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From edwardy...@apache.org
Subject svn commit: r744798 [2/2] - in /incubator/hama/trunk: ./ src/examples/org/apache/hama/examples/ src/java/org/apache/hama/ src/java/org/apache/hama/algebra/ src/java/org/apache/hama/io/ src/java/org/apache/hama/mapred/ src/test/org/apache/hama/ src/test...
Date Mon, 16 Feb 2009 04:35:24 GMT
Modified: incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyReduce.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyReduce.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyReduce.java Mon Feb 16 04:35:23 2009
@@ -1,69 +1,69 @@
-/**
- * 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.hbase.io.BatchUpdate;
-import org.apache.hadoop.io.IntWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-import org.apache.hama.io.VectorUpdate;
-import org.apache.hama.io.VectorWritable;
-import org.apache.hama.mapred.VectorOutputFormat;
-import org.apache.log4j.Logger;
-
-public class SIMDMultiplyReduce extends MapReduceBase implements
-    Reducer<IntWritable, VectorWritable, IntWritable, VectorUpdate> {
-  static final Logger LOG = Logger.getLogger(SIMDMultiplyReduce.class);
-
-  /**
-   * 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<SIMDMultiplyReduce> reducer, JobConf job) {
-    job.setOutputFormat(VectorOutputFormat.class);
-    job.setReducerClass(reducer);
-    job.set(VectorOutputFormat.OUTPUT_TABLE, table);
-    job.setOutputKeyClass(IntWritable.class);
-    job.setOutputValueClass(BatchUpdate.class);
-  }
-  
-  @Override
-  public void reduce(IntWritable key, Iterator<VectorWritable> values,
-      OutputCollector<IntWritable, VectorUpdate> output, Reporter reporter)
-      throws IOException {
-
-    VectorUpdate update = new VectorUpdate(key.get());
-    update.putAll(values.next().entrySet());
-
-    output.collect(key, update);
-  }
-
-}
+/**
+ * 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.hbase.io.BatchUpdate;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.io.VectorUpdate;
+import org.apache.hama.mapred.VectorOutputFormat;
+import org.apache.log4j.Logger;
+
+public class SIMDMultiplyReduce extends MapReduceBase implements
+    Reducer<IntWritable, MapWritable, IntWritable, VectorUpdate> {
+  static final Logger LOG = Logger.getLogger(SIMDMultiplyReduce.class);
+
+  /**
+   * 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<SIMDMultiplyReduce> reducer, JobConf job) {
+    job.setOutputFormat(VectorOutputFormat.class);
+    job.setReducerClass(reducer);
+    job.set(VectorOutputFormat.OUTPUT_TABLE, table);
+    job.setOutputKeyClass(IntWritable.class);
+    job.setOutputValueClass(BatchUpdate.class);
+  }
+  
+  @Override
+  public void reduce(IntWritable key, Iterator<MapWritable> values,
+      OutputCollector<IntWritable, VectorUpdate> output, Reporter reporter)
+      throws IOException {
+
+    VectorUpdate update = new VectorUpdate(key.get());
+    update.putAll(values.next());
+
+    output.collect(key, update);
+  }
+
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/io/VectorUpdate.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/io/VectorUpdate.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/io/VectorUpdate.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/io/VectorUpdate.java Mon Feb 16 04:35:23 2009
@@ -25,6 +25,9 @@
 
 import org.apache.hadoop.hbase.io.BatchUpdate;
 import org.apache.hadoop.hbase.util.Bytes;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Writable;
 import org.apache.hama.Constants;
 import org.apache.hama.util.BytesUtil;
 
@@ -76,4 +79,10 @@
       put(e.getKey(), e.getValue().getValue());
     }
   }
+  
+  public void putAll(MapWritable entries) {
+    for (Map.Entry<Writable, Writable> e : entries.entrySet()) {
+      put(((IntWritable) e.getKey()).get(), ((DoubleEntry) e.getValue()).getValue());
+    }
+  }
 }

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMap.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMap.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMap.java Mon Feb 16 04:35:23 2009
@@ -16,11 +16,11 @@
  */
 package org.apache.hama.mapred;
 
+import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.io.Writable;
 import org.apache.hadoop.io.WritableComparable;
 import org.apache.hadoop.mapred.Mapper;
 import org.apache.hama.io.BlockID;
-import org.apache.hama.io.VectorWritable;
 
 /**
  * Scan an table/file to collect blocks.
@@ -30,5 +30,5 @@
  */
 @SuppressWarnings("unchecked")
 public interface CollectBlocksMap<K extends WritableComparable, V extends Writable>
-    extends Mapper<K, V, BlockID, VectorWritable> {
+    extends Mapper<K, V, BlockID, MapWritable> {
 }

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapReduceBase.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapReduceBase.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapReduceBase.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapReduceBase.java Mon Feb 16 04:35:23 2009
@@ -16,11 +16,11 @@
  */
 package org.apache.hama.mapred;
 
+import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.mapred.JobConf;
 import org.apache.hadoop.mapred.MapReduceBase;
 import org.apache.hama.io.BlockID;
 import org.apache.hama.io.BlockWritable;
-import org.apache.hama.io.VectorWritable;
 
 /**
  * Abstract Blocking Map/Reduce Class to configure the job.
