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

Example 16 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class RandomLocalClockModel method recalculateScaleFactor.

private void recalculateScaleFactor() {
    BooleanParameter indicators = indicatorParamInput.get();
    RealParameter rates = rateParamInput.get();
    calculateUnscaledBranchRates(m_tree.getRoot(), 1.0, indicators, rates);
    double timeTotal = 0.0;
    double branchTotal = 0.0;
    for (int i = 0; i < m_tree.getNodeCount(); i++) {
        Node node = m_tree.getNode(i);
        if (!node.isRoot()) {
            double branchInTime = node.getParent().getHeight() - node.getHeight();
            double branchLength = branchInTime * unscaledBranchRates[node.getNr()];
            timeTotal += branchInTime;
            branchTotal += branchLength;
        }
    }
    scaleFactor = timeTotal / branchTotal;
    scaleFactor *= meanRate.getValue();
}

Example 17 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class GeneTreeForSpeciesTreeDistribution method calculateLogP.

@Override
public double calculateLogP() {
    logP = 0;
    for (final PriorityQueue<Double> m_interval : intervalsInput) {
        m_interval.clear();
    }
    Arrays.fill(nrOfLineages, 0);
    final TreeInterface stree = speciesTreeInput.get();
    final Node[] speciesNodes = stree.getNodesAsArray();
    traverseLineageTree(speciesNodes, treeInput.get().getRoot());
    // if the gene tree does not fit the species tree, logP = -infinity by now
    if (logP == 0) {
        traverseSpeciesTree(stree.getRoot());
    }
    // System.err.println("logp=" + logP);
    return logP;
}

Example 18 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class SpeciesTreePrior method calculateLogP.

@Override
public double calculateLogP() {
    logP = 0;
    // make sure the root branch length is positive
    // if (m_rootHeightParameter.get().getValue() < m_speciesTree.get().getRoot().getHeight()) {
    // logP = Double.NEGATIVE_INFINITY;
    // return logP;
    // }
    final Node[] speciesNodes = treeInput.get().getNodesAsArray();
    try {
        switch(popFunction) {
            case constant:
                // constant pop size function
                logP += gamma2Prior.calcLogP(popSizesBottom);
                // }
                break;
            case linear:
                for (int i = 0; i < speciesNodes.length; i++) {
                    final Node node = speciesNodes[i];
                    final double popSizeBottom;
                    if (node.isLeaf()) {
                        // Gamma(4, psi) prior
                        popSizeBottom = popSizesBottom.getValue(i);
                        logP += gamma4Prior.logDensity(popSizeBottom);
                    }
                    final double popSizeTop = popSizesTop.getValue(i);
                    logP += gamma2Prior.logDensity(popSizeTop);
                }
                break;
            case linear_with_constant_root:
                for (int i = 0; i < speciesNodes.length; i++) {
                    final Node node = speciesNodes[i];
                    if (node.isLeaf()) {
                        final double popSizeBottom = popSizesBottom.getValue(i);
                        logP += gamma4Prior.logDensity(popSizeBottom);
                    }
                    if (!node.isRoot()) {
                        if (i < speciesNodes.length - 1) {
                            final double popSizeTop = popSizesTop.getArrayValue(i);
                            logP += gamma2Prior.logDensity(popSizeTop);
                        } else {
                            final int nodeIndex = treeInput.get().getRoot().getNr();
                            final double popSizeTop = popSizesTop.getArrayValue(nodeIndex);
                            logP += gamma2Prior.logDensity(popSizeTop);
                        }
                    }
                }
                break;
        }
    } catch (Exception e) {
        // exceptions can be thrown by the gamma priors
        e.printStackTrace();
        return Double.NEGATIVE_INFINITY;
    }
    return logP;
}

Example 19 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class ScaleOperatorTest method testTreeScaling.

@Test
public void testTreeScaling() {
    String newick = "((0:1.0,1:1.0)4:1.0,(2:1.0,3:1.0)5:0.5)6:0.0;";
    TreeParser tree = new TreeParser(newick, false, false, false, 0);
    Node[] node = tree.getNodesAsArray();
    ScaleOperator operator = new ScaleOperator();
    operator.initByName("tree", tree, "weight", 1.0);
    operator.proposal();
    // leaf node
    node = tree.getNodesAsArray();
    assertEquals(0.0, node[0].getHeight(), EPSILON);
    assertEquals(0.0, node[1].getHeight(), EPSILON);
    // leaf node, not scaled
    assertEquals(0.5, node[2].getHeight(), EPSILON);
    assertEquals(0.5, node[3].getHeight(), EPSILON);
    // internal nodes, all scaled
    // first determine scale factor
    double scale = node[4].getHeight() / 1.0;
    assertEquals(1.0 * scale, node[4].getHeight(), EPSILON);
    assertEquals(1.5 * scale, node[5].getHeight(), EPSILON);
    assertEquals(2.0 * scale, node[6].getHeight(), EPSILON);
}

Example 20 with Node

use of beast.evolution.tree.Node in project beast2 by CompEvol.

the class TreeAnnotator method processMetaData.

private void processMetaData(Node node) {
    for (Node child : node.getChildren()) {
        processMetaData(child);
    }
    Set<String> metaDataNames = node.getMetaDataNames();
    if (metaDataNames != null && !metaDataNames.isEmpty()) {
        String metadata = "";
        for (String name : metaDataNames) {
            Object value = node.getMetaData(name);
            metadata += name + "=";
            if (value instanceof Object[]) {
                Object[] values = (Object[]) value;
                metadata += "{";
                for (int i = 0; i < values.length; i++) {
                    metadata += values[i].toString();
                    if (i < values.length - 1) {
                        metadata += ",";
                    }
                }
                metadata += "}";
            } else {
                metadata += value.toString();
            }
            metadata += ",";
        }
        metadata = metadata.substring(0, metadata.length() - 1);
        node.metaDataString = metadata;
    }
}