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

Example 36 with TaxonList

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

the class RestrictedPartialsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getId();
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    TaxonList taxa = MonophylyStatisticParser.parseTaxonListOrTaxa(xo.getChild(MonophylyStatisticParser.MRCA));
    Parameter meanParameter = (Parameter) xo.getElementFirstChild(MultivariateDistributionLikelihood.MVN_MEAN);
    Parameter priorSampleSize = (Parameter) xo.getElementFirstChild(AbstractMultivariateTraitLikelihood.PRIOR_SAMPLE_SIZE);
    RestrictedPartials rp = null;
    try {
        rp = new RestrictedPartials(name, tree, taxa, meanParameter, priorSampleSize);
    } catch (TreeUtils.MissingTaxonException e) {
        throw new XMLParseException("Unable to find taxa for " + xo.getId());
    }
    return rp;
}

Example 37 with TaxonList

use of dr.evolution.util.TaxonList 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 38 with TaxonList

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

the class TMRCAStatisticParser 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 = null;
    if (xo.hasChildNamed(MRCA)) {
        taxa = (TaxonList) xo.getElementFirstChild(MRCA);
    }
    boolean isAbsolute = xo.getAttribute(ABSOLUTE, false);
    boolean includeStem = false;
    if (xo.hasAttribute(PARENT) && xo.hasAttribute(STEM)) {
        throw new XMLParseException("Please use either " + PARENT + " or " + STEM + "!");
    } else if (xo.hasAttribute(PARENT)) {
        includeStem = xo.getBooleanAttribute(PARENT);
    } else if (xo.hasAttribute(STEM)) {
        includeStem = xo.getBooleanAttribute(STEM);
    }
    try {
        return new TMRCAStatistic(name, tree, taxa, isAbsolute, includeStem);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 39 with TaxonList

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

the class AttributePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String attributeName = xo.getStringAttribute(ATTRIBUTE);
    String secondaryAttributeName = xo.getAttribute(SECONDARY_ATTRIBUTE, (String) null);
    TaxonList taxa = (TaxonList) xo.getChild(TaxonList.class);
    DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null) {
        throw new XMLParseException("dataType expected for attributePatterns element");
    }
    // using a SimpleSiteList rather than Patterns to allow ancestral reconstruction
    SimpleSiteList patterns = new SimpleSiteList(dataType, taxa);
    int[] pattern = new int[taxa.getTaxonCount()];
    boolean attributeFound = false;
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        if (secondaryAttributeName == null || secondaryAttributeName.isEmpty()) {
            Object value = taxon.getAttribute(attributeName);
            if (value != null) {
                int state = dataType.getState(value.toString());
                if (state < 0) {
                    throw new XMLParseException("State for attribute, " + attributeName + ", in taxon, " + taxon.getId() + ", is unknown: " + value.toString());
                }
                pattern[i] = state;
                attributeFound = true;
            } else {
                pattern[i] = dataType.getUnknownState();
            }
        } else {
            Object value1 = taxon.getAttribute(attributeName);
            Object value2 = taxon.getAttribute(secondaryAttributeName);
            if (value1 != null && value2 != null) {
                String code = value1.toString() + CompositeDataTypeParser.COMPOSITE_STATE_SEPARATOR + value2.toString();
                int state = dataType.getState(code);
                if (state < 0) {
                    throw new XMLParseException("State for attributes, " + attributeName + " & " + secondaryAttributeName + ", in taxon, " + taxon.getId() + ", is unknown: " + code);
                }
                pattern[i] = state;
                attributeFound = true;
            } else {
                pattern[i] = dataType.getUnknownState();
            }
        }
    }
    if (!attributeFound) {
        throw new XMLParseException("The attribute, " + attributeName + " was missing in all taxa. Check the name of the attribute.");
    }
    patterns.addPattern(pattern);
    if (xo.hasAttribute(XMLParser.ID)) {
        Logger.getLogger("dr.evoxml").info("Read attribute patterns, '" + xo.getId() + "' for attribute, " + attributeName);
    } else {
        Logger.getLogger("dr.evoxml").info("Read attribute patterns for attribute, " + attributeName);
    }
    return patterns;
}

Example 40 with TaxonList

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

the class TipDateSamplingComponentGenerator method generate.

protected void generate(final InsertionPoint point, final Object item, final String prefix, final XMLWriter writer) {
    TipDateSamplingComponentOptions comp = (TipDateSamplingComponentOptions) options.getComponentOptions(TipDateSamplingComponentOptions.class);
    TaxonList taxa = comp.getTaxonSet();
    switch(point) {
        case IN_TREE_MODEL:
            {
                writeLeafHeightParameters(writer, (PartitionTreeModel) item, taxa);
            }
            break;
        case AFTER_TREE_MODEL:
            if (options.getPartitionTreeModels().size() > 1) {
                // we have multiple treeModels with some or all the same taxa - create a JointParameter for each...
                writeJointParameters(writer, taxa);
            }
            if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
                writer.writeOpenTag("compoundParameter", new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "treeModel.tipDates") });
                for (int i = 0; i < taxa.getTaxonCount(); i++) {
                    Taxon taxon = taxa.getTaxon(i);
                    writer.writeIDref(ParameterParser.PARAMETER, "age(" + taxon.getId() + ")");
                }
                writer.writeCloseTag("compoundParameter");
            }
            break;
        case IN_MCMC_PRIOR:
            if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_INDIVIDUALLY || comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
            // nothing to do - individual parameter priors are written automatically
            } else if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
            }
            break;
        case IN_FILE_LOG_PARAMETERS:
            if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_INDIVIDUALLY || comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
                for (int i = 0; i < taxa.getTaxonCount(); i++) {
                    Taxon taxon = taxa.getTaxon(i);
                    writer.writeIDref(ParameterParser.PARAMETER, "age(" + taxon.getId() + ")");
                }
            } else if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
                writer.writeIDref(ParameterParser.PARAMETER, "treeModel.tipDates");
            }
            break;
        default:
            throw new IllegalArgumentException("This insertion point is not implemented for " + this.getClass().getName());
    }
}