net.maizegenetics.taxa.tree.SimpleTree Maven / Gradle / Ivy
// SimpleTree.java
//
// (c) 1999-2001 PAL Development Core Team
//
// This package may be distributed under the
// terms of the Lesser GNU General Public License (LGPL)
package net.maizegenetics.taxa.tree;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.Serializable;
import java.io.StringWriter;
import java.io.Writer;
import java.util.Hashtable;
import net.maizegenetics.taxa.Taxon;
/**
* data structure for a binary/non-binary rooted/unrooted trees
*
* @author Alexei Drummond
* @author Korbinian Strimmer
*
*/
public class SimpleTree implements Tree, Serializable {
/**
* root node
*/
private Node root;
/**
* list of internal nodes (including root)
*/
private Node[] internalNode = null;
/**
* number of internal nodes (including root)
*/
private int numInternalNodes;
/**
* list of external nodes
*/
private Node[] externalNode = null;
/**
* number of external nodes
*/
private int numExternalNodes;
/**
* attributes attached to this tree.
*/
private Hashtable[] attributes = null;
/**
* holds the units of the trees branches.
*/
private int units = EXPECTED_SUBSTITUTIONS;
//
// Serialization Stuff
//
static final long serialVersionUID = -7330318631600898531L;
//serialver -classpath ./classes net.maizegenetics.pal.tree.SimpleTree
/**
* I like doing things my self!
*/
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException {
out.writeByte(1); //Version number
out.writeObject(root);
out.writeObject(attributes);
out.writeInt(units);
}
private void readObject(java.io.ObjectInputStream in) throws IOException, ClassNotFoundException {
byte version = in.readByte();
switch (version) {
default: {
root = (Node) in.readObject();
createNodeList();
attributes = (Hashtable[]) in.readObject();
units = in.readInt();
}
}
}
/**
* constructor tree consisting solely of root node
*/
public SimpleTree() {
// Default configuration
root = new SimpleNode();
//root.setIdentifier(new Taxon("ROOT"));
root.setBranchLength(0.0);
root.setBranchLengthSE(0.0);
}
/**
* constructor taking a root node
*/
public SimpleTree(Node r) {
root = r;
createNodeList();
}
/**
* clone constructor
*/
public SimpleTree(Tree tree) {
root = new SimpleNode(tree.getRoot());
setUnits(tree.getUnits());
createNodeList();
}
/**
* clone constructor
*/
public SimpleTree(Tree tree, boolean keepIdentifiers) {
root = new SimpleNode(tree.getRoot(), keepIdentifiers);
setUnits(tree.getUnits());
createNodeList();
}
/**
* clone constructor
*
* @param lm - a label mapping use for translating the original label names
* into something else
*/
public SimpleTree(Tree tree, LabelMapping lm) {
root = new SimpleNode(tree.getRoot(), lm);
setUnits(tree.getUnits());
createNodeList();
}
/**
* Return the units that this tree is expressed in.
*/
public final int getUnits() {
return units;
}
/**
* Sets the units that this tree is expressed in.
*/
public final void setUnits(int units) {
this.units = units;
}
/**
* Returns the number of external nodes.
*/
public final int getExternalNodeCount() {
if (externalNode == null) {
createNodeList();
}
return numExternalNodes;
}
/**
* Returns the ith external node.
*/
public final Node getExternalNode(int i) {
if (externalNode == null) {
createNodeList();
}
return externalNode[i];
}
/**
* Returns the number of internal nodes.
*/
public final int getInternalNodeCount() {
if (internalNode == null) {
createNodeList();
}
return numInternalNodes;
}
/**
* Returns the ith internal node.
*/
public final Node getInternalNode(int i) {
if (internalNode == null) {
createNodeList();
}
return internalNode[i];
}
/**
* Returns the root node of this tree.
*/
public final Node getRoot() {
return root;
}
/**
* Set a new node as root node.
*/
public final void setRoot(Node r) {
root = r;
createNodeList();
}
/**
* count and list external and internal nodes and compute heights of each
* node
*/
public void createNodeList() {
numInternalNodes = 0;
numExternalNodes = 0;
Node node = root;
do {
node = NodeUtils.postorderSuccessor(node);
if (node.isLeaf()) {
node.setNumber(numExternalNodes);
numExternalNodes++;
} else {
node.setNumber(numInternalNodes);
numInternalNodes++;
}
} while (node != root);
internalNode = new Node[numInternalNodes];
externalNode = new Node[numExternalNodes];
node = root;
do {
node = NodeUtils.postorderSuccessor(node);
if (node.isLeaf()) {
externalNode[node.getNumber()] = node;
} else {
internalNode[node.getNumber()] = node;
}
} while (node != root);
// compute heights if it seems necessary
if (root.getNodeHeight() == 0.0) {
NodeUtils.lengths2Heights(root);
}
}
public String toString() {
StringWriter sw = new StringWriter();
try {
NodeUtils.printNH(new PrintWriter(sw), getRoot(), true, false, 0, false);
sw.write(";");
} catch (Exception e) {
e.printStackTrace();
}
return sw.toString();
}
/**
* return node with number num (as displayed in ASCII tree)
*
* @param num number of node
*
* @return node
*/
public Node findNode(int num) {
createNodeList();
if (num <= numExternalNodes) {
return externalNode[num - 1];
} else {
return internalNode[num - 1 - numExternalNodes];
}
}
private int getIndex(Node node) {
if (node.isLeaf()) {
return node.getNumber();
}
return getExternalNodeCount() + node.getNumber();
}
/**
* Sets an named attribute for a given node.
*
* @param node the node whose attribute is being set.
* @param name the name of the attribute.
* @param value the new value of the attribute.
*/
public void setAttribute(Node node, String name, Object value) {
if (node instanceof AttributeNode) {
((AttributeNode) node).setAttribute(name, value);
} else {
int index = getIndex(node);
if (attributes == null) {
attributes = new Hashtable[getExternalNodeCount() + getInternalNodeCount()];
}
if (attributes[index] == null) {
attributes[index] = new Hashtable();
}
attributes[index].put(name, value);
}
}
@Override
public int whichIdNumber(Taxon t) {
for (int i = 0; i < this.getExternalNodeCount(); i++) {
if (t.equals(getExternalNode(i).getIdentifier())) {
return i;
}
}
return -1;
}
/**
* @return an object representing the named attributed for the numbered
* node.
* @param node the node being interrogated.
* @param name the name of the attribute of interest.
*/
public Object getAttribute(Node node, String name) {
if (node instanceof AttributeNode) {
return ((AttributeNode) node).getAttribute(name);
} else {
int index = getIndex(node);
if (attributes == null || attributes[index] == null) {
return null;
}
return attributes[index].get(name);
}
}
/**
* make node with number num to root node
*
* @param num number of node
*/
public void reroot(int num) {
TreeUtils.reroot(this, findNode(num));
}
/**
* make provided node the root node
*
* @param node the node to make the root.
*/
public void reroot(Node node) {
TreeUtils.reroot(this, node);
}
public void report(Writer out) throws IOException {
TreeUtils.report(this, out);
}
public Tree getCopy() {
return new SimpleTree(this);
}
}