svn commit: r671120 [3/4] - in /incubator/hama/trunk: ./ lib/ lib/findbugs/ lib/findbugs/plugin/ lib/jetty-ext/ src/ src/docs/ src/docs/src/ src/docs/src/documentation/ src/docs/src/documentation/classes/ src/docs/src/documentation/content/ src/docs/sr...

[ed...@apache.org]

Added: 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=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/Matrix.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/Matrix.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,303 @@
+/**
+ * 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.conf.Configuration;
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HColumnDescriptor;
+import org.apache.hadoop.hbase.HTableDescriptor;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.JobClient;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hama.algebra.AdditionSubtractionMap;
+import org.apache.hama.algebra.AdditionSubtractionReduce;
+import org.apache.hama.algebra.CholeskyDecompositionMap;
+import org.apache.hama.algebra.CroutDecompositionMap;
+import org.apache.hama.algebra.DeterminantMap;
+import org.apache.hama.algebra.DeterminantReduce;
+import org.apache.hama.algebra.MultiplicationMap;
+import org.apache.hama.algebra.MultiplicationReduce;
+import org.apache.hama.mapred.MatrixInputFormat;
+import org.apache.hama.mapred.MatrixOutputFormat;
+
+/**
+ * A library for mathematical operations on matrices of double.
+ */
+public class Matrix extends AbstractMatrix {
+
+  /**
+   * Construct
+   * 
+   * @param conf configuration object
+   */
+  public Matrix(Configuration conf) {
+    setConfiguration(conf);
+  }
+
+  /**
+   * Construct an matrix
+   * 
+   * @param conf configuration object
+   * @param matrixName the name of the matrix
+   */
+  public Matrix(Configuration conf, Text 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 Matrix(HBaseConfiguration conf, int m, int n, double s) {
+    try {
+      setConfiguration(conf);
+      matrixName = new Text(Constants.RANDOM + System.currentTimeMillis());
+
+      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(Configuration conf, int m, int n) {
+    Text name = new Text(Constants.RANDOM + System.currentTimeMillis());
+    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);
+
+    return rand;
+  }
+
+  /**
+   * Generate matrix with identity elements
+   * 
+   * @param conf configuration object
+   * @param m the number of rows.
+   * @param n the number of columns.
+   * @return an m-by-n matrix with ones on the diagonal and zeros elsewhere.
+   */
+  public static Matrix identity(HBaseConfiguration conf, int m, int n) {
+    // TODO
+    return null;
+  }
+
+  /** {@inheritDoc} */
+  public Matrix multiply(Matrix b) {
+    String output = Constants.RESULT + System.currentTimeMillis();
+    Matrix c = new Matrix(config, new Text(output));
+
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("parallel matrix multiplication of " + getName() + " and " + b.getName());
+    jobConf.setInputFormat(MatrixInputFormat.class);
+    jobConf.setOutputFormat(MatrixOutputFormat.class);
+    MultiplicationMap.initJob(getName(), b.getName(), MultiplicationMap.class, jobConf);
+    MultiplicationReduce.initJob(output, MultiplicationReduce.class, jobConf);
+    
+    jobConf.setNumMapTasks(mapper);
+    jobConf.setNumReduceTasks(reducer);
+    
+    try {
+      JobClient.runJob(jobConf);
+    } catch (IOException e) {
+      LOG.info(e);
+    }
+
+    return c;
+  }
+
+  /** {@inheritDoc} */
+  public Matrix addition(Matrix b) {
+    return additionSubtraction(b, Constants.PLUS);
+  }
+
+  /** {@inheritDoc} */
+  public Matrix subtraction(Matrix b) {
+    return additionSubtraction(b, Constants.PLUS);
+  }
+
+  /**
+   * Method for add or subtract operation 
+   * 
+   * @param target
+   * @param operator
+   * @return matrix
+   */  
+  public Matrix additionSubtraction(Matrix target, String operator) {
+    String b = target.getName();
+    String output = Constants.RESULT + System.currentTimeMillis();
+    Matrix c = new Matrix(config, new Text(output));
+    String jobName = "parallel matrix " + operator + " of " + getName() + " and " + b;
+    LOG.info(jobName);
+    
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName(jobName);
+    jobConf.setInputFormat(MatrixInputFormat.class);
+    jobConf.setOutputFormat(MatrixOutputFormat.class);
+    AdditionSubtractionMap.initJob(getName(), b, operator,
+        AdditionSubtractionMap.class, jobConf);
+    AdditionSubtractionReduce.initJob(output,
+        AdditionSubtractionReduce.class, jobConf);
+    
+    jobConf.setNumMapTasks(mapper);
+    jobConf.setNumReduceTasks(reducer);
+    
+    try {
+      JobClient.runJob(jobConf);
+    } catch (IOException e) {
+      LOG.info(e);
+    }
+
+    return c;
+  }
+
+  /** {@inheritDoc} */
+  public double determinant() {
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("matrix determinant");
+
+    String check = Constants.RESULT + System.currentTimeMillis();
+    Matrix c = new Matrix(config, new Text(check));
+    for (int i = 0; i < getRowDimension(); i++) {
+      c.set(i, 0, 1.0);
+    }
+    c.setDimension(getRowDimension(), 0);
+    jobConf.setInputFormat(MatrixInputFormat.class);
+    jobConf.setOutputFormat(MatrixOutputFormat.class);
+    DeterminantMap.initJob(getName(), check, DeterminantMap.class, jobConf);
+    DeterminantReduce.initJob(getName(), DeterminantReduce.class, jobConf);
+    
+    jobConf.setNumMapTasks(mapper);
+    jobConf.setNumReduceTasks(reducer);
+    
+    try {
+      JobClient.runJob(jobConf);
+    } catch (IOException e) {
+      LOG.info(e);
+    }
+
+    c.clear();
+    return getDeterminant();
+  }
+
+  /** {@inheritDoc} */
+  public TriangularMatrix decompose(Decomposition technique) {
+    if (technique.equals(Decomposition.Cholesky))
+      return choleskyDecompose();
+    else if (technique.equals(Decomposition.Crout))
+      return croutDecompose();
+    else
+      return null;
+  }
+
+  private TriangularMatrix croutDecompose() {
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("Crout Decomposition");
+
+    String output = Constants.RESULT + System.currentTimeMillis();
+    TriangularMatrix b = new TriangularMatrix(config, new Text(output));
+    jobConf.setInputFormat(MatrixInputFormat.class);
+    jobConf.setOutputFormat(MatrixOutputFormat.class);
+    CroutDecompositionMap.initJob(getName(), output,
+        CroutDecompositionMap.class, jobConf);
+
+    jobConf.setNumMapTasks(mapper);
+    jobConf.setNumReduceTasks(reducer);
+    
+    try {
+      JobClient.runJob(jobConf);
+    } catch (IOException e) {
+      LOG.info(e);
+    }
+
+    return b;
+  }
+
+  private TriangularMatrix choleskyDecompose() {
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("Cholesky Decomposition");
+
+    String output = Constants.RESULT + System.currentTimeMillis();
+    TriangularMatrix b = new TriangularMatrix(config, new Text(output));
+    jobConf.setInputFormat(MatrixInputFormat.class);
+    jobConf.setOutputFormat(MatrixOutputFormat.class);
+    CholeskyDecompositionMap.initJob(getName(), output,
+        CholeskyDecompositionMap.class, jobConf);
+
+    jobConf.setNumMapTasks(mapper);
+    jobConf.setNumReduceTasks(reducer);
+    
+    try {
+      JobClient.runJob(jobConf);
+    } catch (IOException e) {
+      LOG.info(e);
+    }
+
+    return b;
+  }
+
+}

Added: 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=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/MatrixInterface.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,178 @@
+/**
+ * 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;
+
+
+/**
+ * Basic matrix interface. It holds <code>double</code>s in a rectangular 2D
+ * array, and it is used alongside <code>Vector</code> in numerical
+ * computations. Implementing classes decides on the actual storage.
