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

Example 86 with Node

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

the class ConvertedEdgeHopContemp method proposal.

@Override
public double proposal() {
    if (acg.getTotalConvCount() == 0)
        return Double.NEGATIVE_INFINITY;
    // Select recombination at random
    Conversion conv = chooseConversion();
    // Choose whether to move departure or arrival point
    boolean moveDeparture = conv.getNode2().isRoot() || Randomizer.nextBoolean();
    double pointHeight = moveDeparture ? conv.getHeight1() : conv.getHeight2();
    Node convNode = moveDeparture ? conv.getNode1() : conv.getNode2();
    // Find list of CF edges alive at pointHeight
    List<Node> intersectingEdges = new ArrayList<>();
    for (Node node : acg.getNodesAsArray()) {
        if (node.isRoot() || node == convNode || node.getHeight() > pointHeight || node.getParent().getHeight() < pointHeight) {
            continue;
        }
        intersectingEdges.add(node);
    }
    if (intersectingEdges.isEmpty())
        return Double.NEGATIVE_INFINITY;
    // Select new attachment point:
    if (moveDeparture)
        conv.setNode1(intersectingEdges.get(Randomizer.nextInt(intersectingEdges.size())));
    else
        conv.setNode2(intersectingEdges.get(Randomizer.nextInt(intersectingEdges.size())));
    return 0.0;
}

Example 87 with Node

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

the class ConversionGraph method fromStringOld.

/**
 * Load ACG from old string representation.
 *
 * @param str string representation of ACG
 */
@Deprecated
public void fromStringOld(String str) {
    // Extract clonal frame and recombination components of string
    Pattern cfPattern = Pattern.compile("^[^\\(]*(\\(.*)$");
    Matcher cfMatcher = cfPattern.matcher(str);
    if (!cfMatcher.find())
        throw new RuntimeException("Error parsing ACG state string.");
    // Process clonal frame
    String sNewick = cfMatcher.group(cfMatcher.groupCount());
    try {
        TreeParser parser = new TreeParser();
        parser.thresholdInput.setValue(1e-10, parser);
        parser.offsetInput.setValue(0, parser);
        setRoot(parser.parseNewick(sNewick));
    } catch (Exception ex) {
        Logger.getLogger(ConversionGraph.class.getName()).log(Level.SEVERE, null, ex);
    }
    initArrays();
    Pattern convPattern = Pattern.compile("\\[&([^]]*)]");
    Matcher convMatcher = convPattern.matcher(str);
    // Process recombinations
    for (Locus locus : getLoci()) convs.get(locus).clear();
    while (convMatcher.find()) {
        String[] elements = convMatcher.group(1).split(",");
        Locus locus = getLocusByID(elements[0]);
        if (locus == null)
            throw new RuntimeException("Uknown locus id " + elements[0] + ".  Aborting.");
        Node node1 = getNode(Integer.parseInt(elements[1]));
        int startLocus = Integer.parseInt(elements[2]);
        double height1 = Double.parseDouble(elements[3]);
        Node node2 = getNode(Integer.parseInt(elements[4]));
        int endLocus = Integer.parseInt(elements[5]);
        double height2 = Double.parseDouble(elements[6]);
        Conversion conv = new Conversion(node1, height1, node2, height2, startLocus, endLocus, this, locus);
        addConversion(conv);
    }
    if (isInvalid()) {
        throw new IllegalArgumentException("Invalid ACG read from string. Aborting.");
    }
}

Example 88 with Node

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

the class ConversionGraph method init.

/*
     * Loggable implementation.
     */
@Override
public void init(PrintStream out) {
    Node node = getRoot();
    out.println("#NEXUS\n");
    out.println("Begin taxa;");
    out.println("\tDimensions ntax=" + getLeafNodeCount() + ";");
    out.println("\t\tTaxlabels");
    printTaxa(node, out, getNodeCount() / 2);
    out.println("\t\t\t;");
    out.println("End;\n");
    out.println("Begin bacter;");
    out.print("\tloci");
    for (Locus locus : loci) out.print(" " + locus.getID() + ":" + locus.getSiteCount());
    out.println(";\nEnd;\n");
    out.println("Begin trees;");
    out.println("\tTranslate");
    printTranslate(node, out, getNodeCount() / 2);
    out.print(";");
}

Example 89 with Node

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

the class StructuredCoalescentTreeDensity method updateEventSequence.

