本文整理汇总了Java中beast.evolution.tree.Node.setParent方法的典型用法代码示例。如果您正苦于以下问题：Java Node.setParent方法的具体用法？Java Node.setParent怎么用？Java Node.setParent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.setParent方法的9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: removeSingleChildNodes
import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
* Extract the sampled tree by discarding all the nodes that have -1 number simultaneously suppress single
* child nodes (nodes with only one child numbered by non-negative number)
* @param node
*/
public void removeSingleChildNodes(Node node) {
if (!node.isLeaf()) {
Node left = node.getLeft();
Node right = node.getRight();
removeSingleChildNodes(left);
removeSingleChildNodes(right);
for (Node child:node.getChildren()) {
if (child.getNr() == -1) {
node.removeChild(child);
}
}
if (node.getChildCount() == 1 && node.getParent() != null) {
Node parent = node.getParent();
Node newChild = node.getLeft();
parent.removeChild(node);
parent.addChild(newChild);
newChild.setParent(parent);
//node.setParent(null);
}
}
}
开发者ID:CompEvol，项目名称:sampled-ancestors，代码行数:28，代码来源:SABDSkylineTreeSimulatorArbitraryRateChanges.java
示例2: convertTree
import beast.evolution.tree.Node; //导入方法依赖的package包/类
private void convertTree(Node node) {
if (!node.isLeaf()) {
if (node.isFake()) {
Node directAncestor = node.getDirectAncestorChild();
node.removeChild(directAncestor);
node.setNr(directAncestor.getNr());
node.setID(directAncestor.getID());
directAncestor.setParent(null);
}
for (int i = 0; i < node.getChildCount(); i++) {
Node childNode = node.getChild(i);
convertTree(childNode);
}
}
}
示例3: randomYuleTree
import beast.evolution.tree.Node; //导入方法依赖的package包/类
static Tree randomYuleTree (int nodes, double l) throws Exception {
Tree tr = new Tree();
ArrayList<Node> nodeList = new ArrayList<Node>();
double t = 0.0;
int label = 1;
for (int i = 0; i < nodes; i++) {
Node n = new Node();
n.setHeight(t);
n.setNr(label);
label++;
nodeList.add(n);
}
while (nodeList.size() > 1) {
t += Randomizer.nextExponential(nodeList.size()*l);
int p_1_index = Randomizer.nextInt(nodeList.size());
Node p1 = nodeList.remove(p_1_index);
int p_2_index = Randomizer.nextInt(nodeList.size());
Node p2 = nodeList.remove(p_2_index);
Node parent = new Node();
parent.setHeight(t);
parent.setNr(label);
label++;
p1.setParent(parent);
parent.addChild(p1);
p2.setParent(parent);
parent.addChild(p2);
nodeList.add(parent);
}
tr.setRoot(nodeList.get(0));
return new Tree(tr.toString());
}
示例4: randomYuleTree
import beast.evolution.tree.Node; //导入方法依赖的package包/类
private static Tree randomYuleTree (int nodes, double l) throws Exception {
Tree tr = new Tree();
ArrayList<Node> nodeList = new ArrayList<Node>();
double t = 0.0;
int label = 1;
for (int i = 0; i < nodes; i++) {
Node n = new Node();
n.setHeight(t);
n.setNr(label);
label++;
nodeList.add(n);
}
while (nodeList.size() > 1) {
t += Randomizer.nextExponential(nodeList.size()*l);
int p_1_index = Randomizer.nextInt(nodeList.size());
Node p1 = nodeList.remove(p_1_index);
int p_2_index = Randomizer.nextInt(nodeList.size());
Node p2 = nodeList.remove(p_2_index);
Node parent = new Node();
parent.setHeight(t);
parent.setNr(label);
label++;
p1.setParent(parent);
parent.addChild(p1);
p2.setParent(parent);
parent.addChild(p2);
nodeList.add(parent);
}
tr.setRoot(nodeList.get(0));
return new Tree(tr.toString());
}
示例5: convertToFakeSATree
import beast.evolution.tree.Node; //导入方法依赖的package包/类
public static void convertToFakeSATree(Node node, int[] nextNr) {
if (!node.isLeaf()) {
convertToFakeSATree(node.getLeft(), nextNr);
if (node.getRight() != null) {
convertToFakeSATree(node.getRight(), nextNr);
}
}
if (node.getChildCount() == 1) {
Node parent = new Node();
parent.setHeight(node.getHeight());
Node child = node.getLeft();
parent.setLeft(child);
child.setParent(parent);
node.removeChild(child);
parent.setRight(node);
parent.setNr(nextNr[0]);
nextNr[0]++;
if (!node.isRoot()) {
Node grandparent = node.getParent();
if (grandparent.getLeft().getNr() == node.getNr()) {
grandparent.setLeft(parent);
} else {
grandparent.setRight(parent);
}
parent.setParent(grandparent);
} else {
node.getTree().setRoot(parent);
}
node.setParent(parent);
}
}
示例6: removeFossils
import beast.evolution.tree.Node; //导入方法依赖的package包/类
public void removeFossils(Node node, Tree tree, ArrayList<Node> removedNodes) {
if (node.isLeaf()) {
if (!extantTaxa.contains(node.getID())) {
node.getParent().removeChild(node);
node.setParent(null);
removedNodes.add(node);
}
} else {
Node left = node.getLeft();
Node right = node.getRight();
removeFossils(left, tree, removedNodes);
removeFossils(right, tree, removedNodes);
if (node.isLeaf()) {
node.getParent().removeChild(node);
node.setParent(null);
removedNodes.add(node);
}
if (node.getChildCount() == 1) {
Node child = node.getChild(0);
if (node.getParent() != null) {
Node grandParent = node.getParent();
grandParent.removeChild(node);
grandParent.addChild(child);
child.setParent(grandParent);
node.setParent(null);
}
else {
child.setParent(null);
tree.setRootOnly(child);
}
removedNodes.add(node);
}
}
}
示例7: convertToFakeSATree
import beast.evolution.tree.Node; //导入方法依赖的package包/类
/**
* convert a tree with single child node to ZeroBranchSATree.