+ */
+public interface MatrixInterface {
+
+  /**
+   * 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);
+
+  /**
+   * Gets the vector of row
+   * 
+   * @param row the row index of the matrix
+   * @return the feature vector of row
+   */
+  public FeatureVector getRowVector(int row);
+
+  /**
+   * Sets the double value of (i, j)
+   * 
+   * @param i ith row of the matrix
+   * @param j jth column of the matrix
+   * @param d the value of entry
+   */
+  public void set(int i, int j, double d);
+
+  /**
+   * Adds value to (i, j)
+   * 
+   * @param i i th row of the matrix
+   * @param j j th column of the matrix
+   * @param d the value of entry
+   */
+  public void add(int i, int j, double d);
+
+  /**
+   * Delete a Row to Matrix.
+   * 
+   * @param i row number to delete
+   */
+  public void deleteRowEquals(int i);
+
+  /**
+   * Delete a Column to Matrix.
+   * 
+   * @param j column number to delete
+   */
+  public void deleteColumnEquals(int j);
+
+  /**
+   * Get a number of row of the matrix from the meta-data column
+   * 
+   * @return a number of rows of the matrix
+   */
+  public int getRowDimension();
+
+  /**
+   * Get a number of column of the matrix from the meta-data column
+   * 
+   * @return a number of columns of the matrix
+   */
+  public int getColumnDimension();
+
+  /**
+   * Sets the dimension of matrix
+   * 
+   * @param rows the number of rows
+   * @param columns the number of columns
+   */
+  public void setDimension(int rows, int columns);
+
+  /**
+   * Modify dimensions of matrix
+   * 
+   * @param m number of rows
+   * @param n number of columns
+   */
+  public void reset(int m, int n);
+
+  /**
+   * Return the matrix name
+   * 
+   * @return the name of the matrix
+   */
+  public String getName();
+
+  /**
+   * Make a deep copy of a matrix
+   * 
+   * @return clone matrix
+   */
+  public Matrix copy();
+
+  /**
+   * Multiply two matrices
+   * 
+   * @param b matrix b
+   * @return the result of the multiplication of matrix a and matrix b
+   */
+  public Matrix multiply(Matrix b);
+
+  /**
+   * Add two matrices
+   * 
+   * @param b matrix b
+   * @return the result of the addition of matrix a and matrix b
+   */
+  public Matrix addition(Matrix b);
+
+  /**
+   * Subtract two matrices
+   * 
+   * @param b matrix b
+   * @return the result of the substraction of matrix a and matrix b
+   */
+  public Matrix subtraction(Matrix b);
+
+  /**
+   * Calculates determinant of a matrix
+   * 
+   * @return the value of determinant
+   */
+  public double determinant();
+
+  /**
+   * Save the matrix to table
+   * 
+   * @param matrixName the name of the matrix
+   */
+  public void save(String matrixName);
+
+  /**
+   * Decomposition
+   * 
+   * @return the decomposed result
+   */
+  public TriangularMatrix decompose(Decomposition technique);
+
+  /**
+   * Clear object
+   */
+  public void clear();
+
+  /**
+   * Close object
+   */
+  public void close();
+
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/RandomVariable.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/RandomVariable.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/RandomVariable.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/RandomVariable.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,209 @@
+/**
+ * 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;
+
+/**
+ * The RandomVaraibale Class provides static methods for generating random
+ * numbers.
+ */
+public class RandomVariable {
+
+  /**
+   * Generate a random number between 0 and 1.
+   * 
+   * @return a double between 0 and 1.
+   */
+  protected static double rand() {
+    double x = Math.random();
+    return x;
+  }
+
+  /**
+   * Generate a random integer.
+   * 
+   * @param i0 min of the random variable.
+   * @param i1 max of the random variable.
+   * @return an int between i0 and i1.
+   */
+  protected static int randInt(int i0, int i1) {
+    double x = rand();
+    int i = i0 + (int) Math.floor((i1 - i0 + 1) * x);
+    return i;
+  }
+
+  /**
+   * Generate a random number from a uniform random variable.
+   * 
+   * @param min min of the random variable.
+   * @param max max of the random variable.
+   * @return a double.
+   */
+  public static double uniform(double min, double max) {
+    double x = min + (max - min) * rand();
+    return x;
+  }
+
+  /**
+   * Generate a random number from a discrete random variable.
+   * 
+   * @param values discrete values.
+   * @param prob probability of each value.
+   * @return a double.
+   */
+  public static double dirac(double[] values, double[] prob) {
+    double[] prob_cumul = new double[values.length];
+    prob_cumul[0] = prob[0];
+    for (int i = 1; i < values.length; i++) {
+      prob_cumul[i] = prob_cumul[i - 1] + prob[i];
+    }
+    double y = rand();
+    double x = 0;
+    for (int i = 0; i < values.length - 1; i++) {
+      if ((y > prob_cumul[i]) && (y < prob_cumul[i + 1])) {
+        x = values[i];
+      }
+    }
+    return x;
+  }
+
+  /**
+   * Generate a random number from a Gaussian (Normal) random variable.
+   * 
+   * @param mu mean of the random variable.
+   * @param sigma standard deviation of the random variable.
+   * @return a double.
+   */
+  public static double normal(double mu, double sigma) {
+    double x = mu + sigma * Math.cos(2 * Math.PI * rand())
+        * Math.sqrt(-2 * Math.log(rand()));
+    return x;
+  }
+
+  /**
+   * Generate a random number from a Chi-2 random variable.
+   * 
+   * @param n degrees of freedom of the chi2 random variable.
+   * @return a double.
+   */
+  public static double chi2(int n) {
+    double x = 0;
+    for (int i = 0; i < n; i++) {
+      double norm = normal(0, 1);
+      x += norm * norm;
+    }
+    return x;
+  }
+
+  /**
+   * Generate a random number from a LogNormal random variable.
+   * 
+   * @param mu mean of the Normal random variable.
+   * @param sigma standard deviation of the Normal random variable.
+   * @return a double.
+   */
+  public static double logNormal(double mu, double sigma) {
+    double x = mu + sigma * Math.cos(2 * Math.PI * rand())
+        * Math.sqrt(-2 * Math.log(rand()));
+    return x;
+  }
+
+  /**
+   * Generate a random number from an exponantial random variable (Mean =
+   * 1/lambda, variance = 1/lambda^2).
