diff --git a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Edge.java b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Edge.java
index 1abd486..4af35fe 100644
--- a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Edge.java
+++ b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Edge.java
@@ -27,8 +27,7 @@
 import edu.uci.ics.pregelix.api.util.BspUtils;
 
 /**
- * A complete edge, the destination vertex and the edge value. Can only be one
- * edge with a destination vertex id per edge map.
+ * The Edge class, represent an outgoing edge inside an {@link Vertex} object.
  * 
  * @param <I>
  *            Vertex index
@@ -41,8 +40,9 @@
     private I destVertexId = null;
     /** Edge value */
     private E edgeValue = null;
-    /** Configuration - Used to instiantiate classes */
+    /** Configuration - Used to instantiate classes */
     private Configuration conf = null;
+    /** Whether the edgeValue field is not null*/
     private boolean hasEdgeValue = false;
 
     /**
diff --git a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Vertex.java b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Vertex.java
index 3220bb1..b0cd533 100644
--- a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Vertex.java
+++ b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/graph/Vertex.java
@@ -36,8 +36,8 @@
 import edu.uci.ics.pregelix.api.util.SerDeUtils;
 
 /**
- * User applications should all subclass {@link Vertex}. Package access should
- * prevent users from accessing internal methods.
+ * User applications should all inherit {@link Vertex}, and implement their own
+ * compute method.
  * 
  * @param <I>
  *            Vertex id type
@@ -50,324 +50,393 @@
  */
 @SuppressWarnings("rawtypes")
 public abstract class Vertex<I extends WritableComparable, V extends Writable, E extends Writable, M extends Writable>
-        implements Writable {
-    private static long superstep = 0;
-    /** Class-wide number of vertices */
-    private static long numVertices = -1;
-    /** Class-wide number of edges */
-    private static long numEdges = -1;
-    /** Vertex id */
-    private I vertexId = null;
-    /** Vertex value */
-    private V vertexValue = null;
-    /** Map of destination vertices and their edge values */
-    private final List<Edge<I, E>> destEdgeList = new ArrayList<Edge<I, E>>();
-    /** If true, do not do anymore computation on this vertex. */
-    boolean halt = false;
-    /** List of incoming messages from the previous superstep */
-    private final List<M> msgList = new ArrayList<M>();
-    /** map context */
-    private static Mapper.Context context = null;
-    /** a delegate for hyracks stuff */
-    private VertexDelegate<I, V, E, M> delegate = new VertexDelegate<I, V, E, M>(this);
-    /** this vertex is updated or not */
-    private boolean updated = false;
-    /** has outgoing messages */
-    private boolean hasMessage = false;
+		implements Writable {
+	private static long superstep = 0;
+	/** Class-wide number of vertices */
+	private static long numVertices = -1;
+	/** Class-wide number of edges */
+	private static long numEdges = -1;
+	/** Vertex id */
+	private I vertexId = null;
+	/** Vertex value */
+	private V vertexValue = null;
+	/** Map of destination vertices and their edge values */
+	private final List<Edge<I, E>> destEdgeList = new ArrayList<Edge<I, E>>();
+	/** If true, do not do anymore computation on this vertex. */
+	boolean halt = false;
+	/** List of incoming messages from the previous superstep */
+	private final List<M> msgList = new ArrayList<M>();
+	/** map context */
+	private static Mapper.Context context = null;
+	/** a delegate for hyracks stuff */
+	private VertexDelegate<I, V, E, M> delegate = new VertexDelegate<I, V, E, M>(
+			this);
+	/** this vertex is updated or not */
+	private boolean updated = false;
+	/** has outgoing messages */
+	private boolean hasMessage = false;
 
-    /**
-     * use object pool for re-using objects
-     */
-    private List<Edge<I, E>> edgePool = new ArrayList<Edge<I, E>>();
-    private List<M> msgPool = new ArrayList<M>();
-    private List<V> valuePool = new ArrayList<V>();
-    private int usedEdge = 0;
-    private int usedMessage = 0;
-    private int usedValue = 0;
+	/**
+	 * use object pool for re-using objects
+	 */
+	private List<Edge<I, E>> edgePool = new ArrayList<Edge<I, E>>();
+	private List<M> msgPool = new ArrayList<M>();
+	private List<V> valuePool = new ArrayList<V>();
+	private int usedEdge = 0;
+	private int usedMessage = 0;
+	private int usedValue = 0;
 
-    /**
-     * The key method that users need to implement
-     * 
-     * @param msgIterator
-     */
-    public abstract void compute(Iterator<M> msgIterator);
+	/**
+	 * The key method that users need to implement
+	 * 
+	 * @param msgIterator
+	 *            an iterator of incoming messages
+	 */
+	public abstract void compute(Iterator<M> msgIterator);
 