@@ -59,7 +59,7 @@
       int block_size, int i, int j, JobConf job) {
     job.setReducerClass(CollectBlocksReducer.class);
     job.setMapOutputKeyClass(BlockID.class);
-    job.setMapOutputValueClass(VectorWritable.class);
+    job.setMapOutputValueClass(MapWritable.class);
 
     job.setOutputFormat(BlockOutputFormat.class);
     job.setOutputKeyClass(BlockID.class);

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapper.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapper.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapper.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksMapper.java Mon Feb 16 04:35:23 2009
@@ -1,56 +1,54 @@
-/**
- * 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.io.IntWritable;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reporter;
-import org.apache.hama.DenseVector;
-import org.apache.hama.io.BlockID;
-import org.apache.hama.io.VectorWritable;
-
-/**
- * A Map/Reduce help class for blocking a DenseMatrix to a block-formated matrix
- */
-public class CollectBlocksMapper extends CollectBlocksMapReduceBase implements
-    CollectBlocksMap<IntWritable, VectorWritable> {
-
-  @Override
-  public void map(IntWritable key, VectorWritable value,
-      OutputCollector<BlockID, VectorWritable> output, Reporter reporter)
-      throws IOException {
-    int startColumn;
-    int endColumn;
-    int blkRow = key.get() / mBlockRowSize;
-    DenseVector dv = value.getDenseVector();
-
-    int i = 0;
-    do {
-      startColumn = i * mBlockColSize;
-      endColumn = startColumn + mBlockColSize - 1;
-      if (endColumn >= mColumns) // the last sub vector
-        endColumn = mColumns - 1;
-      output.collect(new BlockID(blkRow, i), new VectorWritable(key.get(), dv
-          .subVector(startColumn, endColumn)));
-
-      i++;
-    } while (endColumn < (mColumns - 1));
-  }
-
-}
+/**
+ * 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.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.DenseVector;
+import org.apache.hama.io.BlockID;
+import org.apache.log4j.Logger;
+
+/**
+ * A Map/Reduce help class for blocking a DenseMatrix to a block-formated matrix
+ */
+public class CollectBlocksMapper extends CollectBlocksMapReduceBase implements
+    CollectBlocksMap<IntWritable, MapWritable> {
+  static final Logger LOG = Logger.getLogger(CollectBlocksMapper.class);
+  
+  @Override
+  public void map(IntWritable key, MapWritable value,
+      OutputCollector<BlockID, MapWritable> output, Reporter reporter)
+      throws IOException {
+    int startColumn, endColumn, blkRow = key.get() / mBlockRowSize, i = 0;
+    DenseVector dv = new DenseVector(key.get(), value);
+
+    do {
+      startColumn = i * mBlockColSize;
+      endColumn = startColumn + mBlockColSize - 1;
+      if (endColumn >= mColumns) // the last sub vector
+        endColumn = mColumns - 1;
+      output.collect(new BlockID(blkRow, i), dv.subVector(startColumn, endColumn).getEntries());
+
+      i++;
+    } while (endColumn < (mColumns - 1));
+  }
+
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksReducer.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksReducer.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksReducer.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/CollectBlocksReducer.java Mon Feb 16 04:35:23 2009
@@ -19,13 +19,16 @@
 import java.io.IOException;
 import java.util.Iterator;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.mapred.OutputCollector;
 import org.apache.hadoop.mapred.Reducer;
 import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.DenseVector;
 import org.apache.hama.SubMatrix;
 import org.apache.hama.io.BlockID;
 import org.apache.hama.io.BlockWritable;
-import org.apache.hama.io.VectorWritable;
 
 /**
  * Rows are named as c(i, j) with sequential number ((N^2 * i) + ((j * N) + k)
@@ -33,10 +36,11 @@
  * b(k, j).
  */
 public class CollectBlocksReducer extends CollectBlocksMapReduceBase implements
-    Reducer<BlockID, VectorWritable, BlockID, BlockWritable> {
-
+    Reducer<BlockID, MapWritable, BlockID, BlockWritable> {
+  static final Log LOG = LogFactory.getLog(CollectBlocksReducer.class);
+  
   @Override
-  public void reduce(BlockID key, Iterator<VectorWritable> values,
+  public void reduce(BlockID key, Iterator<MapWritable> values,
       OutputCollector<BlockID, BlockWritable> output, Reporter reporter)
       throws IOException {
     // Note: all the sub-vectors are grouped by {@link
@@ -60,11 +64,12 @@
     // i, j is the current offset in the sub-matrix
     int i = 0, j = 0;
     while (values.hasNext()) {
-      VectorWritable vw = values.next();
+      DenseVector vw = new DenseVector(values.next());
       // check the size is suitable
       if (vw.size() != smCols)
         throw new IOException("Block Column Size dismatched.");
-      i = vw.row - rowBase;
+      i = vw.getRow() - rowBase;
+      
       if (i >= smRows || i < 0)
         throw new IOException("Block Row Size dismatched.");
 

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixMap.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixMap.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixMap.java Mon Feb 16 04:35:23 2009
@@ -1,60 +1,60 @@
-/**
- * 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.io.IntWritable;
-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.DenseVector;
-import org.apache.hama.io.VectorWritable;
-import org.apache.hama.util.RandomVariable;
-import org.apache.log4j.Logger;
-
-/**
- * Generate matrix with random elements
- */
-public class RandomMatrixMap extends MapReduceBase implements
-    Mapper<IntWritable, IntWritable, IntWritable, VectorWritable> {
-  static final Logger LOG = Logger.getLogger(RandomMatrixMap.class);
-  protected int column;
-  protected DenseVector vector = new DenseVector();
-  
-  @Override
-  public void map(IntWritable key, IntWritable value,
-      OutputCollector<IntWritable, VectorWritable> output, Reporter report)
-      throws IOException {
-    vector.clear();
-    for (int i = key.get(); i <= value.get(); i++) {
-      for (int j = 0; j < column; j++) {
-        vector.set(j, RandomVariable.rand());
-      }
-      output.collect(new IntWritable(i), new VectorWritable(i, vector));
-    }
-  }
-
-  public void configure(JobConf job) {
-    column = Integer.parseInt(job.get("matrix.column"));
-  }
-}
+/**
+ * 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.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+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.DenseVector;
+import org.apache.hama.util.RandomVariable;
+import org.apache.log4j.Logger;
+
+/**
+ * Generate matrix with random elements
+ */
+public class RandomMatrixMap extends MapReduceBase implements
+    Mapper<IntWritable, IntWritable, IntWritable, MapWritable> {
+  static final Logger LOG = Logger.getLogger(RandomMatrixMap.class);
+  protected int column;
+  protected DenseVector vector = new DenseVector();
+  
+  @Override
+  public void map(IntWritable key, IntWritable value,