+   * 
+   * @param lambda parmaeter of the exponential random variable.
+   * @return a double.
+   */
+  public static double exponential(double lambda) {
+    double x = -1 / lambda * Math.log(rand());
+    return x;
+  }
+
+  /**
+   * Generate a random number from a symetric triangular random variable.
+   * 
+   * @param min min of the random variable.
+   * @param max max of the random variable.
+   * @return a double.
+   */
+  public static double triangular(double min, double max) {
+    double x = min / 2 + (max - min) * rand() / 2 + min / 2 + (max - min)
+        * rand() / 2;
+    return x;
+  }
+
+  /**
+   * Generate a random number from a non-symetric triangular random variable.
+   * 
+   * @param min min of the random variable.
+   * @param med value of the random variable with max density.
+   * @param max max of the random variable.
+   * @return a double.
+   */
+  public static double triangular(double min, double med, double max) {
+    double y = rand();
+    double x = (y < ((med - min) / (max - min))) ? (min + Math.sqrt(y
+        * (max - min) * (med - min))) : (max - Math.sqrt((1 - y) * (max - min)
+        * (max - med)));
+    return x;
+  }
+
+  /**
+   * Generate a random number from a beta random variable.
+   * 
+   * @param a first parameter of the Beta random variable.
+   * @param b second parameter of the Beta random variable.
+   * @return a double.
+   */
+  public static double beta(double a, double b) {
+    double try_x;
+    double try_y;
+    do {
+      try_x = Math.pow(rand(), 1 / a);
+      try_y = Math.pow(rand(), 1 / b);
+    } while ((try_x + try_y) > 1);
+    return try_x / (try_x + try_y);
+  }
+
+  /**
+   * Generate a random number from a Cauchy random variable (Mean = Inf, and
+   * Variance = Inf).
+   * 
+   * @param mu median of the Weibull random variable
+   * @param sigma second parameter of the Cauchy random variable.
+   * @return a double.
+   */
+  public static double cauchy(double mu, double sigma) {
+    double x = sigma * Math.tan(Math.PI * (rand() - 0.5)) + mu;
+    return x;
+  }
+
+  /**
+   * Generate a random number from a Weibull random variable.
+   * 
+   * @param lambda first parameter of the Weibull random variable.
+   * @param c second parameter of the Weibull random variable.
+   * @return a double.
+   */
+  public static double weibull(double lambda, double c) {
+    double x = Math.pow(-Math.log(1 - rand()), 1 / c) / lambda;
+    return x;
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/TriangularMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/TriangularMatrix.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/TriangularMatrix.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/TriangularMatrix.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,174 @@
+/**
+ * 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.conf.Configuration;
+import org.apache.hadoop.hbase.HBaseConfiguration;
+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.BatchUpdate;
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hadoop.io.Text;
+
+/**
+ * A library for mathematical operations on matrices of triangle forms
+ */
+public class TriangularMatrix extends AbstractMatrix {
+
+  /**
+   * Construct
+   * 
+   * @param conf configuration object
+   */
+  public TriangularMatrix(Configuration conf) {
+    setConfiguration(conf);
+  }
+
+  /**
+   * Construct an triangular matrix
+   * 
+   * @param conf configuration object
+   * @param matrixName the name of the triangular matrix
+   */
+  public TriangularMatrix(HBaseConfiguration conf, Text matrixName) {
+    try {
+      setConfiguration(conf);
+      this.matrixName = matrixName;
+
+      if (!admin.tableExists(matrixName)) {
+        tableDesc = new HTableDescriptor(matrixName.toString());
+        tableDesc.addFamily(new HColumnDescriptor(Constants.LOWER.toString()));
+        tableDesc.addFamily(new HColumnDescriptor(Constants.UPPER.toString()));
+        create();
+      }
+
+      table = new HTable(conf, matrixName);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+    }
+  }
+
+  /** {@inheritDoc} */
+  public Matrix multiply(Matrix b) {
+    return null;
+  }
+
+  /** {@inheritDoc} */
+  public Matrix addition(Matrix b) {
+    return null;
+  }
+
+  /** {@inheritDoc} */
+  public double determinant() {
+    return 0;
+  }
+
+  /** {@inheritDoc} */
+  public Matrix subtraction(Matrix b) {
+    return null;
+  }
+
+  /** {@inheritDoc} */
+  public TriangularMatrix decompose(Decomposition technique) {
+    return null;
+  }
+
+  /**
+   * Gets the entry value of lower matrix L(i, j)
+   * 
+   * @param i ith row of lower matrix L
+   * @param j jth column of lower matrix L
+   * @return the value of entry
+   */
+  public double getFromLower(int i, int j) {
+    // If row doesn't exist, return the null pointer exception.
+    //So, we need to make a Cell object. -- Edward
+    
+    Text row = new Text(String.valueOf(i));
+    Text column = new Text(Constants.LOWER + String.valueOf(j));
+
+    try {
+      Cell c = table.get(row, column);
+      if (c == null) {
+        return 0;
+      } else {
+        return toDouble(c.getValue());
+      }
+    } catch (IOException e) {
+      LOG.error(e, e);
+      return 0;
+    }
+  }
+
+  /**
+   * Gets the entry value of upper matrix U(i, j)
+   * 
+   * @param i ith row of upper matrix U
+   * @param j jth column of upper matrix U
+   * @return the value of entry
+   */
+  public double getFromUpper(int i, int j) {
+    try {
+      return toDouble(table.get(new Text(String.valueOf(i)),
+          new Text(Constants.UPPER + String.valueOf(j))).getValue());
+    } catch (IOException e) {
+      LOG.error(e, e);
+      return 0;
+    }
+  }
+
+  /**
+   * Sets the double value of lower matrix L(i, j)
+   * 
+   * @param i ith row of lower matrix L
+   * @param j jth column of lower matrix L
+   * @param d the value of entry
+   */
+  public void setToLower(int i, int j, double d) {
+    BatchUpdate b = new BatchUpdate(new Text(String.valueOf(i)));
+    b.put(new Text(Constants.LOWER + String.valueOf(j)), toBytes(d));
+    try {
+      table.commit(b);
+    } catch (IOException e) {
+      LOG.error(e, e);
+    }
+  }
+
+  /**
+   * Sets the double value of upper matrix U(i, j)
+   * 
+   * @param i ith row of upper matrix U
+   * @param j jth column of upper matrix U
+   * @param d the value of entry
+   */
+  public void setToUpper(int i, int j, double d) {
+    BatchUpdate b = new BatchUpdate(new Text(String.valueOf(i)));
+    b.put(new Text(Constants.UPPER + String.valueOf(j)), toBytes(d));
+    try {
+      table.commit(b);
+    } catch (IOException e) {
+      LOG.error(e, e);
+    }
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionMap.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionMap.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,86 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+import org.apache.hama.Matrix;
+import org.apache.hama.mapred.MatrixMap;
+import org.apache.log4j.Logger;
+
+/**
+ * Matrix addition/subtraction map
+ */
