Examples with DataType dr.evolution.datatype.DataType used on opensource projects

Example 51 with DataType

use of dr.evolution.datatype.DataType in project beast-mcmc by beast-dev.

the class LewisMkSubstitutionModelParser method parseXMLObject.

//public static XMLObjectParser PARSER=new LewisMkSubstitutionModelParser();
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(FREQUENCIES);
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    DataType dataType = freqModel.getDataType();
    int k = dataType.getStateCount();
    System.err.println("Number of states " + k);
    Parameter ratesParameter;
    if (xo.hasAttribute(TOTAL_ORDER) && xo.getBooleanAttribute(TOTAL_ORDER)) {
        //TOTAL ORDERING OF THE STATES BASED ON DATATYPE
        ratesParameter = new Parameter.Default(k * (k - 1) / 2, 0);
        int j = k - 1;
        for (int i = 0; i < (k - 1) * k / 2; i = i + j + 1) {
            ratesParameter.setParameterValue(i, 1);
            j -= 1;
        }
    } else if (xo.hasChildNamed(ORDER)) {
        // USER-SPECIFIED ORDERING OF THE STATES
        ratesParameter = new Parameter.Default(k * (k - 1) / 2, 0);
        for (int i = 0; i < xo.getChildCount(); ++i) {
            if (xo.getChildName(i).equals(ORDER)) {
                cxo = (XMLObject) xo.getChild(i);
                if (cxo.getName().equals(ORDER)) {
                    int from = dataType.getState(cxo.getStringAttribute(STATE).charAt(0));
                    int to = dataType.getState(cxo.getStringAttribute(ADJACENT).charAt(0));
                    if (from > to) {
                        //SWAP: from should have the smaller state number
                        to += from;
                        from = to - from;
                        to -= from;
                    }
                    int ratesIndex = (from * (2 * k - 3) - from * from) / 2 + to - 1;
                    ratesParameter.setParameterValue(ratesIndex, 1);
                }
            }
        }
    } else {
        ratesParameter = new Parameter.Default(k * (k - 1) / 2, 1);
    }
    System.err.println(ratesParameter.toString());
    System.err.println("Infinitesimal matrix:");
    for (int i = 0; i < k; ++i) {
        for (int j = 0; j < k; ++j) {
            int from, to;
            if (i < j) {
                from = i;
                to = j;
            } else {
                from = j;
                to = i;
            }
            //This is right now!!! Thanks, Marc!
            int ratesIndex = (from * (2 * k - 3) - from * from) / 2 + to - 1;
            if (i != j)
                System.err.print(Double.toString(ratesParameter.getValue(ratesIndex)) + "\t(" + ratesIndex + ")\t");
            else
                System.err.print("-\t\t");
        }
        //newline
        System.err.println("");
    }
    System.err.println("");
    if (!checkConnected(ratesParameter.getValues(), k)) {
        throw (new XMLParseException("The state transitions form a disconnected graph! This model is not suited for this case."));
    }
    return new GeneralSubstitutionModel(LEWIS_MK_MODEL, dataType, freqModel, ratesParameter, -1);
}

Example 52 with DataType

use of dr.evolution.datatype.DataType in project beast-mcmc by beast-dev.

the class MarkovModulatedGY94CodonModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    DataType dataType = DataTypeUtils.getDataType(xo);
    HiddenCodons codons;
    if (dataType instanceof HiddenCodons)
        codons = (HiddenCodons) dataType;
    else
        throw new XMLParseException("Must construct " + MARKOV_MODULATED_YANG_MODEL + " with hidden codons");
    Parameter omegaParam = (Parameter) xo.getElementFirstChild(OMEGA);
    Parameter kappaParam = (Parameter) xo.getElementFirstChild(KAPPA);
    Parameter switchingParam = (Parameter) xo.getElementFirstChild(SWITCHING_RATES);
    FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    EigenSystem eigenSystem;
    if (xo.getAttribute(DIAGONALIZATION, "default").compareToIgnoreCase("colt") == 0)
        eigenSystem = new ColtEigenSystem(dataType.getStateCount());
    else
        eigenSystem = new DefaultEigenSystem(dataType.getStateCount());
    return new MarkovModulatedGY94CodonModel(codons, switchingParam, omegaParam, kappaParam, freqModel, eigenSystem);
}

