Examples with XMLParseException dr.xml.XMLParseException used on opensource projects

Example 1 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class ConjugateRootTraitPrior method parseConjugateRootTraitPrior.

public static ConjugateRootTraitPrior parseConjugateRootTraitPrior(XMLObject xo, final int dim) throws XMLParseException {
    XMLObject cxo = xo.getChild(CONJUGATE_ROOT_PRIOR);
    Parameter meanParameter = (Parameter) cxo.getChild(MultivariateDistributionLikelihood.MVN_MEAN).getChild(Parameter.class);
    if (meanParameter.getDimension() != dim) {
        throw new XMLParseException("Root prior mean dimension (" + meanParameter.getDimension() + ") does not match trait diffusion dimension (" + dim + ")");
    }
    Parameter sampleSizeParameter = (Parameter) cxo.getChild(PRIOR_SAMPLE_SIZE).getChild(Parameter.class);
    return new ConjugateRootTraitPrior(meanParameter, sampleSizeParameter);
}

Example 2 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class DataTypeUtils method getDataType.

public static DataType getDataType(XMLObject xo) throws XMLParseException {
    DataType dataType = null;
    if (xo.hasAttribute(DataType.DATA_TYPE)) {
        String dataTypeStr = xo.getStringAttribute(DataType.DATA_TYPE);
        if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
            dataTypeStr += "-" + xo.getStringAttribute(GeneticCode.GENETIC_CODE);
        }
        dataType = DataType.getRegisteredDataTypeByName(dataTypeStr);
    }
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof DataType) {
            if (dataType != null) {
                throw new XMLParseException("Multiple dataTypes defined for alignment element");
            }
            dataType = (DataType) child;
        }
    }
    return dataType;
}

Example 3 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class ParameterIntegerParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    int[] values = null;
    if (xo.hasAttribute(VALUE)) {
        if (values == null) {
            values = xo.getIntegerArrayAttribute(VALUE);
        } else {
            int[] v = xo.getIntegerArrayAttribute(VALUE);
            if (v.length == values.length) {
                System.arraycopy(v, 0, values, 0, v.length);
            } else if (v.length == 1) {
                for (int i = 0; i < values.length; i++) {
                    values[i] = v[0];
                }
            } else {
                throw new XMLParseException("value string must have 1 value or dimension values");
            }
        }
    } else {
        if (xo.hasAttribute(DIMENSION)) {
            values = new int[xo.getIntegerAttribute(DIMENSION)];
        } else {
            // parameter dimension will get set correctly by TreeModel presumably.
            // if (!xo.hasChildNamed(RANDOMIZE)) {
            // return new Parameter.Default(1);
            // }
            values = new int[1];
            values[0] = 0;
        }
    }
    // uppers = new double[values.length];
    // for(int i = 0; i < values.length; i++) {
    // uppers[i] = Double.POSITIVE_INFINITY;
    // }
    // 
    // lowers = new double[values.length];
    // for(int i = 0; i < values.length; i++) {
    // lowers[i] = Double.NEGATIVE_INFINITY;
    // }
    // if( xo.hasAttribute(UPPER) ) {
    // double[] v = xo.getDoubleArrayAttribute(UPPER);
    // if( v.length == uppers.length ) {
    // System.arraycopy(v, 0, uppers, 0, v.length);
    // } else if( v.length == 1 ) {
    // for(int i = 0; i < uppers.length; i++) {
    // uppers[i] = v[0];
    // }
    // } else {
    // throw new XMLParseException("uppers string must have 1 value or dimension values");
    // }
    // }
    // 
    // if( xo.hasAttribute(LOWER) ) {
    // double[] v = xo.getDoubleArrayAttribute(LOWER);
    // if( v.length == lowers.length ) {
    // System.arraycopy(v, 0, lowers, 0, v.length);
    // } else if( v.length == 1 ) {
    // for(int i = 0; i < lowers.length; i++) {
    // lowers[i] = v[0];
    // }
    // } else {
    // throw new XMLParseException("lowers string must have 1 value or dimension values");
    // }
    // }
    // assert uppers != null && lowers != null;
    // if( (uppers.length != values.length) ) {
    // throw new XMLParseException("value and upper limit strings have different dimension, in parameter");
    // }
    // 
    // if( (lowers.length != values.length) ) {
    // throw new XMLParseException("value and lower limit strings have different dimension, in parameter");
    // }
    // 
    // // check if uppers and lowers are consistent
    // for(int i = 0; i < values.length; i++) {
    // if( uppers[i] < lowers[i] ) {
    // throw new XMLParseException("upper is lower than lower, in parameter");
    // }
    // }
    // 
    // if (xo.hasChildNamed(RANDOMIZE)) {
    // 
    // Distribution distribution = (Distribution) xo.getChild(RANDOMIZE).getChild(Distribution.class);
    // for (int i = 0; i < values.length; i++) {
    // do {
    // // Not an efficient way to draw random variables, but this is currently the only general interface
    // values[i] = distribution.quantile(MathUtils.nextDouble());
    // } while (values[i] < lowers[i] || values[i] > uppers[i]);
    // }
    // 
    // } else {
    // 
    // // make values consistent with bounds
    // for(int i = 0; i < values.length; i++) {
    // if( uppers[i] < values[i] ) values[i] = uppers[i];
    // }
    // 
    // for(int i = 0; i < values.length; i++) {
    // if (lowers[i] > values[i]) values[i] = lowers[i];
    // }
    // }
    Variable<Integer> param = new Variable.I(values);
    param.addBounds(new Bounds.Staircase(param));
    return param;
}

