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

Example 61 with Node

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

the class ConvertedEdgeHop method proposal.

@Override
public double proposal() {
    if (acg.getTotalConvCount() == 0)
        return Double.NEGATIVE_INFINITY;
    // Select recombination at random
    Conversion recomb = chooseConversion();
    // Choose whether to move departure or arrival point
    boolean moveDeparture;
    moveDeparture = recomb.getNode2().isRoot() || Randomizer.nextBoolean();
    // Select new attachment point:
    double u = Randomizer.nextDouble() * acg.getClonalFrameLength();
    Node nodeBelow = null;
    double newHeight = -1;
    for (Node node : acg.getNodesAsArray()) {
        if (node.isRoot())
            continue;
        if (u < node.getLength()) {
            newHeight = node.getHeight() + u;
            nodeBelow = node;
            break;
        }
        u -= node.getLength();
    }
    if (newHeight < 0.0)
        throw new IllegalStateException("Problem with recombinant edge " + "hop operator!  This is a bug.");
    // Check that new height does not lie out of bounds
    if (moveDeparture) {
        if (newHeight > recomb.getHeight2())
            return Double.NEGATIVE_INFINITY;
        else {
            recomb.setHeight1(newHeight);
            recomb.setNode1(nodeBelow);
        }
    } else {
        if (newHeight < recomb.getHeight1())
            return Double.NEGATIVE_INFINITY;
        else {
            recomb.setHeight2(newHeight);
            recomb.setNode2(nodeBelow);
        }
    }
    return 0.0;
}

Example 62 with Node

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

the class ConvertedEdgeSlide method proposal.

@Override
public double proposal() {
    double logHR = 0.0;
    if (acg.getTotalConvCount() == 0)
        return Double.NEGATIVE_INFINITY;
    // Select edge at random:
    Conversion conv = chooseConversion();
    // Decide whether to move departure or arrival point
    boolean moveDeparture = Randomizer.nextBoolean();
    // Get current (old) attachment height
    double oldHeight;
    if (moveDeparture) {
        oldHeight = conv.getHeight1();
    } else {
        oldHeight = conv.getHeight2();
    }
    // Choose window:
    double w = apertureSizeInput.get() * acg.getRoot().getHeight();
    // Set new height
    double newHeight = oldHeight + (Randomizer.nextDouble() - 0.5) * w;
    // Check for boundary violation
    if (moveDeparture) {
        if (newHeight > conv.getHeight2() || newHeight > acg.getRoot().getHeight())
            return Double.NEGATIVE_INFINITY;
    } else {
        if (newHeight < conv.getHeight1())
            return Double.NEGATIVE_INFINITY;
    }
    // Get node below current (old) attachment point
    Node nodeBelow;
    if (moveDeparture)
        nodeBelow = conv.getNode1();
    else
        nodeBelow = conv.getNode2();
    // Choose node below new attachment point
    if (newHeight < oldHeight) {
        while (newHeight < nodeBelow.getHeight()) {
            if (nodeBelow.isLeaf())
                return Double.NEGATIVE_INFINITY;
            if (Randomizer.nextBoolean())
                nodeBelow = nodeBelow.getLeft();
            else
                nodeBelow = nodeBelow.getRight();
            logHR += -Math.log(0.5);
        }
    } else {
        while (!nodeBelow.isRoot() && newHeight > nodeBelow.getParent().getHeight()) {
            nodeBelow = nodeBelow.getParent();
            logHR += Math.log(0.5);
        }
    }
    // Write changes back to recombination object
    if (moveDeparture) {
        conv.setHeight1(newHeight);
        conv.setNode1(nodeBelow);
    } else {
        conv.setHeight2(newHeight);
        conv.setNode2(nodeBelow);
    }
    return logHR;
}

Example 63 with Node

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

the class CFConvSwapExperiment method connectEdge.

public static void connectEdge(ConversionGraph acg, Node node, Node destEdgeBase, double destTime) {
    if (node.isRoot())
        throw new IllegalArgumentException("Programmer error: " + "root argument passed to connectEdge().");
    Node parent = node.getParent();
    if (destEdgeBase.isRoot()) {
        parent.addChild(destEdgeBase);
    } else {
        Node grandParent = destEdgeBase.getParent();
        grandParent.removeChild(destEdgeBase);
        grandParent.addChild(parent);
        parent.addChild(destEdgeBase);
    }
    parent.setHeight(destTime);
    for (Locus locus : acg.getLoci()) {
        for (Conversion conv : acg.getConversions(locus)) {
            if (conv.getNode1() == destEdgeBase && conv.getHeight1() > destTime)
                conv.setNode1(parent);
            if (conv.getNode2() == destEdgeBase && conv.getHeight2() > destTime)
                conv.setNode2(parent);
        }
    }
}

Example 64 with Node

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

the class AffectedSiteList method haveReachedAllMRCAs.

/**
 * Test to see whether MRCA of every site has been found.
 * This is actually pretty expensive.  There's got to be a better way...
 *
 * @param activeCFNodes set of active CF nodes and the sites they represent
 * @param activeConversions set of active conversions and the sites they represent
 * @return true if all sites have found an MRCA, false otherwise
 */
protected boolean haveReachedAllMRCAs(Map<Node, Map<Locus, List<Integer>>> activeCFNodes, Map<Locus, Set<Conversion>> activeConversions) {
    for (Locus locus : acg.getLoci()) {
        List<Integer> startSites = new ArrayList<>();
        List<Integer> endSites = new ArrayList<>();
        for (Node node : activeCFNodes.keySet()) {
            for (int i = 0; i < activeCFNodes.get(node).get(locus).size(); i += 2) {
                startSites.add(activeCFNodes.get(node).get(locus).get(i));
                endSites.add(activeCFNodes.get(node).get(locus).get(i + 1));
            }
        }
        for (Conversion conv : activeConversions.get(locus)) {
            for (int i = 0; i < affectedSites.get(conv).size(); i += 2) {
                startSites.add(affectedSites.get(conv).get(i));
                endSites.add(affectedSites.get(conv).get(i + 1));
            }
        }
        Collections.sort(startSites);
        Collections.sort(endSites);
        for (int i = 0; i < startSites.size() - 1; i++) {
            if (startSites.get(i + 1) < endSites.get(i))
                return false;
        }
    }
    return true;
}

Example 65 with Node

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

the class CFEventList method updateEvents.

/**
 * Assemble sorted list of events on clonal frame and a map from nodes
 * to these events.
 */
public void updateEvents() {
    if (!dirty)
        return;
    events.clear();
    // Create event list
    for (Node node : acg.getNodesAsArray()) {
        Event event = new Event(node);
        events.add(event);
    }
    // Sort events in increasing order of their times
    Collections.sort(events, (Event o1, Event o2) -> {
        if (o1.t < o2.t)
            return -1;
        if (o2.t < o1.t)
            return 1;
        return 0;
    });
    // Compute lineage counts:
    int k = 0;
    for (Event event : events) {
        if (event.type == EventType.SAMPLE)
            k += 1;
        else
            k -= 1;
        event.lineages = k;
    }
    dirty = false;
}