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

Example 6 with DataType

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

the class ComplexSubstitutionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter ratesParameter;
    XMLObject cxo;
    if (xo.hasChildNamed(FREQUENCIES)) {
        cxo = xo.getChild(FREQUENCIES);
    } else {
        cxo = xo.getChild(ROOT_FREQUENCIES);
    }
    FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
    DataType dataType = freqModel.getDataType();
    cxo = xo.getChild(RATES);
    int states = dataType.getStateCount();
    Logger.getLogger("dr.app.beagle.evomodel").info("  Complex Substitution Model (stateCount=" + states + ")");
    ratesParameter = (Parameter) cxo.getChild(Parameter.class);
    int rateCount = (dataType.getStateCount() - 1) * dataType.getStateCount();
    if (ratesParameter == null) {
        if (rateCount == 1) {
        // simplest model for binary traits...
        } else {
            throw new XMLParseException("No rates parameter found in " + getParserName());
        }
    } else if (ratesParameter.getDimension() != rateCount) {
        throw new XMLParseException("Rates parameter in " + getParserName() + " element should have " + rateCount + " dimensions.");
    }
    boolean checkConditioning = xo.getAttribute(CHECK_CONDITIONING, true);
    if (!xo.hasChildNamed(INDICATOR)) {
        if (!checkConditioning) {
            return new ComplexSubstitutionModel(COMPLEX_SUBSTITUTION_MODEL, dataType, freqModel, ratesParameter) {

                protected EigenSystem getDefaultEigenSystem(int stateCount) {
                    return new ComplexColtEigenSystem(stateCount, false, ColtEigenSystem.defaultMaxConditionNumber, ColtEigenSystem.defaultMaxIterations);
                }
            };
        } else {
            return new ComplexSubstitutionModel(COMPLEX_SUBSTITUTION_MODEL, dataType, freqModel, ratesParameter);
        }
    }
    cxo = xo.getChild(INDICATOR);
    Parameter indicatorParameter = (Parameter) cxo.getChild(Parameter.class);
    if (indicatorParameter == null || ratesParameter == null || indicatorParameter.getDimension() != ratesParameter.getDimension())
        throw new XMLParseException("Rates and indicator parameters in " + getParserName() + " element must be the same dimension.");
    if (xo.hasAttribute(BSSVS_TOLERANCE)) {
        double tolerance = xo.getAttribute(BSSVS_TOLERANCE, BayesianStochasticSearchVariableSelection.Utils.getTolerance());
        if (tolerance > BayesianStochasticSearchVariableSelection.Utils.getTolerance()) {
            // Only increase smallest allowed tolerance
            BayesianStochasticSearchVariableSelection.Utils.setTolerance(tolerance);
            Logger.getLogger("dr.app.beagle.evomodel").info("\tIncreasing BSSVS tolerance to " + tolerance);
        }
    }
    if (xo.hasAttribute(BSSVS_SCALAR)) {
        double scalar = xo.getAttribute(BSSVS_SCALAR, BayesianStochasticSearchVariableSelection.Utils.getScalar());
        if (scalar < BayesianStochasticSearchVariableSelection.Utils.getScalar()) {
            BayesianStochasticSearchVariableSelection.Utils.setScalar(scalar);
            Logger.getLogger("dr.app.beagle.evomodel").info("\tDecreasing BSSVS scalar to " + scalar);
        }
    }
    SVSComplexSubstitutionModel model;
    if (!checkConditioning) {
        model = new SVSComplexSubstitutionModel(SVS_COMPLEX_SUBSTITUTION_MODEL, dataType, freqModel, ratesParameter, indicatorParameter) {

            protected EigenSystem getDefaultEigenSystem(int stateCount) {
                return new ComplexColtEigenSystem(stateCount, false, ColtEigenSystem.defaultMaxConditionNumber, ColtEigenSystem.defaultMaxIterations);
            }
        };
    } else {
        model = new SVSComplexSubstitutionModel(SVS_COMPLEX_SUBSTITUTION_MODEL, dataType, freqModel, ratesParameter, indicatorParameter);
    }
    boolean randomize = xo.getAttribute(RANDOMIZE, false);
    if (randomize) {
        // Randomization may need multiple tries
        int tries = 0;
        boolean valid = false;
        while (!valid && tries < maxRandomizationTries) {
            BayesianStochasticSearchVariableSelection.Utils.randomize(indicatorParameter, dataType.getStateCount(), false);
            valid = !Double.isInfinite(model.getLogLikelihood());
            tries++;
        }
        Logger.getLogger("dr.app.beagle.evomodel").info("\tRandomization attempts: " + tries);
    }
    if (!xo.getAttribute(NORMALIZED, true)) {
        model.setNormalization(false);
        Logger.getLogger("dr.app.beagle.evomodel").info("\tNormalization: false");
    }
    Logger.getLogger("dr.app.beagle.evomodel").info("\t\tPlease cite: Edwards, Suchard et al. (2011)\n");
    return model;
}

