter biasConst = null;
    if (xo.hasChildNamed(BIAS_CONSTANT)) {
        biasConst = (Parameter) xo.getElementFirstChild(BIAS_CONSTANT);
    }
    Parameter biasLin = null;
    if (xo.hasChildNamed(BIAS_LINEAR)) {
        biasLin = (Parameter) xo.getElementFirstChild(BIAS_LINEAR);
    }
    //get FrequencyModel
    FrequencyModel freqModel = null;
    if (xo.hasChildNamed(FrequencyModelParser.FREQUENCIES)) {
        freqModel = (FrequencyModel) xo.getElementFirstChild(FrequencyModelParser.FREQUENCIES);
    }
    boolean estimateSubmodelParams = false;
    if (xo.hasAttribute(ESTIMATE_SUBMODEL_PARAMS)) {
        estimateSubmodelParams = xo.getBooleanAttribute(ESTIMATE_SUBMODEL_PARAMS);
    }
    System.out.println("Is estimating submodel parameter(s): " + estimateSubmodelParams);
    boolean logistics = false;
    if (xo.hasAttribute(LOGISTICS)) {
        logistics = xo.getBooleanAttribute(LOGISTICS);
    }
    System.out.println("Using logistic regression: " + logistics);
    boolean isSubmodel = false;
    if (xo.hasAttribute(IS_SUBMODEL)) {
        isSubmodel = xo.getBooleanAttribute(IS_SUBMODEL);
    }
    System.out.println("Is a submodel: " + isSubmodel);
    return new LinearBiasModel(dataType, freqModel, subModel, biasConst, biasLin, logistics, estimateSubmodelParams, isSubmodel);
}