Examples with Node jebl.evolution.graphs.Node used on opensource projects

Example 21 with Node

use of jebl.evolution.graphs.Node in project beast-mcmc by beast-dev.

the class TempestPanel method treeSelectionChanged.

private void treeSelectionChanged() {
    Set<Node> selectedTips = treePanel.getTreeViewer().getSelectedTips();
    frame.getCopyAction().setEnabled(selectedTips != null && selectedTips.size() > 0);
    selectedPoints = new HashSet<Integer>();
    for (Node node : selectedTips) {
        selectedPoints.add(pointMap.get(node));
    }
    if (rootToTipPlot != null) {
        rootToTipPlot.setSelectedPoints(selectedPoints);
    }
    if (residualPlot != null) {
        residualPlot.setSelectedPoints(selectedPoints);
    }
    if (SHOW_NODE_DENSITY && nodeDensityPlot != null) {
        nodeDensityPlot.setSelectedPoints(selectedPoints);
    }
    selectMRCA();
}

Example 22 with Node

use of jebl.evolution.graphs.Node in project beast-mcmc by beast-dev.

the class TreeGeoJSONGenerator method traverseTree.

private GeoPoint traverseTree(RootedTree tree, Node node) {
    GeoPoint point = new GeoPoint();
    point.time = tree.getHeight(node);
    point.location = (String) node.getAttribute("location");
    point.host = (String) node.getAttribute("host");
    point.longitude = locationMap.get(point.location).getLongitude();
    point.latitude = locationMap.get(point.location).getLatitude();
    if (tree.isExternal(node)) {
        point.label = tree.getTaxon(node).getName();
        point.probability = 1;
    } else {
        point.label = "";
        point.probability = (Double) node.getAttribute("posterior");
        for (Node child : tree.getChildren(node)) {
            GeoPoint point1 = traverseTree(tree, child);
            GeoLine line = new GeoLine();
            line.label = "";
            line.time0 = point.time;
            line.time1 = point1.time;
            line.location0 = point.location;
            line.location1 = point1.location;
            line.host0 = point.host;
            line.host1 = point1.host;
            line.longitude0 = point.longitude;
            line.longitude1 = point1.longitude;
            line.latitude0 = point.latitude;
            line.latitude1 = point1.latitude;
            lines.add(line);
        }
    }
    points.add(point);
    return point;
}

Example 23 with Node

use of jebl.evolution.graphs.Node in project beast-mcmc by beast-dev.

the class LineageCountThroughTime method getLTT.

public static Variate[] getLTT(String treeFile, double minTime, double maxTime, int binCount, // number of trees to skip
int skip) throws IOException, ImportException {
    double delta = (maxTime - minTime) / (binCount - 1);
    BufferedReader reader = new BufferedReader(new FileReader(treeFile));
    String line = reader.readLine();
    TreeImporter importer;
    if (line.toUpperCase().startsWith("#NEXUS")) {
        importer = new NexusImporter(reader);
    } else {
        importer = new NewickImporter(reader, false);
    }
    int state = 0;
    while (importer.hasTree() && state < skip) {
        importer.importNextTree();
        state += 1;
    }
    // the age of the end of this group
    List<double[]> branchingTimes = new ArrayList<double[]>();
    state = 0;
    while (importer.hasTree()) {
        RootedTree tree = (RootedTree) importer.importNextTree();
        double[] bt = new double[tree.getInternalNodes().size()];
        int i = 0;
        for (Node node : tree.getInternalNodes()) {
            bt[i] = tree.getHeight(node);
            i++;
        }
        Arrays.sort(bt);
        branchingTimes.add(bt);
        state += 1;
    }
    Variate[] bins = new Variate[binCount];
    double height = 0;
    double n = branchingTimes.get(0).length;
    for (int k = 0; k < binCount; k++) {
        bins[k] = new Variate.D();
        if (height >= 0.0 && height <= maxTime) {
            for (state = 0; state < branchingTimes.size(); state++) {
                int index = 0;
                while (index < branchingTimes.get(state).length && branchingTimes.get(state)[index] < height) {
                    index += 1;
                }
                double lineageCount = 1;
                if (index < branchingTimes.get(state).length) {
                    lineageCount = n - index + 1;
                }
                bins[k].add(lineageCount);
            }
        }
        height += delta;
    }
    Variate xData = new Variate.D();
    Variate yDataMean = new Variate.D();
    Variate yDataMedian = new Variate.D();
    Variate yDataUpper = new Variate.D();
    Variate yDataLower = new Variate.D();
    double t = minTime;
    for (Variate bin : bins) {
        xData.add(t);
        if (bin.getCount() > 0) {
            yDataMean.add(bin.getMean());
            yDataMedian.add(bin.getQuantile(0.5));
            yDataLower.add(bin.getQuantile(0.025));
            yDataUpper.add(bin.getQuantile(0.975));
        } else {
            yDataMean.add(Double.NaN);
            yDataMedian.add(Double.NaN);
            yDataLower.add(Double.NaN);
            yDataUpper.add(Double.NaN);
        }
        t += delta;
    }
    return new Variate[] { xData, yDataMean };
}