Example 7 with DataType

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

the class MarkovJumpsTreeLikelihoodParser method createTreeLikelihood.

protected BeagleTreeLikelihood createTreeLikelihood(PatternList patternList, MutableTreeModel treeModel, BranchModel branchModel, GammaSiteRateModel siteRateModel, BranchRateModel branchRateModel, TipStatesModel tipStatesModel, boolean useAmbiguities, PartialsRescalingScheme scalingScheme, boolean delayScaling, Map<Set<String>, Parameter> partialsRestrictions, XMLObject xo) throws XMLParseException {
    DataType dataType = branchModel.getRootSubstitutionModel().getDataType();
    String stateTag = xo.getAttribute(RECONSTRUCTION_TAG_NAME, RECONSTRUCTION_TAG);
    String jumpTag = xo.getAttribute(JUMP_TAG_NAME, JUMP_TAG);
    boolean scaleRewards = xo.getAttribute(SCALE_REWARDS, true);
    boolean useMAP = xo.getAttribute(MAP_RECONSTRUCTION, false);
    boolean useMarginalLogLikelihood = xo.getAttribute(MARGINAL_LIKELIHOOD, true);
    boolean conditionalProbabilitiesInLogSpace = xo.getAttribute(CONDITIONAL_PROBABILITIES_IN_LOG_SPACE, false);
    boolean useUniformization = xo.getAttribute(USE_UNIFORMIZATION, false);
    boolean reportUnconditionedColumns = xo.getAttribute(REPORT_UNCONDITIONED_COLUMNS, false);
    int nSimulants = xo.getAttribute(NUMBER_OF_SIMULANTS, 1);
    if (patternList.areUnique()) {
        throw new XMLParseException("Markov Jumps reconstruction cannot be used with compressed (unique) patterns.");
    }
    MarkovJumpsBeagleTreeLikelihood treeLikelihood = new MarkovJumpsBeagleTreeLikelihood(patternList, treeModel, branchModel, siteRateModel, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling, partialsRestrictions, dataType, stateTag, useMAP, useMarginalLogLikelihood, useUniformization, reportUnconditionedColumns, nSimulants, conditionalProbabilitiesInLogSpace);
    int registersFound = parseAllChildren(xo, treeLikelihood, dataType.getStateCount(), jumpTag, MarkovJumpsType.COUNTS, // For backwards compatibility
    false);
    XMLObject cxo = xo.getChild(COUNTS);
    if (cxo != null) {
        registersFound += parseAllChildren(cxo, treeLikelihood, dataType.getStateCount(), jumpTag, MarkovJumpsType.COUNTS, false);
    }
    cxo = xo.getChild(REWARDS);
    if (cxo != null) {
        registersFound += parseAllChildren(cxo, treeLikelihood, dataType.getStateCount(), jumpTag, MarkovJumpsType.REWARDS, scaleRewards);
    }
    if (registersFound == 0) {
    // Some default values for testing
    // double[] registration = new double[dataType.getStateCount()*dataType.getStateCount()];
    // MarkovJumpsCore.fillRegistrationMatrix(registration,dataType.getStateCount()); // Count all transitions
    // Parameter registerParameter = new Parameter.Default(registration);
    // registerParameter.setId(jumpTag);
    // treeLikelihood.addRegister(registerParameter,
    // MarkovJumpsType.COUNTS,
    // false);
    // Do nothing, should run the same as AncestralStateBeagleTreeLikelihood
    }
    boolean saveCompleteHistory = xo.getAttribute(SAVE_HISTORY, false);
    if (saveCompleteHistory) {
        Parameter allCounts = new Parameter.Default(dataType.getStateCount() * dataType.getStateCount());
        for (int i = 0; i < dataType.getStateCount(); ++i) {
            for (int j = 0; j < dataType.getStateCount(); ++j) {
                if (j == i) {
                    allCounts.setParameterValue(i * dataType.getStateCount() + j, 0.0);
                } else {
                    allCounts.setParameterValue(i * dataType.getStateCount() + j, 1.0);
                }
            }
        }
        allCounts.setId(MarkovJumpsBeagleTreeLikelihood.TOTAL_COUNTS);
        treeLikelihood.setLogHistories(xo.getAttribute(LOG_HISTORY, false));
        treeLikelihood.setUseCompactHistory(xo.getAttribute(COMPACT_HISTORY, false));
        treeLikelihood.addRegister(allCounts, MarkovJumpsType.HISTORY, false);
    }
    return treeLikelihood;
}