+public class AdditionSubtractionMap extends MatrixMap<Text, MapWritable> {
+  static final Logger LOG = Logger.getLogger(AdditionSubtractionMap.class);
+  
+  protected Matrix matrix_b;
+  protected String operator;
+  public static final String MATRIX_B = "hama.addition.substraction.matrix.b";
+  public static final String OPERATOR = "hama.addition.substraction.operator";
+
+  public void configure(JobConf job) {
+    operator = job.get(OPERATOR, "");
+    Text b_name = new Text(job.get(MATRIX_B, ""));
+    matrix_b = new Matrix(new HBaseConfiguration(), b_name);
+  }
+
+  public static void initJob(String matrix_a, String matrix_b, String operator,
+      Class<AdditionSubtractionMap> map, JobConf jobConf) {
+    initJob(matrix_a, map, jobConf);
+    jobConf.set(MATRIX_B, matrix_b);
+    jobConf.set(OPERATOR, operator);
+  }
+
+  @Override
+  public void map(HStoreKey key, MapWritable value,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    Text tKey = key.getRow();
+    MapWritable sum = new MapWritable();
+
+    for (Map.Entry<Writable, Writable> e : value.entrySet()) {
+      double a = getDouble(e.getValue());
+      double b = matrix_b.get(Integer.parseInt(tKey.toString()),
+          getIndex((Text) e.getKey()));
+      byte[] result = null;
+
+      if (operator.equals(Constants.PLUS)) {
+        result = toBytes(a + b);
+      } else if (operator.equals(Constants.MINUS)) {
+        result = toBytes(a - b);
+      }
+
+      sum.put(e.getKey(), new ImmutableBytesWritable(result));
+    }
+    output.collect(tKey, sum);
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionReduce.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionReduce.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/AdditionSubtractionReduce.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,43 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.mapred.MatrixReduce;
+
+/**
+ * Matrix addition/subtraction reduce
+ */
+public class AdditionSubtractionReduce extends MatrixReduce<Text, MapWritable> {
+
+  @Override
+  public void reduce(Text key, Iterator<MapWritable> values,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    output.collect(key, values.next());
+  }
+
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/CholeskyDecompositionMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/CholeskyDecompositionMap.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/CholeskyDecompositionMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/CholeskyDecompositionMap.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,107 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.FeatureVector;
+import org.apache.hama.Matrix;
+import org.apache.hama.TriangularMatrix;
+import org.apache.hama.mapred.MatrixMap;
+import org.apache.hama.mapred.MatrixOutputFormat;
+
+/**
+ * Cholesky Decomposition.
+ * <p>
+ * For a symmetric, positive definite matrix A, the Cholesky decomposition is an
+ * lower triangular matrix L so that A = L*L'.
+ * </p>
+ */
+public class CholeskyDecompositionMap extends MatrixMap<Text, MapWritable> {
+  protected Matrix matrix_a;
+  protected TriangularMatrix matrix_l;
+
+  public static final String MATRIX_A = "cholesky.decomposition.matrix.a";
+  public static final String MATRIX_L = "cholesky.decomposition.matrix.l";
+
+  public void configure(JobConf job) {
+    HBaseConfiguration conf = new HBaseConfiguration();
+    Text a_name = new Text(job.get(MATRIX_A, ""));
+    Text l_name = new Text(job.get(MATRIX_L, ""));
+    matrix_a = new Matrix(conf, a_name);
+    matrix_l = new TriangularMatrix(conf, l_name);
+  }
+
+  /**
+   * @param matrix_a
+   * @param matrix_l
+   * @param map
+   * @param jobConf
+   */
+  public static void initJob(String matrix_a, String matrix_l,
+      Class<CholeskyDecompositionMap> map, JobConf jobConf) {
+    initJob(matrix_a, map, jobConf);
+    jobConf.set(MatrixOutputFormat.OUTPUT, matrix_l);
+    jobConf.set(MATRIX_A, matrix_a);
+    jobConf.set(MATRIX_L, matrix_l);
+  }
+
+  @Override
+  public void map(HStoreKey key, MapWritable value,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    int i = Integer.parseInt(String.valueOf(key.getRow()));
+
+    double[] ithRowOfL = new double[matrix_a.getRowDimension()];
+    double[] jthRowOfL = new double[matrix_a.getRowDimension()];
+
+    // Vector was added. I don't figure out the result. -- edward
+    FeatureVector iOfV = matrix_l.getRowVector(i);
+    for(int x = 0; x < iOfV.size(); x++) {
+      ithRowOfL[x] = iOfV.getDimAt(x);
+    }
+
+    for (int j = i; j < value.size(); j++) {
+      FeatureVector jOfV = matrix_l.getRowVector(i);
+      for(int x = 0; x < jOfV.size(); x++) {
+        jthRowOfL[x] = jOfV.getDimAt(x);
+      }
+
+      double sum = matrix_a.get(i, j);
+      for (int k = i - 1; k >= 0; k--) {
+        sum -= ithRowOfL[k] * jthRowOfL[k];
+      }
+
+      if (i == j) {
+        matrix_l.setToLower(j, i, Math.sqrt(sum));
+      } else {
+        double c = matrix_l.get(i, i);
+        matrix_l.setToLower(j, i, (sum / c));
+      }
+    }
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/CroutDecompositionMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/CroutDecompositionMap.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/CroutDecompositionMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/CroutDecompositionMap.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,131 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.FractionMatrix;
+import org.apache.hama.TriangularMatrix;
+import org.apache.hama.mapred.MatrixMap;
+import org.apache.hama.mapred.MatrixOutputFormat;
+import org.apache.log4j.Logger;
+
+/**
+ * Crout Decomposition
+ */
+public class CroutDecompositionMap extends MatrixMap<Text, MapWritable> {
+  static final Logger LOG = Logger.getLogger(CroutDecompositionMap.class
+      .getName());
+  protected FractionMatrix matrix_a;
+  protected TriangularMatrix matrix_lu;
+
+  public static final String MATRIX_A = "crout.decompositionMap.matrix.a";
+  public static final String MATRIX_LU = "crout.decompositionMap.matrix.lu";
+
+  public void configure(JobConf job) {
+    HBaseConfiguration conf = new HBaseConfiguration();
+    Text a_name = new Text(job.get(MATRIX_A, ""));
+    Text lu_name = new Text(job.get(MATRIX_LU, ""));
+    matrix_a = new FractionMatrix(conf, a_name);
+    matrix_lu = new TriangularMatrix(conf, lu_name);
+    matrix_lu.setDimension(matrix_a.getRowDimension(), matrix_a
+        .getColumnDimension());
+  }
+
+  /**
+   * @param matrix_a
+   * @param matrix_lu
+   * @param map
+   * @param jobConf
+   */
+  public static void initJob(String matrix_a, String matrix_lu,
+      Class<CroutDecompositionMap> map, JobConf jobConf) {
+    initJob(matrix_a, map, jobConf);
+    jobConf.set(MatrixOutputFormat.OUTPUT, matrix_lu);
+    jobConf.set(MATRIX_A, matrix_a);
+    jobConf.set(MATRIX_LU, matrix_lu);
+  }
+
+  @SuppressWarnings("deprecation")
+  @Override
+  public void map(HStoreKey key, MapWritable value,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    Text tKey = key.getRow();
+    int i = Integer.parseInt(String.valueOf(tKey.toString()));
