Index: /trunk/EventBenchCore/src/de/ugoe/cs/eventbench/models/TrieBasedModel.java
===================================================================
--- /trunk/EventBenchCore/src/de/ugoe/cs/eventbench/models/TrieBasedModel.java	(revision 99)
+++ /trunk/EventBenchCore/src/de/ugoe/cs/eventbench/models/TrieBasedModel.java	(revision 100)
@@ -14,36 +14,90 @@
 import edu.uci.ics.jung.graph.Tree;
 
+/**
+ * <p>
+ * Implements a skeleton for stochastic processes that can calculate
+ * probabilities based on a trie. The skeleton provides all functionalities of
+ * {@link IStochasticProcess} except
+ * {@link IStochasticProcess#getProbability(List, Event)}.
+ * </p>
+ * 
+ * @author Steffen Herbold
+ * @version 1.0
+ */
 public abstract class TrieBasedModel implements IStochasticProcess {
 
 	/**
+	 * <p>
 	 * Id for object serialization.
+	 * </p>
 	 */
 	private static final long serialVersionUID = 1L;
 
+	/**
+	 * <p>
+	 * The order of the trie, i.e., the maximum length of subsequences stored in
+	 * the trie.
+	 * </p>
+	 */
 	protected int trieOrder;
 
+	/**
+	 * <p>
+	 * Trie on which the probability calculations are based.
+	 * </p>
+	 */
 	protected Trie<Event<?>> trie;
+
+	/**
+	 * <p>
+	 * Random number generator used by probabilistic sequence generation
+	 * methods.
+	 * </p>
+	 */
 	protected final Random r;
 
-	
+	/**
+	 * <p>
+	 * Constructor. Creates a new TrieBasedModel that can be used for stochastic
+	 * processes with a Markov order less than or equal to {@code markovOrder}.
+	 * </p>
+	 * 
+	 * @param markovOrder
+	 *            Markov order of the model
+	 * @param r
+	 *            random number generator used by probabilistic methods of the
+	 *            class
+	 */
 	public TrieBasedModel(int markovOrder, Random r) {
 		super();
-		this.trieOrder = markovOrder+1;
+		this.trieOrder = markovOrder + 1;
 		this.r = r;
 	}
 
+	/**
+	 * <p>
+	 * Trains the model by generating a trie from which probabilities are
+	 * calculated.
+	 * </p>
+	 * 
+	 * @param sequences
+	 *            training data
+	 */
 	public void train(List<List<Event<?>>> sequences) {
 		trie = new Trie<Event<?>>();
-		
-		for(List<Event<?>> sequence : sequences) {
-			List<Event<?>> currentSequence = new LinkedList<Event<?>>(sequence); // defensive copy
+
+		for (List<Event<?>> sequence : sequences) {
+			List<Event<?>> currentSequence = new LinkedList<Event<?>>(sequence); // defensive
+																					// copy
 			currentSequence.add(0, Event.STARTEVENT);
 			currentSequence.add(Event.ENDEVENT);
-			
+
 			trie.train(currentSequence, trieOrder);
 		}
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see de.ugoe.cs.eventbench.models.IStochasticProcess#randomSequence()
 	 */
@@ -51,22 +105,24 @@
 	public List<? extends Event<?>> randomSequence() {
 		List<Event<?>> sequence = new LinkedList<Event<?>>();
-		
-		IncompleteMemory<Event<?>> context = new IncompleteMemory<Event<?>>(trieOrder-1);
+
+		IncompleteMemory<Event<?>> context = new IncompleteMemory<Event<?>>(
+				trieOrder - 1);
 		context.add(Event.STARTEVENT);
-		
+
 		Event<?> currentState = Event.STARTEVENT;
-		
+
 		boolean endFound = false;
-		
-		while(!endFound) {
+
+		while (!endFound) {
 			double randVal = r.nextDouble();
 			double probSum = 0.0;
 			List<Event<?>> currentContext = context.getLast(trieOrder);
-			for( Event<?> symbol : trie.getKnownSymbols() ) {
+			for (Event<?> symbol : trie.getKnownSymbols()) {
 				probSum += getProbability(currentContext, symbol);
-				if( probSum>=randVal ) {
-					endFound = (symbol==Event.ENDEVENT);
-					if( !(symbol==Event.STARTEVENT || symbol==Event.ENDEVENT) ) {
-						// only add the symbol the sequence if it is not START or END
+				if (probSum >= randVal) {
+					endFound = (symbol == Event.ENDEVENT);
+					if (!(symbol == Event.STARTEVENT || symbol == Event.ENDEVENT)) {
+						// only add the symbol the sequence if it is not START
+						// or END
 						context.add(symbol);
 						currentState = symbol;
@@ -79,26 +135,61 @@
 		return sequence;
 	}
-	
+
+	/**
+	 * <p>
+	 * Returns a Dot representation of the internal trie.
+	 * </p>
+	 * 
+	 * @return dot representation of the internal trie
+	 */
 	public String getTrieDotRepresentation() {
 		return trie.getDotRepresentation();
 	}
-	
+
+	/**
+	 * <p>
+	 * Returns a {@link Tree} of the internal trie that can be used for
+	 * visualization.
+	 * </p>
+	 * 
+	 * @return {@link Tree} depicting the internal trie
+	 */
 	public Tree<TrieVertex, Edge> getTrieGraph() {
 		return trie.getGraph();
 	}
 