-    public final boolean addEdge(I targetVertexId, E edgeValue) {
-        Edge<I, E> edge = this.allocateEdge();
-        edge.setDestVertexId(targetVertexId);
-        edge.setEdgeValue(edgeValue);
-        destEdgeList.add(edge);
-        return true;
-    }
+	/**
+	 * Add an edge for the vertex.
+	 * 
+	 * @param targetVertexId
+	 * @param edgeValue
+	 * @return successful or not
+	 */
+	public final boolean addEdge(I targetVertexId, E edgeValue) {
+		Edge<I, E> edge = this.allocateEdge();
+		edge.setDestVertexId(targetVertexId);
+		edge.setEdgeValue(edgeValue);
+		destEdgeList.add(edge);
+		return true;
+	}
 
-    public void initialize(I vertexId, V vertexValue, Map<I, E> edges, List<M> messages) {
-        if (vertexId != null) {
-            setVertexId(vertexId);
-        }
-        if (vertexValue != null) {
-            setVertexValue(vertexValue);
-        }
-        destEdgeList.clear();
-        if (edges != null && !edges.isEmpty()) {
-            for (Map.Entry<I, E> entry : edges.entrySet()) {
-                destEdgeList.add(new Edge<I, E>(entry.getKey(), entry.getValue()));
-            }
-        }
-        if (messages != null && !messages.isEmpty()) {
-            msgList.addAll(messages);
-        }
-    }
+	/**
+	 * Initialize a new vertex
+	 * 
+	 * @param vertexId
+	 * @param vertexValue
+	 * @param edges
+	 * @param messages
+	 */
+	public void initialize(I vertexId, V vertexValue, Map<I, E> edges,
+			List<M> messages) {
+		if (vertexId != null) {
+			setVertexId(vertexId);
+		}
+		if (vertexValue != null) {
+			setVertexValue(vertexValue);
+		}
+		destEdgeList.clear();
+		if (edges != null && !edges.isEmpty()) {
+			for (Map.Entry<I, E> entry : edges.entrySet()) {
+				destEdgeList.add(new Edge<I, E>(entry.getKey(), entry
+						.getValue()));
+			}
+		}
+		if (messages != null && !messages.isEmpty()) {
+			msgList.addAll(messages);
+		}
+	}
 
-    public void reset() {
-        usedEdge = 0;
-        usedMessage = 0;
-        usedValue = 0;
-    }
+	/**
+	 * reset a vertex object: clear its internal states
+	 */
+	public void reset() {
+		usedEdge = 0;
+		usedMessage = 0;
+		usedValue = 0;
+	}
 
-    private Edge<I, E> allocateEdge() {
-        Edge<I, E> edge;
-        if (usedEdge < edgePool.size()) {
-            edge = edgePool.get(usedEdge);
-            usedEdge++;
-        } else {
-            edge = new Edge<I, E>();
-            edgePool.add(edge);
-            usedEdge++;
-        }
-        return edge;
-    }
+	private Edge<I, E> allocateEdge() {
+		Edge<I, E> edge;
+		if (usedEdge < edgePool.size()) {
+			edge = edgePool.get(usedEdge);
+			usedEdge++;
+		} else {
+			edge = new Edge<I, E>();
+			edgePool.add(edge);
+			usedEdge++;
+		}
+		return edge;
+	}
 
-    private M allocateMessage() {
-        M message;
-        if (usedMessage < msgPool.size()) {
-            message = msgPool.get(usedEdge);
-            usedMessage++;
-        } else {
-            message = BspUtils.<M> createMessageValue(getContext().getConfiguration());
-            msgPool.add(message);
-            usedMessage++;
-        }
-        return message;
-    }
+	private M allocateMessage() {
+		M message;
+		if (usedMessage < msgPool.size()) {
+			message = msgPool.get(usedEdge);
+			usedMessage++;
+		} else {
+			message = BspUtils.<M> createMessageValue(getContext()
+					.getConfiguration());
+			msgPool.add(message);
+			usedMessage++;
+		}
+		return message;
+	}
 
-    private V allocateValue() {
-        V value;
-        if (usedValue < valuePool.size()) {
-            value = valuePool.get(usedEdge);
-            usedValue++;
-        } else {
-            value = BspUtils.<V> createVertexValue(getContext().getConfiguration());
-            valuePool.add(value);
-            usedValue++;
-        }
-        return value;
-    }
+	private V allocateValue() {
+		V value;
+		if (usedValue < valuePool.size()) {
+			value = valuePool.get(usedEdge);
+			usedValue++;
+		} else {
+			value = BspUtils.<V> createVertexValue(getContext()
+					.getConfiguration());
+			valuePool.add(value);
+			usedValue++;
+		}
+		return value;
+	}
 