+
+    for (Map.Entry<Writable, Writable> e : value.entrySet()) {
+      int j = getIndex((Text) e.getKey());
+      matrix_lu.setToUpper(i, j, upper(i, j));
+      matrix_lu.setToLower(i, j, lower(i, j));
+    }
+
+  }
+
+  public double upper(int i, int j) throws IOException {
+    double sum;
+    if (i == j)
+      return 1.0;
+    else if (i > j)
+      return 0.0;
+    else if (i == 0) {
+      return matrix_a.getFromOriginal(0, j) / matrix_a.getFromOriginal(0, 0);
+    } else {
+      sum = 0.0;
+      for (int k = 0; k < i; k++) {
+        sum += matrix_lu.getFromLower(i, k) * matrix_lu.getFromUpper(k, j);
+      }
+      double a = matrix_a.getFromOriginal(i, j) - sum;
+      double b = matrix_lu.getFromLower(i, i);
+      return a / b;
+    }
+  }
+
+  public double lower(int j, int i) throws IOException {
+    double sum, value;
+    if (i == 0)
+      value = matrix_a.getFromOriginal(j, 0);
+    else if (i > j)
+      value = 0.0;
+    else if (j == i) {
+      sum = 0.0;
+      for (int k = 0; k < i; k++) {
+        sum += matrix_lu.getFromLower(j, k) * matrix_lu.getFromUpper(k, i);
+      }
+      value = matrix_a.getFromOriginal(i, i) - sum;
+    } else {
+      sum = 0.0;
+      for (int k = 0; k < i; k++) {
+        sum += matrix_lu.getFromLower(j, k) * matrix_lu.getFromUpper(k, i);
+      }
+      value = matrix_a.getFromOriginal(j, i) - sum;
+    }
+    return value;
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantMap.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantMap.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,110 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+import org.apache.hama.Matrix;
+import org.apache.hama.mapred.MatrixMap;
+import org.apache.hama.mapred.MatrixOutputFormat;
+import org.apache.log4j.Logger;
+
+/**
+ * Determinant map
+ */
+public class DeterminantMap extends MatrixMap<Text, MapWritable> {
+  static final Logger LOG = Logger.getLogger(DeterminantMap.class.getName());
+
+  protected Matrix matrix_a;
+  protected Matrix checkObj;
+
+  public static final String _CHECK = "hama.determinant.check";
+  public static final String MATRIX_A = "hama.determinant.matrix.a";
+  protected int row = 0;
+
+  public void configure(JobConf job) {
+    HBaseConfiguration conf = new HBaseConfiguration();
+    Text name_a = new Text(job.get(MATRIX_A, ""));
+    Text check = new Text(job.get(_CHECK, ""));
+    
+    matrix_a = new Matrix(conf, name_a);
+    checkObj = new Matrix(conf, check);
+    row = matrix_a.getRowDimension();
+  }
+
+  /**
+   * @param matrix_a
+   * @param check
+   * @param map
+   * @param jobConf
+   */
+  public static void initJob(String matrix_a, String check,
+      Class<DeterminantMap> map, JobConf jobConf) {
+    initJob(matrix_a, map, jobConf);
+    jobConf.set(MatrixOutputFormat.OUTPUT, matrix_a);
+    jobConf.set(_CHECK, check);
+    jobConf.set(MATRIX_A, matrix_a);
+  }
+
+  @Override
+  public void map(HStoreKey key, MapWritable value,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+
+    int r = Integer.parseInt(String.valueOf(key.getRow()));
+
+    checkObj.set(r, 0,  0.0);
+    double d = matrix_a.get(r, 0) * Math.pow(-1.0, r) * minor(r, 1);
+    checkObj.set(r, 0, 1.0);
+
+    MapWritable val = new MapWritable();
+    val.put(Constants.COLUMN, getBytesWritable(d));
+    output.collect(Constants.DETERMINANT, val);
+  }
+
+  private double minor(int processRow, int processColumn)
+      throws IOException {
+    double result = 0.0;
+    int i = 0;
+    if ((row - processColumn) == 0) {
+      return 1.0;
+    }
+    for (int r = 0; r < row; r++) {
+      double trans = checkObj.get(r, 0);
+      if (trans != 0.0) {
+        checkObj.set(r, 0, 0.0);
+        result += matrix_a.get(r, processColumn) * Math.pow(-1.0, i)
+            * minor(r, processColumn + 1);
+        checkObj.set(r, 0, 1.0);
+
+        i++;
+      }
+    }
+    return result;
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantReduce.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantReduce.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/DeterminantReduce.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,53 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+import org.apache.hama.mapred.MatrixReduce;
+import org.apache.log4j.Logger;
+
+/**
+ * Aggregate determinant value
+ */
+public class DeterminantReduce extends MatrixReduce<Text, MapWritable> {
+  static final Logger LOG = Logger.getLogger(DeterminantReduce.class.getName());
+
+  @Override
+  public void reduce(Text key, Iterator<MapWritable> values,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    double sum = 0;
+    while (values.hasNext()) {
+      sum += getDouble(values.next().get(Constants.COLUMN));
+    }
+
+    MapWritable value = new MapWritable();
+    value.put(Constants.COLUMN, getBytesWritable(sum));
+    output.collect(key, value);
+  }
+
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationMap.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationMap.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,83 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.FeatureVector;
+import org.apache.hama.Matrix;
+import org.apache.hama.mapred.MatrixMap;
+import org.apache.log4j.Logger;
+
+/**
+ * Each map processor requires O(n^2).
+ */
+public class MultiplicationMap extends MatrixMap<Text, MapWritable> {
+  static final Logger LOG = Logger.getLogger(MultiplicationMap.class.getName());
+
+  protected Matrix matrix_b;
+  public static final String MATRIX_B = "hama.multiplication.matrix.b";
+
+  public void configure(JobConf job) {
+    Text name = new Text(job.get(MATRIX_B, ""));
+    matrix_b = new Matrix(new HBaseConfiguration(), name);
+  }
+
+  /**
+   * @param matrix_a
+   * @param matrix_b
+   * @param map
+   * @param jobConf
+   */
+  public static void initJob(String matrix_a, String matrix_b,
+      Class<MultiplicationMap> map, JobConf jobConf) {
+    initJob(matrix_a, map, jobConf);
+    jobConf.set(MATRIX_B, matrix_b);
+  }
+
+  @Override
+  public void map(HStoreKey key, MapWritable value,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    MapWritable multipliedValue = new MapWritable();
+
+    for (Map.Entry<Writable, Writable> e : value.entrySet()) {
+      int row = getIndex((Text) e.getKey());
+      double c = getDouble(e.getValue());
+
+      FeatureVector v = matrix_b.getRowVector(row);
+      for(int i = 0; i < v.size(); i++) {
+        // GetColumnText doesn't needed -- edward 
+        multipliedValue.put(getColumnText(i), getBytesWritable(v.getValueAt(i) * c));
+      }
+      
+      output.collect(key.getRow(), multipliedValue);
+    }
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationReduce.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationReduce.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/MultiplicationReduce.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,64 @@
+/**
+ * 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.algebra;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.mapred.MatrixReduce;
+
+/**
+ * Accumulate the multiplied values.