+      OutputCollector<IntWritable, MapWritable> output, Reporter report)
+      throws IOException {
+    vector.clear();
+    for (int i = key.get(); i <= value.get(); i++) {
+      for (int j = 0; j < column; j++) {
+        vector.set(j, RandomVariable.rand());
+      }
+      output.collect(new IntWritable(i), vector.getEntries());
+    }
+  }
+
+  public void configure(JobConf job) {
+    column = Integer.parseInt(job.get("matrix.column"));
+  }
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixReduce.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixReduce.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixReduce.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/RandomMatrixReduce.java Mon Feb 16 04:35:23 2009
@@ -1,69 +1,69 @@
-/**
- * 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.hbase.io.BatchUpdate;
-import org.apache.hadoop.io.IntWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-import org.apache.hama.io.VectorUpdate;
-import org.apache.hama.io.VectorWritable;
-import org.apache.log4j.Logger;
-
-public class RandomMatrixReduce extends MapReduceBase implements
-    Reducer<IntWritable, VectorWritable, IntWritable, VectorUpdate> {
-  static final Logger LOG = Logger.getLogger(RandomMatrixReduce.class);
-
-  /**
-   * 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<RandomMatrixReduce> reducer,
-      JobConf job) {
-    job.setOutputFormat(VectorOutputFormat.class);
-    job.setReducerClass(reducer);
-    job.set(VectorOutputFormat.OUTPUT_TABLE, table);
-    job.setOutputKeyClass(IntWritable.class);
-    job.setOutputValueClass(BatchUpdate.class);
-  }
-
-  @Override
-  public void reduce(IntWritable key, Iterator<VectorWritable> values,
-      OutputCollector<IntWritable, VectorUpdate> output, Reporter reporter)
-      throws IOException {
-    VectorUpdate update = new VectorUpdate(key.get());
-    update.putAll(values.next().entrySet());
-    output.collect(key, update);
-    
-    if(values.hasNext())
-      throw new IOException("Unexpected data.");
-  }
-
-}
+/**
+ * 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.hbase.io.BatchUpdate;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.io.VectorUpdate;
+import org.apache.log4j.Logger;
+
+public class RandomMatrixReduce extends MapReduceBase implements
+    Reducer<IntWritable, MapWritable, IntWritable, VectorUpdate> {
+  static final Logger LOG = Logger.getLogger(RandomMatrixReduce.class);
+
+  /**
+   * 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<RandomMatrixReduce> reducer,
+      JobConf job) {
+    job.setOutputFormat(VectorOutputFormat.class);
+    job.setReducerClass(reducer);
+    job.set(VectorOutputFormat.OUTPUT_TABLE, table);
+    job.setOutputKeyClass(IntWritable.class);
+    job.setOutputValueClass(BatchUpdate.class);
+  }
+
+  @Override
+  public void reduce(IntWritable key, Iterator<MapWritable> values,
+      OutputCollector<IntWritable, VectorUpdate> output, Reporter reporter)
+      throws IOException {
+    VectorUpdate update = new VectorUpdate(key.get());
+    update.putAll(values.next());
+    output.collect(key, update);
+    
+    if(values.hasNext())
+      throw new IOException("Unexpected data.");
+  }
+
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/mapred/VectorInputFormat.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/mapred/VectorInputFormat.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/mapred/VectorInputFormat.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/mapred/VectorInputFormat.java Mon Feb 16 04:35:23 2009
@@ -1,168 +1,168 @@
-/**
- * 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.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.hadoop.hbase.UnknownScannerException;
-import org.apache.hadoop.hbase.io.RowResult;
-import org.apache.hadoop.hbase.mapred.TableSplit;
-import org.apache.hadoop.hbase.util.Bytes;
-import org.apache.hadoop.hbase.util.Writables;
-import org.apache.hadoop.io.IntWritable;
-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.hadoop.util.StringUtils;
-import org.apache.hama.io.VectorWritable;
-import org.apache.hama.util.BytesUtil;
-
-public class VectorInputFormat extends HTableInputFormatBase implements
-    InputFormat<IntWritable, VectorWritable>, JobConfigurable {
-  static final Log LOG = LogFactory.getLog(VectorInputFormat.class);
-  private TableRecordReader tableRecordReader;
-  
-  /**
-   * Iterate over an HBase table data, return (IntWritable, VectorWritable) pairs
-   */
-  protected static class TableRecordReader extends HTableRecordReaderBase
-      implements RecordReader<IntWritable, VectorWritable> {
-
-   private int totalRows;
-   private int processedRows;
-
-   @Override
-   public void init() throws IOException {
-     super.init();
-     if(endRow.length == 0) { // the last split, we don't know the end row
-       totalRows = 0;         // so we just skip it.
-     } else {
-       if(startRow.length == 0) { // the first split, start row is 0
-         totalRows = BytesUtil.bytesToInt(endRow);
-       } else {
-         totalRows = BytesUtil.bytesToInt(endRow) - BytesUtil.bytesToInt(startRow);
-       }
-     }
-     processedRows = 0;
-     LOG.info("Split (" + Bytes.toString(startRow) + ", " + Bytes.toString(endRow) + 
-       ") -> " + totalRows);
-   }
-
-
-    /**
-     * @return IntWritable
-     * 
-     * @see org.apache.hadoop.mapred.RecordReader#createKey()
-     */
-    public IntWritable createKey() {
-      return new IntWritable();
-    }
-
-    /**
-     * @return VectorWritable
-     * 
-     * @see org.apache.hadoop.mapred.RecordReader#createValue()
-     */
-    public VectorWritable createValue() {
-      return new VectorWritable();
-    }
-
-    /**
-     * @param key IntWritable as input key.
-     * @param value VectorWritable as input value
-     * 
-     * Converts Scanner.next() to IntWritable, VectorWritable
-     * 
-     * @return true if there was more data
-     * @throws IOException
-     */
-    public boolean next(IntWritable key, VectorWritable value)
-        throws IOException {
-      RowResult result;
-      try {
-        result = this.scanner.next();
-      } catch (UnknownScannerException e) {
-        LOG.debug("recovered from " + StringUtils.stringifyException(e));  
-        restart(lastRow);
-        this.scanner.next();    // skip presumed already mapped row
-        result = this.scanner.next();
-      }
-      
-      boolean hasMore = result != null && result.size() > 0;
-      if (hasMore) {
-        byte[] row = result.getRow();
-        key.set(BytesUtil.bytesToInt(row));
-        lastRow = row;
-        Writables.copyWritable(result, value);
-        processedRows++;
-      }
-      return hasMore;
-    }
-
-    @Override
-    public float getProgress() {
-      if(totalRows <= 0) {
-        return 0;
-      } else {
-        return Math.min(1.0f, processedRows / (float)totalRows);
-      }
-    }
-   
-  }
-  
-  /**
-   * Builds a TableRecordReader. If no TableRecordReader was provided, uses the
-   * default.
