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Posted to commits@hama.apache.org by ed...@apache.org on 2008/08/25 09:57:55 UTC

svn commit: r688643 - in /incubator/hama/trunk/src: docs/src/documentation/content/xdocs/ examples/org/apache/hama/examples/ java/org/apache/hama/ java/org/apache/hama/algebra/ java/org/apache/hama/io/ java/org/apache/hama/mapred/ test/org/apache/hama/...

Author: edwardyoon
Date: Mon Aug 25 00:57:54 2008
New Revision: 688643

URL: http://svn.apache.org/viewvc?rev=688643&view=rev
Log:
Color Logo.

Added:
    incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java
    incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java
    incubator/hama/trunk/src/java/org/apache/hama/mapred/DenseMap.java
Modified:
    incubator/hama/trunk/src/docs/src/documentation/content/xdocs/index.xml
    incubator/hama/trunk/src/docs/src/documentation/content/xdocs/who_we_are.xml
    incubator/hama/trunk/src/examples/org/apache/hama/examples/MatrixAddition.java
    incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java
    incubator/hama/trunk/src/java/org/apache/hama/Matrix.java
    incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java
    incubator/hama/trunk/src/java/org/apache/hama/Vector.java
    incubator/hama/trunk/src/java/org/apache/hama/VectorInterface.java
    incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionMap.java
    incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionReduce.java
    incubator/hama/trunk/src/java/org/apache/hama/io/VectorWritable.java
    incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormatBase.java
    incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java
    incubator/hama/trunk/src/test/org/apache/hama/TestMatrix.java
    incubator/hama/trunk/src/test/org/apache/hama/TestVector.java
    incubator/hama/trunk/src/test/org/apache/hama/mapred/TestMatrixMapReduce.java

Modified: incubator/hama/trunk/src/docs/src/documentation/content/xdocs/index.xml
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/docs/src/documentation/content/xdocs/index.xml?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/docs/src/documentation/content/xdocs/index.xml (original)
+++ incubator/hama/trunk/src/docs/src/documentation/content/xdocs/index.xml Mon Aug 25 00:57:54 2008
@@ -28,7 +28,7 @@
     <section>
       <title> Introduction </title>
       <table class="NonBorderTable">
-      <tr><td><img src="./images/hama_logo.png" alt="Hama Logo" /></td>
+      <tr><td><img src="./images/hama_paint_logo.png" alt="Hama Logo" /></td>
       <td><strong>Hama</strong> (means a hippopotamus in Korean) is a 
       parallel matrix computational package,
       which provides an library of matrix operations for the large-scale

Modified: incubator/hama/trunk/src/docs/src/documentation/content/xdocs/who_we_are.xml
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/docs/src/documentation/content/xdocs/who_we_are.xml?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/docs/src/documentation/content/xdocs/who_we_are.xml (original)
+++ incubator/hama/trunk/src/docs/src/documentation/content/xdocs/who_we_are.xml Mon Aug 25 00:57:54 2008
@@ -114,7 +114,8 @@
 	<title>Contributors</title>
 	<p>Contributors are:</p>
 	<ul>
-	  <li>Su-kyung Kim, a contributor of Hama logos artwork.</li>
+	  <li>Su-kyung Kim, a contributor of Hama logo sketch.</li>
+	  <li>Morakot, a contributor of Hama logo paint.</li>
 	</ul>
 	</section>
 

Modified: incubator/hama/trunk/src/examples/org/apache/hama/examples/MatrixAddition.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/examples/org/apache/hama/examples/MatrixAddition.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/examples/org/apache/hama/examples/MatrixAddition.java (original)
+++ incubator/hama/trunk/src/examples/org/apache/hama/examples/MatrixAddition.java Mon Aug 25 00:57:54 2008
@@ -19,6 +19,7 @@
  */
 package org.apache.hama.examples;
 
+import org.apache.hama.DenseMatrix;
 import org.apache.hama.HamaConfiguration;
 import org.apache.hama.Matrix;
 
@@ -35,8 +36,8 @@
 
     HamaConfiguration conf = new HamaConfiguration();
 
-    Matrix a = Matrix.random(conf, row, column);
-    Matrix b = Matrix.random(conf, row, column);
+    Matrix a = DenseMatrix.random(conf, row, column);
+    Matrix b = DenseMatrix.random(conf, row, column);
 
     Matrix c = a.add(b);
 

Modified: incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java Mon Aug 25 00:57:54 2008
@@ -36,7 +36,7 @@
 /**
  * Methods of the matrix classes
  */
-public abstract class AbstractMatrix implements MatrixInterface {
+public abstract class AbstractMatrix implements Matrix {
   static final Logger LOG = Logger.getLogger(AbstractMatrix.class);
 
   /** Hama Configuration */
@@ -94,25 +94,6 @@
   }
 
   /** {@inheritDoc} */
-  public Vector getRow(int row) {
-    try {
-      return new Vector(row, table.getRow(String.valueOf(row)));
-    } catch (IOException e) {
-      LOG.error(e, e);
-    }
-    return null;
-  }
-
-  public Vector getRow(byte[] row) {
-    try {
-      return new Vector(Numeric.bytesToInt(row), table.getRow(row));
-    } catch (IOException e) {
-      LOG.error(e, e);
-    }
-    return null;
-  }
-
-  /** {@inheritDoc} */
   public int getRows() {
     Cell rows = null;
     try {