+ */
+public class MultiplicationReduce extends MatrixReduce<Text, MapWritable> {
+
+  @Override
+  public void reduce(Text key, Iterator<MapWritable> values,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException {
+    Map<String, Double> sum = new HashMap<String, Double>();
+
+    while (values.hasNext()) {
+      for (Map.Entry<Writable, Writable> e : values.next().entrySet()) {
+        String sKey = e.getKey().toString();
+        if (sum.containsKey(sKey)) {
+          double before = sum.get(e.getKey().toString());
+          sum.put(sKey, before + getDouble(e.getValue()));
+        } else {
+          sum.put(sKey, getDouble(e.getValue()));
+        }
+      }
+    }
+
+    MapWritable value = new MapWritable();
+    for (Map.Entry<String, Double> f : sum.entrySet()) {
+      Writable val = getBytesWritable(f.getValue());
+      value.put(new Text(f.getKey()), val);
+    }
+    output.collect(key, value);
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/algebra/package.html
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/package.html?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/package.html (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/package.html Tue Jun 24 03:36:21 2008
@@ -0,0 +1,23 @@
+<html>
+
+<!--
+   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.
+-->
+
+<body>
+Map/Reduce-Based Basic Linear Algebra Classes
+</body>
+</html>

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/FractionMatrixInputFormat.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/FractionMatrixInputFormat.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/FractionMatrixInputFormat.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/FractionMatrixInputFormat.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,77 @@
+/**
+ * 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.mapred;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.InputFormat;
+import org.apache.hadoop.mapred.InputSplit;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.JobConfigurable;
+import org.apache.hadoop.mapred.RecordReader;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+
+public class FractionMatrixInputFormat extends InputFormatBase implements
+    InputFormat<HStoreKey, MapWritable>, JobConfigurable {
+
+  Text[] m_cols = new Text[] { Constants.DENOMINATOR, Constants.NUMERATOR,
+      Constants.ORIGINAL };
+
+  public RecordReader<HStoreKey, MapWritable> getRecordReader(InputSplit split,
+      JobConf job, Reporter reporter) throws IOException {
+    MatrixSplit tSplit = (MatrixSplit) split;
+
+    Text start = tSplit.getStartRow();
+    Text end = tSplit.getEndRow();
+
+    return new FractionMatrixReader(start, end, m_table, m_cols);
+  }
+
+  class FractionMatrixReader extends MatrixRecordReader {
+
+    public FractionMatrixReader(Text startRow, Text endRow, HTable table,
+        Text[] cols) throws IOException {
+      super(startRow, endRow, table, cols);
+    }
+
+    public boolean next(HStoreKey key, MapWritable value) throws IOException {
+      m_row.clear();
+      HStoreKey tKey = key;
+
+      boolean hasMore = m_scanner.next(tKey, m_row);
+      if (hasMore) {
+        value.clear();
+        for (Map.Entry<Text, byte[]> e : m_row.entrySet()) {
+          if (e.getKey().toString().startsWith(Constants.ORIGINAL.toString())) {
+            value.put(e.getKey(), new ImmutableBytesWritable(e.getValue()));
+          }
+        }
+      }
+      return hasMore;
+    }
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/InputFormatBase.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/InputFormatBase.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/InputFormatBase.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/InputFormatBase.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,94 @@
+/**
+ * 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.mapred;
+
+import java.io.IOException;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.InputFormat;
+import org.apache.hadoop.mapred.InputSplit;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.JobConfigurable;
+import org.apache.hadoop.mapred.RecordReader;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+import org.apache.log4j.Logger;
+
+public abstract class InputFormatBase extends MatrixMapReduce implements
+    InputFormat<HStoreKey, MapWritable>, JobConfigurable {
+  static final Logger LOG = Logger.getLogger(InputFormatBase.class.getName());
+
+  private Text m_tableName;
+  Text[] m_cols;
+  HTable m_table;
+
+  public abstract RecordReader<HStoreKey, MapWritable> getRecordReader(
+      InputSplit split, JobConf job, Reporter report) throws IOException;
+
+  /**
+   * @see org.apache.hadoop.mapred.InputFormat#getSplits(org.apache.hadoop.mapred.JobConf, int)
+   */
+  @SuppressWarnings("unused")
+  public InputSplit[] getSplits(JobConf job, int numSplits) throws IOException {
+    Cell meta = m_table.get(Constants.METADATA, Constants.METADATA_ROWS);
+
+    if (bytesToInt(meta.getValue()) < numSplits) {
+      numSplits = bytesToInt(meta.getValue());
+    }
+
+    Text[] startKeys = new Text[numSplits];
+    int interval = bytesToInt(meta.getValue()) / numSplits;
+
+    for (int i = 0; i < numSplits; i++) {
+      int row = (i * interval);
+      startKeys[i] = new Text(String.valueOf(row));
+    }
+
+    InputSplit[] splits = new InputSplit[startKeys.length];
+    for (int i = 0; i < startKeys.length; i++) {
+      splits[i] = new MatrixSplit(m_tableName, startKeys[i],
+          ((i + 1) < startKeys.length) ? startKeys[i + 1] : new Text());
+    }
+    return splits;
+  }
+
+  public void configure(JobConf job) {
+    Path[] tableNames = job.getInputPaths();
+    m_tableName = new Text(tableNames[0].getName());
+    try {
+      m_table = new HTable(new HBaseConfiguration(job), m_tableName);
+    } catch (IOException e) {
+      LOG.info(e);
+    }
+  }
+
+  public void validateInput(JobConf job) throws IOException {
+    Path[] tableNames = job.getInputPaths();
+    if (tableNames == null || tableNames.length > 1) {
+      throw new IOException("expecting one table name");
+    }
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormat.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormat.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormat.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixInputFormat.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,84 @@
+/**
+ * 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.mapred;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.InputFormat;
+import org.apache.hadoop.mapred.InputSplit;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.JobConfigurable;
+import org.apache.hadoop.mapred.RecordReader;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.Constants;
+
+public class MatrixInputFormat extends InputFormatBase implements
+    InputFormat<HStoreKey, MapWritable>, JobConfigurable {
+  Text[] m_cols = new Text[] { Constants.COLUMN };
+
+  public RecordReader<HStoreKey, MapWritable> getRecordReader(InputSplit split,
+      JobConf job, Reporter reporter) throws IOException {
+    MatrixSplit tSplit = (MatrixSplit) split;
+
+    Text start = tSplit.getStartRow();
+    Text end = tSplit.getEndRow();
+
+    return new MatrixReader(start, end, m_table, m_cols);
+  }
+
+  class MatrixReader extends MatrixRecordReader {
+
+    public MatrixReader(Text startRow, Text endRow, HTable table, Text[] cols)
+        throws IOException {
+      super(startRow, endRow, table, cols);
+    }
+
+    /**
+     * @param key HStoreKey as input key.
