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

Example 21 with TaxonList

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

the class Defects method readNexusFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private static Alignment readNexusFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                // ignore tree block
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return alignment;
}

Example 22 with TaxonList

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

the class PartitionedTreeModelParser 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);
    AbstractOutbreak outbreak = (AbstractOutbreak) xo.getElementFirstChild(OUTBREAK);
    PartitionedTreeModel treeModel;
    if (xo.hasAttribute(STARTING_TT_FILE)) {
        treeModel = new PartitionedTreeModel(xo.getId(), tree, outbreak, xo.getStringAttribute(STARTING_TT_FILE));
    } else {
        treeModel = new PartitionedTreeModel(xo.getId(), tree, outbreak);
    }
    Logger.getLogger("dr.evomodel").info("Creating the partitioned 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);
                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");
                }
                ParameterParser.replaceParameter(cxo, treeModel.createNodeTraitsParameter(name, dim, initialValues, rootNode, internalNodes, leafNodes, fireTreeEvents));
            } 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 {
                if (!cxo.getName().equals(OUTBREAK)) {
                    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 23 with TaxonList

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

the class SpeciationLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(MODEL);
    final SpeciationModel specModel = (SpeciationModel) cxo.getChild(SpeciationModel.class);
    cxo = xo.getChild(TREE);
    final Tree tree = (Tree) cxo.getChild(Tree.class);
    Set<Taxon> excludeTaxa = null;
    if (xo.hasChildNamed(INCLUDE)) {
        excludeTaxa = new HashSet<Taxon>();
        for (int i = 0; i < tree.getTaxonCount(); i++) {
            excludeTaxa.add(tree.getTaxon(i));
        }
        cxo = xo.getChild(INCLUDE);
        for (int i = 0; i < cxo.getChildCount(); i++) {
            TaxonList taxonList = (TaxonList) cxo.getChild(i);
            for (int j = 0; j < taxonList.getTaxonCount(); j++) {
                excludeTaxa.remove(taxonList.getTaxon(j));
            }
        }
    }
    if (xo.hasChildNamed(EXCLUDE)) {
        excludeTaxa = new HashSet<Taxon>();
        cxo = xo.getChild(EXCLUDE);
        for (int i = 0; i < cxo.getChildCount(); i++) {
            TaxonList taxonList = (TaxonList) cxo.getChild(i);
            for (int j = 0; j < taxonList.getTaxonCount(); j++) {
                excludeTaxa.add(taxonList.getTaxon(j));
            }
        }
    }
    if (excludeTaxa != null) {
        Logger.getLogger("dr.evomodel").info("Speciation model excluding " + excludeTaxa.size() + " taxa from prior - " + (tree.getTaxonCount() - excludeTaxa.size()) + " taxa remaining.");
    }
    final XMLObject cal = xo.getChild(CALIBRATION);
    if (cal != null) {
        if (excludeTaxa != null) {
            throw new XMLParseException("Sorry, not implemented: internal calibration prior + excluded taxa");
        }
        List<Distribution> dists = new ArrayList<Distribution>();
        List<Taxa> taxa = new ArrayList<Taxa>();
        List<Boolean> forParent = new ArrayList<Boolean>();
        // (Statistic) cal.getChild(Statistic.class);
        Statistic userPDF = null;
        for (int k = 0; k < cal.getChildCount(); ++k) {
            final Object ck = cal.getChild(k);
            if (DistributionLikelihood.class.isInstance(ck)) {
                dists.add(((DistributionLikelihood) ck).getDistribution());
            } else if (Distribution.class.isInstance(ck)) {
                dists.add((Distribution) ck);
            } else if (Taxa.class.isInstance(ck)) {
                final Taxa tx = (Taxa) ck;
                taxa.add(tx);
                forParent.add(tx.getTaxonCount() == 1);
            } else if (Statistic.class.isInstance(ck)) {
                if (userPDF != null) {
                    throw new XMLParseException("more than one userPDF correction???");
                }
                userPDF = (Statistic) cal.getChild(Statistic.class);
            } else {
                XMLObject cko = (XMLObject) ck;
                assert cko.getChildCount() == 2;
                for (int i = 0; i < 2; ++i) {
                    final Object chi = cko.getChild(i);
                    if (DistributionLikelihood.class.isInstance(chi)) {
                        dists.add(((DistributionLikelihood) chi).getDistribution());
                    } else if (Distribution.class.isInstance(chi)) {
                        dists.add((Distribution) chi);
                    } else if (Taxa.class.isInstance(chi)) {
                        taxa.add((Taxa) chi);
                        boolean fp = ((Taxa) chi).getTaxonCount() == 1;
                        if (cko.hasAttribute(PARENT)) {
                            boolean ufp = cko.getBooleanAttribute(PARENT);
                            if (fp && !ufp) {
                                throw new XMLParseException("forParent==false for a single taxon?? (must be true)");
                            }
                            fp = ufp;
                        }
                        forParent.add(fp);
                    } else {
                        assert false;
                    }
                }
            }
        }
        if (dists.size() != taxa.size()) {
            throw new XMLParseException("Mismatch in number of distributions and taxa specs");
        }
        try {
            final String correction = cal.getAttribute(CORRECTION, EXACT);
            final CalibrationPoints.CorrectionType type = correction.equals(EXACT) ? CalibrationPoints.CorrectionType.EXACT : (correction.equals(APPROX) ? CalibrationPoints.CorrectionType.APPROXIMATED : (correction.equals(NONE) ? CalibrationPoints.CorrectionType.NONE : (correction.equals(PEXACT) ? CalibrationPoints.CorrectionType.PEXACT : null)));
            if (cal.hasAttribute(CORRECTION) && type == null) {
                throw new XMLParseException("correction type == " + correction + "???");
            }
            final CalibrationPoints calib = new CalibrationPoints(tree, specModel.isYule(), dists, taxa, forParent, userPDF, type);
            final SpeciationLikelihood speciationLikelihood = new SpeciationLikelihood(tree, specModel, null, calib);
            return speciationLikelihood;
        } catch (IllegalArgumentException e) {
            throw new XMLParseException(e.getMessage());
        }
    }
    return new SpeciationLikelihood(tree, specModel, excludeTaxa, null);
}