*
* @param node all the nodes that are under this node and have single child will be
* replaced with zero branches
* @throws Exception
*/
private void convertToFakeSATree(Node node, int[] lastLabel) throws Exception {
if (!node.isLeaf()) {
convertToFakeSATree(node.getLeft(), lastLabel);
if (node.getRight() != null) {
convertToFakeSATree(node.getRight(), lastLabel);
}
}
if (node.getChildCount() == 1) {
Node parent = newNode();
parent.setNr(-1);
parent.setHeight(node.getHeight());
Node child = node.getLeft();
parent.setLeft(child);
child.setParent(parent);
node.removeChild(child);
parent.setRight(node);
if (!node.isRoot()) {
Node grandparent = node.getParent();
if (grandparent.getLeft().equals(node)) {
grandparent.setLeft(parent);
} else {
grandparent.setRight(parent);
}
parent.setParent(grandparent);
}
node.setParent(parent);
if (node.getNr() == -1) {
node.setNr(lastLabel[0]+1);
lastLabel[0]++;
}
}
}
示例8: connectParentToChildren
import beast.evolution.tree.Node; //导入方法依赖的package包/类
public void connectParentToChildren(Node parent, Node left, Node right) {
parent.setLeft(left);
parent.setRight(right);
left.setParent(parent);
right.setParent(parent);
}
示例9: main
import beast.evolution.tree.Node; //导入方法依赖的package包/类
public static void main (String[] arg) throws Exception{
Node root = new Node();
root.setNr(4);
root.setHeight(2.0);
Node left = new Node();
left.setNr(3);
left.setHeight(1.0);
root.setLeft(left);
left.setParent(root);
Node right = new Node();
right.setNr(2);
right.setHeight(2.0);
root.setRight(right);
right.setParent(root);
Node leftLeft = new Node();
leftLeft.setNr(0);
leftLeft.setHeight(0.0);
left.setLeft(leftLeft);
leftLeft.setParent(left);
Node leftRight = new Node();
leftRight.setNr(1);
leftRight.setHeight(1.0);
left.setRight(leftRight);
leftRight.setParent(left);
Tree tree = new Tree(root);
System.out.println("The tree is " + tree.getRoot().toShortNewick(false));
SATreeComparingAnalysis analysis = new SATreeComparingAnalysis();
//process tree. consider Fake SA trees
ArrayList<Integer> dAPattern = new ArrayList<Integer>();
for (int i=tree.getLeafNodeCount(); i< tree.getNodeCount(); i++){
if (((ZeroBranchSANode)tree.getNode(i)).isFake()) {
int descendantsCount = tree.getNode(i).getLeafNodeCount() - 1;
if (descendantsCount > 0) {
for(int j=dAPattern.size(); j<descendantsCount; j++){
dAPattern.add(0);
}
int tmp = dAPattern.get(descendantsCount-1);
tmp++;
dAPattern.set(descendantsCount - 1, tmp);
}
}
}
SATreeComparingAnalysis.TreeSummary treeSummary = analysis.new TreeSummary(tree.getRoot().getHeight(), tree.getLeafNodeCount() - ((ZeroBranchSATree)tree).getDirectAncestorNodeCount(), dAPattern);
System.out.println(treeSummary.dAPattern.toString());
ArrayList<Integer> a = new ArrayList<Integer> (Arrays.asList(new Integer[]{1, 1}));
System.out.println(treeSummary.dAPattern.equals(a));
}