+	/**
+	 * <p>
+	 * The string representation of the model is {@link Trie#toString()} of
+	 * {@link #trie}.
+	 * </p>
+	 * 
+	 * @see java.lang.Object#toString()
+	 */
 	@Override
 	public String toString() {
 		return trie.toString();
 	}
-	
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.ugoe.cs.eventbench.models.IStochasticProcess#getNumStates()
+	 */
+	@Override
 	public int getNumStates() {
 		return trie.getNumSymbols();
 	}
-	
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.ugoe.cs.eventbench.models.IStochasticProcess#getStateStrings()
+	 */
+	@Override
 	public String[] getStateStrings() {
 		String[] stateStrings = new String[getNumStates()];
-		int i=0;
-		for( Event<?> symbol : trie.getKnownSymbols() ) {
+		int i = 0;
+		for (Event<?> symbol : trie.getKnownSymbols()) {
 			stateStrings[i] = symbol.toString();
 			i++;
@@ -106,29 +197,63 @@
 		return stateStrings;
 	}
-	
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.ugoe.cs.eventbench.models.IStochasticProcess#getEvents()
+	 */
+	@Override
 	public Set<? extends Event<?>> getEvents() {
 		return trie.getKnownSymbols();
 	}
-	
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see
+	 * de.ugoe.cs.eventbench.models.IStochasticProcess#generateSequences(int)
+	 */
+	@Override
 	public Set<List<? extends Event<?>>> generateSequences(int length) {
 		return generateSequences(length, false);
-		/*Set<List<? extends Event<?>>> sequenceSet = new LinkedHashSet<List<? extends Event<?>>>();;
-		if( length<1 ) {
-			throw new InvalidParameterException("Length of generated subsequences must be at least 1.");
-		}
-		if( length==1 ) {
-			for( Event<?> event : getEvents() ) {
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see
+	 * de.ugoe.cs.eventbench.models.IStochasticProcess#generateSequences(int,
+	 * boolean)
+	 */
+	@Override
+	public Set<List<? extends Event<?>>> generateSequences(int length,
+			boolean fromStart) {
+		Set<List<? extends Event<?>>> sequenceSet = new LinkedHashSet<List<? extends Event<?>>>();
+		;
+		if (length < 1) {
+			throw new InvalidParameterException(
+					"Length of generated subsequences must be at least 1.");
+		}
+		if (length == 1) {
+			if (fromStart) {
 				List<Event<?>> subSeq = new LinkedList<Event<?>>();
-				subSeq.add(event);
+				subSeq.add(Event.STARTEVENT);
 				sequenceSet.add(subSeq);
+			} else {
+				for (Event<?> event : getEvents()) {
+					List<Event<?>> subSeq = new LinkedList<Event<?>>();
+					subSeq.add(event);
+					sequenceSet.add(subSeq);
+				}
 			}
 			return sequenceSet;
 		}
 		Set<? extends Event<?>> events = getEvents();
-		Set<List<? extends Event<?>>> seqsShorter = generateSequences(length-1);
-		for( Event<?> event : events ) {