+     * @param value MapWritable as input value
+     * 
+     * Converts HScannerInterface.next(IntWritable, SortedMap<Text, byte[]>) to
+     * IntWritable, MapWritable<Text, ImmutableBytesWritable>
+     * 
+     * @return true if there was more data
+     * @throws IOException
+     */
+    @SuppressWarnings("unchecked")
+    public boolean next(HStoreKey key, MapWritable value) throws IOException {
+      m_row.clear();
+      HStoreKey tKey = key;
+
+      boolean hasMore = m_scanner.next(tKey, m_row);
+      if (hasMore) {
+        value.clear();
+        for (Map.Entry<Text, byte[]> e : m_row.entrySet()) {
+          value.put(e.getKey(), new ImmutableBytesWritable(e.getValue()));
+        }
+      }
+      return hasMore;
+    }
+  }
+}

Added: 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=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMap.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,72 @@
+/**
+ * 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.mapred;
+
+import java.io.IOException;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+
+/**
+ * Scan an HBase table to sort by a specified sort column. If the column does
+ * not exist, the record is not passed to Reduce.
+ * 
+ */
+@SuppressWarnings("unchecked")
+public abstract class MatrixMap<K extends WritableComparable, V extends Writable>
+    extends MatrixMapReduce implements Mapper<HStoreKey, MapWritable, K, V> {
+
+  /**
+   * Use this before submitting a MatrixMap job. It will appropriately set up
+   * the JobConf.
+   * 
+   * @param matrixA table name
+   * @param mapper mapper class
+   * @param job job configuration
+   */
+  public static void initJob(String matrixA, Class<? extends MatrixMap> mapper,
+      JobConf job) {
+    job.setOutputKeyClass(Text.class);
+    job.setOutputValueClass(MapWritable.class);
+    job.setMapperClass(mapper);
+    job.setInputPath(new Path(matrixA));
+  }
+
+  /**
+   * Call a user defined function on a single HBase record, represented by a key
+   * and its associated record value.
+   * 
+   * @param key
+   * @param value
+   * @param output
+   * @param reporter
+   * @throws IOException
+   */
+  public abstract void map(HStoreKey key, MapWritable value,
+      OutputCollector<K, V> output, Reporter reporter) throws IOException;
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMapReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMapReduce.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMapReduce.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixMapReduce.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,137 @@
+/**
+ * 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.mapred;
+
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hama.Constants;
+
+public class MatrixMapReduce extends MapReduceBase {
+
+  /**
+   * Converts the double to bytes
+   * 
+   * @param doubleVal
+   * @return bytes
+   */
+  public byte[] toBytes(double doubleVal) {
+    byte[] dByteArray = new byte[8];
+    long n = Double.doubleToLongBits(doubleVal);
+
+    for (int i = 0; i < dByteArray.length; i++) {
+      dByteArray[i] = (byte) (n >> (i * 8) & 0xFF);
+    }
+
+    return dByteArray;
+  }
+
+  /**
+   * Converts the bytes to double
+   * 
+   * @param inBytes
+   * @return double
+   */
+  public double toDouble(byte[] inBytes) {
+    if (inBytes == null) {
+      return 0;
+    }
+
+    long n = 0;
+    for (int i = 0; i < inBytes.length; i++) {
+      n |= ((long) (inBytes[i] & 0377) << (i * 8));
+    }
+
+    double doubleValue = Double.longBitsToDouble(n);
+
+    return doubleValue;
+  }
+  
+  /**
+   * Converts the int to byte array
+   * 
+   * @param i
+   * @return Byte Array
+   */
+  public byte[] intToBytes(int i) {
+    ByteBuffer bb = ByteBuffer.allocate(4);
+    bb.order(ByteOrder.nativeOrder());
+    bb.putInt(i);
+    return bb.array();
+  }
+
+  /**
+   * Converts the bytes to int
+   * 
+   * @param bytes
+   * @return Integer value
+   */
+  public int bytesToInt(byte[] bytes) {
+    ByteBuffer bb = ByteBuffer.wrap(bytes);
+    bb.order(ByteOrder.nativeOrder());
+    return bb.getInt();
+  }
+
+  /**
+   * Converts the double to ImmutableBytesWritable
+   * 
+   * @param d
+   * @return ImmutableBytesWritable
+   */
+  public ImmutableBytesWritable getBytesWritable(double d) {
+    return new ImmutableBytesWritable(toBytes(d));
+  }
+  
+  /**
+   * Converts the writable to double
+   * 
+   * @param value
+   * @return double
+   */
+  public double getDouble(Writable value) {
+    return toDouble(((ImmutableBytesWritable) value).get());
+  }
+
+  /**
+   * Return the integer index
+   * 
+   * @param key
+   * @return integer
+   */
+  public int getIndex(Text key) {
+    String sKey = key.toString();
+    return Integer.parseInt(sKey
+        .substring(sKey.indexOf(":") + 1, sKey.length()));
+  }
+
+  /**
+   * Return the column key
+   * 
+   * @param i
+   * @return text
+   */
+  public Text getColumnText(int i) {
+    return new Text(Constants.COLUMN + String.valueOf(i));
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixOutputFormat.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixOutputFormat.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixOutputFormat.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixOutputFormat.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,153 @@
+/**
+ * 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.mapred;
+
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.util.Map;
+
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.hbase.HBaseConfiguration;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.BatchUpdate;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.mapred.FileAlreadyExistsException;
+import org.apache.hadoop.mapred.InvalidJobConfException;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputFormatBase;
+import org.apache.hadoop.mapred.RecordWriter;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hadoop.util.Progressable;
+import org.apache.hama.Constants;
+import org.apache.log4j.Logger;
+
+public class MatrixOutputFormat extends OutputFormatBase<Text, MapWritable> {
+
+  /** JobConf parameter that specifies the output */
+  public static final String OUTPUT = "hbase.mapred.output";
+  public int rowCount = 0;
+  public int columnCount = 0;
+  static final Logger LOG = Logger
+      .getLogger(MatrixOutputFormat.class.getName());
+
+  /** constructor */
+  public MatrixOutputFormat() {
+    super();
+  }
+
+  /**
+   * Convert Reduce output (key, value) to (HStoreKey, KeyedDataArrayWritable)
+   * and write to an HBase table
+   */
+  protected class TableRecordWriter implements RecordWriter<Text, MapWritable> {
+    private HTable m_table;
+
+    /**
+     * Instantiate a TableRecordWriter with the HBase HClient for writing.
