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

Example 41 with Taxon

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

the class TransmissionLikelihood method setupIntervals.

private int setupIntervals(NodeRef node) throws IncompatibleException {
    double height = virusTree.getNodeHeight(node);
    int host;
    if (virusTree.isExternal(node)) {
        Taxon hostTaxon = (Taxon) virusTree.getTaxonAttribute(node.getNumber(), "host");
        if (transmissionHistoryModel != null) {
            host = transmissionHistoryModel.getHostIndex(hostTaxon);
        } else {
            host = hostTree.getTaxonIndex(hostTaxon);
        }
        intervals[host].addSampleEvent(height);
    } else {
        // Tree should be bifurcating...
        int host1 = setupIntervals(virusTree.getChild(node, 0));
        int host2 = setupIntervals(virusTree.getChild(node, 1));
        while (height > transmissionTime[host1]) {
            double time = transmissionTime[host1];
            intervals[host1].addNothingEvent(time);
            host1 = donorHost[host1];
            intervals[host1].addSampleEvent(time);
        }
        while (height > transmissionTime[host2]) {
            double time = transmissionTime[host2];
            intervals[host2].addNothingEvent(time);
            host2 = donorHost[host2];
            intervals[host2].addSampleEvent(time);
        }
        if (host1 != host2) {
            throw new IncompatibleException("Virus tree is not compatible with transmission history");
        }
        host = host1;
        intervals[host].addCoalescentEvent(height);
    }
    return host;
}

Example 42 with Taxon

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

the class NewickParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    //        boolean usingDates = xo.getAttribute(USING_DATES, true);
    boolean usingDates = true;
    if (xo.hasAttribute(USING_DATES)) {
        usingDates = xo.getAttribute(USING_DATES, true);
    }
    boolean usingHeights = false;
    if (xo.hasAttribute(USING_HEIGHTS)) {
        usingHeights = xo.getAttribute(USING_HEIGHTS, true);
    }
    if (usingDates && usingHeights) {
        throw new XMLParseException("Unable to use both dates and node heights. Specify value of usingDates attribute.");
    }
    //		else if (!usingDates && !usingHeights) {
    //			System.out.println("Tree is assumed to be ultrametric");
    //		}
    StringBuffer buffer = new StringBuffer();
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof String) {
            buffer.append((String) xo.getChild(i));
        } else {
            throw new XMLParseException("illegal element in newick element");
        }
    }
    java.io.Reader reader = new java.io.StringReader(buffer.toString());
    NewickImporter importer = new NewickImporter(reader);
    FlexibleTree tree;
    try {
        tree = (FlexibleTree) importer.importTree(null);
    } catch (IOException ioe) {
        throw new XMLParseException("error parsing tree in newick element");
    } catch (NewickImporter.BranchMissingException bme) {
        throw new XMLParseException("branch missing in tree in newick element");
    } catch (Importer.ImportException ime) {
        throw new XMLParseException("error parsing tree in newick element - " + ime.getMessage());
    }
    if (tree == null) {
        throw new XMLParseException("Failed to read tree");
    }
    tree.setUnits(units);
    for (int i = 0; i < tree.getTaxonCount(); i++) {
        FlexibleNode node = (FlexibleNode) tree.getExternalNode(i);
        String id = node.getTaxon().getId();
        Taxon taxon = null;
        XMLObject obj = getStore().get(id);
        if (obj != null && obj.getNativeObject() instanceof Taxon) {
            taxon = (Taxon) obj.getNativeObject();
        }
        if (taxon != null) {
            node.setTaxon(taxon);
        } else {
            throw new XMLParseException("unknown taxon, " + id + ", in newick tree");
        }
    }
    if (usingDates) {
        for (int i = 0; i < tree.getTaxonCount(); i++) {
            NodeRef node = tree.getExternalNode(i);
            dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getTaxonAttribute(i, dr.evolution.util.Date.DATE);
            if (date == null) {
                date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getExternalNode(i), dr.evolution.util.Date.DATE);
            }
            double height = 0.0;
            double nodeHeight = tree.getNodeHeight(node);
            if (date != null) {
                height = Taxon.getHeightFromDate(date);
            }
            if (Math.abs(nodeHeight - height) > 1e-5) {
                System.out.println("  Changing height of node " + tree.getTaxon(node.getNumber()) + " from " + nodeHeight + " to " + height);
                tree.setNodeHeight(node, height);
            }
        }
        for (int i = 0; i < tree.getInternalNodeCount(); i++) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getInternalNode(i), dr.evolution.util.Date.DATE);
            if (date != null) {
                double height = Taxon.getHeightFromDate(date);
                tree.setNodeHeight(tree.getInternalNode(i), height);
            }
        }
        // END: i loop
        MutableTree.Utils.correctHeightsForTips(tree);
    } else if (!usingDates && !usingHeights) {
        System.out.println("Tree is assumed to be ultrametric");
        // not using dates or heights
        for (int i = 0; i < tree.getTaxonCount(); i++) {
            final NodeRef leaf = tree.getExternalNode(i);
            final double h = tree.getNodeHeight(leaf);
            if (h != 0.0) {
                double zero = 0.0;
                System.out.println("  Changing height of leaf node " + tree.getTaxon(leaf.getNumber()) + " from " + h + " to " + zero);
                tree.setNodeHeight(leaf, zero);
            }
        }
    // END: i loop
    } else {
        System.out.println("Using node heights.");
    }
    if (xo.hasAttribute(RESCALE_HEIGHT)) {
        double rescaleHeight = xo.getDoubleAttribute(RESCALE_HEIGHT);
        double scale = rescaleHeight / tree.getNodeHeight(tree.getRoot());
        for (int i = 0; i < tree.getInternalNodeCount(); i++) {
            NodeRef n = tree.getInternalNode(i);
            tree.setNodeHeight(n, tree.getNodeHeight(n) * scale);
        }
    }
    if (xo.hasAttribute(RESCALE_LENGTH)) {
        double rescaleLength = xo.getDoubleAttribute(RESCALE_LENGTH);
        double scale = rescaleLength / TreeUtils.getTreeLength(tree, tree.getRoot());
        for (int i = 0; i < tree.getInternalNodeCount(); i++) {
            NodeRef n = tree.getInternalNode(i);
            tree.setNodeHeight(n, tree.getNodeHeight(n) * scale);
        }
    }
    //System.out.println("Constructed newick tree = " + Tree.Utils.uniqueNewick(tree, tree.getRoot()));
    return tree;
}