-			for( List<? extends Event<?>> seqShorter : seqsShorter ) {
+		Set<List<? extends Event<?>>> seqsShorter = generateSequences(
+				length - 1, fromStart);
+		for (Event<?> event : events) {
+			for (List<? extends Event<?>> seqShorter : seqsShorter) {
 				Event<?> lastEvent = event;
-				if( getProbability(seqShorter, lastEvent)>0.0 ) {
+				if (getProbability(seqShorter, lastEvent) > 0.0) {
 					List<Event<?>> subSeq = new ArrayList<Event<?>>(seqShorter);
 					subSeq.add(lastEvent);
@@ -138,49 +263,22 @@
 		}
 		return sequenceSet;
-		*/
-	}
-	
-	// if startValid, all sequences will start in Event.STARTEVENT
-	public Set<List<? extends Event<?>>> generateSequences(int length, boolean fromStart) {
-		Set<List<? extends Event<?>>> sequenceSet = new LinkedHashSet<List<? extends Event<?>>>();;
-		if( length<1 ) {
-			throw new InvalidParameterException("Length of generated subsequences must be at least 1.");
-		}
-		if( length==1 ) {
-			if( fromStart ) {
-				List<Event<?>> subSeq = new LinkedList<Event<?>>();
-				subSeq.add(Event.STARTEVENT);
-				sequenceSet.add(subSeq);
-			} else {
-				for( Event<?> event : getEvents() ) {
-					List<Event<?>> subSeq = new LinkedList<Event<?>>();
-					subSeq.add(event);
-					sequenceSet.add(subSeq);
-				}
-			}
-			return sequenceSet;
-		}
-		Set<? extends Event<?>> events = getEvents();
-		Set<List<? extends Event<?>>> seqsShorter = generateSequences(length-1, fromStart);
-		for( Event<?> event : events ) {
-			for( List<? extends Event<?>> seqShorter : seqsShorter ) {
-				Event<?> lastEvent = event;
-				if( getProbability(seqShorter, lastEvent)>0.0 ) {
-					List<Event<?>> subSeq = new ArrayList<Event<?>>(seqShorter);
-					subSeq.add(lastEvent);
-					sequenceSet.add(subSeq);
-				}
-			}
-		}
-		return sequenceSet;
-	}
-	
-	// sequences from start to end
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see
+	 * de.ugoe.cs.eventbench.models.IStochasticProcess#generateValidSequences
+	 * (int)
+	 */
+	@Override
 	public Set<List<? extends Event<?>>> generateValidSequences(int length) {
 		// check for min-length implicitly done by generateSequences
-		Set<List<? extends Event<?>>> allSequences = generateSequences(length, true);
+		Set<List<? extends Event<?>>> allSequences = generateSequences(length,
+				true);
 		Set<List<? extends Event<?>>> validSequences = new LinkedHashSet<List<? extends Event<?>>>();
-		for( List<? extends Event<?>> sequence : allSequences ) {
-			if( sequence.size()==length && Event.ENDEVENT.equals(sequence.get(sequence.size()-1)) ) {
+		for (List<? extends Event<?>> sequence : allSequences) {
+			if (sequence.size() == length
+					&& Event.ENDEVENT.equals(sequence.get(sequence.size() - 1))) {
 				validSequences.add(sequence);
 			}