Added: incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java?rev=688643&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java Mon Aug 25 00:57:54 2008
@@ -0,0 +1,185 @@
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.hama;
+
+import java.io.IOException;
+
+import org.apache.hadoop.hbase.HColumnDescriptor;
+import org.apache.hadoop.hbase.HTableDescriptor;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.mapred.JobClient;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hama.algebra.AdditionMap;
+import org.apache.hama.algebra.AdditionReduce;
+import org.apache.hama.mapred.DenseMap;
+import org.apache.hama.mapred.MatrixReduce;
+import org.apache.hama.util.RandomVariable;
+
+public class DenseMatrix extends AbstractMatrix implements Matrix {
+
+  /**
+   * Construct
+   * 
+   * @param conf configuration object
+   */
+  public DenseMatrix(HamaConfiguration conf) {
+    setConfiguration(conf);
+  }
+
+  /**
+   * Construct an matrix
+   * 
+   * @param conf configuration object
+   * @param matrixName the name of the matrix
+   */
+  public DenseMatrix(HamaConfiguration conf, String matrixName) {
+    try {
+      setConfiguration(conf);
+      this.matrixName = matrixName;
+
+      if (!admin.tableExists(matrixName)) {
+        tableDesc = new HTableDescriptor(matrixName.toString());
+        tableDesc.addFamily(new HColumnDescriptor(Constants.COLUMN.toString()));
+        create();
+      }
+
+      table = new HTable(config, matrixName);
+    } catch (Exception e) {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * Construct an m-by-n constant matrix.
+   * 
+   * @param conf configuration object
+   * @param m the number of rows.
+   * @param n the number of columns.
+   * @param s fill the matrix with this scalar value.
+   */
+  public DenseMatrix(HamaConfiguration conf, int m, int n, double s) {
+    try {
+      setConfiguration(conf);
+      matrixName = RandomVariable.randMatrixName();
+
+      if (!admin.tableExists(matrixName)) {
+        tableDesc = new HTableDescriptor(matrixName.toString());
+        tableDesc.addFamily(new HColumnDescriptor(Constants.COLUMN.toString()));
+        create();
+      }
+
+      table = new HTable(config, matrixName);
+
+      for (int i = 0; i < m; i++) {
+        for (int j = 0; j < n; j++) {
+          set(i, j, s);
+        }
+      }
+
+      setDimension(m, n);
+    } catch (IOException e) {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * Generate matrix with random elements
+   * 
+   * @param conf configuration object
+   * @param m the number of rows.
+   * @param n the number of columns.
+   * @return an m-by-n matrix with uniformly distributed random elements.
+   */
+  public static Matrix random(HamaConfiguration conf, int m, int n) {
+    String name = RandomVariable.randMatrixName();
+    Matrix rand = new DenseMatrix(conf, name);
+    for (int i = 0; i < m; i++) {
+      for (int j = 0; j < n; j++) {
+        rand.set(i, j, RandomVariable.rand());
+      }
+    }
+
+    rand.setDimension(m, n);
+    LOG.info("Create the " + m + " * " + n + " random matrix : " + name);
+    return rand;
+  }
+
+  public Matrix add(Matrix B) {
+    String output = RandomVariable.randMatrixName();
+    Matrix C = new DenseMatrix(config, output);
+
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("addition MR job");
+
+    DenseMap.initJob(this.getName(), B.getName(), AdditionMap.class,
+        ImmutableBytesWritable.class, DenseVector.class, jobConf);
+    MatrixReduce.initJob(C.getName(), AdditionReduce.class, jobConf);
+
+    try {
+      JobClient.runJob(jobConf);
+    } catch (IOException e) {
+      // TODO Auto-generated catch block
+      e.printStackTrace();
+    }
+
+    return C;
+  }
+
+  public Matrix add(double alpha, Matrix B) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  public DenseVector getRow(int row) {
+    try {
+      return new DenseVector(row, table.getRow(String.valueOf(row)));
+    } catch (IOException e) {
+      LOG.error(e, e);
+    }
+    return null;
+  }
+  
+  public Matrix mult(Matrix B) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  public Matrix multAdd(double alpha, Matrix B, Matrix C) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  public double norm(Norm type) {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  public Matrix set(double alpha, Matrix B) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  public Matrix set(Matrix B) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java?rev=688643&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java Mon Aug 25 00:57:54 2008
@@ -0,0 +1,154 @@
+package org.apache.hama;
+
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hadoop.hbase.io.HbaseMapWritable;
+import org.apache.hadoop.hbase.io.RowResult;
+import org.apache.hadoop.hbase.util.Bytes;
+import org.apache.hama.io.VectorWritable;
+import org.apache.hama.util.Numeric;
+import org.apache.log4j.Logger;
+
+public class DenseVector extends VectorWritable implements Vector {
+  static final Logger LOG = Logger.getLogger(Vector.class);
+
+  public DenseVector() {
+    this(null, new HbaseMapWritable<byte[], Cell>());
+  }
+
+  public DenseVector(final byte[] row, final HbaseMapWritable<byte[], Cell> m) {
+    this.row = row;
+    this.cells = m;
+  }
+
+  public DenseVector(int row, RowResult rowResult) {
+    this.cells = new HbaseMapWritable<byte[], Cell>();
+    this.row = Numeric.intToBytes(row);
+    for (Map.Entry<byte[], Cell> f : rowResult.entrySet()) {
+      this.cells.put(f.getKey(), f.getValue());
+    }
+  }
+
+  /**
+   * Get the row for this Vector
+   */
+  public byte[] getRow() {
+    return row;
+  }
+
+  public HbaseMapWritable<byte[], Cell> getCells() {
+    return cells;
+  }
+
+  public void add(int index, double value) {
+    // TODO Auto-generated method stub
+
+  }
+
+  public Vector add(double alpha, Vector v) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  public Vector add(Vector v2) {
+    HbaseMapWritable<byte[], Cell> trunk = new HbaseMapWritable<byte[], Cell>();
+    for (int i = 0; i < this.size(); i++) {
+      double value = (this.get(i) + v2.get(i));
+      Cell cValue = new Cell(String.valueOf(value), System.currentTimeMillis());
+      trunk.put(Bytes.toBytes("column:" + i), cValue);
+    }
+
+    return new DenseVector(row, trunk);
+  }
+
+  public double dot(Vector v) {
+    double cosine = 0.0;
+    double q_i, d_i;
+    for (int i = 0; i < Math.min(this.size(), v.size()); i++) {
+      q_i = v.get(i);
+      d_i = this.get(i);
+      cosine += q_i * d_i;
+    }
+    return cosine / (this.getNorm2() * ((DenseVector) v).getNorm2());
+  }
+
+  public Vector scale(double alpha) {
+    Set<byte[]> keySet = cells.keySet();
+    Iterator<byte[]> it = keySet.iterator();
+
+    while (it.hasNext()) {
+      byte[] key = it.next();
+      double oValue = Numeric.bytesToDouble(get(key).getValue());
+      double nValue = oValue * alpha;
+      Cell cValue = new Cell(String.valueOf(nValue), System.currentTimeMillis());
+      cells.put(key, cValue);
+    }
+
+    return this;
+  }
+
+  public double get(int index) {
+    return Numeric.bytesToDouble(cells.get(Numeric.getColumnIndex(index))
+        .getValue());
+  }
+
+  public double norm(Norm type) {
+    if (type == Norm.One)
+      return getNorm1();
+    else if (type == Norm.Two)
+      return getNorm2();
+    else if (type == Norm.TwoRobust)
+      return getNorm2Robust();
+    else
+      return getNormInf();
+  }
+
+  public void set(int index, double value) {
+    Cell cValue = new Cell(String.valueOf(value), System.currentTimeMillis());
+    cells.put(Numeric.getColumnIndex(index), cValue);
+  }
+
+  public DenseVector set(Vector v) {
+    return new DenseVector(((DenseVector) v).getRow(), ((DenseVector) v).getCells());
+  }
+
+  public double getNorm1() {
+    double sum = 0.0;
+
+    Set<byte[]> keySet = cells.keySet();
+    Iterator<byte[]> it = keySet.iterator();
+
+    while (it.hasNext()) {
+      sum += Numeric.bytesToDouble(get(it.next()).getValue());
+    }
+
+    return sum;
+  }
+
+  public double getNorm2() {
+    double square_sum = 0.0;
+
+    Set<byte[]> keySet = cells.keySet();
+    Iterator<byte[]> it = keySet.iterator();
+
+    while (it.hasNext()) {
+      double value = Numeric.bytesToDouble(get(it.next()).getValue());
+      square_sum += value * value;
+    }
+
+    return Math.sqrt(square_sum);
+  }
+
+  public double getNorm2Robust() {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  public double getNormInf() {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+}
\ No newline at end of file

