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

Example 1 with Taxon

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

the class TreeUtils method getTipDates.

/**
     * Gets the tip dates from a tree.
     */
public static void getTipDates(Tree tree, Variate dates) {
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        Object date = taxon.getAttribute("date");
        if (date != null) {
            if (date instanceof Date) {
                dates.add(((Date) date).getTimeValue());
            } else {
                try {
                    dates.add(Double.parseDouble(date.toString()));
                } catch (NumberFormatException nfe) {
                    dates.add(0.0);
                }
            }
        } else {
            dates.add(0.0);
        }
    }
}

Example 2 with Taxon

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

the class CheckPointTreeModifier method incorporateAdditionalTaxa.

/**
     * Add the remaining taxa, which can be identified through the TreeDataLikelihood XML elements.
     */
public ArrayList<NodeRef> incorporateAdditionalTaxa(CheckPointUpdaterApp.UpdateChoice choice, BranchRates rateModel) {
    System.out.println("Tree before adding taxa:\n" + treeModel.toString() + "\n");
    ArrayList<NodeRef> newTaxaNodes = new ArrayList<NodeRef>();
    for (String str : newTaxaNames) {
        for (int i = 0; i < treeModel.getExternalNodeCount(); i++) {
            if (treeModel.getNodeTaxon(treeModel.getExternalNode(i)).getId().equals(str)) {
                newTaxaNodes.add(treeModel.getExternalNode(i));
                //always take into account Taxon dates vs. dates set through a TreeModel
                System.out.println(treeModel.getNodeTaxon(treeModel.getExternalNode(i)).getId() + " with height " + treeModel.getNodeHeight(treeModel.getExternalNode(i)) + " or " + treeModel.getNodeTaxon(treeModel.getExternalNode(i)).getHeight());
            }
        }
    }
    System.out.println("newTaxaNodes length = " + newTaxaNodes.size());
    ArrayList<Taxon> currentTaxa = new ArrayList<Taxon>();
    for (int i = 0; i < treeModel.getExternalNodeCount(); i++) {
        boolean taxonFound = false;
        for (String str : newTaxaNames) {
            if (str.equals((treeModel.getNodeTaxon(treeModel.getExternalNode(i))).getId())) {
                taxonFound = true;
            }
        }
        if (!taxonFound) {
            System.out.println("Adding " + treeModel.getNodeTaxon(treeModel.getExternalNode(i)).getId() + " to list of current taxa");
            currentTaxa.add(treeModel.getNodeTaxon(treeModel.getExternalNode(i)));
        }
    }
    System.out.println("Current taxa count = " + currentTaxa.size());
    //iterate over both current taxa and to be added taxa
    boolean originTaxon = true;
    for (Taxon taxon : currentTaxa) {
        if (taxon.getHeight() == 0.0) {
            originTaxon = false;
            System.out.println("Current taxon " + taxon.getId() + " has node height 0.0");
        }
    }
    for (NodeRef newTaxon : newTaxaNodes) {
        if (treeModel.getNodeTaxon(newTaxon).getHeight() == 0.0) {
            originTaxon = false;
            System.out.println("New taxon " + treeModel.getNodeTaxon(newTaxon).getId() + " has node height 0.0");
        }
    }
    //check the Tree(Data)Likelihoods in the connected set of likelihoods
    //focus on TreeDataLikelihood, which has getTree() to get the tree for each likelihood
    //also get the DataLikelihoodDelegate from TreeDataLikelihood
    ArrayList<TreeDataLikelihood> likelihoods = new ArrayList<TreeDataLikelihood>();
    ArrayList<Tree> trees = new ArrayList<Tree>();
    ArrayList<DataLikelihoodDelegate> delegates = new ArrayList<DataLikelihoodDelegate>();
    for (Likelihood likelihood : Likelihood.CONNECTED_LIKELIHOOD_SET) {
        if (likelihood instanceof TreeDataLikelihood) {
            likelihoods.add((TreeDataLikelihood) likelihood);
            trees.add(((TreeDataLikelihood) likelihood).getTree());
            delegates.add(((TreeDataLikelihood) likelihood).getDataLikelihoodDelegate());
        }
    }
    //suggested to go through TreeDataLikelihoodParser and give it an extra option to create a HashMap
    //keyed by the tree; am currently not overly fond of this approach
    ArrayList<PatternList> patternLists = new ArrayList<PatternList>();
    for (DataLikelihoodDelegate del : delegates) {
        if (del instanceof BeagleDataLikelihoodDelegate) {
            patternLists.add(((BeagleDataLikelihoodDelegate) del).getPatternList());
        } else if (del instanceof MultiPartitionDataLikelihoodDelegate) {
            MultiPartitionDataLikelihoodDelegate mpdld = (MultiPartitionDataLikelihoodDelegate) del;
            List<PatternList> list = mpdld.getPatternLists();
            for (PatternList pList : list) {
                patternLists.add(pList);
            }
        }
    }
    if (patternLists.size() == 0) {
        throw new RuntimeException("No patterns detected. Please make sure the XML file is BEAST 1.9 compatible.");
    }
    //aggregate all patterns to create distance matrix
    //TODO What about different trees for different partitions?
    Patterns patterns = new Patterns(patternLists.get(0));