Example 4 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class PartitionParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    int from = 0;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    DataType dataType = null;
    if (xo.hasAttribute(FROM)) {
        from = xo.getIntegerAttribute(FROM) - 1;
        if (from < 0) {
            throw new XMLParseException("Illegal 'from' attribute in patterns element");
        }
    }
    if (xo.hasAttribute(TO)) {
        to = xo.getIntegerAttribute(TO) - 1;
        if (to < 0 || to < from) {
            throw new XMLParseException("Illegal 'to' attribute in patterns element");
        }
    }
    if (every <= 0) {
        throw new XMLParseException("Illegal 'every' attribute in patterns element");
    }
    if (xo.hasAttribute(DATA_TYPE)) {
        dataType = DataTypeUtils.getDataType(xo);
    }
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    GammaSiteRateModel siteModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
    // FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    FrequencyModel freqModel;
    List<FrequencyModel> freqModels = new ArrayList<FrequencyModel>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object cxo = xo.getChild(i);
        if (cxo instanceof FrequencyModel) {
            freqModels.add((FrequencyModel) cxo);
        }
    }
    if (freqModels.size() == 1) {
        freqModel = freqModels.get(0);
    } else {
        double[] freqParameter = new double[freqModels.size() * freqModels.get(0).getFrequencyCount()];
        int index = 0;
        for (int i = 0; i < freqModels.size(); i++) {
            for (int j = 0; j < freqModels.get(i).getFrequencyCount(); j++) {
                freqParameter[index] = (freqModels.get(i).getFrequency(j)) / freqModels.size();
                index++;
            }
        }
        freqModel = new FrequencyModel(dataType, freqParameter);
    }
    Sequence rootSequence = (Sequence) xo.getChild(Sequence.class);
    BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    if (rateModel == null) {
        rateModel = new DefaultBranchRateModel();
    }
    BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
    if (branchModel == null) {
        SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
        branchModel = new HomogeneousBranchModel(substitutionModel);
    }
    Partition partition = new Partition(tree, branchModel, siteModel, rateModel, freqModel, from, to, every, dataType);
    if (rootSequence != null) {
        partition.setRootSequence(rootSequence);
    }
    return partition;
}

Example 5 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class RatioParameterParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter parameter1 = (Parameter) xo.getElementFirstChild(PARAMETER1);
    Parameter parameter2 = (Parameter) xo.getElementFirstChild(PARAMETER2);
    if (parameter1.getDimension() != parameter2.getDimension()) {
        throw new XMLParseException("Parameters in ratio '" + xo.getId() + "' must have the same dimension");
    }
    return new RatioParameter(parameter1, parameter2);
}