Example 53 with DataType

use of dr.evolution.datatype.DataType in project beast-mcmc by beast-dev.

the class FrequencyModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    DataType dataType = DataTypeUtils.getDataType(xo);
    Parameter freqsParam = (Parameter) xo.getElementFirstChild(FREQUENCIES);
    double[] frequencies = null;
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object obj = xo.getChild(i);
        if (obj instanceof PatternList) {
            PatternList patternList = (PatternList) obj;
            if (xo.getAttribute(COMPRESS, false) && (patternList.getDataType() instanceof HiddenDataType)) {
                double[] hiddenFrequencies = patternList.getStateFrequencies();
                int hiddenCount = ((HiddenDataType) patternList.getDataType()).getHiddenClassCount();
                int baseStateCount = hiddenFrequencies.length / hiddenCount;
                frequencies = new double[baseStateCount];
                for (int j = 0; j < baseStateCount; ++j) {
                    for (int k = 0; k < hiddenCount; ++k) {
                        frequencies[j] += hiddenFrequencies[j + k * baseStateCount];
                    }
                }
            } else {
                // TODO
                if (xo.hasAttribute(COMPOSITION)) {
                    String type = xo.getStringAttribute(COMPOSITION);
                    if (type.equalsIgnoreCase(FREQ_3x4)) {
                        frequencies = getEmpirical3x4Freqs(patternList);
                    }
                } else {
                    frequencies = patternList.getStateFrequencies();
                }
            // END: composition check
            }
            break;
        }
    // END: patternList check
    }
    StringBuilder sb = new StringBuilder("\nCreating state frequencies model '" + freqsParam.getParameterName() + "': ");
    if (frequencies != null) {
        if (freqsParam.getDimension() != frequencies.length) {
            throw new XMLParseException("dimension of frequency parameter and number of sequence states don't match.");
        }
        for (int j = 0; j < frequencies.length; j++) {
            freqsParam.setParameterValue(j, frequencies[j]);
        }
        sb.append("Using empirical frequencies from data ");
    } else {
        sb.append("Initial frequencies ");
    }
    sb.append("= {");
    if (xo.getAttribute(NORMALIZE, false)) {
        double sum = 0;
        for (int j = 0; j < freqsParam.getDimension(); j++) sum += freqsParam.getParameterValue(j);
        for (int j = 0; j < freqsParam.getDimension(); j++) {
            if (sum != 0)
                freqsParam.setParameterValue(j, freqsParam.getParameterValue(j) / sum);
            else
                freqsParam.setParameterValue(j, 1.0 / freqsParam.getDimension());
        }
    }
    NumberFormat format = NumberFormat.getNumberInstance();
    format.setMaximumFractionDigits(5);
    sb.append(format.format(freqsParam.getParameterValue(0)));
    for (int j = 1; j < freqsParam.getDimension(); j++) {
        sb.append(", ");
        sb.append(format.format(freqsParam.getParameterValue(j)));
    }
    sb.append("}");
    Logger.getLogger("dr.evomodel").info(sb.toString());
    return new FrequencyModel(dataType, freqsParam);
}

Example 54 with DataType

use of dr.evolution.datatype.DataType in project beast-mcmc by beast-dev.

the class OldGLMSubstitutionModelParser 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();
    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(dr.oldevomodelxml.substmodel.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 OldGLMSubstitutionModel(xo.getId(), dataType, rootFreq, glm);
}

Example 55 with DataType

use of dr.evolution.datatype.DataType 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();
    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);
}