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// (c) 1999-2001 PAL Development Core Team
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// This package may be distributed under the
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// terms of the Lesser GNU General Public License (LGPL)
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import java.util.Hashtable;
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import java.util.Enumeration;
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* data structure for a node (includes branch) in a binary/non-binary
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* rooted/unrooted tree
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* @version $Id: SimpleNode.java,v 1.27 2003/10/19 02:35:26 matt Exp $
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* @author Korbinian Strimmer
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* @author Alexei Drummond
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public class SimpleNode implements AttributeNode {
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/** number of node as displayed */
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/** sequences associated with node */
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private byte[] sequence;
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/** length of branch to parent node */
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private double length;
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/** standard error of length of branch to parent node */
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private double lengthSE;
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/** height of this node */
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private double height;
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/** identifier of node/associated branch */
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private Identifier identifier;
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/** the attributes associated with this node. */
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private Hashtable attributes = null;
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// Serialization Stuff
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static final long serialVersionUID=3472432765038556717L;
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//serialver -classpath ./classes pal.tree.SimpleNode
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/** I like doing things my self! */
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private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException {
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out.writeByte(3); //Version number
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out.writeObject(parent);
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out.writeObject(sequence);
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out.writeDouble(length);
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out.writeDouble(lengthSE);
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out.writeDouble(height);
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out.writeObject(identifier);
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out.writeObject(child);
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out.writeObject(attributes);
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private void readObject(java.io.ObjectInputStream in) throws IOException, ClassNotFoundException{
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byte version = in.readByte();
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parent = (Node)in.readObject();
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number = in.readInt();
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sequence = (byte[])in.readObject();
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Object partial = (double[][][])in.readObject();
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length = in.readDouble();
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lengthSE = in.readDouble();
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height = in.readDouble();
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identifier = (Identifier)in.readObject();
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child = (Node[])in.readObject();
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//attributes are transient
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parent = (Node)in.readObject();
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number = in.readInt();
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sequence = (byte[])in.readObject();
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length = in.readDouble();
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lengthSE = in.readDouble();
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height = in.readDouble();
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identifier = (Identifier)in.readObject();
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child = (Node[])in.readObject();
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//attributes are not transient!
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parent = (Node)in.readObject();
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number = in.readInt();
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sequence = (byte[])in.readObject();
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length = in.readDouble();
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lengthSE = in.readDouble();
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height = in.readDouble();
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identifier = (Identifier)in.readObject();
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child = (Node[])in.readObject();
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attributes = (Hashtable)in.readObject();
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// the following constructors should eventually become
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// "friendly" to prevent anyone calling them directly.
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// Instead, the NodeFactory should be used!
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/** constructor default node */
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identifier = Identifier.ANONYMOUS;
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public SimpleNode(String name, double branchLength) {
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identifier = new Identifier(name);
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length = branchLength;
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* @param branchLength
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* @throws IllegalArgumentException if only one child!
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protected SimpleNode(Node[] children, double branchLength) {
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this.child = children;
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if(children.length==1) {
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throw new IllegalArgumentException("Must have more than one child!");
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for(int i = 0 ; i < child.length ; i++) {
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child[i].setParent(this);
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this.length = branchLength;
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protected SimpleNode(Node[] children) {
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this(children, BranchLimits.MINARC);
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/** constructor used to clone a node and all children */
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public SimpleNode(Node n)
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identifier = Identifier.ANONYMOUS;
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public SimpleNode(Node n, boolean keepIds) {
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for (int i = 0; i < n.getChildCount(); i++) {
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addChild(new SimpleNode(n.getChild(i), keepIds));
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public SimpleNode(Node n, LabelMapping lm) {
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for (int i = 0; i < n.getChildCount(); i++) {
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addChild(new SimpleNode(n.getChild(i), lm));
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protected void init(Node n) {
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* Initialized node instance variables based on given Node.
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* children are ignored.
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protected void init(Node n, boolean keepId) {
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* Initialized node instance variables based on given Node.
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* children are ignored.
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* @param lm - may be null
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protected void init(Node n, boolean keepId, LabelMapping lm) {
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length = n.getBranchLength();
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lengthSE = n.getBranchLengthSE();
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height = n.getNodeHeight();
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identifier = lm.getLabelIdentifier(n.getIdentifier());
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identifier = n.getIdentifier();
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} else { identifier = Identifier.ANONYMOUS; }
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number = n.getNumber();
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sequence = n.getSequence();
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if (n instanceof AttributeNode) {
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AttributeNode attNode = (AttributeNode)n;
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Enumeration e = attNode.getAttributeNames();
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while ((e != null) && e.hasMoreElements()) {
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String name = (String)e.nextElement();
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setAttribute(name, attNode.getAttribute(name));
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* Returns the parent node of this node.
