Examples with TaxonList dr.evolution.util.TaxonList used on opensource projects

Example 51 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class SequenceErrorModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SequenceErrorModel.ErrorType errorType = SequenceErrorModel.ErrorType.ALL_SUBSTITUTIONS;
    if (xo.hasAttribute(TYPE)) {
        if (xo.getStringAttribute(TYPE).equalsIgnoreCase("transitions")) {
            errorType = SequenceErrorModel.ErrorType.TRANSITIONS_ONLY;
        } else if (!xo.getStringAttribute(TYPE).equalsIgnoreCase("all")) {
            throw new XMLParseException("unrecognized option for attribute, 'type': " + xo.getStringAttribute(TYPE));
        }
    }
    Parameter baseDamageRateParameter = null;
    if (xo.hasChildNamed(BASE_ERROR_RATE)) {
        baseDamageRateParameter = (Parameter) xo.getElementFirstChild(BASE_ERROR_RATE);
    }
    Parameter ageRelatedRateParameter = null;
    if (xo.hasChildNamed(AGE_RELATED_RATE)) {
        ageRelatedRateParameter = (Parameter) xo.getElementFirstChild(AGE_RELATED_RATE);
    }
    if (baseDamageRateParameter == null && ageRelatedRateParameter == null) {
        throw new XMLParseException("You must specify one or other or both of " + BASE_ERROR_RATE + " and " + AGE_RELATED_RATE + " parameters");
    }
    Parameter indicatorParameter = null;
    if (xo.hasChildNamed(INDICATORS)) {
        indicatorParameter = (Parameter) xo.getElementFirstChild(INDICATORS);
    }
    TaxonList includeTaxa = null;
    TaxonList excludeTaxa = null;
    if (xo.hasChildNamed(INCLUDE)) {
        includeTaxa = (TaxonList) xo.getElementFirstChild(INCLUDE);
    }
    if (xo.hasChildNamed(EXCLUDE)) {
        excludeTaxa = (TaxonList) xo.getElementFirstChild(EXCLUDE);
    }
    SequenceErrorModel aDNADamageModel = new SequenceErrorModel(includeTaxa, excludeTaxa, errorType, baseDamageRateParameter, ageRelatedRateParameter, indicatorParameter);
    Logger.getLogger("dr.evomodel").info("Using sequence error model, assuming errors cause " + (errorType == SequenceErrorModel.ErrorType.TRANSITIONS_ONLY ? "transitions only." : "any substitution."));
    return aDNADamageModel;
}

Example 52 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class AncestralTraitTreeModelParser method parseAncestor.

private static AncestralTaxonInTree parseAncestor(MutableTreeModel tree, XMLObject xo, final int index) throws XMLParseException {
    Taxon ancestor = (Taxon) xo.getChild(Taxon.class);
    Parameter pseudoBranchLength = (Parameter) xo.getChild(Parameter.class);
    AncestralTaxonInTree ancestorInTree;
    NodeRef node = new NodeRef() {

        @Override
        public int getNumber() {
            return index;
        }

        @Override
        public void setNumber(int n) {
            throw new RuntimeException("Do not set");
        }
    };
    if (xo.hasChildNamed(MonophylyStatisticParser.MRCA)) {
        TaxonList descendants = MonophylyStatisticParser.parseTaxonListOrTaxa(xo.getChild(MonophylyStatisticParser.MRCA));
        try {
            ancestorInTree = new AncestralTaxonInTree(ancestor, tree, descendants, pseudoBranchLength, null, node, index, 0.0);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to find taxa for " + ancestor.getId());
        }
    } else {
        XMLObject cxo = xo.getChild(ANCESTRAL_PATH);
        Taxon taxon = (Taxon) cxo.getChild(Taxon.class);
        Parameter time = (Parameter) cxo.getChild(Parameter.class);
        boolean relativeHeight = cxo.getAttribute(RELATIVE_HEIGHT, false);
        double offset = 0;
        if (relativeHeight) {
            Object date = taxon.getAttribute("date");
            if (date != null && date instanceof Date) {
                offset = taxon.getHeight();
            } else {
                throw new XMLParseException("Taxon '" + taxon.getId() + "' has no specified date");
            }
        } else {
            if (time.getParameterValue(0) <= taxon.getHeight()) {
                throw new XMLParseException("Ancestral path time must be > sampling time for taxon '" + taxon.getId() + "'");
            }
        }
        Taxa descendent = new Taxa();
        descendent.addTaxon(taxon);
        try {
            ancestorInTree = new AncestralTaxonInTree(ancestor, tree, descendent, pseudoBranchLength, time, node, index, // TODO Refactor into separate class from MRCA version
            offset);
        } catch (TreeUtils.MissingTaxonException e) {
            throw new XMLParseException("Unable to find taxa for " + ancestor.getId());
        }
    }
    return ancestorInTree;
}

Example 53 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class ExternalLengthStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    TaxonList taxa = (TaxonList) xo.getChild(Taxa.class);
    try {
        return new ExternalLengthStatistic(name, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 54 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class MRCATraitStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(NAME, xo.getId());
    String trait = xo.getStringAttribute(TRAIT);
    DefaultTreeModel tree = (DefaultTreeModel) xo.getChild(DefaultTreeModel.class);
    TaxonList taxa = (TaxonList) xo.getElementFirstChild(MRCA);
    try {
        return new MRCATraitStatistic(name, trait, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 55 with TaxonList

use of dr.evolution.util.TaxonList in project beast-mcmc by beast-dev.

the class MonophylyStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Boolean inverse = xo.getAttribute(INVERSE, false);
    Tree tree = (Tree) xo.getChild(Tree.class);
    TaxonList taxa = parseTaxonListOrTaxa(xo.getChild(MRCA));
    TaxonList ignore = null;
    if (xo.hasChildNamed(IGNORE)) {
        ignore = parseTaxonListOrTaxa(xo.getChild(IGNORE));
    }
    try {
        return new MonophylyStatistic(name, tree, taxa, ignore, inverse);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}