-   * 
-   * @see org.apache.hadoop.mapred.InputFormat#getRecordReader(InputSplit,
-   *      JobConf, Reporter)
-   */
-  public RecordReader<IntWritable, VectorWritable> getRecordReader(
-      InputSplit split, JobConf job, Reporter reporter) throws IOException {
-    TableSplit tSplit = (TableSplit) split;
-    TableRecordReader trr = this.tableRecordReader;
-    // if no table record reader was provided use default
-    if (trr == null) {
-      trr = new TableRecordReader();
-    }
-    trr.setStartRow(tSplit.getStartRow());
-    trr.setEndRow(tSplit.getEndRow());
-    trr.setHTable(this.table);
-    trr.setInputColumns(this.inputColumns);
-    trr.setRowFilter(this.rowFilter);
-    trr.init();
-    return trr;
-  }
-  
-  /**
-   * Allows subclasses to set the {@link TableRecordReader}.
-   * 
-   * @param tableRecordReader to provide other {@link TableRecordReader}
-   *                implementations.
-   */
-  protected void setTableRecordReader(TableRecordReader tableRecordReader) {
-    this.tableRecordReader = tableRecordReader;
-  }
-}
+/**
+ * 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.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.hbase.UnknownScannerException;
+import org.apache.hadoop.hbase.io.RowResult;
+import org.apache.hadoop.hbase.mapred.TableSplit;
+import org.apache.hadoop.hbase.util.Bytes;
+import org.apache.hadoop.hbase.util.Writables;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+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.hadoop.util.StringUtils;
+import org.apache.hama.DenseVector;
+import org.apache.hama.util.BytesUtil;
+
+public class VectorInputFormat extends HTableInputFormatBase implements
+    InputFormat<IntWritable, MapWritable>, JobConfigurable {
+  static final Log LOG = LogFactory.getLog(VectorInputFormat.class);
+  private TableRecordReader tableRecordReader;
+  
+  /**
+   * Iterate over an HBase table data, return (IntWritable, MapWritable) pairs
+   */
+  protected static class TableRecordReader extends HTableRecordReaderBase
+      implements RecordReader<IntWritable, MapWritable> {
+
+   private int totalRows;
+   private int processedRows;
+
+   @Override
+   public void init() throws IOException {
+     super.init();
+     if(endRow.length == 0) { // the last split, we don't know the end row
+       totalRows = 0;         // so we just skip it.
+     } else {
+       if(startRow.length == 0) { // the first split, start row is 0
+         totalRows = BytesUtil.bytesToInt(endRow);
+       } else {
+         totalRows = BytesUtil.bytesToInt(endRow) - BytesUtil.bytesToInt(startRow);
+       }
+     }
+     processedRows = 0;
+     LOG.info("Split (" + Bytes.toString(startRow) + ", " + Bytes.toString(endRow) + 
+       ") -> " + totalRows);
+   }
+
+
+    /**
+     * @return IntWritable
+     * 
+     * @see org.apache.hadoop.mapred.RecordReader#createKey()
+     */
+    public IntWritable createKey() {
+      return new IntWritable();
+    }
+
+    /**
+     * @return MapWritable
+     * 
+     * @see org.apache.hadoop.mapred.RecordReader#createValue()
+     */
+    public MapWritable createValue() {
+      return new MapWritable();
+    }
+
+    /**
+     * @param key IntWritable as input key.
+     * @param value MapWritable as input value
+     * 
+     * Converts Scanner.next() to IntWritable, MapWritable
+     * 
+     * @return true if there was more data
+     * @throws IOException
+     */
+    public boolean next(IntWritable key, MapWritable value)
+        throws IOException {
+      RowResult result;
+      try {
+        result = this.scanner.next();
+      } catch (UnknownScannerException e) {
+        LOG.debug("recovered from " + StringUtils.stringifyException(e));  
+        restart(lastRow);
+        this.scanner.next();    // skip presumed already mapped row
+        result = this.scanner.next();
+      }
+      
+      boolean hasMore = result != null && result.size() > 0;
+      if (hasMore) {
+        byte[] row = result.getRow();
+        key.set(BytesUtil.bytesToInt(row));
+        lastRow = row;
+        Writables.copyWritable(new DenseVector(result).getEntries(), value);
+        processedRows++;
+      }
+      return hasMore;
+    }
+
+    @Override
+    public float getProgress() {
+      if(totalRows <= 0) {
+        return 0;
+      } else {
+        return Math.min(1.0f, processedRows / (float)totalRows);
+      }
+    }
+  }
+  
+  /**
+   * Builds a TableRecordReader. If no TableRecordReader was provided, uses the
+   * default.
+   * 
+   * @see org.apache.hadoop.mapred.InputFormat#getRecordReader(InputSplit,
+   *      JobConf, Reporter)
+   */
+  public RecordReader<IntWritable, MapWritable> getRecordReader(
+      InputSplit split, JobConf job, Reporter reporter) throws IOException {
+    TableSplit tSplit = (TableSplit) split;
+    TableRecordReader trr = this.tableRecordReader;
+    // if no table record reader was provided use default
+    if (trr == null) {
+      trr = new TableRecordReader();
+    }
+    trr.setStartRow(tSplit.getStartRow());
+    trr.setEndRow(tSplit.getEndRow());
+    trr.setHTable(this.table);
+    trr.setInputColumns(this.inputColumns);
+    trr.setRowFilter(this.rowFilter);
+    trr.init();
+    return trr;
+  }
+  
+  /**
+   * Allows subclasses to set the {@link TableRecordReader}.
+   * 
+   * @param tableRecordReader to provide other {@link TableRecordReader}
+   *                implementations.
+   */
+  protected void setTableRecordReader(TableRecordReader tableRecordReader) {
+    this.tableRecordReader = tableRecordReader;
+  }
+}

Modified: incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java Mon Feb 16 04:35:23 2009
@@ -1,341 +1,342 @@
-/**
- * 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 java.util.Iterator;
-
-import junit.extensions.TestSetup;
-import junit.framework.Test;
-import junit.framework.TestCase;
-import junit.framework.TestSuite;
-
-import org.apache.hadoop.hbase.client.HBaseAdmin;
-import org.apache.hama.io.DoubleEntry;
-import org.apache.hama.util.RandomVariable;
-import org.apache.log4j.Logger;
-
-/**
- * Matrix test
- */
-public class TestDenseMatrix extends TestCase {
-  static final Logger LOG = Logger.getLogger(TestDenseMatrix.class);
-  private static int SIZE = 10;
-  private static Matrix m1;
-  private static Matrix m2;
-  private final static String aliase1 = "matrix_aliase_A";
-  private final static String aliase2 = "matrix_aliase_B";
-  private static HamaConfiguration conf;
-  private static HBaseAdmin admin;
-  private static HamaAdmin hamaAdmin;
-
-  public static Test suite() {
-    TestSetup setup = new TestSetup(new TestSuite(TestDenseMatrix.class)) {
-      protected void setUp() throws Exception {
-        HCluster hCluster = new HCluster();
-        hCluster.setUp();
-
-        conf = hCluster.getConf();
-        admin = new HBaseAdmin(conf);
-        hamaAdmin = new HamaAdminImpl(conf, admin);
-
-        m1 = DenseMatrix.random(hCluster.getConf(), SIZE, SIZE);
-        m2 = DenseMatrix.random(hCluster.getConf(), SIZE, SIZE);
-      }
-
-      protected void tearDown() {
-        try {
-          closeTest();
-        } catch (IOException e) {
-          e.printStackTrace();
-        }
-      }
-    };
-    return setup;
-  }
-
-  public static void closeTest() throws IOException {
-    m1.close();
-    m2.close();
-  }
-
-  public void testEntryAdd() throws IOException {
-    double origin = m1.get(1, 1);
-    m1.add(1, 1, 0.5);
-
-    assertEquals(m1.get(1, 1), origin + 0.5);
-  }
-
-  /**
-   * Column vector test.
