Examples with NodeRef dr.evolution.tree.NodeRef used on opensource projects

Example 66 with NodeRef

use of dr.evolution.tree.NodeRef in project beast-mcmc by beast-dev.

the class ARGTraceAnalysis method analyzeARG.

/**
	 * Actually analyzes a particular tree using the trace given the burnin
	 */
public final Tree analyzeARG(String target) {
    int n = getTreeCount();
    FlexibleTree meanTree = null;
    for (int i = 0; i < n; i++) {
        Tree tree = getARG(i);
        if (TreeUtils.uniqueNewick(tree, tree.getRoot()).equals(target)) {
            meanTree = new FlexibleTree(tree);
            break;
        }
    }
    if (meanTree == null)
        throw new RuntimeException("No target tree in trace");
    int m = meanTree.getInternalNodeCount();
    for (int j = 0; j < m; j++) {
        double[] heights = new double[n];
        NodeRef node1 = meanTree.getInternalNode(j);
        Set<String> leafSet = TreeUtils.getDescendantLeaves(meanTree, node1);
        for (int i = 0; i < n; i++) {
            Tree tree = getARG(i);
            NodeRef node2 = TreeUtils.getCommonAncestorNode(tree, leafSet);
            heights[i] = tree.getNodeHeight(node2);
        }
        meanTree.setNodeHeight(node1, dr.stats.DiscreteStatistics.mean(heights));
        meanTree.setNodeAttribute(node1, "upper", new Double(dr.stats.DiscreteStatistics.quantile(0.975, heights)));
        meanTree.setNodeAttribute(node1, "lower", new Double(dr.stats.DiscreteStatistics.quantile(0.025, heights)));
    }
    return meanTree;
}

Example 67 with NodeRef

use of dr.evolution.tree.NodeRef in project beast-mcmc by beast-dev.

the class ARGCoalescentLikelihood method calculateIntervals.

public void calculateIntervals() {
    intervals.clear();
    intervals.ensureCapacity(arg.getNodeCount());
    NodeRef x;
    for (int i = 0; i < arg.getInternalNodeCount(); i++) {
        x = arg.getInternalNode(i);
        if (arg.isReassortment(x)) {
            intervals.add(new CoalescentInterval(arg.getNodeHeight(x), RECOMBINATION));
        } else {
            intervals.add(new CoalescentInterval(arg.getNodeHeight(x), COALESCENT));
        }
    }
    for (int i = 0; i < arg.getExternalNodeCount(); i++) {
        x = arg.getExternalNode(i);
        if (arg.getNodeHeight(x) > 0.0) {
            intervals.add(new CoalescentInterval(arg.getNodeHeight(x), NEW_SAMPLE));
        }
    }
    dr.util.HeapSort.sort(intervals);
    double a = 0, b = 0;
    for (int i = 0; i < intervals.size(); i++) {
        b = intervals.get(i).length;
        intervals.get(i).length = intervals.get(i).length - a;
        a = b;
    }
    intervalsKnown = true;
}

Example 68 with NodeRef

use of dr.evolution.tree.NodeRef in project beast-mcmc by beast-dev.

the class ClusterLabelsVirusesStatistic method determine_membership_v2.

//traverse down the tree, top down, do calculation
int[] determine_membership_v2(TreeModel treeModel) {
    NodeRef root = treeModel.getRoot();
    int numClusters = 1;
    LinkedList<NodeRef> list = new LinkedList<NodeRef>();
    list.addFirst(root);
    int[] membership = new int[treeModel.getNodeCount()];
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        membership[i] = -1;
    }
    //root always given the first cluster
    membership[root.getNumber()] = 0;
    while (!list.isEmpty()) {
        //do things with the current object
        NodeRef curElement = list.pop();
        //String content = "node #" + curElement.getNumber() +", taxon=" + treeModel.getNodeTaxon(curElement) + " and parent is = " ;
        String content = "node #" + curElement.getNumber() + ", taxon= ";
        if (treeModel.getNodeTaxon(curElement) == null) {
            content += "internal node\t";
        } else {
            content += treeModel.getNodeTaxon(curElement).getId() + "\t";
        //content += treeModel.getTaxonIndex(treeModel.getNodeTaxon(curElement)) + "\t";
        }
        if (treeModel.getParent(curElement) == null) {
        //content += "no parent";
        } else {
        //content += "parent node#=" + treeModel.getParent(curElement).getNumber();
        }
        //cluster assignment:
        if (!treeModel.isRoot(curElement)) {
            if ((int) indicators.getParameterValue(curElement.getNumber()) == 1) {
                numClusters++;
                membership[curElement.getNumber()] = numClusters - 1;
            } else {
                //inherit from parent's cluster assignment
                membership[curElement.getNumber()] = membership[treeModel.getParent(curElement).getNumber()];
            }
        }
        //is not Root
        content += " cluster = " + membership[curElement.getNumber()];
        for (int childNum = 0; childNum < treeModel.getChildCount(curElement); childNum++) {
            list.addFirst(treeModel.getChild(curElement, childNum));
        }
    }
    return (membership);
}