/**
 * Determines the sequence of migration, coalescence and sampling events
 * which make up the coloured tree.
 */
protected void updateEventSequence() {
    // Clean up previous list:
    eventList.clear();
    lineageCountList.clear();
    Node rootNode = mtTree.getRoot();
    // Initialise map of active nodes to active change indices:
    Map<Node, Integer> changeIdx = new HashMap<>();
    changeIdx.put(rootNode, -1);
    // Initialise lineage count per colour array:
    Integer[] lineageCount = new Integer[migrationModel.getNTypes()];
    for (int c = 0; c < migrationModel.getNTypes(); c++) if (c == ((MultiTypeNode) rootNode).getNodeType())
        lineageCount[c] = 1;
    else
        lineageCount[c] = 0;
    // Calculate event sequence:
    while (!changeIdx.isEmpty()) {
        SCEvent nextEvent = new SCEvent();
        nextEvent.time = Double.NEGATIVE_INFINITY;
        // Initial assignment not significant
        nextEvent.node = rootNode;
        // Determine next event
        for (Node node : changeIdx.keySet()) if (changeIdx.get(node) < 0) {
            if (node.isLeaf()) {
                // Next event is a sample
                if (node.getHeight() > nextEvent.time) {
                    nextEvent.time = node.getHeight();
                    nextEvent.kind = SCEventKind.SAMPLE;
                    nextEvent.type = ((MultiTypeNode) node).getNodeType();
                    nextEvent.node = node;
                }
            } else {
                // Next event is a coalescence
                if (node.getHeight() > nextEvent.time) {
                    nextEvent.time = node.getHeight();
                    nextEvent.kind = SCEventKind.COALESCE;
                    nextEvent.type = ((MultiTypeNode) node).getNodeType();
                    nextEvent.node = node;
                }
            }
        } else {
            // Next event is a migration
            double thisChangeTime = ((MultiTypeNode) node).getChangeTime(changeIdx.get(node));
            if (thisChangeTime > nextEvent.time) {
                nextEvent.time = thisChangeTime;
                nextEvent.kind = SCEventKind.MIGRATE;
                nextEvent.destType = ((MultiTypeNode) node).getChangeType(changeIdx.get(node));
                if (changeIdx.get(node) > 0)
                    nextEvent.type = ((MultiTypeNode) node).getChangeType(changeIdx.get(node) - 1);
                else
                    nextEvent.type = ((MultiTypeNode) node).getNodeType();
                nextEvent.node = node;
            }
        }
        // Update active node list (changeIdx) and lineage count appropriately:
        switch(nextEvent.kind) {
            case COALESCE:
                Node leftChild = nextEvent.node.getLeft();
                Node rightChild = nextEvent.node.getRight();
                changeIdx.remove(nextEvent.node);
                changeIdx.put(leftChild, ((MultiTypeNode) leftChild).getChangeCount() - 1);
                changeIdx.put(rightChild, ((MultiTypeNode) rightChild).getChangeCount() - 1);
                lineageCount[nextEvent.type]++;
                break;
            case SAMPLE:
                changeIdx.remove(nextEvent.node);
                lineageCount[nextEvent.type]--;
                break;
            case MIGRATE:
                lineageCount[nextEvent.destType]--;
                lineageCount[nextEvent.type]++;
                int oldIdx = changeIdx.get(nextEvent.node);
                changeIdx.put(nextEvent.node, oldIdx - 1);
                break;
        }
        // Add event to list:
        eventList.add(nextEvent);
        lineageCountList.add(Arrays.copyOf(lineageCount, lineageCount.length));
    }
    // Reverse event and lineage count lists (order them from tips to root):
    eventList = Lists.reverse(eventList);
    lineageCountList = Lists.reverse(lineageCountList);
}

Example 90 with Node

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

the class MultiTypeUniform method proposal.

/**
 * Change the node height and return the hastings ratio.
 *
 * @return log of Hastings Ratio
 */
@Override
public double proposal() {
    // Randomly select event on tree:
    int event = Randomizer.nextInt(mtTree.getInternalNodeCount() + mtTree.getTotalNumberOfChanges());
    MultiTypeNode node = null;
    int changeIdx = -1;
    if (event < mtTree.getInternalNodeCount()) {
        node = (MultiTypeNode) mtTree.getNode(mtTree.getLeafNodeCount() + event);
        if (!includeRootInput.get() && node.isRoot())
            return Double.NEGATIVE_INFINITY;
    } else {
        event -= mtTree.getInternalNodeCount();
        for (Node thisNode : mtTree.getNodesAsArray()) {
            if (thisNode.isRoot())
                continue;
            if (event < ((MultiTypeNode) thisNode).getChangeCount()) {
                node = (MultiTypeNode) thisNode;
                changeIdx = event;
                break;
            }
            event -= ((MultiTypeNode) thisNode).getChangeCount();
        }
    }
    if (node == null)
        throw new IllegalStateException("Event selection loop fell through!");
    if (changeIdx == -1) {
        if (node.isRoot()) {
            // Scale distance root and closest event
            double tmin = Math.max(((MultiTypeNode) node.getLeft()).getFinalChangeTime(), ((MultiTypeNode) node.getRight()).getFinalChangeTime());
            double u = Randomizer.nextDouble();
            double f = u * rootScaleFactorInput.get() + (1 - u) / rootScaleFactorInput.get();
            double tnew = tmin + f * (node.getHeight() - tmin);
            node.setHeight(tnew);
            return -Math.log(f);
        } else {
            // Reposition node randomly between closest events
            double tmin = Math.max(((MultiTypeNode) node.getLeft()).getFinalChangeTime(), ((MultiTypeNode) node.getRight()).getFinalChangeTime());
            double tmax = node.getChangeCount() > 0 ? node.getChangeTime(0) : node.getParent().getHeight();
            double u = Randomizer.nextDouble();
            double tnew = u * tmin + (1.0 - u) * tmax;
            node.setHeight(tnew);
            return 0.0;
        }
    } else {
        double tmin, tmax;
        if (changeIdx + 1 < node.getChangeCount())
            tmax = node.getChangeTime(changeIdx + 1);
        else
            tmax = node.getParent().getHeight();
        if (changeIdx - 1 < 0)
            tmin = node.getHeight();
        else
            tmin = node.getChangeTime(changeIdx - 1);
        double u = Randomizer.nextDouble();
        double tnew = u * tmin + (1 - u) * tmax;
        node.setChangeTime(changeIdx, tnew);
        return 0.0;
    }
}