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

Example 56 with TaxonList

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

the class AncestralTraitParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String traitName = xo.getAttribute(TRAIT_NAME, STATES);
    String name = xo.getAttribute(NAME, traitName);
    Tree tree = (Tree) xo.getChild(Tree.class);
    TreeTraitProvider treeTraitProvider = (TreeTraitProvider) xo.getChild(TreeTraitProvider.class);
    TaxonList taxa = null;
    if (xo.hasChildNamed(MRCA)) {
        taxa = (TaxonList) xo.getElementFirstChild(MRCA);
    }
    TreeTrait trait = treeTraitProvider.getTreeTrait(traitName);
    if (trait == null) {
        throw new XMLParseException("A trait called, " + traitName + ", was not available from the TreeTraitProvider supplied to " + getParserName() + (xo.hasId() ? ", with ID " + xo.getId() : ""));
    }
    try {
        return new AncestralTrait(name, trait, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 57 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 = true;
    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;
            } else {
                attributeFound = false;
            }
        } 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;
            } else {
                attributeFound = false;
            }
        }
    }
    if (!attributeFound) {
        throw new XMLParseException("The attribute, " + attributeName + " was not found 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 58 with TaxonList

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

the class TreeTraitParserUtilities method jitter.

public void jitter(XMLObject xo, int length, List<Integer> missingIndices) throws XMLParseException {
    XMLObject cxo = xo.getChild(TreeTraitParserUtilities.JITTER);
    Parameter traits = (Parameter) cxo.getChild(Parameter.class);
    // Must be included, no default value
    double[] window = cxo.getDoubleArrayAttribute(TreeTraitParserUtilities.WINDOW);
    // default = true
    boolean duplicates = cxo.getAttribute(TreeTraitParserUtilities.DUPLICATES, true);
    TaxonList taxonList = (TaxonList) cxo.getChild(TaxonList.class);
    jitter(traits, length, missingIndices, window, taxonList, duplicates, true);
}

Example 59 with TaxonList

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

the class EmpiricalTreeDistributionModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final String fileName = xo.getStringAttribute(FILE_NAME);
    // default is random tree
    int startingTree = xo.getAttribute(STARTING_TREE, -1);
    // default is random draw
    boolean iterate = xo.getAttribute(ITERATE, false);
    if (iterate && startingTree < 0) {
        startingTree = 0;
    }
    Logger.getLogger("dr.evomodel").info("Creating the empirical tree distribution model, '" + xo.getId() + "'");
    TaxonList taxa = (TaxonList) xo.getChild(TaxonList.class);
    final File file = FileHelpers.getFile(fileName);
    Tree[] trees = null;
    NexusImporter importer = null;
    try {
        FileReader reader = new FileReader(file);
        importer = new NexusImporter(reader);
        if (!iterate) {
            // Re-order taxon numbers to original TaxonList order
            trees = importer.importTrees(taxa, true);
            reader.close();
        }
    } catch (FileNotFoundException e) {
        throw new XMLParseException(e.getMessage());
    } catch (IOException e) {
        throw new XMLParseException(e.getMessage());
    } catch (Importer.ImportException e) {
        throw new XMLParseException(e.getMessage());
    }
    if (iterate) {
        Logger.getLogger("dr.evomodel").info("    Iterate over each tree from file, " + fileName);
        return new EmpiricalTreeDistributionModel(importer, startingTree);
    } else {
        Logger.getLogger("dr.evomodel").info("    Randomly jump between " + trees.length + " trees from file, " + fileName);
        return new EmpiricalTreeDistributionModel(trees, startingTree);
    }
}

Example 60 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.");
    }
}