Example 43 with Taxon

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

the class UncertainAttributePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String attributeName = xo.getStringAttribute(ATTRIBUTE);
    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
    UncertainSiteList patterns = new UncertainSiteList(dataType, taxa);
    boolean normalize = xo.getAttribute(NORMALIZE, true);
    if (dataType == null) {
        // TODO Is this necessary given XMLSyntaxRules?
        throw new XMLParseException("dataType expected for attributePatterns element");
    }
    double[][] uncertainPattern = new double[taxa.getTaxonCount()][];
    // Parse attributes
    boolean attributeFound = false;
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        Object value = taxon.getAttribute(attributeName);
        if (value != null) {
            attributeFound = true;
            List<StateProbability> stateProbabilities;
            try {
                stateProbabilities = parseStates(value.toString(), dataType);
            } catch (StateParseException e) {
                throw new XMLParseException("State or probability for attribute (" + attributeName + ") in taxon " + taxon.getId() + " is invalid; state = \"" + e.getState() + "\" and probability =\"" + e.getProbability() + "\"");
            }
            uncertainPattern[i] = convertToPartials(stateProbabilities, dataType, normalize);
        } else {
            throw new XMLParseException("State for attribute (" + attributeName + ") in taxon " + taxon.getId() + " is unknown.");
        }
    }
    if (!attributeFound) {
        throw new XMLParseException("The attribute (" + attributeName + ") was missing in all taxa. Check the name of the attribute.");
    }
    patterns.addPattern(uncertainPattern);
    Logger.getLogger("dr.evolution").info("\n ---------------------------------\nCreating an uncertain attribute model for attribute \"" + attributeName + "\"");
    Logger.getLogger("dr.evolution").info("\tIf you publish results using this model, please reference:");
    Logger.getLogger("dr.evolution").info("\t" + Citable.Utils.getCitationString(patterns));
    Logger.getLogger("dr.evolution").info("\n");
    return patterns;
}

Example 44 with Taxon

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

the class SequenceParser method parseXMLObject.

/**
     * @return a sequence object based on the XML element it was passed.
     */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Sequence sequence = new Sequence();
    Taxon taxon = (Taxon) xo.getChild(Taxon.class);
    DataType dataType = null;
    if (xo.hasAttribute(DataType.DATA_TYPE)) {
        String dataTypeStr = xo.getStringAttribute(DataType.DATA_TYPE);
        if (dataTypeStr.equals(Nucleotides.DESCRIPTION)) {
            dataType = Nucleotides.INSTANCE;
        } else if (dataTypeStr.equals(AminoAcids.DESCRIPTION)) {
            dataType = AminoAcids.INSTANCE;
        } else if (dataTypeStr.equals(Codons.DESCRIPTION)) {
            dataType = Codons.UNIVERSAL;
        } else if (dataTypeStr.equals(TwoStates.DESCRIPTION)) {
            dataType = TwoStates.INSTANCE;
        }
    }
    StringBuffer seqBuf = new StringBuffer();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof String) {
            StringTokenizer st = new StringTokenizer((String) child);
            while (st.hasMoreTokens()) {
                seqBuf.append(st.nextToken());
            }
        }
    }
    // We really need to filter the input string to check for illegal characters.
    // Perhaps sequence.setSequenceString could throw an exception if any characters
    // don't fit the dataType.
    String sequenceString = seqBuf.toString();
    if (sequenceString.length() == 0) {
        throw new XMLParseException("Sequence data missing from sequence element!");
    }
    if (dataType != null) {
        sequence.setDataType(dataType);
    }
    sequence.setSequenceString(sequenceString);
    sequence.setTaxon(taxon);
    return sequence;
}

Example 45 with Taxon

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

the class HiddenLinkageLikelihood method getLogLikelihood.

public double getLogLikelihood() {
    double logL = 0;
    // first check whether the reads are linked together
    // according to the linkage constraints provided as data in the
    // input file
    ArrayList<LinkedGroup> linkedGroups = hlm.getData().getConstraints();
    for (LinkedGroup lg : linkedGroups) {
        TaxonList tl = lg.getLinkedReads();
        int found = 0;
        for (int l = 0; l < hlm.getLinkageGroupCount(); l++) {
            Set<Taxon> group = hlm.getGroup(l);
            for (int i = 0; i < tl.getTaxonCount(); i++) {
                if (group.contains(tl.getTaxon(i)))
                    found++;
            }
            if (found == tl.getTaxonCount()) {
                logL += Math.log(lg.getLinkageProbability());
                break;
            } else if (found > 0) {
                logL += Math.log(1.0 - lg.getLinkageProbability());
                break;
            }
        }
    }
    // reference tree topology
    if (hlm.getData().getFixedReferenceTree()) {
        // not yet implemented.
        logL += Double.NEGATIVE_INFINITY;
    }
    return logL;
}