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

Example 76 with Tree

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

the class BeagleSeqSimTest method ancestralSequenceTree.

//END: simulateRandomBranchAssignment
static void ancestralSequenceTree() {
    try {
        LinkedHashMap<NodeRef, int[]> sequenceMap = new LinkedHashMap<NodeRef, int[]>();
        DataType dataType = Nucleotides.INSTANCE;
        // 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);
        for (NodeRef node : treeModel.getNodes()) {
            if (treeModel.isExternal(node)) {
                int[] seq = new int[] { 1, 1, 1 };
                sequenceMap.put(node, seq);
            } else {
                int[] seq = new int[] { 2, 2, 2 };
                sequenceMap.put(node, seq);
            }
        }
        // END: nodes loop
        AncestralSequenceTrait ancestralSequence = new AncestralSequenceTrait(sequenceMap, dataType);
        TreeTraitProvider[] treeTraitProviders = new TreeTraitProvider[] { ancestralSequence };
        StringBuffer buffer = new StringBuffer();
        NumberFormat format = NumberFormat.getNumberInstance(Locale.ENGLISH);
        boolean useTipLabels = true;
        //
        TreeUtils.newick(//
        treeModel, //
        treeModel.getRoot(), //
        useTipLabels, //
        TreeUtils.BranchLengthType.LENGTHS_AS_TIME, //
        format, //
        null, //
        treeTraitProviders, null, buffer);
        System.out.println(buffer);
    } catch (IOException e) {
        e.printStackTrace();
    } catch (ImportException e) {
        e.printStackTrace();
    }
// END: try-catch
}

Example 77 with Tree

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

the class BeagleSeqSimTest method simulateTopology.

// END: annotateTree
static void simulateTopology() {
    try {
        System.out.println("Test case 1: simulateTopology");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        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);
        // set demographic function
        ExponentialGrowth exponentialGrowth = new ExponentialGrowth(Units.Type.YEARS);
        exponentialGrowth.setN0(10);
        exponentialGrowth.setGrowthRate(0.5);
        Taxa taxa = new Taxa();
        for (Taxon taxon : tree.asList()) {
            double absoluteHeight = Utils.getAbsoluteTaxonHeight(taxon, tree);
            taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, absoluteHeight);
            // taxon.setAttribute("date", new Date(absoluteHeight,
            // Units.Type.YEARS, true));
            taxa.addTaxon(taxon);
        }
        // END: taxon loop
        CoalescentSimulator topologySimulator = new CoalescentSimulator();
        TreeModel treeModel = new TreeModel(topologySimulator.simulateTree(taxa, exponentialGrowth));
        System.out.println(treeModel.toString());
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        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);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 78 with Tree

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

the class BeagleSeqSimTest method simulateOnePartition.

// END: simulate topology
static void simulateOnePartition() {
    try {
        MathUtils.setSeed(666);
        System.out.println("Test case 2: simulateOnePartition");
        int sequenceLength = 10;
        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 substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAAGTGAGG");
        partition1.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        SimpleAlignment alignment = simulator.simulate(simulateInPar, false);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 79 with Tree

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

the class DebugTreeImporter method main.

