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

Example 11 with Node

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

the class TreeKMLGenerator method generateTree.

private Element generateTree(RootedTree tree, Settings settings, TreeSettings treeSettings, List<Element> styles) {
    BranchStyle branchStyle = treeSettings.getBranchStyle();
    Element element = generateContainer("Folder", treeSettings.getName(), treeSettings.getDescription(), true, null);
    double scaleFactor = settings.getPlotAltitude() / tree.getHeight(tree.getRootNode());
    int nodeNumber = 0;
    for (Node node : tree.getNodes()) {
        nodeNumber++;
        double latitude;
        double longitude;
        Object[] location = getArrayNodeAttribute(node, settings.getTraitName());
        if (location != null) {
            latitude = (Double) location[0];
            longitude = (Double) location[0];
        } else {
            latitude = getDoubleNodeAttribute(node, settings.getLatitudeName());
            longitude = getDoubleNodeAttribute(node, settings.getLongitudeName());
        }
        double altitude = (tree.getHeight(node) * scaleFactor);
        double date = settings.getMostRecentDate() - tree.getHeight(node);
        if (tree.isExternal(node)) {
            System.out.println(tree.getTaxon(node).getName() + "\t" + latitude + "\t" + longitude);
        }
        if (!tree.isRoot(node)) {
            // Create each branch of the tree..
            Element branch;
            String nodeName = treeSettings.getName() + "_node" + nodeNumber;
            if (tree.isExternal(node)) {
                Element tip = generateTaxonLabel(tree, node, tree.getTaxon(node).getName(), tree.getHeight(node), date, latitude, longitude);
                element.addContent(tip);
            }
            Node parentNode = tree.getParent(node);
            double parentLatitude = getDoubleNodeAttribute(parentNode, settings.getLatitudeName());
            double parentLongitude = getDoubleNodeAttribute(parentNode, settings.getLongitudeName());
            double parentAltitude = (tree.getHeight(parentNode) * scaleFactor);
            double parentDate = settings.getMostRecentDate() - tree.getHeight(parentNode);
            double width = branchStyle.getWidthBase();
            if (branchStyle.getWidthProperty() != null) {
                double property = getDoubleNodeAttribute(node, branchStyle.getWidthProperty(), 0.0);
                width += ((property - branchStyle.getWidthPropertyMinimum()) / (branchStyle.getWidthPropertyMaximum() - branchStyle.getWidthPropertyMinimum())) * branchStyle.getWidthScale();
            }
            Color color = branchStyle.getColorStart();
            if (branchStyle.getColorProperty() != null) {
                double property;
                if (branchStyle.getColorProperty().equalsIgnoreCase("height")) {
                    property = tree.getHeight(node) / maxHeight;
                } else {
                    property = getDoubleNodeAttribute(node, branchStyle.getColorProperty());
                    property = ((property - branchStyle.getWidthPropertyMinimum()) / (branchStyle.getWidthPropertyMaximum() - branchStyle.getWidthPropertyMinimum())) * branchStyle.getWidthScale();
                }
                color = getBlendedColor((float) property, branchStyle.getColorStart(), branchStyle.getColorFinish());
            }
            LineStyle lineStyle = new LineStyle(width, color);
            if (treeSettings.getTreeType() == TreeType.RECTANGLE_TREE || treeSettings.getTreeType() == TreeType.TRIANGLE_TREE) {
                branch = generateBranch(treeSettings.getTreeType(), tree, node, nodeName, parentLatitude, latitude, parentLongitude, longitude, parentAltitude, altitude, 0.0, parentAltitude, date, date, settings.getAgeCutOff(), lineStyle, null, 0, styles);
            } else if (treeSettings.getTreeType() == TreeType.ARC_TREE) {
                LineStyle lineStyle2 = null;
                // color range from the parent height to the node height.
                if (branchStyle.getColorProperty() != null && branchStyle.getColorProperty().equalsIgnoreCase("height")) {
                    double divisor = (settings.getAgeCutOff() > 0 ? settings.getMostRecentDate() - settings.getAgeCutOff() : maxHeight);
                    color = getBlendedColor((float) (tree.getHeight(parentNode) / divisor), branchStyle.getColorStart(), branchStyle.getColorFinish());
                    lineStyle = new LineStyle(width, color);
                    color = getBlendedColor((float) (tree.getHeight(node) / divisor), branchStyle.getColorStart(), branchStyle.getColorFinish());
                    lineStyle2 = new LineStyle(width, color);
                }
                branch = generateBranch(treeSettings.getTreeType(), tree, node, nodeName, parentLatitude, latitude, parentLongitude, longitude, parentAltitude, altitude, 0.0, parentAltitude, parentDate, date, settings.getAgeCutOff(), lineStyle, lineStyle2, 50, styles);
            } else if (treeSettings.getTreeType() == TreeType.SURFACE_TREE) {
                double maxAltitude = settings.getPlotAltitude() * (tree.getHeight(parentNode) - tree.getHeight(node)) / maxBranchLength;
                LineStyle lineStyle2 = null;
                // color range from the parent height to the node height.
                if (branchStyle.getColorProperty() != null && branchStyle.getColorProperty().equalsIgnoreCase("height")) {
                    double divisor = (settings.getAgeCutOff() > 0 ? settings.getMostRecentDate() - settings.getAgeCutOff() : maxHeight);
                    color = getBlendedColor((float) (tree.getHeight(parentNode) / divisor), branchStyle.getColorStart(), branchStyle.getColorFinish());
                    lineStyle = new LineStyle(width, color);
                    color = getBlendedColor((float) (tree.getHeight(node) / divisor), branchStyle.getColorStart(), branchStyle.getColorFinish());
                    lineStyle2 = new LineStyle(width, color);
                }
                branch = generateBranch(treeSettings.getTreeType(), tree, node, nodeName, parentLatitude, latitude, parentLongitude, longitude, 0.0, 0.0, 0.5, maxAltitude, parentDate, date, settings.getAgeCutOff(), lineStyle, lineStyle2, settings.getTimeDivisionCount(), styles);
            } else {
                throw new IllegalArgumentException("Unknown TreeType");
            }
            element.addContent(branch);
        }
    }
    return element;
}

