Examples with Node beast.evolution.tree.Node used on opensource projects

Example 81 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class CFConvSwapExperiment method main.

public static void main(String[] args) throws Exception {
    // Load model
    XMLParser parser = new XMLParser();
    MCMC mcmc = (MCMC) parser.parseFile(new File("inferencePreSimulatedData.xml"));
    State state = mcmc.startStateInput.get();
    state.setStateFileName("problem.state");
    state.restoreFromFile();
    double oldPosterior = state.robustlyCalcPosterior(mcmc.posteriorInput.get());
    ConversionGraph acg = (ConversionGraph) state.getStateNode(0);
    PrintStream ps = new PrintStream("proposal.trees");
    ps.println(acg);
    Node srcNode = acg.getNode(3);
    Node srcNodeS = getSibling(srcNode);
    Node destNode = acg.getNode(6);
    double t_srcNodeP = srcNode.getParent().getHeight();
    disconnectEdge(acg, srcNode);
    Locus locus = acg.getLoci().get(0);
    Conversion convToReplace = acg.getConversions(locus).get(27);
    acg.deleteConversion(convToReplace);
    Node srcNodeP = srcNode.getParent();
    connectEdge(acg, srcNode, destNode, convToReplace.getHeight2());
    // Move Conversions
    for (Conversion conv : acg.getConversions(locus)) {
        boolean moved = false;
        if (conv.getNode1() == srcNode && conv.getHeight1() > srcNodeP.getHeight()) {
            conv.setNode1(destNode);
            moved = true;
        }
        if (conv.getNode2() == srcNode && conv.getHeight2() > srcNodeP.getHeight()) {
            conv.setNode2(destNode);
            moved = true;
        }
        if (moved) {
            while (conv.getHeight1() > conv.getNode1().getParent().getHeight()) conv.setNode1(conv.getNode1().getParent());
            while (conv.getHeight2() > conv.getNode2().getParent().getHeight()) conv.setNode2(conv.getNode2().getParent());
        }
    }
    Conversion convNew = new Conversion();
    convNew.setLocus(locus);
    convNew.setStartSite(0);
    convNew.setEndSite(4000);
    convNew.setNode1(srcNode);
    convNew.setNode2(srcNodeS);
    convNew.setHeight1(convToReplace.getHeight1());
    convNew.setHeight2(t_srcNodeP);
    acg.addConversion(convNew);
    ps.println(acg);
    double newPosterior = state.robustlyCalcPosterior(mcmc.posteriorInput.get());
    System.out.println(newPosterior - oldPosterior);
// state.setStateFileName("proposal.state");
// state.storeToFile(1);
// Open state file
}

Example 82 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class CFConvSwapExperiment method disconnectEdge.

public static void disconnectEdge(ConversionGraph acg, Node node) {
    if (node.isRoot())
        throw new IllegalArgumentException("Programmer error: " + "root argument passed to disconnectEdge().");
    Node parent = node.getParent();
    Node sister = getSibling(node);
    if (parent.isRoot()) {
        parent.removeChild(sister);
        sister.setParent(null);
    } else {
        Node grandParent = parent.getParent();
        grandParent.removeChild(parent);
        parent.setParent(null);
        parent.removeChild(sister);
        grandParent.addChild(sister);
    }
    for (Locus locus : acg.getLoci()) {
        for (Conversion conv : acg.getConversions(locus)) {
            if (conv.getNode1() == parent)
                conv.setNode1(sister);
            if (conv.getNode2() == parent)
                conv.setNode2(sister);
        }
    }
}

Example 83 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class ClonalFrameLogger method init.

public void init(PrintStream out) {
    Node node = acg.getRoot();
    out.println("#NEXUS\n");
    out.println("Begin taxa;");
    out.println("\tDimensions ntax=" + acg.getLeafNodeCount() + ";");
    out.println("\t\tTaxlabels");
    acg.printTaxa(node, out, acg.getNodeCount() / 2);
    out.println("\t\t\t;");
    out.println("End;");
    out.println("Begin trees;");
    out.println("\tTranslate");
    acg.printTranslate(node, out, acg.getNodeCount() / 2);
    out.print(";");
}

Example 84 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class CFOperator method expandConversions.

