Examples with CompoundParameter dr.inference.model.CompoundParameter used on opensource projects

Example 16 with CompoundParameter

use of dr.inference.model.CompoundParameter in project beast-mcmc by beast-dev.

the class TreeModelParser method parseXMLObject.

/**
     * @return a tree object based on the XML element it was passed.
     */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Tree tree = (Tree) xo.getChild(Tree.class);
    boolean fixHeights = xo.getAttribute(FIX_HEIGHTS, false);
    boolean fixTree = xo.getAttribute(FIX_TREE, false);
    TreeModel treeModel = new TreeModel(xo.getId(), tree, fixHeights, fixTree);
    Logger.getLogger("dr.evomodel").info("\nCreating the tree model, '" + xo.getId() + "'");
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject cxo = (XMLObject) xo.getChild(i);
            if (cxo.getName().equals(ROOT_HEIGHT)) {
                ParameterParser.replaceParameter(cxo, treeModel.getRootHeightParameter());
            } else if (cxo.getName().equals(LEAF_HEIGHT)) {
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafHeight element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon " + taxonName + " not found for leafHeight element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter newParameter = treeModel.getLeafHeightParameter(node);
                ParameterParser.replaceParameter(cxo, newParameter);
                Taxon taxon = treeModel.getTaxon(index);
                setPrecisionBounds(newParameter, taxon);
            } else if (cxo.getName().equals(LEAF_HEIGHTS)) {
                // get a set of leaf height parameters out as a compound parameter...
                TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
                Parameter offsetParameter = (Parameter) cxo.getChild(Parameter.class);
                CompoundParameter leafHeights = new CompoundParameter("leafHeights");
                for (Taxon taxon : taxa) {
                    int index = treeModel.getTaxonIndex(taxon);
                    if (index == -1) {
                        throw new XMLParseException("taxon " + taxon.getId() + " not found for leafHeight element in treeModel element");
                    }
                    NodeRef node = treeModel.getExternalNode(index);
                    Parameter newParameter = treeModel.getLeafHeightParameter(node);
                    leafHeights.addParameter(newParameter);
                    setPrecisionBounds(newParameter, taxon);
                }
                ParameterParser.replaceParameter(cxo, leafHeights);
            } else if (cxo.getName().equals(NODE_HEIGHTS)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeHeights element");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeHeightsParameter(rootNode, internalNodes, leafNodes));
            } else if (cxo.getName().equals(NODE_RATES)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                double[] initialValues = null;
                if (cxo.hasAttribute(INITIAL_VALUE)) {
                    initialValues = cxo.getDoubleArrayAttribute(INITIAL_VALUE);
                }
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeRates element");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeRatesParameter(initialValues, rootNode, internalNodes, leafNodes));
            } else if (cxo.getName().equals(NODE_TRAITS)) {
                boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
                boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
                boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
                boolean fireTreeEvents = cxo.getAttribute(FIRE_TREE_EVENTS, false);
                boolean asMatrix = cxo.getAttribute(AS_MATRIX, false);
                String name = cxo.getAttribute(NAME, "trait");
                int dim = cxo.getAttribute(MULTIVARIATE_TRAIT, 1);
                double[] initialValues = null;
                if (cxo.hasAttribute(INITIAL_VALUE)) {
                    initialValues = cxo.getDoubleArrayAttribute(INITIAL_VALUE);
                }
                if (!rootNode && !internalNodes && !leafNodes) {
                    throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeTraits element");
                }
                Parameter newParameter = asMatrix ? treeModel.createNodeTraitsParameterAsMatrix(name, dim, initialValues, rootNode, internalNodes, leafNodes, fireTreeEvents) : treeModel.createNodeTraitsParameter(name, dim, initialValues, rootNode, internalNodes, leafNodes, fireTreeEvents);
                ParameterParser.replaceParameter(cxo, newParameter);
            } else if (cxo.getName().equals(LEAF_TRAIT)) {
                String name = cxo.getAttribute(NAME, "trait");
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafTrait element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon '" + taxonName + "' not found for leafTrait element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter parameter = treeModel.getNodeTraitParameter(node, name);
                if (parameter == null)
                    throw new XMLParseException("trait '" + name + "' not found for leafTrait (taxon, " + taxonName + ") element in treeModel element");
                ParameterParser.replaceParameter(cxo, parameter);
            } else {
                throw new XMLParseException("illegal child element in " + getParserName() + ": " + cxo.getName());
            }
        } else if (xo.getChild(i) instanceof Tree) {
        // do nothing - already handled
        } else {
            throw new XMLParseException("illegal child element in  " + getParserName() + ": " + xo.getChildName(i) + " " + xo.getChild(i));
        }
    }
    // AR this is doubling up the number of bounds on each node.
    //        treeModel.setupHeightBounds();
    //System.err.println("done constructing treeModel");
    Logger.getLogger("dr.evomodel").info("  initial tree topology = " + TreeUtils.uniqueNewick(treeModel, treeModel.getRoot()));
    Logger.getLogger("dr.evomodel").info("  tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
    return treeModel;
}

Example 17 with CompoundParameter

use of dr.inference.model.CompoundParameter in project beast-mcmc by beast-dev.

the class SampleQuantileLociRatesParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final boolean normalize = xo.getAttribute(NORMALIZE, false);
    final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_MEAN_LOCI_RATE_TO, Double.NaN);
    CompoundParameter lociRates = (CompoundParameter) xo.getElementFirstChild(LOCI_RATES);
    Parameter rateQuantilesParameter = (Parameter) xo.getElementFirstChild(RATE_QUANTILES);
    ParametricDistributionModel distributionModel = (ParametricDistributionModel) xo.getElementFirstChild(DISTRIBUTION);
    Logger.getLogger("dr.evomodel").info("Using sample quantile loci rates model.");
    Logger.getLogger("dr.evomodel").info("  parametric model = " + distributionModel.getModelName());
    if (normalize) {
        Logger.getLogger("dr.evomodel").info("   mean rate is normalized to " + normalizeBranchRateTo);
    }
    return new SampleQuantileLociRates(lociRates, rateQuantilesParameter, distributionModel, normalize, normalizeBranchRateTo);
}