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

Example 1 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 2 with TaxonList

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

the class ARGTrace method loadARGTrace.

/**
 * Loads the trace for with trees from a reader
 *
 * @return the TreeTrace
 */
public static ARGTrace loadARGTrace(Reader r) throws IOException, Importer.ImportException {
    BufferedReader reader = new BufferedReader(r);
    ARGTrace trace = new ARGTrace();
    dr.evolution.util.TaxonList taxonList = null;
    int minState = -1;
    int stepSize = 0;
    String line;
    ARGModel nullARG = new ARGModel(null, null, 0, 0);
    ArrayList<String> nameList = new ArrayList<String>();
    taxonList = (TaxonList) nullARG;
    while ((line = reader.readLine()) != null) {
        // String line = reader.readLine();
        line.trim();
        if (line.toUpperCase().startsWith("ARG")) {
            StringTokenizer st = new StringTokenizer(line, "=");
            nameList.add(st.nextToken());
            ARGModel arg = nullARG.fromGraphStringCompressed(st.nextToken().trim());
            trace.add(arg);
        }
    }
    if (nameList.size() < 2) {
        throw new Importer.ImportException("Less than two ARGs in the trace file");
    }
    minState = getStateNumber(nameList.get(0));
    stepSize = getStateNumber(nameList.get(1)) - minState;
    // if (line.toUpperCase().startsWith("#NEXUS")) {
    // NexusImporter importer = new NexusImporter(reader);
    // Tree [] trees = importer.importTrees(null);
    // 
    // if (trees.length < 2) {
    // throw new Importer.ImportException("Less than two trees in the trace file");
    // }
    // 
    // String id1 = trees[0].getId();
    // String id2 = trees[1].getId();
    // 
    // minState = getStateNumber(id1);
    // stepSize = getStateNumber(id2) - minState;
    // 
    // for (int i = 0; i < trees.length; i++) {
    // args.add(args[i]);
    // }
    // } else {
    // NewickImporter importer = new NewickImporter(reader);
    // 
    // while (true) {
    // 
    // int state = 0;
    // Tree tree;
    // 
    // try {
    // state = importer.readInteger();
    // tree = importer.importTree(taxonList);
    // 
    // if (taxonList == null) {
    // // The first tree becomes the taxon list. This means
    // // that all subsequent trees will look up their taxa
    // // in that taxon list rather than creating their own
    // // duplicitous ones.
    // taxonList = tree;
    // }
    // } catch (Importer.ImportException ie) {
    // System.out.println("Error reading tree for state " + state);
    // throw ie;
    // } catch (EOFException e) {
    // break;
    // }
    // 
    // if (minState == -1) {
    // minState = state;
    // } else if (stepSize == 0) {
    // stepSize = state - minState;
    // }
    // 
    // trace.add(tree);
    // }
    // }
    trace.setMinimumState(minState);
    trace.setStepSize(stepSize);
    return trace;
}

Example 3 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 4 with TaxonList

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

the class GhostTreeModelParser 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);
    TaxonList ghostTaxa = (TaxonList) xo.getElementFirstChild(GHOST_TAXA);
    GhostTreeModel treeModel = new GhostTreeModel(xo.getId(), tree, ghostTaxa);
    Logger.getLogger("dr.evomodel").info("\nCreating the tree model, '" + xo.getId() + "'" + "\n\nwith " + ghostTaxa.getTaxonCount() + " ghost lineages.");
    Logger.getLogger("dr.evomodel").info("  taxon count = " + treeModel.getExternalNodeCount());
    Logger.getLogger("dr.evomodel").info("  tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
    return treeModel;
}

Example 5 with TaxonList

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

the class BranchSpecificBranchModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing clade-specific branch model.");
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    BranchSpecificBranchModel branchModel = new BranchSpecificBranchModel(tree, substitutionModel);
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject xoc = (XMLObject) xo.getChild(i);
            if (xoc.getName().equals(CLADE)) {
                double stemWeight = xoc.getAttribute(STEM_WEIGHT, 0.0);
                substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                if (taxonList.getTaxonCount() == 1) {
                    throw new XMLParseException("A clade must be defined by at least two taxa");
                }
                try {
                    branchModel.addClade(taxonList, substitutionModel, stemWeight);
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            } else if (xoc.getName().equals(EXTERNAL_BRANCHES)) {
                substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                try {
                    branchModel.addExternalBranches(taxonList, substitutionModel);
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            } else if (xoc.getName().equals(BACKBONE)) {
                substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
                try {
                    branchModel.addBackbone(taxonList, substitutionModel);
                } catch (TreeUtils.MissingTaxonException mte) {
                    throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
                }
            }
        }
    }
    return branchModel;
}