-   * 
-   * @param rand
-   * @throws IOException
-   */
-  public void testGetColumn() throws IOException {
-    Vector v = m1.getColumn(0);
-    Iterator<DoubleEntry> it = v.iterator();
-    int x = 0;
-    while (it.hasNext()) {
-      assertEquals(m1.get(x, 0), it.next().getValue());
-      x++;
-    }
-  }
-
-  public void testGetSetAttribute() throws IOException {
-    m1.setRowLabel(0, "row1");
-    assertEquals(m1.getRowLabel(0), "row1");
-    assertEquals(m1.getRowLabel(1), null);
-
-    m1.setColumnLabel(0, "column1");
-    assertEquals(m1.getColumnLabel(0), "column1");
-    assertEquals(m1.getColumnLabel(1), null);
-  }
-
-  public void testSubMatrix() throws IOException {
-    SubMatrix a = m1.subMatrix(2, 4, 2, 5); // A : 3 * 4
-    for (int i = 0; i < a.getRows(); i++) {
-      for (int j = 0; j < a.getColumns(); j++) {
-        assertEquals(a.get(i, j), m1.get(i + 2, j + 2));
-      }
-    }
-
-    SubMatrix b = m2.subMatrix(0, 3, 0, 2); // B : 4 * 3
-    SubMatrix c = a.mult(b);
-
-    double[][] C = new double[3][3]; // A * B
-    for (int i = 0; i < 3; i++) {
-      for (int j = 0; j < 3; j++) {
-        for (int k = 0; k < 4; k++) {
-          C[i][j] += m1.get(i + 2, k + 2) * m2.get(k, j);
-        }
-      }
-    }
-
-    for (int i = 0; i < 3; i++) {
-      for (int j = 0; j < 3; j++) {
-        assertEquals(C[i][j], c.get(i, j));
-      }
-    }
-  }
-
-  /**
-   * Test matrices addition
-   * 
-   * @throws IOException
-   */
-  public void testMatrixAdd() throws IOException {
-    Matrix result = m1.add(m2);
-
-    assertEquals(result.getRows(), SIZE);
-    assertEquals(result.getColumns(), SIZE);
-
-    for (int i = 0; i < SIZE; i++) {
-      for (int j = 0; j < SIZE; j++) {
-        assertEquals(result.get(i, j), m1.get(i, j) + m2.get(i, j));
-      }
-    }
-  }
-
-  /**
-   * Test matrices multiplication
-   * 
-   * @throws IOException
-   */
-  public void testMatrixMult() throws IOException {
-    Matrix result = m1.mult(m2);
-
-    assertEquals(result.getRows(), SIZE);
-    assertEquals(result.getColumns(), SIZE);
-
-    verifyMultResult(m1, m2, result);
-  }
-
-  public void testSetMatrix() throws IOException {
-    Matrix a = new DenseMatrix(conf);
-    a.set(m1);
-
-    for (int i = 0; i < 5; i++) {
-      int x = RandomVariable.randInt(0, 10);
-      int y = RandomVariable.randInt(0, 10);
-      assertEquals(a.get(x, y), m1.get(x, y));
-    }
-  }
-
-  public void testSetAlphaMatrix() throws IOException {
-    Matrix a = new DenseMatrix(conf);
-    a.set(0.5, m1);
-    
-    for (int i = 0; i < 5; i++) {
-      int x = RandomVariable.randInt(0, 10);
-      int y = RandomVariable.randInt(0, 10);
-      assertEquals(a.get(x, y), (m1.get(x, y) * 0.5));
-    }
-  }
-  
-  public void testAddAlphaMatrix() throws IOException {
-    double value = m1.get(0, 0) + (m2.get(0, 0) * 0.1);
-    Matrix result = m1.add(0.1, m2);
-    assertEquals(value, result.get(0, 0));
-  }
-  
-  public void testSetRow() throws IOException {
-    Vector v = new DenseVector();
-    double[] entries = new double[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 0 };
-
-    for (int i = 0; i < SIZE; i++) {
-      v.set(i, entries[i]);
-    }
-
-    m1.setRow(SIZE + 1, v);
-    Iterator<DoubleEntry> it = m1.getRow(SIZE + 1).iterator();
-
-    int i = 0;
-    while (it.hasNext()) {
-      assertEquals(entries[i], it.next().getValue());
-      i++;
-    }
-  }
-
-  public void testSetColumn() throws IOException {
-    Vector v = new DenseVector();
-    double[] entries = new double[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 0 };
-
-    for (int i = 0; i < SIZE; i++) {
-      v.set(i, entries[i]);
-    }
-
-    m1.setColumn(SIZE + 1, v);
-    Iterator<DoubleEntry> it = m1.getColumn(SIZE + 1).iterator();
-
-    int i = 0;
-    while (it.hasNext()) {
-      assertEquals(entries[i], it.next().getValue());
-      i++;
-    }
-  }
-
-  public void testLoadSave() throws IOException {
-    String path1 = m1.getPath();
-    // save m1 to aliase1
-    m1.save(aliase1);
-    // load matrix m1 using aliase1
-    DenseMatrix loadTest = new DenseMatrix(conf, aliase1, false);
-
-    for (int i = 0; i < loadTest.getRows(); i++) {
-      for (int j = 0; j < loadTest.getColumns(); j++) {
-        assertEquals(m1.get(i, j), loadTest.get(i, j));
-      }
-    }
-
-    assertEquals(path1, loadTest.getPath());
-    // close loadTest, it just disconnect to the table but didn't delete it.