Example 12 with Node

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

the class PathogenPanel method getSelectedTips.

public List<String> getSelectedTips() {
    List<String> tips = new ArrayList<String>();
    jebl.evolution.trees.Tree tree = treePanel.getTreeViewer().getTrees().get(0);
    for (Node node : treePanel.getTreeViewer().getSelectedTips()) {
        tips.add(tree.getTaxon(node).getName());
    }
    return tips;
}

Example 13 with Node

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

the class BranchScoreMetric method getClades.

private void getClades(Map<Taxon, Integer> taxonMap, RootedTree tree, Node node, List<Clade> clades, BitSet bits) {
    BitSet bits2 = new BitSet();
    if (tree.isExternal(node)) {
        int index = taxonMap.get(tree.getTaxon(node));
        bits2.set(index);
    } else {
        for (Node child : tree.getChildren(node)) {
            getClades(taxonMap, tree, child, clades, bits2);
        }
        clades.add(new Clade(bits2, tree.getHeight(node)));
    }
    if (bits != null) {
        bits.or(bits2);
    }
}

Example 14 with Node

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

the class CladeMetric method getClade.

private Clade getClade(Map<Taxon, Integer> taxonMap, RootedTree tree, Node node, BitSet bits) {
    BitSet bits2 = new BitSet();
    Clade c = null;
    if (tree.isExternal(node)) {
        int index = taxonMap.get(tree.getTaxon(node));
        bits2.set(index);
    } else {
        for (Node child : tree.getChildren(node)) {
            getClade(taxonMap, tree, child, bits2);
        }
        c = new Clade(bits2, tree.getHeight(node));
    }
    if (bits != null) {
        bits.or(bits2);
    }
    return c;
}

Example 15 with Node

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

the class CladeMetric method getClades.

private void getClades(Map<Taxon, Integer> taxonMap, RootedTree tree, Node node, List<Clade> clades, BitSet bits) {
    BitSet bits2 = new BitSet();
    if (tree.isExternal(node)) {
        int index = taxonMap.get(tree.getTaxon(node));
        bits2.set(index);
    } else {
        for (Node child : tree.getChildren(node)) {
            getClades(taxonMap, tree, child, clades, bits2);
        }
        clades.add(new Clade(bits2, tree.getHeight(node)));
    }
    if (bits != null) {
        bits.or(bits2);
    }
}