    if (patternLists.size() > 1) {
        for (int i = 1; i < patternLists.size(); i++) {
            patterns.addPatterns(patternLists.get(i));
        }
    }
    //set the patterns for the distance matrix computations
    choice.setPatterns(patterns);
    //add new taxa one at a time
    System.out.println("Adding " + newTaxaNodes.size() + " taxa ...");
    for (NodeRef newTaxon : newTaxaNodes) {
        treeModel.setNodeHeight(newTaxon, treeModel.getNodeTaxon(newTaxon).getHeight());
        System.out.println("\nadding Taxon: " + newTaxon + " (height = " + treeModel.getNodeHeight(newTaxon) + ")");
        //check if this taxon has a more recent sampling date than all other nodes in the current TreeModel
        double offset = checkCurrentTreeNodes(newTaxon, treeModel.getRoot());
        System.out.println("Sampling date offset when adding " + newTaxon + " = " + offset);
        //AND set its current node height to 0.0 IF no originTaxon has been found
        if (offset < 0.0) {
            if (!originTaxon) {
                System.out.println("Updating all node heights with offset " + Math.abs(offset));
                updateAllTreeNodes(Math.abs(offset), treeModel.getRoot());
                treeModel.setNodeHeight(newTaxon, 0.0);
            }
        } else if (offset == 0.0) {
            if (!originTaxon) {
                treeModel.setNodeHeight(newTaxon, 0.0);
            }
        }
        //get the closest Taxon to the Taxon that needs to be added
        //take into account which taxa can currently be chosen
        Taxon closest = choice.getClosestTaxon(treeModel.getNodeTaxon(newTaxon), currentTaxa);
        System.out.println("\nclosest Taxon: " + closest + " with original height: " + closest.getHeight());
        //get the distance between these two taxa
        double distance = choice.getDistance(treeModel.getNodeTaxon(newTaxon), closest);
        System.out.println("at distance: " + distance);
        //TODO what if distance == 0.0 ??? how to choose closest taxon then (in absence of geo info)?
        //find the NodeRef for the closest Taxon (do not rely on node numbering)
        NodeRef closestRef = null;
        //careful with node numbering and subtract number of new taxa
        for (int i = 0; i < treeModel.getExternalNodeCount(); i++) {
            if (treeModel.getNodeTaxon(treeModel.getExternalNode(i)) == closest) {
                closestRef = treeModel.getExternalNode(i);
            }
        }
        System.out.println(closestRef + " with height " + treeModel.getNodeHeight(closestRef));
        //System.out.println("trying to set node height: " + closestRef + " from " + treeModel.getNodeHeight(closestRef) + " to " + closest.getHeight());
        //treeModel.setNodeHeight(closestRef, closest.getHeight());
        double timeForDistance = distance / rateModel.getBranchRate(treeModel, closestRef);
        System.out.println("timeForDistance = " + timeForDistance);
        //get parent node of branch that will be split
        NodeRef parent = treeModel.getParent(closestRef);
        //determine height of new node
        double insertHeight;
        if (treeModel.getNodeHeight(closestRef) == treeModel.getNodeHeight(newTaxon)) {
            insertHeight = treeModel.getNodeHeight(closestRef) + timeForDistance / 2.0;
            System.out.println("treeModel.getNodeHeight(closestRef) == treeModel.getNodeHeight(newTaxon): " + insertHeight);
            if (insertHeight >= treeModel.getNodeHeight(parent)) {
                insertHeight = treeModel.getNodeHeight(closestRef) + EPSILON * (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(closestRef));
            }
        } else {
            double remainder = (timeForDistance - Math.abs(treeModel.getNodeHeight(closestRef) - treeModel.getNodeHeight(newTaxon))) / 2.0;
            if (remainder > 0) {
                insertHeight = Math.max(treeModel.getNodeHeight(closestRef), treeModel.getNodeHeight(newTaxon)) + remainder;
                System.out.println("remainder > 0: " + insertHeight);
                if (insertHeight >= treeModel.getNodeHeight(parent)) {
                    insertHeight = treeModel.getNodeHeight(closestRef) + EPSILON * (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(closestRef));
                }
            } else {
                insertHeight = EPSILON * (treeModel.getNodeHeight(parent) - Math.max(treeModel.getNodeHeight(closestRef), treeModel.getNodeHeight(newTaxon)));
                insertHeight += Math.max(treeModel.getNodeHeight(closestRef), treeModel.getNodeHeight(newTaxon));
                System.out.println("remainder <= 0: " + insertHeight);
            }
        }
        System.out.println("insert at height: " + insertHeight);
        //pass on all the necessary variables to a method that adds the new taxon to the tree
        addTaxonAlongBranch(newTaxon, parent, closestRef, insertHeight);
        //option to print tree after each taxon addition
        System.out.println("\nTree after adding taxon " + newTaxon + ":\n" + treeModel.toString());
        //add newly added Taxon to list of current taxa
        currentTaxa.add(treeModel.getNodeTaxon(newTaxon));
    }
    return newTaxaNodes;
}