-    public final void setVertexId(I vertexId) {
-        this.vertexId = vertexId;
-        delegate.setVertexId(vertexId);
-    }
+	/**
+	 * Set the vertex id
+	 * 
+	 * @param vertexId
+	 */
+	public final void setVertexId(I vertexId) {
+		this.vertexId = vertexId;
+		delegate.setVertexId(vertexId);
+	}
 
-    public final I getVertexId() {
-        return vertexId;
-    }
+	/**
+	 * Get the vertex id
+	 * 
+	 * @return vertex id
+	 */
+	public final I getVertexId() {
+		return vertexId;
+	}
 
-    /**
-     * Set the global superstep folr all the vertices (internal use)
-     * 
-     * @param superstep
-     *            New superstep
-     */
-    public static void setSuperstep(long superstep) {
-        Vertex.superstep = superstep;
-    }
+	/**
+	 * Set the global superstep for all the vertices (internal use)
+	 * 
+	 * @param superstep
+	 *            New superstep
+	 */
+	public static void setSuperstep(long superstep) {
+		Vertex.superstep = superstep;
+	}
 
-    public static long getCurrentSuperstep() {
-        return superstep;
-    }
+	public static long getCurrentSuperstep() {
+		return superstep;
+	}
 
-    public final long getSuperstep() {
-        return superstep;
-    }
+	public final long getSuperstep() {
+		return superstep;
+	}
 
-    public final V getVertexValue() {
-        return vertexValue;
-    }
+	public final V getVertexValue() {
+		return vertexValue;
+	}
 
-    public final void setVertexValue(V vertexValue) {
-        this.vertexValue = vertexValue;
-        this.updated = true;
-    }
+	public final void setVertexValue(V vertexValue) {
+		this.vertexValue = vertexValue;
+		this.updated = true;
+	}
 
-    /**
-     * Set the total number of vertices from the last superstep.
-     * 
-     * @param numVertices
-     *            Aggregate vertices in the last superstep
-     */
-    public static void setNumVertices(long numVertices) {
-        Vertex.numVertices = numVertices;
-    }
+	/**
+	 * Set the total number of vertices from the last superstep.
+	 * 
+	 * @param numVertices
+	 *            Aggregate vertices in the last superstep
+	 */
+	public static void setNumVertices(long numVertices) {
+		Vertex.numVertices = numVertices;
+	}
 
-    public final long getNumVertices() {
-        return numVertices;
-    }
+	public final long getNumVertices() {
+		return numVertices;
+	}
 
-    /**
-     * Set the total number of edges from the last superstep.
-     * 
-     * @param numEdges
-     *            Aggregate edges in the last superstep
-     */
-    public static void setNumEdges(long numEdges) {
-        Vertex.numEdges = numEdges;
-    }
+	/**
+	 * Set the total number of edges from the last superstep.
+	 * 
+	 * @param numEdges
+	 *            Aggregate edges in the last superstep
+	 */
+	public static void setNumEdges(long numEdges) {
+		Vertex.numEdges = numEdges;
+	}
 
-    public final long getNumEdges() {
-        return numEdges;
-    }
+	public final long getNumEdges() {
+		return numEdges;
+	}
 
-    public final void sendMsg(I id, M msg) {
-        if (msg == null) {
-            throw new IllegalArgumentException("sendMsg: Cannot send null message to " + id);
-        }
-        delegate.sendMsg(id, msg);
-        this.hasMessage = true;
-    }
+	/***
+	 * Send a message to a specific vertex
+	 * 
+	 * @param id
+	 *            the receiver vertex id
+	 * @param msg
+	 *            the message
+	 */
+	public final void sendMsg(I id, M msg) {
+		if (msg == null) {
+			throw new IllegalArgumentException(
+					"sendMsg: Cannot send null message to " + id);
+		}
+		delegate.sendMsg(id, msg);
+		this.hasMessage = true;
+	}
 
-    public final void sendMsgToAllEdges(M msg) {
-        if (msg == null) {
-            throw new IllegalArgumentException("sendMsgToAllEdges: Cannot send null message to all edges");
-        }
-        for (Edge<I, E> edge : destEdgeList) {
-            sendMsg(edge.getDestVertexId(), msg);
-        }
-    }
+	/**
+	 * Send a message to all direct outgoing neighbors
+	 * 
+	 * @param msg
+	 *            the message
+	 */
+	public final void sendMsgToAllEdges(M msg) {
+		if (msg == null) {
+			throw new IllegalArgumentException(
+					"sendMsgToAllEdges: Cannot send null message to all edges");
+		}
+		for (Edge<I, E> edge : destEdgeList) {
+			sendMsg(edge.getDestVertexId(), msg);
+		}
+	}
 