Modified: incubator/hama/trunk/src/java/org/apache/hama/Matrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/Matrix.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/Matrix.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/Matrix.java Mon Aug 25 00:57:54 2008
@@ -19,160 +19,140 @@
  */
 package org.apache.hama;
 
-import java.io.IOException;
-
-import org.apache.hadoop.hbase.HColumnDescriptor;
-import org.apache.hadoop.hbase.HTableDescriptor;
-import org.apache.hadoop.hbase.client.HTable;
-import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
-import org.apache.hadoop.mapred.JobClient;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hama.algebra.AdditionMap;
-import org.apache.hama.algebra.AdditionReduce;
-import org.apache.hama.mapred.MatrixMap;
-import org.apache.hama.mapred.MatrixReduce;
-import org.apache.hama.util.RandomVariable;
-
 /**
- * A library for mathematical operations on matrices of double.
+ * Basic matrix interface.
  */
-public class Matrix extends AbstractMatrix {
+public interface Matrix {
+  
+  /**
+   * Gets the double value of (i, j)
+   * 
+   * @param i ith row of the matrix
+   * @param j jth column of the matrix
+   * @return the value of entry
+   */
+  public double get(int i, int j);
 
   /**
-   * Construct
+   * Gets the vector of row
    * 
-   * @param conf configuration object
+   * @param row the row index of the matrix
+   * @return the feature vector of row
    */
-  public Matrix(HamaConfiguration conf) {
-    setConfiguration(conf);
-  }
+  public Vector getRow(int row);
 