Example 69 with NodeRef

use of dr.evolution.tree.NodeRef in project beast-mcmc by beast-dev.

the class PathStatistic method determine_from_membership_v3.

int[] determine_from_membership_v3() {
    int[] printFromCluster = new int[treeModel.getNodeCount()];
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        printFromCluster[i] = -1;
    }
    int[] fromMembership = new int[treeModel.getNodeCount()];
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        fromMembership[i] = -99;
    }
    NodeRef root = treeModel.getRoot();
    int numClusters = 1;
    LinkedList<NodeRef> list = new LinkedList<NodeRef>();
    list.addFirst(root);
    int[] membership = new int[treeModel.getNodeCount()];
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        membership[i] = -1;
    }
    //root always given the first cluster
    membership[root.getNumber()] = 0;
    fromMembership[0] = -1;
    while (!list.isEmpty()) {
        //do things with the current object
        NodeRef curElement = list.pop();
        //cluster assignment:
        if (!treeModel.isRoot(curElement)) {
            if ((int) indicators.getParameterValue(curElement.getNumber()) == 1) {
                numClusters++;
                membership[curElement.getNumber()] = numClusters - 1;
                fromMembership[curElement.getNumber()] = membership[treeModel.getParent(curElement).getNumber()];
            } else {
                //inherit from parent's cluster assignment
                membership[curElement.getNumber()] = membership[treeModel.getParent(curElement).getNumber()];
                fromMembership[curElement.getNumber()] = fromMembership[treeModel.getParent(curElement).getNumber()];
            }
        } else //is not Root
        {
            fromMembership[curElement.getNumber()] = -1;
        }
        for (int childNum = 0; childNum < treeModel.getChildCount(curElement); childNum++) {
            list.addFirst(treeModel.getChild(curElement, childNum));
        }
    }
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        if ((int) indicators.getParameterValue(i) == 1) {
            printFromCluster[membership[i]] = fromMembership[i];
        }
    }
    return (printFromCluster);
}

Example 70 with NodeRef

use of dr.evolution.tree.NodeRef in project beast-mcmc by beast-dev.

the class PathStatistic method determine_from_membership_v2.

//traverse down the tree, top down, do calculation
int[] determine_from_membership_v2() {
    //note: I set MAX_DIM as the most I would print, but in order to avoid bug, I 
    //declare the number of nodes as the most active nodes I can have.
    int[] fromMembership = new int[treeModel.getNodeCount()];
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        fromMembership[i] = -1;
    }
    NodeRef root = treeModel.getRoot();
    int numClusters = 1;
    LinkedList<NodeRef> list = new LinkedList<NodeRef>();
    list.addFirst(root);
    int[] membership = new int[treeModel.getNodeCount()];
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        membership[i] = -1;
    }
    //root always given the first cluster
    membership[root.getNumber()] = 0;
    while (!list.isEmpty()) {
        //do things with the current object
        NodeRef curElement = list.pop();
        //String content = "node #" + curElement.getNumber() +", taxon=" + treeModel.getNodeTaxon(curElement) + " and parent is = " ;
        String content = "node #" + curElement.getNumber() + ", taxon= ";
        if (treeModel.getNodeTaxon(curElement) == null) {
            content += "internal node\t";
        } else {
            content += treeModel.getNodeTaxon(curElement).getId() + "\t";
        //content += treeModel.getTaxonIndex(treeModel.getNodeTaxon(curElement)) + "\t";
        }
        if (treeModel.getParent(curElement) == null) {
        //content += "no parent";
        } else {
        //content += "parent node#=" + treeModel.getParent(curElement).getNumber();
        }
        //cluster assignment:
        if (!treeModel.isRoot(curElement)) {
            if ((int) indicators.getParameterValue(curElement.getNumber()) == 1) {
                //		 System.out.print("indicator # " + curElement.getNumber()  + " ");
                numClusters++;
                membership[curElement.getNumber()] = numClusters - 1;
                fromMembership[numClusters - 1] = membership[treeModel.getParent(curElement).getNumber()];
            //		System.out.println("    membership " + (numClusters-1) + " assigned from " + membership[ treeModel.getParent(curElement).getNumber()] );
            } else {
                //inherit from parent's cluster assignment
                membership[curElement.getNumber()] = membership[treeModel.getParent(curElement).getNumber()];
            }
        }
        //is not Root
        content += " cluster = " + membership[curElement.getNumber()];
        for (int childNum = 0; childNum < treeModel.getChildCount(curElement); childNum++) {
            list.addFirst(treeModel.getChild(curElement, childNum));
        }
    }
    return (fromMembership);
}