本文整理汇总了Java中beast.evolution.tree.Node.getLength方法的典型用法代码示例。如果您正苦于以下问题：Java Node.getLength方法的具体用法？Java Node.getLength怎么用？Java Node.getLength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.getLength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: height
import beast.evolution.tree.Node; //导入方法依赖的package包/类
double height(Node node) {
if (node.isLeaf()) {
return node.getLength();
} else {
return node.getLength() + Math.max(height(node.getLeft()), height(node.getRight()));
}
}
示例2: computeFactor
import beast.evolution.tree.Node; //导入方法依赖的package包/类
private void computeFactor() {
//scale mean rate to 1.0 or separate parameter
double treeRate = 0.0;
double treeTime = 0.0;
for (int i = 0; i < tree.getNodeCount(); i++) {
Node node = tree.getNode(i);
if (!node.isRoot()) {
int nodeNumber = node.getNr();
if (nodeNumber == categories.getDimension()) {
// root node has nr less than #categories, so use that nr
nodeNumber = node.getTree().getRoot().getNr();
}
int rateCategory = categories.getValue(nodeNumber);
treeRate += rates[rateCategory] * node.getLength();
treeTime += node.getLength();
//System.out.println("rates and time\t" + rates[rateCategory] + "\t" + node.getLength());
}
}
//treeRate /= treeTime;
scaleFactor = 1.0 / (treeRate / treeTime);
//System.out.println("scaleFactor\t\t\t\t\t" + scaleFactor);
}
示例3: setTipValues
import beast.evolution.tree.Node; //导入方法依赖的package包/类
void setTipValues(Node node) {
if (node.isRoot()) {
node.setMetaData("p", new Point2D.Double(0, 0));
node.setMetaData("arc", 2 * Math.PI);
node.setMetaData("direction", -Math.PI / 2.0);
} else {
Node parent = node.getParent();
double direction = (Double) node.getMetaData("direction");
double length = node.getLength();
Point2D parentPoint2D = (Point2D) parent.getMetaData("p");
double x = parentPoint2D.getX() + length * Math.cos(direction);
double y = parentPoint2D.getY() + length * Math.sin(direction);
if (x < minX) minX = x;
if (x > maxX) maxX = x;
if (y < minY) minY = y;
if (y > maxY) maxY = y;
node.setMetaData("p", new Point2D.Double(x, y));
}
double arc = (Double) node.getMetaData("arc");
int leafNodeCount = node.getLeafNodeCount();
double childDirection = (Double) node.getMetaData("direction");
for (Node child : node.getChildren()) {
int childLeafNodeCount = child.getLeafNodeCount();
double childArc = arc * (double) childLeafNodeCount / (double) leafNodeCount;
child.setMetaData("arc", childArc);
child.setMetaData("direction", childDirection - childArc / 2);
childDirection += childArc;
}
for (Node childNode : node.getChildren()) {
setTipValues(childNode);
}
}
示例4: getCommonAncestor
import beast.evolution.tree.Node; //导入方法依赖的package包/类
protected Node getCommonAncestor(Node n1, Node n2) {
// assert n1.getTree() == n2.getTree();
if( ! nodesTraversed[n1.getNr()] ) {
nodesTraversed[n1.getNr()] = true;
nseen += 1;
}
if( ! nodesTraversed[n2.getNr()] ) {
nodesTraversed[n2.getNr()] = true;
nseen += 1;
}
while (n1 != n2) {
double h1 = n1.getHeight();
double h2 = n2.getHeight();
if ( h1 < h2 ) {
n1 = n1.getParent();
if( ! nodesTraversed[n1.getNr()] ) {
nodesTraversed[n1.getNr()] = true;
nseen += 1;
}
} else if( h2 < h1 ) {
n2 = n2.getParent();
if( ! nodesTraversed[n2.getNr()] ) {
nodesTraversed[n2.getNr()] = true;
nseen += 1;
}
} else {
//zero length branches hell
Node n;
double b1 = n1.getLength();
double b2 = n2.getLength();
if( b1 > 0 ) {
n = n2;
} else { // b1 == 0
if( b2 > 0 ) {
n = n1;
} else {
// both 0
n = n1;
while( n != null && n != n2 ) {
n = n.getParent();
}
if( n == n2 ) {
// n2 is an ancestor of n1
n = n1;
} else {
// always safe to advance n2
n = n2;
}
}
}
if( n == n1 ) {
n = n1 = n.getParent();
} else {
n = n2 = n.getParent();
}
if( ! nodesTraversed[n.getNr()] ) {
nodesTraversed[n.getNr()] = true;
nseen += 1;
}
}
}
return n1;
}
示例5: toNewick
import beast.evolution.tree.Node; //导入方法依赖的package包/类
String toNewick(Node node, List<Function> metadataList, BranchRateModel branchRateModel, PopulationModel populationModel) {
StringBuffer buf = new StringBuffer();
if (node.getLeft() != null) {
buf.append("(");
buf.append(toNewick(node.getLeft(), metadataList, branchRateModel, populationModel));
if (node.getRight() != null) {
buf.append(',');
buf.append(toNewick(node.getRight(), metadataList, branchRateModel, populationModel));
}
buf.append(")");
} else {
buf.append(node.getNr() + 1);
}
if (someMetaDataNeedsLogging) {
buf.append("[&");
if (metadataList.size() > 0) {
for (Function metadata : metadataList) {
buf.append(((BEASTObject)metadata).getID());
buf.append('=');
if (metadata instanceof Parameter<?>) {
Parameter<?> p = (Parameter<?>) metadata;
int dim = p.getMinorDimension1();
if (dim > 1) {
buf.append('{');
for (int i = 0; i < dim; i++) {
buf.append(p.getMatrixValue(node.getNr(), i));
if (i < dim - 1) {
buf.append(',');
}
}
buf.append('}');
} else {
buf.append(metadata.getArrayValue(node.getNr()));
}
} else {
buf.append(metadata.getArrayValue(node.getNr()));
}
if (metadataList.indexOf(metadata) < metadataList.size() - 1) {
buf.append(",");
}
}
if (branchRateModel != null || populationModel != null) {
buf.append(",");
}
}
if (branchRateModel != null) {
buf.append("rate=");
appendDouble(buf, branchRateModel.getRateForBranch(node));
if (populationModel != null) {
buf.append(",");
}
}
if (populationModel != null) {
populationModel.serialize(node, buf, df);
}
buf.append(']');
}
buf.append(":");
double nodeLength;
if (node.isRoot()) {
nodeLength = getTreeHeight() - node.getHeight();
} else {
nodeLength = node.getLength();
}
if (substitutions) {
appendDouble(buf, nodeLength * branchRateModel.getRateForBranch(node));
} else {
appendDouble(buf, nodeLength);
}
return buf.toString();
}