   /**
-   * Construct an matrix
+   * Get a number of row of the matrix from the meta-data column
    * 
-   * @param conf configuration object
-   * @param matrixName the name of the matrix
+   * @return a number of rows of the matrix
    */
-  public Matrix(HamaConfiguration conf, String matrixName) {
-    try {
-      setConfiguration(conf);
-      this.matrixName = matrixName;
-
-      if (!admin.tableExists(matrixName)) {
-        tableDesc = new HTableDescriptor(matrixName.toString());
-        tableDesc.addFamily(new HColumnDescriptor(Constants.COLUMN.toString()));
-        create();
-      }
-
-      table = new HTable(config, matrixName);
-    } catch (Exception e) {
-      e.printStackTrace();
-    }
-  }
+  public int getRows();
 
   /**
-   * Construct an m-by-n constant matrix.
+   * Get a number of column of the matrix from the meta-data column
    * 
-   * @param conf configuration object
-   * @param m the number of rows.
-   * @param n the number of columns.
-   * @param s fill the matrix with this scalar value.
-   */
-  public Matrix(HamaConfiguration conf, int m, int n, double s) {
-    try {
-      setConfiguration(conf);
-      matrixName = RandomVariable.randMatrixName();
-
-      if (!admin.tableExists(matrixName)) {
-        tableDesc = new HTableDescriptor(matrixName.toString());
-        tableDesc.addFamily(new HColumnDescriptor(Constants.COLUMN.toString()));
-        create();
-      }
-
-      table = new HTable(config, matrixName);
-
-      for (int i = 0; i < m; i++) {
-        for (int j = 0; j < n; j++) {
-          set(i, j, s);
-        }
-      }
-
-      setDimension(m, n);
-    } catch (IOException e) {
-      e.printStackTrace();
-    }
-  }
+   * @return a number of columns of the matrix
+   */
+  public int getColumns();
 
   /**
-   * Generate matrix with random elements
+   * Sets the double value of (i, j)
    * 
-   * @param conf configuration object
-   * @param m the number of rows.
-   * @param n the number of columns.
-   * @return an m-by-n matrix with uniformly distributed random elements.
-   */
-  public static Matrix random(HamaConfiguration conf, int m, int n) {
-    String name = RandomVariable.randMatrixName();
-    Matrix rand = new Matrix(conf, name);
-    for (int i = 0; i < m; i++) {
-      for (int j = 0; j < n; j++) {
-        rand.set(i, j, RandomVariable.rand());
-      }
-    }
-
-    rand.setDimension(m, n);
-    LOG.info("Create the " + m + " * " + n + " random matrix : " + name);
-    return rand;
-  }
+   * @param i ith row of the matrix
+   * @param j jth column of the matrix
+   * @param value the value of entry
+   */
+  public void set(int i, int j, double value);
 
-  public Matrix add(Matrix B) {
-    String output = RandomVariable.randMatrixName();
-    Matrix C = new Matrix(config, output);
-
-    JobConf jobConf = new JobConf(config);
-    jobConf.setJobName("addition MR job");
-
-    MatrixMap.initJob(this.getName(), B.getName(), AdditionMap.class,
-        ImmutableBytesWritable.class, Vector.class, jobConf);
-    MatrixReduce.initJob(C.getName(), AdditionReduce.class, jobConf);
-
-    try {
-      JobClient.runJob(jobConf);
-    } catch (IOException e) {
-      // TODO Auto-generated catch block
-      e.printStackTrace();
-    }
+  /**
+   * A=alpha*B
+   * 
+   * @param alpha
+   * @param B
+   * @return A
+   */
+  public Matrix set(double alpha, Matrix B);
 
-    return C;
-  }
+  /**
+   * A=B
+   * 
+   * @param B
+   * @return A
+   */
+  public Matrix set(Matrix B);
 
-  public Matrix add(double alpha, Matrix B) {
-    // TODO Auto-generated method stub
-    return null;
-  }
+  /**
+   * Sets the dimension of matrix
+   * 
+   * @param rows the number of rows
+   * @param columns the number of columns
+   */
+  public void setDimension(int rows, int columns);
 
-  public Matrix mult(Matrix B) {
-    // TODO Auto-generated method stub
-    return null;
-  }
+  /**
+   * A(i, j) += value
+   * 
+   * @param i
+   * @param j
+   * @param value
+   */
+  public void add(int i, int j, double value);
 
-  public Matrix multAdd(double alpha, Matrix B, Matrix C) {
-    // TODO Auto-generated method stub
-    return null;
-  }
+  /**
+   * A = B + A
+   * 
+   * @param B
+   * @return A
+   */
+  public Matrix add(Matrix B);
 
-  public double norm(Norm type) {
-    // TODO Auto-generated method stub
-    return 0;
-  }
+  /**
+   * A = alpha*B + A
+   * 
+   * @param alpha
+   * @param B
+   * @return A
+   */
+  public Matrix add(double alpha, Matrix B);
 
