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

Example 26 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) {
            frequencies = ((PatternList) obj).getStateFrequencies();
            break;
        }
    }
    StringBuilder sb = new StringBuilder("Creating 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("= {");
    double sum = 0;
    for (int j = 0; j < freqsParam.getDimension(); j++) {
        sum += freqsParam.getParameterValue(j);
    }
    if (xo.getAttribute(NORMALIZE, false)) {
        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());
        }
        sum = 1.0;
    }
    if (Math.abs(sum - 1.0) > 1e-8) {
        throw new XMLParseException("Frequencies do not sum to 1 (they sum to " + sum + ")");
    }
    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 27 with DataType

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

the class SubstitutionEpochModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    DataType dataType = null;
    FrequencyModel freqModel = null;
    List<SubstitutionModel> modelList = new ArrayList<SubstitutionModel>();
    XMLObject cxo = xo.getChild(MODELS);
    for (int i = 0; i < cxo.getChildCount(); i++) {
        SubstitutionModel model = (SubstitutionModel) cxo.getChild(i);
        if (dataType == null) {
            dataType = model.getDataType();
        } else if (dataType != model.getDataType())
            throw new XMLParseException("Substitution models across epoches must use the same data type.");
        if (freqModel == null) {
            freqModel = model.getFrequencyModel();
        } else if (freqModel != model.getFrequencyModel())
            throw new XMLParseException("Substitution models across epoches must currently use the same frequency model.\nHarass Marc to fix this.");
        modelList.add(model);
    }
    Parameter transitionTimes = (Parameter) xo.getChild(Parameter.class);
    if (transitionTimes.getDimension() != modelList.size() - 1) {
        throw new XMLParseException("# of transition times must equal # of substitution models - 1\n" + transitionTimes.getDimension() + "\n" + modelList.size());
    }
    return new SubstitutionEpochModel(SUBSTITUTION_EPOCH_MODEL, modelList, transitionTimes, dataType, freqModel);
}

Example 28 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(dataType, freqModel, ratesParameter, 0);
}

Example 29 with DataType

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

the class MkModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(GeneralSubstitutionModelParser.FREQUENCIES);
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    DataType dataType = freqModel.getDataType();
    int rateCount = ((dataType.getStateCount() - 1) * dataType.getStateCount()) / 2 - 1;
    Parameter ratesParameter = new Parameter.Default(rateCount, 1.0);
    Logger.getLogger("dr.evolution").info("Creating an Mk substitution model with data type: " + dataType.getType() + "on " + dataType.getStateCount() + " states.");
    int relativeTo = 1;
    return new GeneralSubstitutionModel(dataType, freqModel, ratesParameter, relativeTo);
}

Example 30 with DataType

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

the class TwoStateMarkovRewardsTest method testTwoStateRewards.

public void testTwoStateRewards() {
    DataType dataType = TwoStates.INSTANCE;
    FrequencyModel freqModel = new FrequencyModel(TwoStates.INSTANCE, new double[] { 0.5, 0.5 });
    Parameter rates = new Parameter.Default(new double[] { 4.0, 6.0 });
    ComplexSubstitutionModel twoStateModel = new ComplexSubstitutionModel("two", dataType, freqModel, rates) {
    };
    twoStateModel.setNormalization(false);
    MarkovJumpsSubstitutionModel markovRewards = new MarkovJumpsSubstitutionModel(twoStateModel, MarkovJumpsType.REWARDS);
    double[] r = new double[2];
    double[] q = new double[4];
    double[] c = new double[4];
    int mark = 0;
    double weight = 1.0;
    r[mark] = weight;
    markovRewards.setRegistration(r);
    twoStateModel.getInfinitesimalMatrix(q);
    System.out.println("Q = " + new Vector(q));
    System.out.println("Reward for state 0");
    double time = 1.0;
    markovRewards.computeCondStatMarkovJumps(time, c);
    System.out.println("Reward conditional on X(0) = i, X(t) = j: " + new Vector(c));
    double endTime = 10.0;
    int steps = 10;
    for (time = 0.0; time < endTime; time += (endTime / steps)) {
        markovRewards.computeCondStatMarkovJumps(time, c);
        // start = 0, end = 0
        System.out.println(time + "," + c[0]);
    }
}