Examples with ComparableDouble dr.util.ComparableDouble used on opensource projects

Example 1 with ComparableDouble

use of dr.util.ComparableDouble in project beast-mcmc by beast-dev.

the class GaussianProcessSkytrackTreeOperator method collectAllTimes.

private static void collectAllTimes(Tree tree, NodeRef top, NodeRef[] excludeBelow, ArrayList<ComparableDouble> times, ArrayList<Integer> childs) {
    times.add(new ComparableDouble(tree.getNodeHeight(top)));
    childs.add(tree.getChildCount(top));
    for (int i = 0; i < tree.getChildCount(top); i++) {
        NodeRef child = tree.getChild(top, i);
        if (excludeBelow == null) {
            collectAllTimes(tree, child, excludeBelow, times, childs);
        } else {
            // check if this subtree is included in the coalescent density
            boolean include = true;
            for (NodeRef anExcludeBelow : excludeBelow) {
                if (anExcludeBelow.getNumber() == child.getNumber()) {
                    include = false;
                    break;
                }
            }
            if (include)
                collectAllTimes(tree, child, excludeBelow, times, childs);
        }
    }
}

Example 2 with ComparableDouble

use of dr.util.ComparableDouble in project beast-mcmc by beast-dev.

the class VeryOldCoalescentLikelihood method collectAllTimes.

/**
     * extract coalescent times and tip information into ArrayList times from tree.
     *
     * @param node         the node to start from
     * @param excludeBelow an optional array of nodes to exclude (corresponding subtrees) from density.
     */
private static void collectAllTimes(Tree tree, NodeRef node, NodeRef[] excludeBelow, ArrayList times, ArrayList<Integer> childs) {
    times.add(new ComparableDouble(tree.getNodeHeight(node)));
    childs.add(tree.getChildCount(node));
    for (int i = 0; i < tree.getChildCount(node); i++) {
        NodeRef child = tree.getChild(node, i);
        if (excludeBelow == null) {
            collectAllTimes(tree, child, excludeBelow, times, childs);
        } else {
            // check if this subtree is included in the coalescent density
            boolean include = true;
            for (NodeRef anExcludeBelow : excludeBelow) {
                if (anExcludeBelow.getNumber() == child.getNumber()) {
                    include = false;
                    break;
                }
            }
            if (include)
                collectAllTimes(tree, child, excludeBelow, times, childs);
        }
    }
}

Example 3 with ComparableDouble

use of dr.util.ComparableDouble in project beast-mcmc by beast-dev.

the class VeryOldCoalescentLikelihood method setupIntervals.

/**
     * Recalculates all the intervals from the tree model.
     */
protected final void setupIntervals() {
    double MULTIFURCATION_LIMIT = 1e-9;
    ArrayList times = new ArrayList();
    ArrayList<Integer> childs = new ArrayList<Integer>();
    collectAllTimes(tree, getMRCAOfCoalescent(tree), getExcludedMRCAs(tree), times, childs);
    int[] indices = new int[times.size()];
    HeapSort.sort(times, indices);
    int maxIntervalCount = tree.getNodeCount();
    if (intervals == null) {
        intervals = new double[maxIntervalCount];
        lineageCounts = new int[maxIntervalCount];
        storedIntervals = new double[maxIntervalCount];
        storedLineageCounts = new int[maxIntervalCount];
    }
    // start is the time of the first tip
    double start = ((ComparableDouble) times.get(indices[0])).doubleValue();
    int numLines = 0;
    int i = 0;
    intervalCount = 0;
    while (i < times.size()) {
        int lineagesRemoved = 0;
        int lineagesAdded = 0;
        double finish = ((ComparableDouble) times.get(indices[i])).doubleValue();
        double next = finish;
        while (Math.abs(next - finish) < MULTIFURCATION_LIMIT) {
            int children = childs.get(indices[i]);
            if (children == 0) {
                lineagesAdded += 1;
            } else {
                lineagesRemoved += (children - 1);
            }
            i += 1;
            if (i < times.size()) {
                next = ((ComparableDouble) times.get(indices[i])).doubleValue();
            } else
                break;
        }
        //System.out.println("time = " + finish + " removed = " + lineagesRemoved + " added = " + lineagesAdded);
        if (lineagesAdded > 0) {
            if (intervalCount > 0 || ((finish - start) > MULTIFURCATION_LIMIT)) {
                intervals[intervalCount] = finish - start;
                lineageCounts[intervalCount] = numLines;
                intervalCount += 1;
            }
            start = finish;
        }
        // add sample event
        numLines += lineagesAdded;
        if (lineagesRemoved > 0) {
            intervals[intervalCount] = finish - start;
            lineageCounts[intervalCount] = numLines;
            intervalCount += 1;
            start = finish;
        }
        // coalescent event
        numLines -= lineagesRemoved;
    }
    intervalsKnown = true;
}

Example 4 with ComparableDouble

use of dr.util.ComparableDouble in project beast-mcmc by beast-dev.

the class OldAbstractCoalescentLikelihood method collectAllTimes.

/**
     * Extract coalescent times and tip information into ArrayList times from tree.
     * Upon return times contain the time of each node in the subtree below top, and at the corrosponding index
     * of childs is the descendent count for that time.
     *
     * @param top          the node to start from
     * @param excludeBelow an optional array of nodes to exclude (corresponding subtrees) from density.
     * @param tree         given tree
     * @param times        array to fill with times
     * @param childs       array to fill with descendents count
     */
private static void collectAllTimes(Tree tree, NodeRef top, NodeRef[] excludeBelow, ArrayList<ComparableDouble> times, ArrayList<Integer> childs) {
    times.add(new ComparableDouble(tree.getNodeHeight(top)));
    childs.add(tree.getChildCount(top));
    for (int i = 0; i < tree.getChildCount(top); i++) {
        NodeRef child = tree.getChild(top, i);
        if (excludeBelow == null) {
            collectAllTimes(tree, child, excludeBelow, times, childs);
        } else {
            // check if this subtree is included in the coalescent density
            boolean include = true;
            for (NodeRef anExcludeBelow : excludeBelow) {
                if (anExcludeBelow.getNumber() == child.getNumber()) {
                    include = false;
                    break;
                }
            }
            if (include)
                collectAllTimes(tree, child, excludeBelow, times, childs);
        }
    }
}