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

Example 56 with Tree

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

the class MsatSamplingTreeLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    //taxa
    ArrayList<Taxon> taxonList3 = new ArrayList<Taxon>();
    Collections.addAll(taxonList3, new Taxon("Taxon1"), new Taxon("Taxon2"), new Taxon("Taxon3"), new Taxon("Taxon4"), new Taxon("Taxon5"), new Taxon("Taxon6"), new Taxon("Taxon7"));
    Taxa taxa3 = new Taxa(taxonList3);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 6);
    Patterns msatPatterns = new Patterns(msat, taxa3);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 3, 2, 4, 5, 1 });
    //create tree
    NewickImporter importer = new NewickImporter("(((Taxon1:0.3,Taxon2:0.3):0.6,Taxon3:0.9):0.9,((Taxon4:0.5,Taxon5:0.5):0.3,(Taxon6:0.7,Taxon7:0.7):0.1):1.0);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel eu1 = new AsymmetricQuadraticModel(msat, null);
    //create msatSamplerTreeModel
    Parameter internalVal = new Parameter.Default(new double[] { 2, 3, 4, 2, 1, 5 });
    int[] externalValues = msatPatterns.getPattern(0);
    HashMap<String, Integer> taxaMap = new HashMap<String, Integer>(externalValues.length);
    boolean internalValuesProvided = true;
    for (int i = 0; i < externalValues.length; i++) {
        taxaMap.put(msatPatterns.getTaxonId(i), i);
    }
    MicrosatelliteSamplerTreeModel msatTreeModel = new MicrosatelliteSamplerTreeModel("JUnitTestEx", treeModel, internalVal, msatPatterns, externalValues, taxaMap, internalValuesProvided);
    //create msatSamplerTreeLikelihood
    BranchRateModel branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    eu1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, eu1, branchRateModel);
    //eu2
    TwoPhaseModel eu2 = new TwoPhaseModel(msat, null, eu1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    eu2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, eu2, branchRateModel);
    //ec1
    LinearBiasModel ec1 = new LinearBiasModel(msat, null, eu1, new Parameter.Default(0.48), new Parameter.Default(0.0), false, false, false);
    ec1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, ec1, branchRateModel);
    //ec2
    TwoPhaseModel ec2 = new TwoPhaseModel(msat, null, ec1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    ec2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, ec2, branchRateModel);
    //el1
    LinearBiasModel el1 = new LinearBiasModel(msat, null, eu1, new Parameter.Default(0.2), new Parameter.Default(-0.018), true, false, false);
    el1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, el1, branchRateModel);
    AsymmetricQuadraticModel pu1 = new AsymmetricQuadraticModel(msat, null, new Parameter.Default(1.0), new Parameter.Default(0.015), new Parameter.Default(0.0), new Parameter.Default(1.0), new Parameter.Default(0.015), new Parameter.Default(0.0), false);
    pu1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pu1, branchRateModel);
    //ec2
    TwoPhaseModel pu2 = new TwoPhaseModel(msat, null, pu1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    pu2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pu2, branchRateModel);
    //ec1
    LinearBiasModel pc1 = new LinearBiasModel(msat, null, pu1, new Parameter.Default(0.48), new Parameter.Default(0.0), false, false, false);
    pc1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pc1, branchRateModel);
}

Example 57 with Tree

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

the class NormalizedSequenceLikelihoodTest method createSillyTreeModel.

protected TreeModel createSillyTreeModel(int numTaxa) {
    SimpleNode[] nodes = new SimpleNode[2 * numTaxa - 1];
    for (int n = 0; n < 2 * numTaxa - 1; n++) {
        nodes[n] = new SimpleNode();
    }
    nodes[0].setTaxon(taxa[0]);
    nodes[1].setTaxon(taxa[1]);
    nodes[2].setHeight(1);
    nodes[2].addChild(nodes[0]);
    nodes[2].addChild(nodes[1]);
    SimpleNode root = nodes[2];
    if (numTaxa == 3) {
        nodes[3].setTaxon(taxa[2]);
        nodes[4].setHeight(2);
        nodes[4].addChild(nodes[2]);
        nodes[4].addChild(nodes[3]);
        root = nodes[4];
    }
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    //treeModel
    return new TreeModel(tree);
}

Example 58 with Tree

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

the class PathogenFrame method readFromFile.

protected boolean readFromFile(File file) throws IOException {
    Reader reader = new FileReader(file);
    BufferedReader bufferedReader = new BufferedReader(reader);
    String line = bufferedReader.readLine();
    while (line != null && line.length() == 0) {
        line = bufferedReader.readLine();
    }
    boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
    reader = new FileReader(file);
    Tree tree = null;
    try {
        if (isNexus) {
            NexusImporter importer = new NexusImporter(reader);
            tree = importer.importTree(taxa);
        } else {
            NewickImporter importer = new NewickImporter(reader);
            tree = importer.importTree(taxa);
        }
    } catch (Importer.ImportException ime) {
        JOptionPane.showMessageDialog(this, "Error parsing imported file: " + ime, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ime.printStackTrace();
        return false;
    } catch (IOException ioex) {
        JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
        ioex.printStackTrace();
        return false;
    } catch (Exception ex) {
        JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ex.printStackTrace();
        return false;
    }
    if (tree == null) {
        JOptionPane.showMessageDialog(this, "The file is not in a suitable format or contains no trees.", "Error reading file", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    FlexibleTree binaryTree = new FlexibleTree(tree, true);
    binaryTree.resolveTree();
    trees.add(binaryTree);
    if (taxa == null) {
        taxa = binaryTree;
    }
    getExportTreeAction().setEnabled(true);
    getExportDataAction().setEnabled(true);
    return true;
}

Example 59 with Tree

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

the class PathogenFrame method setStatusMessage.

private void setStatusMessage() {
    Tree tree = pathogenPanel.getTree();
    if (tree != null) {
        String message = "";
        message += "Tree loaded, " + tree.getTaxonCount() + " taxa";
        TemporalRooting tr = pathogenPanel.getTemporalRooting();
        if (tr.isContemporaneous()) {
            message += ", contemporaneous tips";
        } else {
            NumberFormatter nf = new NumberFormatter(3);
            message += ", dated tips with range " + nf.format(tr.getDateRange());
        }
        statusLabel.setText(message);
    }
}

Example 60 with Tree

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

the class TreeTrace method loadTreeTrace.

/**
     * Loads the trace for with trees from a reader
     *
     * @param r the reader to load the trees from
     * @return the TreeTrace
     * @throws dr.evolution.io.Importer.ImportException
     *                             thrown when tree file is not correctly formatted
     * @throws java.io.IOException if general I/O error occurs
     */
public static TreeTrace loadTreeTrace(Reader r) throws IOException, Importer.ImportException {
    BufferedReader reader = new BufferedReader(r);
    TreeTrace trace = new TreeTrace();
    dr.evolution.util.TaxonList taxonList = null;
    int minState = -1;
    int stepSize = 0;
    String line = reader.readLine();
    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 (Tree tree : trees) {
            trace.add(tree);
        }
    } 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;
}