Project setup. No real functionality.

.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="lib" path="/Users/maxgarfinkel/.m2/repository/junit/junit/4.8.2/junit-4.8.2.jar" sourcepath="/Users/maxgarfinkel/.m2/repository/junit/junit/4.8.2/junit-4.8.2-sources.jar">
+		<attributes>
+			<attribute name="javadoc_location" value="jar:file:/Users/maxgarfinkel/.m2/repository/junit/junit/4.8.2/junit-4.8.2-javadoc.jar!/"/>
+			<attribute name="maven.groupId" value="junit"/>
+			<attribute name="maven.artifactId" value="junit"/>
+			<attribute name="maven.version" value="4.8.2"/>
+			<attribute name="maven.scope" value="test"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>suffixTree</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.jdt.core.prefs

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+#Tue Aug 28 20:37:12 BST 2012
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.5

.settings/org.eclipse.m2e.core.prefs

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+#Tue Aug 28 20:37:12 BST 2012
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.maxgarfinkel</groupId>
+  <artifactId>suffixTree</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+  <dependencies>
+  	<dependency>
+		<groupId>org.hamcrest</groupId>
+		<artifactId>hamcrest-all</artifactId>
+		<version>1.3</version>
+	</dependency>
+  	<dependency>
+  		<groupId>log4j</groupId>
+  		<artifactId>log4j</artifactId>
+  		<version>1.2.17</version>
+  	</dependency>
+  </dependencies>
+  <build>
+  <plugins>
+	<plugin>
+
+       <groupId>org.apache.maven.plugins</groupId>
+       <artifactId>maven-eclipse-plugin</artifactId>
+       <configuration>
+          <downloadSources>true</downloadSources>
+          <downloadJavadocs>true</downloadJavadocs>
+       </configuration>
+     </plugin>
+    </plugins>
+  </build>
+</project>

src/main/java/com/maxgarfinkel/suffixTree/ActivePoint.java

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+package com.maxgarfinkel.suffixTree;
+
+class ActivePoint<T> {
+	private Node<T> activeNode;
+	private Edge<T> activeEdge;
+	private int activeLength;
+
+	ActivePoint(Node<T> root){
+		activeNode = root;
+		activeEdge = null;
+		activeLength = 0;
+	}
+
+	/**
+	 * Inserts a suffix at the active point.
+	 * @param suffix the suffix to be inserted at the active point
+	 * @return true if suffix was explicitly inserted, false otherwise.
+	 */
+	boolean insertSuffix(Suffix suffix){
+		boolean isExplicitInsert = false;
+		if(activeEdge != null){
+			//insert on the edge
+			isExplicitInsert = activeEdge.insert(suffix, this);
+		}else{
+			//insert on the node
+			isExplicitInsert = activeNode.insert(suffix, this);
+		}
+		return false;
+	}
+
+	void setPosition(Node<T> node, Edge<T> edge, int length){
+		activeNode = node;
+		activeEdge = edge;
+		activeLength = length;
+	}
+}

src/main/java/com/maxgarfinkel/suffixTree/Algorithms.java

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+package com.maxgarfinkel.suffixTree;
+
+public class Algorithms {
+
+	public <T> boolean containsSuffix(Object[] suffix, SuffixTree<T> tree){
+		suffix = Utils.addLeafToSequence(suffix, Leaf.getInstance());
+		Node<T> node = tree.getRoot();
+		Edge<T> edge = null;
+		int position = 0;
+		for(Object item : suffix){
+			position++;
+			if(edge == null){
+				Edge<T> e = node.getEdgeStarting(item);
+				if(e != null){
+					edge = e;
+					position = 0;
+				}else{
+					return false;
+				}
+			}else{
+				int length = edge.getLength();
+				if(position == length && edge.isTerminating()){
+					node = edge.getTerminal();
+					Edge<T> e = node.getEdgeStarting(item);
+					if(e != null){
+						edge = e;
+						position = 0;
+					}
+				}else if(!edge.getItemAt(position).equals(item))
+					return false;
+			}
+		}
+
+		if(edge == null || edge.getItemAt(position) == null )
+			return false;
+		else if(edge.isTerminating())
+			return false;
+		else
+			return true;
+	}
+}

