本文整理汇总了Java中beast.util.TreeParser.getNodesAsArray方法的典型用法代码示例。如果您正苦于以下问题：Java TreeParser.getNodesAsArray方法的具体用法？Java TreeParser.getNodesAsArray怎么用？Java TreeParser.getNodesAsArray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.util.TreeParser的用法示例。
在下文中一共展示了TreeParser.getNodesAsArray方法的4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.util.TreeParser; //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: testTreeScaling
import beast.util.TreeParser; //导入方法依赖的package包/类
@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 treeParser = new TreeParser(newick, false, false, false, 0);
Node [] node = treeParser.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
assertEquals(1.0, node[4].getHeight(), EPSILON);
assertEquals(1.5, node[5].getHeight(), EPSILON);
assertEquals(2.0, node[6].getHeight(), EPSILON);
treeParser.scale(2.0);
// leaf node
node = treeParser.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
assertEquals(2.0, node[4].getHeight(), EPSILON);
assertEquals(3.0, node[5].getHeight(), EPSILON);
assertEquals(4.0, node[6].getHeight(), EPSILON);
}
示例3: testTreeScaling
import beast.util.TreeParser; //导入方法依赖的package包/类
@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);
}
示例4: traverse
import beast.util.TreeParser; //导入方法依赖的package包/类
private double traverse(TreeParser newickTree, double[][] geoBioDiversities, String[] traitsLong, String[] traitsShort, int[][] totalNodes, double[] totalLength) {
if (traitsLong.length < traitsShort.length)
throw new RuntimeException("Error: Trait 1 length = " + traitsLong.length + " < Trait 2 length = " + traitsShort.length);
final int taxonCount = newickTree.getLeafNodeCount();
final Node[] nodes = newickTree.getNodesAsArray();
final String[] taxaNames = newickTree.getTaxaNames();
double totalLengthOverTree = 0;
for (int n = 0; n < taxonCount; n++) {
assert (nodes[n].isLeaf());
int matrixId = getIndexFrom(taxaNames[nodes[n].getNr()], traitsLong, traitsShort);
if (matrixId < 0)
throw new RuntimeException("Cannot find traits from " + taxaNames[nodes[n].getNr()]);
if (matrixId >= traitsLong.length * traitsShort.length)
throw new RuntimeException("Index = " + matrixId + " out of boundary at node " + n);
if (verbose) {
System.out.println(n + ", geoBioDiversities[" + matrixId + "][" + matrixId + "] = " +
geoBioDiversities[matrixId][matrixId] + " + " + nodes[n].getLength());
}
geoBioDiversities[matrixId][matrixId] += nodes[n].getLength();
totalNodes[0][matrixId] ++;
totalNodes[1][matrixId] ++;
totalLength[matrixId] += nodes[n].getLength();
totalLengthOverTree += nodes[n].getLength();
}
for (int n = taxonCount; n < nodes.length - 1; n++) { // exclude nodes[length - 1] which is root
if (nodes[n].isRoot()) System.out.println(n + " is Root : " + nodes[n].getLength());
List<Integer> traitsIndex = getAllTraitsIndexFromInternalNode(nodes[n], taxaNames, traitsLong, traitsShort);
Collections.sort(traitsIndex);
if (verbose) System.out.println(n + ", traitsIndex = " + traitsIndex);
if (traitsIndex.size() < 1) {
throw new RuntimeException("plotsIndex.size() < 1 when n = " + n);
} else if (traitsIndex.size() == 1) {
if (verbose) {
System.out.println(n + ", geoBioDiversities[" + traitsIndex.get(0) + "][" + traitsIndex.get(0) + "] = " +
geoBioDiversities[traitsIndex.get(0)][traitsIndex.get(0)] + " + " + nodes[n].getLength());
}
geoBioDiversities[traitsIndex.get(0)][traitsIndex.get(0)] += nodes[n].getLength();
totalNodes[0][traitsIndex.get(0)] ++;
totalNodes[1][traitsIndex.get(0)] ++;
totalLength[traitsIndex.get(0)] += nodes[n].getLength();
} else {
for (int i = 0; i < traitsIndex.size(); i++) {
for (int j = i + 1; j < traitsIndex.size(); j++) {
if (verbose) {
System.out.println(n + ", geoBioDiversities[" + traitsIndex.get(i) + "][" + traitsIndex.get(j) + "] = " +
geoBioDiversities[traitsIndex.get(i)][traitsIndex.get(j)] + " + " + nodes[n].getLength());
}
geoBioDiversities[traitsIndex.get(i)][traitsIndex.get(j)] += nodes[n].getLength();
}
totalNodes[1][traitsIndex.get(i)] ++;
totalLength[traitsIndex.get(i)] += nodes[n].getLength();
}
}
totalLengthOverTree += nodes[n].getLength();
}
return totalLengthOverTree;
}