Examples with Tree dr.evolution.tree.Tree used on opensource projects

Example 1 with Tree

use of dr.evolution.tree.Tree 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 2 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class BeagleTreeLikelihood method main.

public static void main(String[] args) {
    try {
        MathUtils.setSeed(666);
        System.out.println("Test case 1: simulateOnePartition");
        int sequenceLength = 1000;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create branch model
        Parameter kappa1 = new Parameter.Default(1, 1);
        Parameter kappa2 = new Parameter.Default(1, 1);
        HKY hky1 = new HKY(kappa1, freqModel);
        HKY hky2 = new HKY(kappa2, freqModel);
        HomogeneousBranchModel homogenousBranchSubstitutionModel = new HomogeneousBranchModel(hky1);
        List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
        substitutionModels.add(hky1);
        substitutionModels.add(hky2);
        List<FrequencyModel> freqModels = new ArrayList<FrequencyModel>();
        freqModels.add(freqModel);
        Parameter epochTimes = new Parameter.Default(1, 20);
        // create branch rate model
        Parameter rate = new Parameter.Default(1, 0.001);
        BranchRateModel branchRateModel = new StrictClockBranchRates(rate);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        BranchModel homogeneousBranchModel = new HomogeneousBranchModel(hky1);
        BranchModel epochBranchModel = new EpochBranchModel(treeModel, substitutionModels, epochTimes);
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        homogenousBranchSubstitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        Alignment alignment = simulator.simulate(false, false);
        BeagleTreeLikelihood nbtl = new BeagleTreeLikelihood(alignment, treeModel, homogeneousBranchModel, siteRateModel, branchRateModel, null, false, PartialsRescalingScheme.DEFAULT, false);
        System.out.println("nBTL(homogeneous) = " + nbtl.getLogLikelihood());
        nbtl = new BeagleTreeLikelihood(alignment, treeModel, epochBranchModel, siteRateModel, branchRateModel, null, false, PartialsRescalingScheme.DEFAULT, false);
        System.out.println("nBTL(epoch) = " + nbtl.getLogLikelihood());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 3 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class TiterImporter method importTrees.

/**
     * importTrees.
     */
public Tree[] importTrees(TaxonList taxonList) throws IOException, ImportException {
    boolean done = false;
    ArrayList<FlexibleTree> array = new ArrayList<FlexibleTree>();
    do {
        try {
            skipUntil("(");
            unreadCharacter('(');
            FlexibleNode root = readInternalNode(taxonList);
            FlexibleTree tree = new FlexibleTree(root, false, true);
            array.add(tree);
            if (taxonList == null) {
                taxonList = tree;
            }
            if (readCharacter() != ';') {
                throw new BadFormatException("Expecting ';' after tree");
            }
        } catch (EOFException e) {
            done = true;
        }
    } while (!done);
    Tree[] trees = new Tree[array.size()];
    array.toArray(trees);
    return trees;
}

Example 4 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class OldTreesPanel method createTree.

private void createTree() {
    if (generateTreeDialog == null) {
        generateTreeDialog = new GenerateTreeDialog(frame);
    }
    int result = generateTreeDialog.showDialog(options);
    if (result != JOptionPane.CANCEL_OPTION) {
        GenerateTreeDialog.MethodTypes methodType = generateTreeDialog.getMethodType();
        PartitionData partition = generateTreeDialog.getDataPartition();
        Patterns patterns = new Patterns(partition.getAlignment());
        DistanceMatrix distances = new F84DistanceMatrix(patterns);
        Tree tree;
        TemporalRooting temporalRooting;
        switch(methodType) {
            case NJ:
                tree = new NeighborJoiningTree(distances);
                temporalRooting = new TemporalRooting(tree);
                tree = temporalRooting.findRoot(tree, TemporalRooting.RootingFunction.CORRELATION);
                break;
            case UPGMA:
                tree = new UPGMATree(distances);
                temporalRooting = new TemporalRooting(tree);
                break;
            default:
                throw new IllegalArgumentException("unknown method type");
        }
        tree.setId(generateTreeDialog.getName());
        options.userTrees.add(tree);
        treesTableModel.fireTableDataChanged();
        int row = options.userTrees.size() - 1;
        treesTable.getSelectionModel().setSelectionInterval(row, row);
    }
    fireTreePriorsChanged();
}

Example 5 with Tree

use of dr.evolution.tree.Tree in project beast-mcmc by beast-dev.

the class TimeSlicer method readAndAnalyzeTrees.

// private List<Tree> importTrees(String treeFileName, int burnin) throws IOException, Importer.ImportException {
// 
// int totalTrees = 10000;
// 
// progressStream.println("Reading trees (bar assumes 10,000 trees)...");
// progressStream.println("0              25             50             75            100");
// progressStream.println("|--------------|--------------|--------------|--------------|");
// 
// int stepSize = totalTrees / 60;
// if (stepSize < 1) stepSize = 1;
// 
// List<Tree> treeList = new ArrayList<Tree>();
// BufferedReader reader1 = new BufferedReader(new FileReader(treeFileName));
// 
// String line1 = reader1.readLine();
// TreeImporter importer1;
// if (line1.toUpperCase().startsWith("#NEXUS")) {
// importer1 = new NexusImporter(new FileReader(treeFileName));
// } else {
// importer1 = new NewickImporter(new FileReader(treeFileName));
// }
// totalTrees = 0;
// while (importer1.hasTree()) {
// Tree treeTime = importer1.importNextTree();
// 
// if (totalTrees > burnin)
// treeList.add(treeTime);
// 
// if (totalTrees > 0 && totalTrees % stepSize == 0) {
// progressStream.print("*");
// progressStream.flush();
// }
// totalTrees++;
// }
// return treeList;
// }
private void readAndAnalyzeTrees(String treeFileName, int burnin, int skipEvery, String[] traits, double[] slices, boolean impute, boolean trueNoise, Normalization normalize, boolean divideByBranchLength, BranchSet branchset, Set taxaSet) throws IOException, Importer.ImportException {
    int totalTrees = 10000;
    int totalStars = 0;
    progressStream.println("Reading and analyzing trees (bar assumes 10,000 trees)...");
    progressStream.println("0              25             50             75            100");
    progressStream.println("|--------------|--------------|--------------|--------------|");
    int stepSize = totalTrees / 60;
    if (stepSize < 1)
        stepSize = 1;
    BufferedReader reader1 = new BufferedReader(new FileReader(treeFileName));
    String line1 = reader1.readLine();
    TreeImporter importer1;
    if (line1.toUpperCase().startsWith("#NEXUS")) {
        importer1 = new NexusImporter(new FileReader(treeFileName));
    } else {
        importer1 = new NewickImporter(new FileReader(treeFileName));
    }
    totalTrees = 0;
    while (importer1.hasTree()) {
        Tree treeTime = importer1.importNextTree();
        if (totalTrees % skipEvery == 0) {
            treesRead++;
            if (totalTrees >= burnin) {
                analyzeTree(treeTime, traits, slices, impute, trueNoise, normalize, divideByBranchLength, branchset, taxaSet);
            }
        }
        if (totalTrees > 0 && totalTrees % stepSize == 0) {
            progressStream.print("*");
            totalStars++;
            if (totalStars % 61 == 0)
                progressStream.print("\n");
            progressStream.flush();
        }
        totalTrees++;
    }
    progressStream.print("\n");
}