-    public final void voteToHalt() {
-        halt = true;
-    }
+	/**
+	 * Vote to halt. Once all vertex vote to halt and no more messages, a
+	 * Pregelix job will terminate.
+	 */
+	public final void voteToHalt() {
+		halt = true;
+	}
 
-    public final boolean isHalted() {
-        return halt;
-    }
+	/**
+	 * @return the vertex is halted (true) or not (false)
+	 */
+	public final boolean isHalted() {
+		return halt;
+	}
 
-    @Override
-    final public void readFields(DataInput in) throws IOException {
-        reset();
-        if (vertexId == null)
-            vertexId = BspUtils.<I> createVertexIndex(getContext().getConfiguration());
-        vertexId.readFields(in);
-        delegate.setVertexId(vertexId);
-        boolean hasVertexValue = in.readBoolean();
-        if (hasVertexValue) {
-            vertexValue = allocateValue();
-            vertexValue.readFields(in);
-            delegate.setVertex(this);
-        }
-        destEdgeList.clear();
-        long edgeMapSize = SerDeUtils.readVLong(in);
-        for (long i = 0; i < edgeMapSize; ++i) {
-            Edge<I, E> edge = allocateEdge();
-            edge.setConf(getContext().getConfiguration());
-            edge.readFields(in);
-            addEdge(edge);
-        }
-        msgList.clear();
-        long msgListSize = SerDeUtils.readVLong(in);
-        for (long i = 0; i < msgListSize; ++i) {
-            M msg = allocateMessage();
-            msg.readFields(in);
-            msgList.add(msg);
-        }
-        halt = in.readBoolean();
-        updated = false;
-        hasMessage = false;
-    }
+	@Override
+	final public void readFields(DataInput in) throws IOException {
+		reset();
+		if (vertexId == null)
+			vertexId = BspUtils.<I> createVertexIndex(getContext()
+					.getConfiguration());
+		vertexId.readFields(in);
+		delegate.setVertexId(vertexId);
+		boolean hasVertexValue = in.readBoolean();
+		if (hasVertexValue) {
+			vertexValue = allocateValue();
+			vertexValue.readFields(in);
+			delegate.setVertex(this);
+		}
+		destEdgeList.clear();
+		long edgeMapSize = SerDeUtils.readVLong(in);
+		for (long i = 0; i < edgeMapSize; ++i) {
+			Edge<I, E> edge = allocateEdge();
+			edge.setConf(getContext().getConfiguration());
+			edge.readFields(in);
+			addEdge(edge);
+		}
+		msgList.clear();
+		long msgListSize = SerDeUtils.readVLong(in);
+		for (long i = 0; i < msgListSize; ++i) {
+			M msg = allocateMessage();
+			msg.readFields(in);
+			msgList.add(msg);
+		}
+		halt = in.readBoolean();
+		updated = false;
+		hasMessage = false;
+	}
 
-    @Override
-    public void write(DataOutput out) throws IOException {
-        vertexId.write(out);
-        out.writeBoolean(vertexValue != null);
-        if (vertexValue != null) {
-            vertexValue.write(out);
-        }
-        SerDeUtils.writeVLong(out, destEdgeList.size());
-        for (Edge<I, E> edge : destEdgeList) {
-            edge.write(out);
-        }
-        SerDeUtils.writeVLong(out, msgList.size());
-        for (M msg : msgList) {
-            msg.write(out);
-        }
-        out.writeBoolean(halt);
-    }
+	@Override
+	public void write(DataOutput out) throws IOException {
+		vertexId.write(out);
+		out.writeBoolean(vertexValue != null);
+		if (vertexValue != null) {
+			vertexValue.write(out);
+		}
+		SerDeUtils.writeVLong(out, destEdgeList.size());
+		for (Edge<I, E> edge : destEdgeList) {
+			edge.write(out);
+		}
+		SerDeUtils.writeVLong(out, msgList.size());
+		for (M msg : msgList) {
+			msg.write(out);
+		}
+		out.writeBoolean(halt);
+	}
 
-    private boolean addEdge(Edge<I, E> edge) {
-        edge.setConf(getContext().getConfiguration());
-        destEdgeList.add(edge);
-        return true;
-    }
+	private boolean addEdge(Edge<I, E> edge) {
+		edge.setConf(getContext().getConfiguration());
+		destEdgeList.add(edge);
+		return true;
+	}
 