//args[0]: saved dump file
//args[1]: new XML file
//args[2]: new tree (Newick format)
//args[3]: output file
//e.g.: dump.trump.160 worobey-con-sc-resume-162-taxa.xml newtree.nwk restart.dump
public static void main(String[] args) {
    if (args.length != 4) {
        throw new RuntimeException("Incorrect number of arguments.");
    }
    try {
        FileReader fileIn = new FileReader(args[2]);
        BufferedReader in = new BufferedReader(fileIn);
        String fullTree = in.readLine();
        NewickImporter importer = new NewickImporter(fullTree);
        Tree tree = importer.importNextTree();
        //assume rootHeight in dumpfile is ALWAYS followed by all the nodeHeights
        System.out.println("root height: " + tree.getNodeHeight(tree.getRoot()));
        FileReader dumpFileIn = new FileReader(args[0]);
        BufferedReader dumpIn = new BufferedReader(dumpFileIn);
        FileWriter dumpFileOut = new FileWriter(args[3]);
        BufferedWriter dumpOut = new BufferedWriter(dumpFileOut);
        String original = dumpIn.readLine();
        String[] fields = original.split("\t");
        //write new rootHeight to new output dump file
        while (!fields[0].equals("treeModel.rootHeight")) {
            if (DEBUG) {
                System.out.println(original);
            }
            dumpOut.write(original + "\n");
            original = dumpIn.readLine();
            fields = original.split("\t");
        }
        fields[2] = Double.toString(tree.getNodeHeight(tree.getRoot()));
        for (int i = 0; i < fields.length; i++) {
            dumpOut.write(fields[i] + "\t");
        }
        dumpOut.write("\n");
        //write all new node heights to new output dump file
        int nodeCount = tree.getNodeCount();
        if (DEBUG) {
            System.out.println(nodeCount + " nodes found in tree.");
        }
        for (int i = 0; i < (nodeCount - 1); i++) {
            if (DEBUG) {
                System.out.println(tree.getNode(i).getNumber() + "\t" + tree.getNodeHeight(tree.getNode(i)));
            }
            dumpOut.write(tree.getNode(i).getNumber() + "\t1\t" + tree.getNodeHeight(tree.getNode(i)) + "\n");
        }
        //skip all the node heights in the original dump file
        //no clue as to how many there are ...
        //best I can tell only node heights have integers as parameter names
        original = dumpIn.readLine();
        if (DEBUG) {
            System.out.println(original);
        }
        fields = original.split("\t");
        while (isInteger(fields[0])) {
            original = dumpIn.readLine();
            fields = original.split("\t");
        }
        while (!fields[0].equals("treeModel")) {
            dumpOut.write(original + "\n");
            original = dumpIn.readLine();
            if (DEBUG) {
                System.out.println(original);
            }
            fields = original.split("\t");
        }
        dumpOut.write(fields[0] + "\t" + fullTree);
        dumpOut.flush();
        dumpOut.close();
    } catch (FileNotFoundException fnfe) {
        throw new RuntimeException("Tree file not found.");
    } catch (IOException ioe) {
        throw new RuntimeException("Unable to read file: " + ioe.getMessage());
    } catch (Importer.ImportException ie) {
        throw new RuntimeException("Unable to import tree: " + ie.getMessage());
    }
}

Example 80 with Tree

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

the class IstvanOperator method doOperation.

public double doOperation() {
    Tree tree = likelihood.getTreeModel();
    alignment = likelihood.getAlignment();
    //System.out.println("Incoming alignment");
    //System.out.println(alignment);
    //System.out.println();
    SubstitutionModel substModel = likelihood.getSiteModel().getSubstitutionModel();
    // initialize the iParent and iTau arrays based on the given tree.
    initTree(tree, likelihood.getSiteModel().getMu());
    int[] treeIndex = new int[tree.getTaxonCount()];
    for (int i = 0; i < treeIndex.length; i++) {
        treeIndex[i] = tree.getTaxonIndex(alignment.getTaxonId(i));
    }
    // initialize the iAlignment array from the given alignment.
    initAlignment(alignment, treeIndex);
    // initialize the iProbs array from the substitution model -- must be called after populating tree!
    initSubstitutionModel(substModel);
    DataType dataType = substModel.getDataType();
    proposal.setGapSymbol(dataType.getGapState());
    int[][] returnedAlignment = new int[iAlignment.length][];
    //System.out.println("Initialization done, starting proposal proper...");
    double logq = proposal.propose(iAlignment, iProbs, iBaseFreqs, iParent, iTau, returnedAlignment, tuning, exponent, gapPenalty);
    //System.out.println("Proposal finished, logq=" + logq);
    //create new alignment object
    SimpleAlignment newAlignment = new SimpleAlignment();
    for (int i = 0; i < alignment.getTaxonCount(); i++) {
        StringBuffer seqBuffer = new StringBuffer();
        for (int j = 0; j < returnedAlignment[i].length; j++) {
            seqBuffer.append(dataType.getChar(returnedAlignment[treeIndex[i]][j]));
        }
        // add sequences in order of tree
        String seqString = seqBuffer.toString();
        Sequence sequence = new Sequence(alignment.getTaxon(i), seqString);
        newAlignment.addSequence(sequence);
        String oldunaligned = alignment.getUnalignedSequenceString(i);
        String unaligned = newAlignment.getUnalignedSequenceString(i);
        if (!unaligned.equals(oldunaligned)) {
            System.err.println("Sequence changed from:");
            System.err.println("old:'" + oldunaligned + "'");
            System.err.println("new:'" + unaligned + "'");
            throw new RuntimeException();
        }
    }
    //System.out.println("Outgoing alignment");
    //System.out.println(newAlignment);
    //System.out.println();
    likelihood.setAlignment(newAlignment);
    return logq;
}