Example 3 with Taxon

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

the class ARGModel method fromGraphStringCompressed.

public ARGModel fromGraphStringCompressed(String source) {
    StringTokenizer st1 = new StringTokenizer(source, ":");
    int numberNodes = Integer.parseInt(st1.nextToken());
    int numberPartitions = Integer.parseInt(st1.nextToken());
    int rootNumber = Integer.parseInt(st1.nextToken());
    int external = 0;
    ArrayList<Node> nodes = new ArrayList<Node>();
    for (int i = 0; i < numberNodes; i++) {
        Node node = new Node();
        node.number = i;
        nodes.add(node);
    }
    for (int i = 0; i < numberNodes; i++) {
        String nodeString = st1.nextToken();
        StringTokenizer st2 = new StringTokenizer(nodeString);
        Node node = nodes.get(i);
        int lP = Integer.parseInt(st2.nextToken());
        int rP = Integer.parseInt(st2.nextToken());
        int lC = Integer.parseInt(st2.nextToken());
        int rC = Integer.parseInt(st2.nextToken());
        if (lP != -1)
            node.leftParent = nodes.get(lP);
        if (rP != -1)
            node.rightParent = nodes.get(rP);
        if (lC != -1)
            node.leftChild = nodes.get(lC);
        if (rC != -1)
            node.rightChild = nodes.get(rC);
        double height = Double.parseDouble(st2.nextToken());
        node.heightParameter = new Parameter.Default(height);
        String name = st2.nextToken();
        if (name.compareTo("NA") != 0) {
            // todo saveList
            node.taxon = new Taxon(name);
            external++;
        }
        String p = st2.nextToken();
        if (p.compareTo("NA") == 0)
            node.bifurcation = true;
        else {
            node.bifurcation = false;
            node.partitioning = new Parameter.Default(numberPartitions, 0.0);
            node.partitioning.setParameterValueQuietly(Integer.parseInt(p), 1.0);
            while (st2.hasMoreTokens()) node.partitioning.setParameterValueQuietly(Integer.parseInt(st2.nextToken()), 1.0);
        }
    }
    return new ARGModel(nodes, nodes.get(rootNumber), numberPartitions, external);
// return null;
}

Example 4 with Taxon

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

the class TiterImporter method readExternalNode.

/**
     * Reads an external node in.
     */
private FlexibleNode readExternalNode(TaxonList taxonList) throws IOException, ImportException {
    FlexibleNode node = new FlexibleNode();
    String label = readToken(":(),;");
    Taxon taxon;
    if (taxonList != null) {
        // if a taxon list is given then the taxon must be in it...
        int index = taxonList.getTaxonIndex(label);
        if (index != -1) {
            taxon = taxonList.getTaxon(index);
        } else {
            throw new UnknownTaxonException("Taxon in tree, '" + label + "' is unknown");
        }
    } else {
        // No taxon list given so create new taxa
        taxon = new Taxon(label);
    }
    node.setTaxon(taxon);
    return node;
}

Example 5 with Taxon

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

the class WanderingTaxonLoggerParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(NAME, xo.getId());
    WanderingTaxonLogger.Relative relative = WanderingTaxonLogger.Relative.SISTER;
    if (xo.getAttribute(WanderingTaxonLogger.RELATIVE, "sister").equalsIgnoreCase("parent")) {
        relative = WanderingTaxonLogger.Relative.PARENT;
    }
    Taxon taxon = (Taxon) xo.getChild(Taxon.class);
    return new WanderingTaxonLogger(name, taxon, relative);
}