-  public Matrix set(double alpha, Matrix B) {
-    // TODO Auto-generated method stub
-    return null;
-  }
+  /**
+   * C = A*B
+   * 
+   * @param B
+   * @return C
+   */
+  public Matrix mult(Matrix B);
+
+  /**
+   * C = alpha*A*B + C
+   * 
+   * @param alpha
+   * @param B
+   * @param C
+   * @return C
+   */
+  public Matrix multAdd(double alpha, Matrix B, Matrix C);
+
+  /**
+   * Computes the given norm of the matrix
+   * 
+   * @param type
+   * @return norm of the matrix
+   */
+  public double norm(Norm type);
 
-  public Matrix set(Matrix B) {
-    // TODO Auto-generated method stub
-    return null;
+  /**
+   * Supported matrix-norms.
+   */
+  enum Norm {
+    /** Largest entry in absolute value */
+    Infinity
   }
+
+  /**
+   * Return the matrix name
+   * 
+   * @return the name of the matrix
+   */
+  public String getName();
 }

Modified: incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java Mon Aug 25 00:57:54 2008
@@ -19,9 +19,7 @@
  */
 package org.apache.hama;
 
-/**
- * Basic matrix interface.
- */
+@Deprecated
 public interface MatrixInterface {
 
   /**

Modified: incubator/hama/trunk/src/java/org/apache/hama/Vector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/Vector.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/Vector.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/Vector.java Mon Aug 25 00:57:54 2008
@@ -19,155 +19,110 @@
  */
 package org.apache.hama;
 
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.hadoop.hbase.io.Cell;
-import org.apache.hadoop.hbase.io.HbaseMapWritable;
-import org.apache.hadoop.hbase.io.RowResult;
-import org.apache.hadoop.hbase.util.Bytes;
-import org.apache.hama.io.VectorWritable;
-import org.apache.hama.util.Numeric;
-import org.apache.log4j.Logger;
-
-public class Vector extends VectorWritable implements VectorInterface {
-  static final Logger LOG = Logger.getLogger(Vector.class);
-
-  public Vector() {
-    this(null, new HbaseMapWritable<byte[], Cell>());
-  }
-
-  public Vector(final byte[] row, final HbaseMapWritable<byte[], Cell> m) {
-    this.row = row;
-    this.cells = m;
-  }
-
-  public Vector(int row, RowResult rowResult) {
-    this.cells = new HbaseMapWritable<byte[], Cell>();
-    this.row = Numeric.intToBytes(row);
-    for (Map.Entry<byte[], Cell> f : rowResult.entrySet()) {
-      this.cells.put(f.getKey(), f.getValue());
-    }
-  }
+/**
+ * Basic vector interface.
+ */
+public interface Vector {
 
   /**
-   * Get the row for this Vector
+   * Size of the vector
+   * 
+   * @return size of the vector
    */
-  public byte[] getRow() {
-    return row;
-  }
-
-  public HbaseMapWritable<byte[], Cell> getCells() {
-    return cells;
-  }
-
-  public void add(int index, double value) {
-    // TODO Auto-generated method stub
-
-  }
-
-  public Vector add(double alpha, Vector v) {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  public Vector add(Vector v2) {
-    HbaseMapWritable<byte[], Cell> trunk = new HbaseMapWritable<byte[], Cell>();
-    for (int i = 0; i < this.size(); i++) {
-      double value = (this.get(i) + v2.get(i));
-      Cell cValue = new Cell(String.valueOf(value), System.currentTimeMillis());
-      trunk.put(Bytes.toBytes("column:" + i), cValue);
-    }
-
-    return new Vector(row, trunk);
-  }
-
-  public double dot(Vector v) {
-    double cosine = 0.0;
-    double q_i, d_i;
-    for (int i = 0; i < Math.min(this.size(), v.size()); i++) {
-      q_i = v.get(i);
-      d_i = this.get(i);
-      cosine += q_i * d_i;
-    }
-    return cosine / (this.getNorm2() * v.getNorm2());
-  }
-
-  public Vector scale(double alpha) {
-    Set<byte[]> keySet = cells.keySet();
-    Iterator<byte[]> it = keySet.iterator();
-
-    while (it.hasNext()) {
-      byte[] key = it.next();
-      double oValue = Numeric.bytesToDouble(get(key).getValue());
-      double nValue = oValue * alpha;
-      Cell cValue = new Cell(String.valueOf(nValue), System.currentTimeMillis());
-      cells.put(key, cValue);
-    }
-
-    return this;
-  }
-
-  public double get(int index) {
-    return Numeric.bytesToDouble(cells.get(Numeric.getColumnIndex(index))
-        .getValue());
-  }
+  public int size();
 
-  public double norm(Norm type) {
-    if (type == Norm.One)
-      return getNorm1();
-    else if (type == Norm.Two)
-      return getNorm2();
-    else if (type == Norm.TwoRobust)
-      return getNorm2Robust();
-    else
-      return getNormInf();
-  }
+  /**
+   * Gets the value of index
+   * 
+   * @param index
+   * @return v(index)
+   */
+  public double get(int index);
 
-  public void set(int index, double value) {
-    Cell cValue = new Cell(String.valueOf(value), System.currentTimeMillis());
-    cells.put(Numeric.getColumnIndex(index), cValue);
-  }
+  /**
+   * Sets the value of index
+   * 
+   * @param index
+   * @param value
+   */
+  public void set(int index, double value);
 
-  public Vector set(Vector v) {
-    return new Vector(v.getRow(), v.getCells());
-  }
+  /**
+   * Sets the vector
+   * 
+   * @param v
+   * @return x = v
+   */
+  public Vector set(Vector v);
 