+     * 
+     * @param table
+     */
+    public TableRecordWriter(HTable table) {
+      m_table = table;
+    }
+
+    /** {@inheritDoc} */
+    public void close(@SuppressWarnings("unused")
+    Reporter reporter) {
+      if (rowCount > 0 && columnCount > 0) {
+        BatchUpdate b = new BatchUpdate(Constants.METADATA);
+        b.put(Constants.METADATA_ROWS, intToBytes(rowCount));
+        b.put(Constants.METADATA_COLUMNS, intToBytes(columnCount));
+        try {
+          m_table.commit(b);
+        } catch (IOException e) {
+          e.printStackTrace();
+        }
+      }
+    }
+
+    /**
+     * Converts the int to byte array
+     * 
+     * @param i
+     * @return Byte Array
+     */
+    public byte[] intToBytes(int i) {
+      ByteBuffer bb = ByteBuffer.allocate(4);
+      bb.order(ByteOrder.nativeOrder());
+      bb.putInt(i);
+      return bb.array();
+    }
+
+    /** {@inheritDoc} */
+    public void write(Text key, MapWritable value) throws IOException {
+
+      BatchUpdate b = new BatchUpdate(key);
+      b.put(Constants.METADATA_ROWS, intToBytes(rowCount));
+      b.put(Constants.METADATA_COLUMNS, intToBytes(columnCount));
+
+      rowCount++;
+      LOG.info(columnCount);
+      if (columnCount < value.keySet().size())
+        columnCount = value.keySet().size();
+
+      for (Map.Entry<Writable, Writable> e : value.entrySet()) {
+        b.put((Text) e.getKey(), ((ImmutableBytesWritable) e.getValue()).get());
+      }
+      m_table.commit(b); // end transaction
+    }
+
+  }
+
+  /** {@inheritDoc} */
+  @Override
+  @SuppressWarnings("unchecked")
+  public RecordWriter getRecordWriter(FileSystem ignored, JobConf job, 
+  String name, Progressable progress) throws IOException {
+
+    // expecting exactly one path
+
+    Text tableName = new Text(job.get(OUTPUT));
+    HTable table = null;
+    try {
+      table = new HTable(new HBaseConfiguration(job), tableName);
+    } catch (IOException e) {
+      LOG.error(e);
+      throw e;
+    }
+    return new TableRecordWriter(table);
+  }
+
+  /** {@inheritDoc} */
+  @Override
+  @SuppressWarnings("unused")
+  public void checkOutputSpecs(FileSystem ignored, JobConf job)
+      throws FileAlreadyExistsException, InvalidJobConfException, IOException {
+
+    String tableName = job.get(OUTPUT);
+    if (tableName == null) {
+      throw new IOException("Must specify table name");
+    }
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixRecordReader.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixRecordReader.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixRecordReader.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixRecordReader.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,72 @@
+package org.apache.hama.mapred;
+
+import java.io.IOException;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.apache.hadoop.hbase.HScannerInterface;
+import org.apache.hadoop.hbase.HStoreKey;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.RecordReader;
+
+/**
+ * Iterate over an HBase table data, return (IntWritable, MapWritable<Text,
+ * ImmutableBytesWritable>) pairs
+ */
+public abstract class MatrixRecordReader implements RecordReader<HStoreKey, MapWritable> {
+  protected final HScannerInterface m_scanner;
+  protected final SortedMap<Text, byte[]> m_row = new TreeMap<Text, byte[]>();
+
+  /**
+   * Constructor
+   * 
+   * @param startRow start row of block
+   * @param endRow end row of block
+   * @param table HTable object
+   * @param cols column specification
+   * @throws IOException
+   */
+  public MatrixRecordReader(Text startRow, Text endRow, HTable table,
+      Text[] cols) throws IOException {
+    if (endRow != null && endRow.getLength() > 0) {
+      this.m_scanner = table.obtainScanner(cols, startRow, endRow);
+    } else {
+      this.m_scanner = table.obtainScanner(cols, startRow);
+    }
+  }
+
+  public void close() throws IOException {
+    this.m_scanner.close();
+  }
+
+  /**
+   * @return HStoreKey
+   * 
+   * @see org.apache.hadoop.mapred.RecordReader#createKey()
+   */
+  public HStoreKey createKey() {
+    return new HStoreKey();
+  }
+
+  /**
+   * @return MapWritable
+   * 
+   * @see org.apache.hadoop.mapred.RecordReader#createValue()
+   */
+  @SuppressWarnings("unchecked")
+  public MapWritable createValue() {
+    return new MapWritable();
+  }
+
+  /** {@inheritDoc} */
+  public long getPos() {
+    return 0;
+  }
+
+  /** {@inheritDoc} */
+  public float getProgress() {
+    return 0;
+  }
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixReduce.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixReduce.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixReduce.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,65 @@
+/**
+ * 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.mapred;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.Writable;
+import org.apache.hadoop.io.WritableComparable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+
+/**
+ * Write a table, sorting by the input key
+ */
+@SuppressWarnings("unchecked")
+public abstract class MatrixReduce<K extends WritableComparable, V extends Writable>
+    extends MatrixMapReduce implements Reducer<K, V, Text, MapWritable> {
+
+  /**
+   * Use this before submitting a TableReduce job. It will appropriately set up
+   * the JobConf.
+   * 
+   * @param table
+   * @param reducer
+   * @param job
+   */
+  public static void initJob(String table,
+      Class<? extends MatrixReduce> reducer, JobConf job) {
+    job.setReducerClass(reducer);
+    job.set(MatrixOutputFormat.OUTPUT, table);
+  }
+
+  /**
+   * @param key
+   * @param values
+   * @param output
+   * @param reporter
+   * @throws IOException
+   */
+  public abstract void reduce(K key, Iterator<V> values,
+      OutputCollector<Text, MapWritable> output, Reporter reporter)
+      throws IOException;
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixSplit.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixSplit.java?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixSplit.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/MatrixSplit.java Tue Jun 24 03:36:21 2008
@@ -0,0 +1,99 @@
+/**
+ * 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.mapred;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.InputSplit;
+
+public class MatrixSplit implements InputSplit {
+  private Text m_tableName;
+  private Text m_startRow;
+  private Text m_endRow;
+
+  /** default constructor */
+  public MatrixSplit() {
+    m_tableName = new Text();
+    m_startRow = new Text();
+    m_endRow = new Text();
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param tableName
+   * @param startRow
+   * @param endRow
+   */
+  public MatrixSplit(Text tableName, Text startRow, Text endRow) {
+    this();
+    m_tableName.set(tableName);
+    m_startRow.set(startRow);
+    m_endRow.set(endRow);
+  }
+
+  /** @return table name */
+  public Text getTableName() {
+    return m_tableName;
+  }
+
+  /** @return starting row key */
+  public Text getStartRow() {
+    return m_startRow;
+  }
+
+  /** @return end row key */
+  public Text getEndRow() {
+    return m_endRow;
+  }
+
+  /** {@inheritDoc} */
+  public long getLength() {
+    return 0;
+  }
+
+  /** {@inheritDoc} */
+  public String[] getLocations() {
+    return new String[] {};
+  }
+
+  /** {@inheritDoc} */
+  public void readFields(DataInput in) throws IOException {
+    m_tableName.readFields(in);
+    m_startRow.readFields(in);
+    m_endRow.readFields(in);
+  }
+
+  /** {@inheritDoc} */
+  public void write(DataOutput out) throws IOException {
+    m_tableName.write(out);
+    m_startRow.write(out);
+    m_endRow.write(out);
+  }
+
+  /** {@inheritDoc} */
+  @Override
+  public String toString() {
+    return m_tableName + "," + m_startRow + "," + m_endRow;
+  }
+}
\ No newline at end of file

Added: incubator/hama/trunk/src/java/org/apache/hama/mapred/package.html
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/package.html?rev=671120&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/package.html (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/package.html Tue Jun 24 03:36:21 2008
@@ -0,0 +1,23 @@
+<html>
+
+<!--
+   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.
+-->
+
+<body>
+Matrix Input/Output Formatter
+</body>
+</html>