src/main/java/com/maxgarfinkel/suffixTree/Edge.java

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+package com.maxgarfinkel.suffixTree;
+
+class Edge<T> {
+	private final int start;
+	private int end = -1;
+	private final Node<T> parentNode;
+	private final Object[] sequence;
+	private Node<T> terminal = null;
+	private SuffixTree<T> tree = null;
+
+	/**
+	 * Create a new <code>Edge</code> object.
+	 * @param start The position in the master sequence of the first item in this suffix.
+	 * @param parent The parent {@link Node}
+	 * @param sequence The master sequence which the {@link SuffixTree} indexes.  
+	 * @param tree The master {@link SuffixTree} containing the root element which this edge is a child of.
+	 */
+	Edge(int start, Node<T> parent, Object[] sequence, SuffixTree<T> tree){
+		this.start = start;
+		this.parentNode = parent;
+		this.sequence = sequence;
+		this.tree = tree;
+	}
+
+	boolean isStarting(Object item){
+		return sequence[start].equals(item);
+	}
+
+	/**
+	 * 
+	 * @param suffix
+	 * @param activePoint
+	 * @return
+	 */
+	boolean insert(Suffix<T> suffix, ActivePoint<T> activePoint) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	int getEnd(){
+		return end != -1 ? end : tree.getCurrentEnd();
+	}
+
+	boolean isTerminating(){
+		return terminal != null;
+	}
+
+	int getLength() {
+		int realEnd = getEnd();
+		return realEnd - start;
+	}
+
+	Node<T> getTerminal(){
+		return terminal;
+	}
+
+	T getItemAt(int position){
+		return (T) sequence[start+position];
+	}
+
+	T getStartItem(){
+		return (T) sequence[start];
+	}
+}

src/main/java/com/maxgarfinkel/suffixTree/Leaf.java

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+package com.maxgarfinkel.suffixTree;
+
+class Leaf {
+
+	private static Leaf leafInstance = null;
+
+	static Leaf getInstance(){
+		if(leafInstance == null)
+			leafInstance = new Leaf();
+		return leafInstance;
+	}
+
+	@Override
+	public boolean equals(Object o){
+		return Leaf.class.isInstance(o);
+	}
+
+	@Override
+	public String toString(){
+		return "$";
+	}
+
+}

src/main/java/com/maxgarfinkel/suffixTree/Node.java

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+package com.maxgarfinkel.suffixTree;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+class Node<T> implements Iterable<Edge<T>>{
+	private final Map<T,Edge<T>> edges = new HashMap<T,Edge<T>>();
+	private final Edge<T> incomingEdge;
+	private final Object[] sequence;
+	private final SuffixTree<T> tree;
+	private Node<T> link = null;
+
+	Node(Edge<T> incomingEdge, Object[] sequence, SuffixTree<T> tree){
+		this.incomingEdge = incomingEdge;
+		this.sequence = sequence;
+		this.tree = tree;
+	}
+
+	boolean insert(Suffix<T> suffix, ActivePoint<T> activePoint){
+		if(edges.containsKey(suffix.getEndItem())){
+			Edge<T> edge = edges.get(suffix.getEndItem());
+			activePoint.setPosition(this, edge, 1);
+			return false;
+		}else{
+			Edge<T> edge = new Edge<T>(suffix.getEndPosition(), this, sequence, tree);
+			edges.put(edge.getStartItem(),edge);
+			return true;
+		}
+	}
+
+	Edge<T> getEdgeStarting(Object item){
+		return edges.get(item);
+	}
+
+	boolean hasSuffixLink(){
+		return link != null;
+	}
+
+	int getEdgeCount(){
+		return edges.size();
+
+	}
+
+	public Iterator<Edge<T>> iterator() {
+		return edges.values().iterator();
+	}
+}

src/main/java/com/maxgarfinkel/suffixTree/Suffix.java

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+package com.maxgarfinkel.suffixTree;
+
+class Suffix<T> {
+	private int start;
+	private int end;
+	private Object[] sequence;
+
+	public Suffix(int currentEnd, int remainder, Object[] sequence) {
+		start = currentEnd-(remainder-1);
+		end = currentEnd;
+		this.sequence = sequence;
+	}
+
+	@Override
+	public String toString(){
+		StringBuilder sb = new StringBuilder();
+		int end = getEndPosition();
+		for(int i = start; i < end; i++){
+			sb.append(sequence[i]).append(",");
+		}
+		return sb.toString();
+	}
+
+	/**
+	 * 
+	 * @return The position in the master sequence of the end item in this suffix. 
+	 * This value is inclusive, thus and end of 0 implies the suffix contains only
+	 * the item at <code>sequence[0]</code>
+	 */
+	int getEndPosition(){
+		return end;
+	}
+
+	Object getEndItem(){
+		return sequence[end];
+	}
+}