Example 24 with TaxonList

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

the class Coevolve method readNexusFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private Alignment readNexusFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                // ignore tree block
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return alignment;
}

Example 25 with TaxonList

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

the class CoalescentLikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(MODEL);
    DemographicModel demoModel = (DemographicModel) cxo.getChild(DemographicModel.class);
    List<TreeModel> trees = new ArrayList<TreeModel>();
    List<Double> popFactors = new ArrayList<Double>();
    MultiLociTreeSet treesSet = demoModel instanceof MultiLociTreeSet ? (MultiLociTreeSet) demoModel : null;
    for (int k = 0; k < xo.getChildCount(); ++k) {
        final Object child = xo.getChild(k);
        if (child instanceof XMLObject) {
            cxo = (XMLObject) child;
            if (cxo.getName().equals(POPULATION_TREE)) {
                final TreeModel t = (TreeModel) cxo.getChild(TreeModel.class);
                assert t != null;
                trees.add(t);
                popFactors.add(cxo.getAttribute(POPULATION_FACTOR, 1.0));
            }
        }
    //                in the future we may have arbitrary multi-loci element
    //                else if( child instanceof MultiLociTreeSet )  {
    //                    treesSet = (MultiLociTreeSet)child;
    //                }
    }
    TreeModel treeModel = null;
    if (trees.size() == 1 && popFactors.get(0) == 1.0) {
        treeModel = trees.get(0);
    } else if (trees.size() > 1) {
        treesSet = new MultiLociTreeSet.Default(trees, popFactors);
    } else if (!(trees.size() == 0 && treesSet != null)) {
        throw new XMLParseException("Incorrectly constructed likelihood element");
    }
    TaxonList includeSubtree = null;
    if (xo.hasChildNamed(INCLUDE)) {
        includeSubtree = (TaxonList) xo.getElementFirstChild(INCLUDE);
    }
    List<TaxonList> excludeSubtrees = new ArrayList<TaxonList>();
    if (xo.hasChildNamed(EXCLUDE)) {
        cxo = xo.getChild(EXCLUDE);
        for (int i = 0; i < cxo.getChildCount(); i++) {
            excludeSubtrees.add((TaxonList) cxo.getChild(i));
        }
    }
    if (treeModel != null) {
        try {
            return new CoalescentLikelihood(treeModel, includeSubtree, excludeSubtrees, demoModel);
        } catch (TreeUtils.MissingTaxonException mte) {
            throw new XMLParseException("treeModel missing a taxon from taxon list in " + getParserName() + " element");
        }
    } else {
        if (includeSubtree != null || excludeSubtrees.size() > 0) {
            throw new XMLParseException("Include/Exclude taxa not supported for multi locus sets");
        }
        // a base - and modifing it will probsbly result in a bigger mess.
        return new OldAbstractCoalescentLikelihood(treesSet, demoModel);
    }
}