-  public double getNorm1() {
-    double sum = 0.0;
+  /**
+   * Adds the value to v(index)
+   * 
+   * @param index
+   * @param value
+   */
+  public void add(int index, double value);
 
-    Set<byte[]> keySet = cells.keySet();
-    Iterator<byte[]> it = keySet.iterator();
+  /**
+   * x = alpha*v + x
+   * 
+   * @param alpha
+   * @param v
+   * @return x = alpha*v + x
+   */
+  public Vector add(double alpha, Vector v);
 
-    while (it.hasNext()) {
-      sum += Numeric.bytesToDouble(get(it.next()).getValue());
-    }
+  /**
+   * x = v + x
+   * 
+   * @param v
+   * @return x = v + x
+   */
+  public Vector add(Vector v);
 
-    return sum;
-  }
+  /**
+   * x dot v
+   * 
+   * @param v
+   * @return x dot v
+   */
+  public double dot(Vector v);
 
-  public double getNorm2() {
-    double square_sum = 0.0;
+  /**
+   * v = alpha*v 
+   * 
+   * @param alpha
+   * @return v = alpha*v
+   */
+  public Vector scale(double alpha);
+  
+  
+  /**
+   * Computes the given norm of the vector
+   * 
+   * @param type
+   * @return norm of the vector
+   */
+  public double norm(Norm type);
 
-    Set<byte[]> keySet = cells.keySet();
-    Iterator<byte[]> it = keySet.iterator();
+  /**
+   * Supported vector-norms.
+   */
+  enum Norm {
 
-    while (it.hasNext()) {
-      double value = Numeric.bytesToDouble(get(it.next()).getValue());
-      square_sum += value * value;
-    }
+    /** Sum of the absolute values of the entries */
+    One,
 
-    return Math.sqrt(square_sum);
-  }
+    /** The root of sum of squares */
+    Two,
 
-  public double getNorm2Robust() {
-    // TODO Auto-generated method stub
-    return 0;
-  }
+    /**
+     * As the 2 norm may overflow, an overflow resistant version is also
+     * available. Note that it may be slower.
+     */
+    TwoRobust,
 
-  public double getNormInf() {
-    // TODO Auto-generated method stub
-    return 0;
+    /** Largest entry in absolute value */
+    Infinity
   }
 }

Modified: incubator/hama/trunk/src/java/org/apache/hama/VectorInterface.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/VectorInterface.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/VectorInterface.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/VectorInterface.java Mon Aug 25 00:57:54 2008
@@ -19,9 +19,7 @@
  */
 package org.apache.hama;
 
-/**
- * Basic vector interface.
- */
+@Deprecated
 public interface VectorInterface {
 
   /**

Modified: incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionMap.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionMap.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionMap.java Mon Aug 25 00:57:54 2008
@@ -24,18 +24,20 @@
 import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.DenseVector;
 import org.apache.hama.Vector;
-import org.apache.hama.mapred.MatrixMap;
+import org.apache.hama.mapred.DenseMap;
+import org.apache.hama.util.Numeric;
 
-public class AdditionMap extends MatrixMap<ImmutableBytesWritable, Vector> {
+public class AdditionMap extends DenseMap<ImmutableBytesWritable, DenseVector> {
 
+  @Override
   public void map(ImmutableBytesWritable key, Vector value,
-      OutputCollector<ImmutableBytesWritable, Vector> output,
+      OutputCollector<ImmutableBytesWritable, DenseVector> output,
       Reporter reporter) throws IOException {
-    
-    Vector v1 = B.getRow(key.get());
-    output.collect(key, v1.add(value));
-    
-  }
 
+    Vector v1 = MATRIX_B.getRow(Numeric.bytesToInt(key.get()));
+    output.collect(key, (DenseVector) v1.add(value));
+
+  }
 }

Modified: incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionReduce.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionReduce.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionReduce.java Mon Aug 25 00:57:54 2008
@@ -28,19 +28,19 @@
 import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reporter;
-import org.apache.hama.Vector;
+import org.apache.hama.DenseVector;
 import org.apache.hama.mapred.MatrixReduce;
 
 public class AdditionReduce extends
-    MatrixReduce<ImmutableBytesWritable, Vector> {
+    MatrixReduce<ImmutableBytesWritable, DenseVector> {
 
   @Override
-  public void reduce(ImmutableBytesWritable key, Iterator<Vector> values,
+  public void reduce(ImmutableBytesWritable key, Iterator<DenseVector> values,
       OutputCollector<ImmutableBytesWritable, BatchUpdate> output,
       Reporter reporter) throws IOException {
 
     BatchUpdate b = new BatchUpdate(key.get());
-    Vector vector = values.next();
+    DenseVector vector = values.next();
     for (Map.Entry<byte[], Cell> f : vector.entrySet()) {
       b.put(f.getKey(), f.getValue().getValue());
     }

Modified: incubator/hama/trunk/src/java/org/apache/hama/io/VectorWritable.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/io/VectorWritable.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/io/VectorWritable.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/io/VectorWritable.java Mon Aug 25 00:57:54 2008
@@ -196,5 +196,4 @@
     }
 