Example 8 with DataType

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

the class MarkovModulatedSubstitutionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    DataType dataType = DataTypeUtils.getDataType(xo);
    if (!(dataType instanceof HiddenDataType)) {
        throw new XMLParseException("Must construct " + MARKOV_MODULATED_MODEL + " with hidden data types. " + "You may need to provide the `-universal` extension to your hidden code type.");
    }
    Parameter switchingRates = (Parameter) xo.getElementFirstChild(SWITCHING_RATES);
    List<SubstitutionModel> substModels = new ArrayList<SubstitutionModel>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object cxo = xo.getChild(i);
        if (cxo instanceof SubstitutionModel) {
            substModels.add((SubstitutionModel) cxo);
        }
    }
    boolean geometricRates = xo.getAttribute(GEOMETRIC_RATES, false);
    Parameter rateScalar = xo.hasChildNamed(RATE_SCALAR) ? (Parameter) xo.getChild(RATE_SCALAR).getChild(Parameter.class) : null;
    SiteRateModel siteRateModel = (SiteRateModel) xo.getChild(SiteRateModel.class);
    if (siteRateModel != null) {
        if (siteRateModel.getCategoryCount() != substModels.size() && substModels.size() % siteRateModel.getCategoryCount() != 0) {
            throw new XMLParseException("Number of gamma categories must equal number of substitution models in " + xo.getId());
        }
    }
    MarkovModulatedSubstitutionModel mmsm = new MarkovModulatedSubstitutionModel(xo.getId(), substModels, switchingRates, dataType, null, rateScalar, geometricRates, siteRateModel);
    if (xo.getAttribute(RENORMALIZE, false)) {
        mmsm.setNormalization(true);
    }
    return mmsm;
}

Example 9 with DataType

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

the class AlignmentParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final SimpleAlignment alignment = new SimpleAlignment();
    final DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null) {
        throw new XMLParseException("dataType attribute expected for alignment element");
    }
    alignment.setDataType(dataType);
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        if (child instanceof UncertainSequence) {
            alignment.addSequence((UncertainSequence) child);
        } else if (child instanceof Sequence) {
            alignment.addSequence((Sequence) child);
        } else if (child instanceof DataType) {
        // already dealt with
        } else {
            throw new XMLParseException("Unknown child element found in alignment");
        }
    }
    final Logger logger = Logger.getLogger("dr.evoxml");
    logger.info("\nRead alignment" + (xo.hasAttribute(XMLParser.ID) ? ": " + xo.getId() : "") + "\n  Sequences = " + alignment.getSequenceCount() + "\n      Sites = " + alignment.getSiteCount() + "\n   Datatype = " + alignment.getDataType().getDescription());
    return alignment;
}

Example 10 with DataType

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

the class MutationDeathTypeParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evolution").info("\nCreating an extended data type.");
    Logger.getLogger("dr.evolution").info("\tIf you publish results using this model, please reference Alekseyenko, Lee and Suchard (in submision).\n");
    DataType dataType = DataTypeUtils.getDataType(xo);
    char extantChar = '\0';
    XMLObject cxo = xo.getChild(EXTANT);
    if (cxo != null) {
        extantChar = cxo.getStringAttribute(CODE).charAt(0);
    }
    cxo = xo.getChild(STATE);
    char stateChar;
    if (cxo != null) {
        stateChar = cxo.getStringAttribute(CODE).charAt(0);
    } else {
        stateChar = dataType.getChar(dataType.getGapState());
    }
    Logger.getLogger("dr.evolution").info("\tNon-existent code: " + stateChar);
    if (dataType == null && extantChar == '\0')
        throw new XMLParseException("In " + xo.getName() + " you must either provide a data type or a code for extant state");
    MutationDeathType mdt;
    if (dataType != null) {
        Logger.getLogger("dr.evolution").info("\tBase type: " + dataType.toString());
        mdt = new MutationDeathType(dataType, stateChar);
    } else {
        Logger.getLogger("dr.evolution").info("\tExtant code: " + extantChar);
        mdt = new MutationDeathType(stateChar, extantChar);
    }
    char ambiguityChar = '\0';
    String states;
    Object dxo;
    for (int i = 0; i < xo.getChildCount(); ++i) {
        dxo = xo.getChild(i);
        if (dxo instanceof XMLObject) {
            cxo = (XMLObject) dxo;
            if (cxo.getName().equals(AMBIGUITY)) {
                ambiguityChar = cxo.getStringAttribute(CODE).charAt(0);
                if (cxo.hasAttribute(STATES)) {
                    states = cxo.getStringAttribute(STATES);
                } else {
                    states = "";
                }
                mdt.addAmbiguity(ambiguityChar, states);
                Logger.getLogger("dr.evolution").info("\tAmbiguity code: " + ambiguityChar);
            }
        }
    }
    return mdt;
}