-    loadTest.close();
-
-    // try to close m1 & load matrix m1 using aliase1 again.
-    m1.close();
-    DenseMatrix loadTest2 = new DenseMatrix(conf, aliase1, false);
-    assertEquals(path1, loadTest2.getPath());
-    // remove aliase1
-    // because loadTest2 connect the aliase1, so we just remove aliase entry
-    // but didn't delete the table.
-    hamaAdmin.delete(aliase1);
-    assertEquals(true, admin.tableExists(path1));
-    // close loadTest2, because it is the last one who reference table 'path1'
-    // it will do the gc!
-    loadTest2.close();
-    assertEquals(false, admin.tableExists(path1));
-
-    // if we try to load non-existed matrix using aliase name, it should fail.
-    DenseMatrix loadTest3 = null;
-    try {
-      loadTest3 = new DenseMatrix(conf, aliase1, false);
-      fail("Try to load a non-existed matrix should fail!");
-    } catch (IOException e) {
-
-    } finally {
-      if (loadTest3 != null)
-        loadTest3.close();
-    }
-  }
-
-  public void testForceCreate() throws IOException {
-    String path2 = m2.getPath();
-    // save m2 to aliase2
-    m2.save(aliase2);
-    // load matrix m2 using aliase2
-    DenseMatrix loadTest = new DenseMatrix(conf, aliase2, false);
-
-    for (int i = 0; i < loadTest.getRows(); i++) {
-      for (int j = 0; j < loadTest.getColumns(); j++) {
-        assertEquals(m2.get(i, j), loadTest.get(i, j));
-      }
-    }
-
-    assertEquals(path2, loadTest.getPath());
-
-    // force to create matrix loadTest2 using aliasename 'aliase2'
-    DenseMatrix loadTest2 = new DenseMatrix(conf, aliase2, true);
-    String loadPath2 = loadTest2.getPath();
-    assertFalse(path2.equals(loadPath2));
-    assertEquals(loadPath2, hamaAdmin.getPath(aliase2));
-    assertFalse(path2.equals(hamaAdmin.getPath(aliase2)));
-
-    // try to close m2 & loadTest, it table will be deleted finally
-    m2.close();
-    assertEquals(true, admin.tableExists(path2));
-    loadTest.close();
-    assertEquals(false, admin.tableExists(path2));
-
-    // remove 'aliase2' & close loadTest2
-    loadTest2.close();
-    assertEquals(true, admin.tableExists(loadPath2));
-    hamaAdmin.delete(aliase2);
-    assertEquals(false, admin.tableExists(loadPath2));
-  }
-
-  /**
-   * Verifying multiplication result
-   * 
-   * @param m1
-   * @param m2
-   * @param result
-   * @throws IOException
-   */
-  private void verifyMultResult(Matrix m1, Matrix m2, Matrix result)
-      throws IOException {
-    double[][] c = new double[SIZE][SIZE];
-
-    for (int i = 0; i < SIZE; i++) {
-      for (int j = 0; j < SIZE; j++) {
-        for (int k = 0; k < SIZE; k++) {
-          c[i][k] += m1.get(i, j) * m2.get(j, k);
-        }
-      }
-    }
-
-    for (int i = 0; i < SIZE; i++) {
-      for (int j = 0; j < SIZE; j++) {
-        double gap = (c[i][j] - result.get(i, j));
-        assertTrue(gap < 0.000001 || gap < -0.000001);
-      }
-    }
-  }
-}
+/**
+ * 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 java.util.Iterator;
+
+import junit.extensions.TestSetup;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.apache.hadoop.hbase.client.HBaseAdmin;
+import org.apache.hadoop.io.Writable;
+import org.apache.hama.io.DoubleEntry;
+import org.apache.hama.util.RandomVariable;
+import org.apache.log4j.Logger;
+
+/**
+ * Matrix test
+ */
+public class TestDenseMatrix extends TestCase {
+  static final Logger LOG = Logger.getLogger(TestDenseMatrix.class);
+  private static int SIZE = 10;
+  private static Matrix m1;
+  private static Matrix m2;
+  private final static String aliase1 = "matrix_aliase_A";
+  private final static String aliase2 = "matrix_aliase_B";
+  private static HamaConfiguration conf;
+  private static HBaseAdmin admin;
+  private static HamaAdmin hamaAdmin;
+
+  public static Test suite() {
+    TestSetup setup = new TestSetup(new TestSuite(TestDenseMatrix.class)) {
+      protected void setUp() throws Exception {
+        HCluster hCluster = new HCluster();
+        hCluster.setUp();
+
+        conf = hCluster.getConf();
+        admin = new HBaseAdmin(conf);
+        hamaAdmin = new HamaAdminImpl(conf, admin);
+
+        m1 = DenseMatrix.random(hCluster.getConf(), SIZE, SIZE);
+        m2 = DenseMatrix.random(hCluster.getConf(), SIZE, SIZE);
+      }
+
+      protected void tearDown() {
+        try {
+          closeTest();
+        } catch (IOException e) {
+          e.printStackTrace();
+        }
+      }
+    };
+    return setup;
+  }
+
+  public static void closeTest() throws IOException {
+    m1.close();
+    m2.close();
+  }
+
+  public void testEntryAdd() throws IOException {
+    double origin = m1.get(1, 1);
+    m1.add(1, 1, 0.5);
+
+    assertEquals(m1.get(1, 1), origin + 0.5);
+  }
+
+  /**
+   * Column vector test.