   }
-
 }

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/DenseMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/DenseMap.java?rev=688643&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/DenseMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/DenseMap.java Mon Aug 25 00:57:54 2008
@@ -0,0 +1,43 @@
+package org.apache.hama.mapred;
+
+import java.io.IOException;
+
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+import org.apache.hama.DenseMatrix;
+import org.apache.hama.HamaConfiguration;
+import org.apache.hama.Matrix;
+import org.apache.hama.Vector;
+
+@SuppressWarnings("unchecked")
+public abstract class DenseMap<K extends WritableComparable, V extends Writable>
+    extends MapReduceBase implements
+    Mapper<ImmutableBytesWritable, Vector, K, V> {
+  protected static Matrix MATRIX_B;
+
+  public static void initJob(String matrixA, String matrixB,
+      Class<? extends DenseMap> mapper,
+      Class<? extends WritableComparable> outputKeyClass,
+      Class<? extends Writable> outputValueClass, JobConf job) {
+
+    job.setInputFormat(MatrixInputFormat.class);
+    job.setMapOutputValueClass(outputValueClass);
+    job.setMapOutputKeyClass(outputKeyClass);
+    job.setMapperClass(mapper);
+    FileInputFormat.addInputPaths(job, matrixA);
+
+    MATRIX_B = new DenseMatrix(new HamaConfiguration(), matrixB);
+    job.set(MatrixInputFormat.COLUMN_LIST, Constants.COLUMN);
+  }
+
+  public abstract void map(ImmutableBytesWritable key, Vector value,
+      OutputCollector<K, V> output, Reporter reporter) throws IOException;
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormatBase.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormatBase.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormatBase.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormatBase.java Mon Aug 25 00:57:54 2008
@@ -22,11 +22,10 @@
 import org.apache.hadoop.mapred.JobConf;
 import org.apache.hadoop.mapred.RecordReader;
 import org.apache.hadoop.mapred.Reporter;
-import org.apache.hama.Vector;
-import org.apache.hama.io.VectorWritable;
+import org.apache.hama.DenseVector;
 
 public abstract class MatrixInputFormatBase implements
-    InputFormat<ImmutableBytesWritable, Vector> {
+    InputFormat<ImmutableBytesWritable, DenseVector> {
   private final Log LOG = LogFactory.getLog(MatrixInputFormatBase.class);
   private byte[][] inputColumns;
   private HTable table;
@@ -34,10 +33,10 @@
   private RowFilterInterface rowFilter;
 
   /**
-   * Iterate over an HBase table data, return (Text, VectorResult) pairs
+   * Iterate over an HBase table data, return (Text, DenseVector) pairs
    */
   protected class TableRecordReader implements
-      RecordReader<ImmutableBytesWritable, Vector> {
+      RecordReader<ImmutableBytesWritable, DenseVector> {
     private byte[] startRow;
     private byte[] endRow;
     private RowFilterInterface trrRowFilter;
@@ -77,7 +76,7 @@
     }
 
     /**
-     * @param inputColumns the columns to be placed in {@link VectorWritable}.
+     * @param inputColumns the columns to be placed in {@link DenseVector}.
      */
     public void setInputColumns(final byte[][] inputColumns) {
       this.trrInputColumns = inputColumns;
@@ -120,12 +119,12 @@
     }
 
     /**
-     * @return VectorResult
+     * @return DenseVector
      * 
      * @see org.apache.hadoop.mapred.RecordReader#createValue()
      */
-    public Vector createValue() {
-      return new Vector();
+    public DenseVector createValue() {
+      return new DenseVector();
     }
 
     /** {@inheritDoc} */
@@ -145,13 +144,13 @@
      * @param key HStoreKey as input key.
      * @param value MapWritable as input value
      * 
-     *          Converts Scanner.next() to Text, VectorResult
+     *          Converts Scanner.next() to Text, DenseVector
      * 
      * @return true if there was more data
      * @throws IOException
      */
     @SuppressWarnings("unchecked")
-    public boolean next(ImmutableBytesWritable key, Vector value)
+    public boolean next(ImmutableBytesWritable key, DenseVector value)
         throws IOException {
       RowResult result = this.scanner.next();
       boolean hasMore = result != null && result.size() > 0;
@@ -170,7 +169,7 @@
    * @see org.apache.hadoop.mapred.InputFormat#getRecordReader(InputSplit,
    *      JobConf, Reporter)
    */
-  public RecordReader<ImmutableBytesWritable, Vector> getRecordReader(
+  public RecordReader<ImmutableBytesWritable, DenseVector> getRecordReader(
       InputSplit split, @SuppressWarnings("unused") JobConf job,
       @SuppressWarnings("unused") Reporter reporter) throws IOException {
     TableSplit tSplit = (TableSplit) split;
@@ -238,7 +237,7 @@
   }
 
   /**
-   * @param inputColumns to be passed in {@link VectorWritable} to the map task.
+   * @param inputColumns to be passed in {@link DenseVector} to the map task.
    */
   protected void setInputColums(byte[][] inputColumns) {
     this.inputColumns = inputColumns;

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java Mon Aug 25 00:57:54 2008
@@ -31,18 +31,19 @@
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reporter;
 import org.apache.hama.Constants;
+import org.apache.hama.DenseMatrix;
 import org.apache.hama.HamaConfiguration;
 import org.apache.hama.Matrix;
 import org.apache.hama.Vector;
 