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public final Node getParent() {
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/** Set the parent node of this node. */
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public void setParent(Node node)
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public final void removeParent() {
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* Returns the sequence at this node, in the form of a String.
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public String getSequenceString() {
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return new String(sequence);
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* Returns the sequence at this node, in the form of an array of bytes.
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public byte[] getSequence() {
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* Sets the sequence at this node, in the form of an array of bytes.
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public void setSequence(byte[] s) {
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* Get the length of the branch attaching this node to its parent.
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public final double getBranchLength() {
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* Set the length of the branch attaching this node to its parent.
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public final void setBranchLength(double value) {
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* Get the length SE of the branch attaching this node to its parent.
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public final double getBranchLengthSE() {
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* Set the length SE of the branch attaching this node to its parent.
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public final void setBranchLengthSE(double value) {
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* Get the height of this node relative to the most recent node.
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public final double getNodeHeight() {
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* Set the height of this node relative to the most recent node.
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* @note corrects children branch lengths
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public final void setNodeHeight(double value) {
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for(int i = 0 ; i<child.length ; i++) {
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child[i].setBranchLength(height-child[i].getNodeHeight());
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* Set the height of this node relative to the most recent node.
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* @param adjustChildBranchLengths if true
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public final void setNodeHeight(double value,boolean adjustChildBranchLengths) {
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if(adjustChildBranchLengths &&child!=null) {
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for(int i = 0 ; i<child.length ; i++) {
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child[i].setBranchLength(height-child[i].getNodeHeight());
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* Returns the identifier for this node.
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public final Identifier getIdentifier() {
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* Set identifier for this node.
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public final void setIdentifier(Identifier id) {
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public void setNumber(int n) {
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public int getNumber() {
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* @param n number of child
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public Node getChild(int n)
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* @node node new child node
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public void setChild(int n, Node node)
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child[n].setParent(this);
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* check whether this node is an internal node
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* @return result (true or false)
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public boolean hasChildren()
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* check whether this node is an external node
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* @return result (true or false)
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public boolean isLeaf() {
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return (getChildCount() == 0);
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* check whether this node is a root node
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* @return result (true or false)
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public boolean isRoot()
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* @param n new child node
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public void addChild(Node n)
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insertChild(n, getChildCount());
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* add new child node (insertion at a specific position)
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* @param n new child node
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+ @param pos position
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public void insertChild(Node n, int pos)
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int numChildren = getChildCount();
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Node[] newChild = new Node[numChildren + 1];
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for (int i = 0; i < pos; i++)
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newChild[i] = child[i];
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for (int i = pos; i < numChildren; i++)
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newChild[i+1] = child[i];
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* @param n number of child to be removed
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public Node removeChild(int n)
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int numChildren = getChildCount();
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if (n >= numChildren)
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throw new IllegalArgumentException("Nonexistent child");
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Node[] newChild = new Node[numChildren-1];
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for (int i = 0; i < n; i++)
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newChild[i] = child[i];
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for (int i = n; i < numChildren-1; i++)
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newChild[i] = child[i+1];
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Node removed = child[n];
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//remove parent link from removed child!
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removed.setParent(null);
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* determines the height of this node and its descendants
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* from branch lengths, assuming contemporaneous tips.
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public void lengths2HeightsContemp()
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double largestHeight = 0.0;
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for (int i = 0; i < getChildCount(); i++)
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NodeUtils.lengths2Heights(getChild(i));
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getChild(i).getNodeHeight() + getChild(i).getBranchLength();
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if (newHeight > largestHeight)
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largestHeight = newHeight;
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setNodeHeight(largestHeight);
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* Sets a named attribute to the given value.
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* @param name the name of the attribute
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* @param value the value to set the attribute
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public final void setAttribute(String name, Object value) {
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if (attributes == null) attributes = new Hashtable();
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attributes.put(name, value);
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* @return the attribute with the given name or null if it doesn't exist.
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* @param name the name of the attribute.
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public final Object getAttribute(String name) {
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if (attributes == null) return null;
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return attributes.get(name);
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* @return an enumeration of the attributes that this node has or null if the
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* node has no attributes.
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public final Enumeration getAttributeNames() {
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if (attributes == null) return null;
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return attributes.keys();
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* Returns the number of children this node has.
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public final int getChildCount() {
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if (child == null) return 0;
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public String toString() {
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StringWriter sw = new StringWriter();
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NodeUtils.printNH(new PrintWriter(sw), this, true, false, 0, false);
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return sw.toString();
added
removed
src/pal/tree/SimpleNode.java