+   * 
+   * @param rand
+   * @throws IOException
+   */
+  public void testGetColumn() throws IOException {
+    Vector v = m1.getColumn(0);
+    Iterator<Writable> it = v.iterator();
+    int x = 0;
+    while (it.hasNext()) {
+      assertEquals(m1.get(x, 0), ((DoubleEntry) it.next()).getValue());
+      x++;
+    }
+  }
+
+  public void testGetSetAttribute() throws IOException {
+    m1.setRowLabel(0, "row1");
+    assertEquals(m1.getRowLabel(0), "row1");
+    assertEquals(m1.getRowLabel(1), null);
+
+    m1.setColumnLabel(0, "column1");
+    assertEquals(m1.getColumnLabel(0), "column1");
+    assertEquals(m1.getColumnLabel(1), null);
+  }
+
+  public void testSubMatrix() throws IOException {
+    SubMatrix a = m1.subMatrix(2, 4, 2, 5); // A : 3 * 4
+    for (int i = 0; i < a.getRows(); i++) {
+      for (int j = 0; j < a.getColumns(); j++) {
+        assertEquals(a.get(i, j), m1.get(i + 2, j + 2));
+      }
+    }
+
+    SubMatrix b = m2.subMatrix(0, 3, 0, 2); // B : 4 * 3
+    SubMatrix c = a.mult(b);
+
+    double[][] C = new double[3][3]; // A * B
+    for (int i = 0; i < 3; i++) {
+      for (int j = 0; j < 3; j++) {
+        for (int k = 0; k < 4; k++) {
+          C[i][j] += m1.get(i + 2, k + 2) * m2.get(k, j);
+        }
+      }
+    }
+
+    for (int i = 0; i < 3; i++) {
+      for (int j = 0; j < 3; j++) {
+        assertEquals(C[i][j], c.get(i, j));
+      }
+    }
+  }
+
+  /**
+   * Test matrices addition
+   * 
+   * @throws IOException
+   */
+  public void testMatrixAdd() throws IOException {
+    Matrix result = m1.add(m2);
+
+    assertEquals(result.getRows(), SIZE);
+    assertEquals(result.getColumns(), SIZE);
+
+    for (int i = 0; i < SIZE; i++) {
+      for (int j = 0; j < SIZE; j++) {
+        assertEquals(result.get(i, j), m1.get(i, j) + m2.get(i, j));
+      }
+    }
+  }
+
+  /**
+   * Test matrices multiplication
+   * 
+   * @throws IOException
+   */
+  public void testMatrixMult() throws IOException {
+    Matrix result = m1.mult(m2);
+
+    assertEquals(result.getRows(), SIZE);
+    assertEquals(result.getColumns(), SIZE);
+
+    verifyMultResult(m1, m2, result);
+  }
+
+  public void testSetMatrix() throws IOException {
+    Matrix a = new DenseMatrix(conf);
+    a.set(m1);
+
+    for (int i = 0; i < 5; i++) {
+      int x = RandomVariable.randInt(0, 10);
+      int y = RandomVariable.randInt(0, 10);
+      assertEquals(a.get(x, y), m1.get(x, y));
+    }
+  }
+
+  public void testSetAlphaMatrix() throws IOException {
+    Matrix a = new DenseMatrix(conf);
+    a.set(0.5, m1);
+    
+    for (int i = 0; i < 5; i++) {
+      int x = RandomVariable.randInt(0, 10);
+      int y = RandomVariable.randInt(0, 10);
+      assertEquals(a.get(x, y), (m1.get(x, y) * 0.5));
+    }
+  }
+  
+  public void testAddAlphaMatrix() throws IOException {
+    double value = m1.get(0, 0) + (m2.get(0, 0) * 0.1);
+    Matrix result = m1.add(0.1, m2);
+    assertEquals(value, result.get(0, 0));
+  }
+  
+  public void testSetRow() throws IOException {
+    Vector v = new DenseVector();
+    double[] entries = new double[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 0 };
+
+    for (int i = 0; i < SIZE; i++) {
+      v.set(i, entries[i]);
+    }
+
+    m1.setRow(SIZE + 1, v);
+    Iterator<Writable> it = m1.getRow(SIZE + 1).iterator();
+
+    int i = 0;
+    while (it.hasNext()) {
+      assertEquals(entries[i], ((DoubleEntry) it.next()).getValue());
+      i++;
+    }
+  }
+
+  public void testSetColumn() throws IOException {
+    Vector v = new DenseVector();
+    double[] entries = new double[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 0 };
+
+    for (int i = 0; i < SIZE; i++) {
+      v.set(i, entries[i]);
+    }
+
+    m1.setColumn(SIZE + 1, v);
+    Iterator<Writable> it = m1.getColumn(SIZE + 1).iterator();
+
+    int i = 0;
+    while (it.hasNext()) {
+      assertEquals(entries[i], ((DoubleEntry) it.next()).getValue());
+      i++;
+    }
+  }
+
+  public void testLoadSave() throws IOException {
+    String path1 = m1.getPath();
+    // save m1 to aliase1
+    m1.save(aliase1);
+    // load matrix m1 using aliase1
+    DenseMatrix loadTest = new DenseMatrix(conf, aliase1, false);
+
+    for (int i = 0; i < loadTest.getRows(); i++) {
+      for (int j = 0; j < loadTest.getColumns(); j++) {
+        assertEquals(m1.get(i, j), loadTest.get(i, j));
+      }
+    }
+
+    assertEquals(path1, loadTest.getPath());
+    // close loadTest, it just disconnect to the table but didn't delete it.
+    loadTest.close();
+
+    // try to close m1 & load matrix m1 using aliase1 again.
+    m1.close();
+    DenseMatrix loadTest2 = new DenseMatrix(conf, aliase1, false);
+    assertEquals(path1, loadTest2.getPath());
+    // remove aliase1
+    // because loadTest2 connect the aliase1, so we just remove aliase entry
+    // but didn't delete the table.
+    hamaAdmin.delete(aliase1);
+    assertEquals(true, admin.tableExists(path1));
+    // close loadTest2, because it is the last one who reference table 'path1'
+    // it will do the gc!
+    loadTest2.close();
+    assertEquals(false, admin.tableExists(path1));
+
+    // if we try to load non-existed matrix using aliase name, it should fail.
