本文整理汇总了Java中dr.evolution.tree.MutableTree.getChildCount方法的典型用法代码示例。如果您正苦于以下问题：Java MutableTree.getChildCount方法的具体用法？Java MutableTree.getChildCount怎么用？Java MutableTree.getChildCount使用的例子？那么, 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dr.evolution.tree.MutableTree的用法示例。
在下文中一共展示了MutableTree.getChildCount方法的5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: adjustInternalHeights
import dr.evolution.tree.MutableTree; //导入方法依赖的package包/类
private static void adjustInternalHeights(MutableTree tree, NodeRef node) {
if (!tree.isExternal(node)) {
// pre-order recursion
for (int i = 0; i < tree.getChildCount(node); i++) {
adjustInternalHeights(tree, tree.getChild(node, i));
}
}
NodeRef parent = tree.getParent(node);
if (parent != null) {
if (tree.getNodeHeight(parent) < tree.getNodeHeight(node)) {
tree.setNodeHeight(parent, tree.getNodeHeight(node));
}
}
}
示例2: addNewClades
import dr.evolution.tree.MutableTree; //导入方法依赖的package包/类
private BitSet addNewClades(final MutableTree tree, final NodeRef node) {
final BitSet bitSet = new BitSet(tree.getTaxonCount());
if (tree.isExternal(node)) {
bitSet.set(hostTaxonList.getTaxonIndex(tree.getNodeTaxon(node).getId()));
} else {
for (int i = 0; i < tree.getChildCount(node); ++i) {
bitSet.or(addNewClades(tree, tree.getChild(node, i)));
}
}
if (!clades.containsKey(bitSet))
clades.put(bitSet, clades.size());
final int id = clades.get(bitSet);
ids[(Integer) tree.getNodeAttribute(node, NODE_REF)] = id;
tree.setNodeAttribute(node, NODE_REF, id);
return bitSet;
}
示例3: simulate
import dr.evolution.tree.MutableTree; //导入方法依赖的package包/类
private void simulate(MutableTree tree, NodeRef node, double value) {
tree.setNodeAttribute(node, traitName, new Double(value));
int childCount = tree.getChildCount(node);
double height = tree.getNodeHeight(node);
for (int i = 0; i < childCount; i++) {
NodeRef child = tree.getChild(node, i);
simulate(tree, child, diffusionModel.simulateForward(value, height - tree.getNodeHeight(child)));
}
}
示例4: annotateTree
import dr.evolution.tree.MutableTree; //导入方法依赖的package包/类
public void annotateTree(MutableTree tree, NodeRef node, BitSet bits, HeightsSummary heightsOption) {
BitSet bits2 = new BitSet();
if (tree.isExternal(node)) {
int index = taxonList.getTaxonIndex(tree.getNodeTaxon(node).getId());
bits2.set(index);
annotateNode(tree, node, bits2, true, heightsOption);
} else {
for (int i = 0; i < tree.getChildCount(node); i++) {
NodeRef node1 = tree.getChild(node, i);
annotateTree(tree, node1, bits2, heightsOption);
}
annotateNode(tree, node, bits2, false, heightsOption);
}
if (bits != null) {
bits.or(bits2);
}
}
示例5: annotateRates
import dr.evolution.tree.MutableTree; //导入方法依赖的package包/类
private static void annotateRates(
MutableTree targetTree, NodeRef node, Tree timeTree, Tree mutationTree) {
Set<String> leafSet = Tree.Utils.getDescendantLeaves(targetTree, node);
if (Tree.Utils.isMonophyletic(timeTree, leafSet)) {
NodeRef timeNode = Tree.Utils.getCommonAncestorNode(timeTree, leafSet);
NodeRef mutationNode = Tree.Utils.getCommonAncestorNode(mutationTree, leafSet);
double height = timeTree.getNodeHeight(timeNode);
if (!targetTree.isRoot(node)) {
double time = timeTree.getNodeHeight(timeTree.getParent(timeNode)) - height;
double mutations = mutationTree.getNodeHeight(mutationTree.getParent(mutationNode)) - mutationTree.getNodeHeight(mutationNode);
//double rate = mutations/time;
Number totalMutations = (Number)targetTree.getNodeAttribute(node, "totalMutations");
Number totalTime = (Number)targetTree.getNodeAttribute(node, "totalTime");
if (totalMutations == null) {
targetTree.setNodeAttribute(node, "totalMutations", mutations);
targetTree.setNodeAttribute(node, "totalTime", time);
targetTree.setNodeAttribute(node, "count", 1);
} else {
Integer count = (Integer)targetTree.getNodeAttribute(node, "count");
targetTree.setNodeAttribute(node, "totalMutations", totalMutations.doubleValue() + mutations);
targetTree.setNodeAttribute(node, "totalTime", totalTime.doubleValue() + time);
targetTree.setNodeAttribute(node, "count", count + 1);
}
}
if (!targetTree.isExternal(node)) {
java.util.List<Double> list = (java.util.List<Double>)targetTree.getNodeAttribute(node, "heightList");
if (list == null) {
list = new ArrayList<Double>() ;
targetTree.setNodeAttribute(node, "heightList", list);
}
list.add(height);
}
}
for (int i = 0; i < targetTree.getChildCount(node); i++) {
annotateRates(targetTree, targetTree.getChild(node, i), timeTree, mutationTree);
}
}