-    public List<M> getMsgList() {
-        return msgList;
-    }
+	/**
+	 * Get the list of incoming messages
+	 * 
+	 * @return the list of messages
+	 */
+	public List<M> getMsgList() {
+		return msgList;
+	}
 
-    public List<Edge<I, E>> getEdges() {
-        return this.destEdgeList;
-    }
+	/**
+	 * Get outgoing edge list
+	 * 
+	 * @return a list of outgoing edges
+	 */
+	public List<Edge<I, E>> getEdges() {
+		return this.destEdgeList;
+	}
 
-    public final Mapper<?, ?, ?, ?>.Context getContext() {
-        return context;
-    }
+	public final Mapper<?, ?, ?, ?>.Context getContext() {
+		return context;
+	}
 
-    public final static void setContext(Mapper<?, ?, ?, ?>.Context context) {
-        Vertex.context = context;
-    }
+	public final static void setContext(Mapper<?, ?, ?, ?>.Context context) {
+		Vertex.context = context;
+	}
 
-    @SuppressWarnings("unchecked")
-    public String toString() {
-        Collections.sort(destEdgeList);
-        StringBuffer edgeBuffer = new StringBuffer();
-        edgeBuffer.append("(");
-        for (Edge<I, E> edge : destEdgeList) {
-            edgeBuffer.append(edge.getDestVertexId()).append(",");
-        }
-        edgeBuffer.append(")");
-        return "Vertex(id=" + getVertexId() + ",value=" + getVertexValue() + ", edges=" + edgeBuffer + ")";
-    }
+	@SuppressWarnings("unchecked")
+	public String toString() {
+		Collections.sort(destEdgeList);
+		StringBuffer edgeBuffer = new StringBuffer();
+		edgeBuffer.append("(");
+		for (Edge<I, E> edge : destEdgeList) {
+			edgeBuffer.append(edge.getDestVertexId()).append(",");
+		}
+		edgeBuffer.append(")");
+		return "Vertex(id=" + getVertexId() + ",value=" + getVertexValue()
+				+ ", edges=" + edgeBuffer + ")";
+	}
 
-    public void setOutputWriters(List<IFrameWriter> writers) {
-        delegate.setOutputWriters(writers);
-    }
+	public void setOutputWriters(List<IFrameWriter> writers) {
+		delegate.setOutputWriters(writers);
+	}
 
-    public void setOutputAppenders(List<FrameTupleAppender> appenders) {
-        delegate.setOutputAppenders(appenders);
-    }
+	public void setOutputAppenders(List<FrameTupleAppender> appenders) {
+		delegate.setOutputAppenders(appenders);
+	}
 
-    public void setOutputTupleBuilders(List<ArrayTupleBuilder> tbs) {
-        delegate.setOutputTupleBuilders(tbs);
-    }
+	public void setOutputTupleBuilders(List<ArrayTupleBuilder> tbs) {
+		delegate.setOutputTupleBuilders(tbs);
+	}
 
-    public void finishCompute() throws IOException {
-        delegate.finishCompute();
-    }
+	public void finishCompute() throws IOException {
+		delegate.finishCompute();
+	}
 
-    public boolean hasUpdate() {
-        return this.updated;
-    }
+	public boolean hasUpdate() {
+		return this.updated;
+	}
 
-    public boolean hasMessage() {
-        return this.hasMessage;
-    }
+	public boolean hasMessage() {
+		return this.hasMessage;
+	}
 
-    public int getNumOutEdges() {
-        return destEdgeList.size();
-    }
+	public int getNumOutEdges() {
+		return destEdgeList.size();
+	}
 
-    @SuppressWarnings("unchecked")
-    public void sortEdges() {
-        Collections.sort((List) destEdgeList);
-    }
+	@SuppressWarnings("unchecked")
+	public void sortEdges() {
+		Collections.sort((List) destEdgeList);
+	}
 
 }
diff --git a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/job/PregelixJob.java b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/job/PregelixJob.java
index d2005c8..754c76e 100644
--- a/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/job/PregelixJob.java
+++ b/pregelix/pregelix-api/src/main/java/edu/uci/ics/pregelix/api/job/PregelixJob.java
@@ -26,8 +26,7 @@
 import edu.uci.ics.pregelix.api.io.VertexOutputFormat;
 
 /**
- * Limits the functions that can be called by the user. Job is too flexible for
- * our needs. For instance, our job should not have any reduce tasks.
+ * This class represents a Pregelix job.
  */
 public class PregelixJob extends Job {
     /** Vertex class - required */