/**
 * Take length of new edge above srcNode that is greater than the
 * original height of srcNode.parent and shifts a random fraction of
 * conversion attachments to it from the lineage above destNode.
 *
 * In the case that destNode was the root, the conversions starting
 * above destNode are drawn from the prior.
 *
 * Assumes topology has not yet been altered.
 *
 * @param srcNode source node for the move
 * @param destNode dest node for the move
 * @param destTime new time drawn for srcNode.P.
 * @return log probability of new conversion configuration.
 */
protected double expandConversions(Node srcNode, Node destNode, double destTime) {
    double logP = 0.0;
    double volatileHeight = acg.getRoot().getHeight();
    boolean forwardRootMove = destTime > volatileHeight;
    Node node = srcNode.getParent();
    while (node != null) {
        for (Locus locus : acg.getLoci()) {
            for (Conversion conv : acg.getConversions(locus)) {
                if (conv.getNode1() == node && conv.getHeight1() < destTime) {
                    if (Randomizer.nextBoolean())
                        conv.setNode1(srcNode);
                    logP += Math.log(0.5);
                }
                if (conv.getNode2() == node && conv.getHeight2() < destTime) {
                    if (Randomizer.nextBoolean())
                        conv.setNode2(srcNode);
                    logP += Math.log(0.5);
                }
            }
        }
        node = node.getParent();
    }
    // Apply topology modifications.
    disconnectEdge(srcNode);
    connectEdge(srcNode, destNode, destTime);
    // this was a forward root move
    if (forwardRootMove) {
        acg.setRoot(srcNode.getParent());
        double L = 2.0 * (destTime - volatileHeight);
        double Nexp = L * rhoInput.get().getValue() * (acg.getTotalSequenceLength() + acg.getLoci().size() * (deltaInput.get().getValue() - 1.0));
        int N = (int) Randomizer.nextPoisson(Nexp);
        // Factorial cancels
        logP += -Nexp + N * Math.log(Nexp);
        for (int i = 0; i < N; i++) {
            Conversion conv = new Conversion();
            double u = Randomizer.nextDouble() * L;
            if (u < 0.5 * L) {
                conv.setNode1(destNode);
                conv.setHeight1(volatileHeight + u);
            } else {
                conv.setNode1(srcNode);
                conv.setHeight1(volatileHeight + u - 0.5 * L);
            }
            logP += Math.log(1.0 / L) + drawAffectedRegion(conv) + coalesceEdge(conv);
            acg.addConversion(conv);
        }
    }
    return logP;
}

Example 85 with Node

use of beast.evolution.tree.Node in project bacter by tgvaughan.

the class CFSubtreeExchange method proposal.

@Override
public double proposal() {
    double logHGF = 0.0;
    if (acg.getLeafNodeCount() < 3)
        return Double.NEGATIVE_INFINITY;
    Node srcNode, srcNodeP, destNode, destNodeP;
    if (isNarrowInput.get()) {
        // Narrow exchange selection:
        do {
            srcNode = acg.getNode(Randomizer.nextInt(acg.getNodeCount() - 1));
        } while (srcNode.getParent().isRoot());
        srcNodeP = srcNode.getParent();
        destNode = getSibling(srcNodeP);
        destNodeP = destNode.getParent();
    } else {
        // Wide exchange selection:
        srcNode = acg.getNode(Randomizer.nextInt(acg.getNodeCount() - 1));
        srcNodeP = srcNode.getParent();
        do {
            destNode = acg.getNode(Randomizer.nextInt(acg.getNodeCount() - 1));
        } while (destNode == srcNode || destNode.getParent() == srcNode.getParent());
        destNodeP = destNode.getParent();
    }
    double t_srcNodeP = srcNodeP.getHeight();
    double t_destNodeP = destNodeP.getHeight();
    // Reject if substitution would result in negative branch lengths:
    if (destNode == srcNodeP || srcNode == destNodeP || destNode.getHeight() > t_srcNodeP || srcNode.getHeight() > t_destNodeP)
        return Double.NEGATIVE_INFINITY;
    if (t_srcNodeP > t_destNodeP) {
        Node srcNodeS = getSibling(srcNode);
        logHGF += collapseConversions(srcNode, destNodeP, t_destNodeP);
        if (!srcNodeS.isRoot() && srcNodeS.getLength() == 0.0)
            srcNodeS = srcNodeS.getParent();
        logHGF -= expandConversions(destNode, srcNodeS, t_srcNodeP);
    } else {
        Node srcNodeS = getSibling(srcNode);
        logHGF -= expandConversions(srcNode, destNodeP, t_destNodeP);
        if (srcNodeP.isRoot())
            acg.setRoot(srcNodeP);
        logHGF += collapseConversions(destNode, srcNodeS, t_srcNodeP);
    }
    assert !acg.isInvalid() : "CFSTX proposed invalid state.";
    return logHGF;
}