-@SuppressWarnings("unchecked")
+@Deprecated
 public abstract class MatrixMap<K extends WritableComparable, V extends Writable>
     extends MapReduceBase implements
     Mapper<ImmutableBytesWritable, Vector, K, V> {
-  protected static Matrix B;
+  protected static Matrix MATRIX_B;
 
   public static void initJob(String matrixA, String matrixB,
-      Class<? extends MatrixMap> mapper,
+      Class<? extends DenseMap> mapper,
       Class<? extends WritableComparable> outputKeyClass,
       Class<? extends Writable> outputValueClass, JobConf job) {
 
@@ -52,7 +53,7 @@
     job.setMapperClass(mapper);
     FileInputFormat.addInputPaths(job, matrixA);
 
-    B = new Matrix(new HamaConfiguration(), matrixB);
+    MATRIX_B = new DenseMatrix(new HamaConfiguration(), matrixB);
     job.set(MatrixInputFormat.COLUMN_LIST, Constants.COLUMN);
   }
 

Modified: incubator/hama/trunk/src/test/org/apache/hama/TestMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestMatrix.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestMatrix.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestMatrix.java Mon Aug 25 00:57:54 2008
@@ -28,7 +28,7 @@
    * Random matrix creation test
    */
   public void testRandomMatrix() {
-    Matrix rand = Matrix.random(conf, SIZE, SIZE);
+    Matrix rand = DenseMatrix.random(conf, SIZE, SIZE);
     assertTrue(rand.getRows() == SIZE);
   }
 }

Modified: incubator/hama/trunk/src/test/org/apache/hama/TestVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestVector.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestVector.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestVector.java Mon Aug 25 00:57:54 2008
@@ -24,12 +24,13 @@
   private final double norm1 = 12.0;
   private final double norm2 = 6.782329983125268;
   private double[][] values = { { 2, 5, 1, 4 }, { 4, 1, 3, 3 } };
+  private final String m = "dotTest";
 
   /**
    * Test vector
    */
   public void testGetVector() {
-    Matrix m1 = new Matrix(conf, "dotTest");
+    Matrix m1 = new DenseMatrix(conf, m);
 
     for (int i = 0; i < 2; i++) {
       for (int j = 0; j < 4; j++) {
@@ -58,11 +59,11 @@
   }
 
   private void norm1Test(Vector v1, Vector v2) {
-    assertEquals(norm1, v1.getNorm1());
+    assertEquals(norm1, ((DenseVector) v1).getNorm1());
   }
 
   private void norm2Test(Vector v1, Vector v2) {
-    assertEquals(norm2, v1.getNorm2());
+    assertEquals(norm2, ((DenseVector) v1).getNorm2());
   }
 
   private void scalingTest(Vector v2) {
@@ -74,7 +75,7 @@
   }
   
   public void testGetSet() {
-    Vector v1 = new Vector();
+    Vector v1 = new DenseVector();
     v1.set(0, 0.2);
     assertEquals(v1.get(0), 0.2);
   }

Modified: incubator/hama/trunk/src/test/org/apache/hama/mapred/TestMatrixMapReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/mapred/TestMatrixMapReduce.java?rev=688643&r1=688642&r2=688643&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/mapred/TestMatrixMapReduce.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/mapred/TestMatrixMapReduce.java Mon Aug 25 00:57:54 2008
@@ -24,9 +24,10 @@
 import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
 import org.apache.hadoop.mapred.JobClient;
 import org.apache.hadoop.mapred.JobConf;
+import org.apache.hama.DenseMatrix;
+import org.apache.hama.DenseVector;
 import org.apache.hama.HamaTestCase;
 import org.apache.hama.Matrix;
-import org.apache.hama.Vector;
 import org.apache.hama.algebra.AdditionMap;
 import org.apache.hama.algebra.AdditionReduce;
 import org.apache.log4j.Logger;
@@ -46,11 +47,11 @@
   }
 
   public void testMatrixMapReduce() throws IOException {
-    Matrix matrixA = new Matrix(conf, A);
+    Matrix matrixA = new DenseMatrix(conf, A);
     matrixA.set(0, 0, 1);
     matrixA.set(0, 1, 0);
 
-    Matrix matrixB = new Matrix(conf, B);
+    Matrix matrixB = new DenseMatrix(conf, B);
     matrixB.set(0, 0, 1);
     matrixB.set(0, 1, 1);
 
@@ -58,13 +59,13 @@
   }
 
   public void miniMRJob() throws IOException {
-    Matrix c = new Matrix(conf, output);
+    Matrix c = new DenseMatrix(conf, output);
 
     JobConf jobConf = new JobConf(conf, TestMatrixMapReduce.class);
     jobConf.setJobName("test MR job");
 
-    MatrixMap.initJob(A, B, AdditionMap.class, ImmutableBytesWritable.class,
-        Vector.class, jobConf);
+    DenseMap.initJob(A, B, AdditionMap.class, ImmutableBytesWritable.class,
+        DenseVector.class, jobConf);
     MatrixReduce.initJob(output, AdditionReduce.class, jobConf);
 
     jobConf.setNumMapTasks(1);