本文整理汇总了Java中beast.evolution.tree.Node.getAllLeafNodes方法的典型用法代码示例。如果您正苦于以下问题：Java Node.getAllLeafNodes方法的具体用法？Java Node.getAllLeafNodes怎么用？Java Node.getAllLeafNodes使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类beast.evolution.tree.Node的用法示例。
在下文中一共展示了Node.getAllLeafNodes方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: findNode
import beast.evolution.tree.Node; //导入方法依赖的package包/类
private Node findNode(final TreeParser tree, final String[] targetArray) {
final Node[] treeNodes = tree.getNodesAsArray();
final Set<String> targetSet = new HashSet<>();
for (int i = 0; i < targetArray.length; i++) {
targetSet.add(targetArray[i]);
}
for (Node node: treeNodes) {
Set<String> nodeSet = new HashSet<>();
if (node.isLeaf()) {
nodeSet.add(node.getID());
} else {
final List<Node> leafNodes = node.getAllLeafNodes();
for (Node leaf: leafNodes) {
nodeSet.add(leaf.getID());
}
}
if (targetSet.equals(nodeSet)) {
return node;
}
}
return null;
}
示例2: visitTree
import beast.evolution.tree.Node; //导入方法依赖的package包/类
@Override
public Node visitTree(@NotNull NewickParser.TreeContext ctx) {
Node root = visit(ctx.node());
// Ensure tree is properly sorted in terms of node numbers.
root.sort();
// Replace lengths read from Newick with heights.
convertLengthToHeight(root);
// Make sure internal nodes are numbered correctly
numberUnnumberedNodes(root);
// Check for duplicate taxa
BitSet nodeNrSeen = new BitSet();
for (Node leaf : root.getAllLeafNodes()) {
if (leaf.getNr()<0)
continue; // Skip unnumbered leaves
if (nodeNrSeen.get(leaf.getNr()))
throw new TreeParsingException("Duplicate taxon found: " + labels.get(leaf.getNr()));
else
nodeNrSeen.set(leaf.getNr());
}
return root;
}
示例3: generateConstraints
import beast.evolution.tree.Node; //导入方法依赖的package包/类
private static Document generateConstraints (Tree tree, double minConstraintHeight) throws Exception {
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.newDocument();
List<Node> constraintNodes = getConstraintNodes(tree, minConstraintHeight);
Element rootElem = doc.createElement("root");
doc.appendChild(rootElem);
for (int i = 0; i < constraintNodes.size(); i++) {
Node n = constraintNodes.get(i);
List<Node> children = n.getAllLeafNodes();
Element distElem = doc.createElement("distribution");
distElem.setAttribute("id", "Constraint_"+(i+1)+".prior");
distElem.setAttribute("spec", "beast.math.distributions.MRCAPrior");
distElem.setAttribute("tree", "@Tree.t:GTR1");
rootElem.appendChild(distElem);
Element taxonSetElem = doc.createElement("taxonset");
taxonSetElem.setAttribute("id", "Constraint_"+(i+1));
taxonSetElem.setAttribute("spec", "TaxonSet");
distElem.appendChild(taxonSetElem);
for (Node c : children) {
Element taxonElem = doc.createElement("taxon");
taxonElem.setAttribute("id", c.getID());
taxonElem.setAttribute("spec", "Taxon");
taxonSetElem.appendChild(taxonElem);
}
Element uniformElem = doc.createElement("Uniform");
uniformElem.setAttribute("id", "Uniform.0"+(i+1));
uniformElem.setAttribute("name", "distr");
double height = n.getHeight();
String upper = Math.ceil(height * 1.1) + "";
String lower = Math.floor(height * 0.9) + "";
uniformElem.setAttribute("lower", lower);
uniformElem.setAttribute("upper", upper);
distElem.appendChild(uniformElem);
}
return doc;
}