+    DenseMatrix loadTest3 = null;
+    try {
+      loadTest3 = new DenseMatrix(conf, aliase1, false);
+      fail("Try to load a non-existed matrix should fail!");
+    } catch (IOException e) {
+
+    } finally {
+      if (loadTest3 != null)
+        loadTest3.close();
+    }
+  }
+
+  public void testForceCreate() throws IOException {
+    String path2 = m2.getPath();
+    // save m2 to aliase2
+    m2.save(aliase2);
+    // load matrix m2 using aliase2
+    DenseMatrix loadTest = new DenseMatrix(conf, aliase2, false);
+
+    for (int i = 0; i < loadTest.getRows(); i++) {
+      for (int j = 0; j < loadTest.getColumns(); j++) {
+        assertEquals(m2.get(i, j), loadTest.get(i, j));
+      }
+    }
+
+    assertEquals(path2, loadTest.getPath());
+
+    // force to create matrix loadTest2 using aliasename 'aliase2'
+    DenseMatrix loadTest2 = new DenseMatrix(conf, aliase2, true);
+    String loadPath2 = loadTest2.getPath();
+    assertFalse(path2.equals(loadPath2));
+    assertEquals(loadPath2, hamaAdmin.getPath(aliase2));
+    assertFalse(path2.equals(hamaAdmin.getPath(aliase2)));
+
+    // try to close m2 & loadTest, it table will be deleted finally
+    m2.close();
+    assertEquals(true, admin.tableExists(path2));
+    loadTest.close();
+    assertEquals(false, admin.tableExists(path2));
+
+    // remove 'aliase2' & close loadTest2
+    loadTest2.close();
+    assertEquals(true, admin.tableExists(loadPath2));
+    hamaAdmin.delete(aliase2);
+    assertEquals(false, admin.tableExists(loadPath2));
+  }
+
+  /**
+   * Verifying multiplication result
+   * 
+   * @param m1
+   * @param m2
+   * @param result
+   * @throws IOException
+   */
+  private void verifyMultResult(Matrix m1, Matrix m2, Matrix result)
+      throws IOException {
+    double[][] c = new double[SIZE][SIZE];
+
+    for (int i = 0; i < SIZE; i++) {
+      for (int j = 0; j < SIZE; j++) {
+        for (int k = 0; k < SIZE; k++) {
+          c[i][k] += m1.get(i, j) * m2.get(j, k);
+        }
+      }
+    }
+
+    for (int i = 0; i < SIZE; i++) {
+      for (int j = 0; j < SIZE; j++) {
+        double gap = (c[i][j] - result.get(i, j));
+        assertTrue(gap < 0.000001 || gap < -0.000001);
+      }
+    }
+  }
+}

Modified: incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java Mon Feb 16 04:35:23 2009
@@ -1,158 +1,159 @@
-/**
- * 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 java.util.Iterator;
-
-import junit.extensions.TestSetup;
-import junit.framework.Test;
-import junit.framework.TestCase;
-import junit.framework.TestSuite;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.hama.io.DoubleEntry;
-
-public class TestDenseVector extends TestCase {
-  final static Log LOG = LogFactory.getLog(TestDenseVector.class.getName());
-  
-  private static final double cosine = 0.6978227007909176;
-  private static final double norm1 = 12.0;
-  private static final double norm2 = 6.782329983125268;
-  private static double[][] values = { { 2, 5, 1, 4 }, { 4, 1, 3, 3 } };
-  private static Matrix m1;
-  private static Vector v1;
-  private static Vector v2;
-
-  public static Test suite() {
-    TestSetup setup = new TestSetup(new TestSuite(TestDenseVector.class)) {
-      protected void setUp() throws Exception {
-        HCluster hCluster = new HCluster();
-        hCluster.setUp();
-
-        m1 = new DenseMatrix(hCluster.getConf());
-
-        for (int i = 0; i < 2; i++)
-          for (int j = 0; j < 4; j++)
-            m1.set(i, j, values[i][j]);
-
-        v1 = m1.getRow(0);
-        v2 = m1.getRow(1);
-      }
-
-      protected void tearDown() {
-        LOG.info("tearDown()");
-      }
-    };
-    return setup;
-  }
-
-  /**
-   * Test |a| dot |b|
-   */
-  public void testDot() {
-    double cos = v1.dot(v2);
-    assertEquals(cos, cosine);
-  }
-
-  public void testSubVector() {
-    int start = 2;
-    Vector subVector = v1.subVector(start, v1.size() - 1);
-    Iterator<DoubleEntry> it = subVector.iterator();
-
-    int i = start;
-    while (it.hasNext()) {
-      assertEquals(v1.get(i), it.next().getValue());
-      i++;
-    }
-  }
-
-  /**
-   * Test norm one
-   */
-  public void testNom1() {
-    double result = ((DenseVector) v1).getNorm1();
-    assertEquals(norm1, result);
-  }
-
-  /**
-   * Test norm two
-   */
-  public void testNom2() {
-    double result = ((DenseVector) v1).getNorm2();
-    assertEquals(norm2, result);
-  }
-
-  /**
-   * Test scaling
-   */
-  public void scalingTest() {
-    v2.scale(0.5);
-
-    for (int i = 0; i < v2.size(); i++) {
-      assertEquals(values[1][i] * 0.5, v2.get(i));
-    }
-  }
-
-  /**
-   * Test get/set methods
-   * @throws IOException 
-   */
-  public void testGetSet() throws IOException {
-    assertEquals(v1.get(0), values[0][0]);
-    assertEquals(m1.getColumn(0).size(), 2);
-  }
-
-  /**
-   * Test add()
-   */
-  public void testAdd() {
-    v1.add(v2);
-    int i = 0;
-    Iterator<DoubleEntry> it = v1.iterator();
-    while (it.hasNext()) {
-      DoubleEntry c = it.next();
-      assertEquals(c.getValue(), values[0][i] + values[1][i]);
-      i++;
-    }
-
-    v1.add(0.5, v2);
-    int j = 0;
-    Iterator<DoubleEntry> itt = v1.iterator();
-    while (itt.hasNext()) {
-      DoubleEntry c = itt.next();
-      assertEquals(c.getValue(), (values[0][j] + values[1][j]) + (0.5 * values[1][j]));
-      j++;
-    }
-    
-    double old = v1.get(0);
-    v1.add(0, norm1);
-    assertEquals(v1.get(0), old + norm1);
-  }
-  
-  /**
-   * Clear test
-   */
-  public void testClear() {
-    ((DenseVector) v1).clear();
-    assertEquals(v1.size(), 0);
-  }
-}
+/**
+ * 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 java.util.Iterator;
+
+import junit.extensions.TestSetup;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.io.Writable;
+import org.apache.hama.io.DoubleEntry;
+
+public class TestDenseVector extends TestCase {
+  final static Log LOG = LogFactory.getLog(TestDenseVector.class.getName());
+  
+  private static final double cosine = 0.6978227007909176;
+  private static final double norm1 = 12.0;
+  private static final double norm2 = 6.782329983125268;
+  private static double[][] values = { { 2, 5, 1, 4 }, { 4, 1, 3, 3 } };
+  private static Matrix m1;
+  private static Vector v1;
+  private static Vector v2;
+
+  public static Test suite() {
+    TestSetup setup = new TestSetup(new TestSuite(TestDenseVector.class)) {
+      protected void setUp() throws Exception {
+        HCluster hCluster = new HCluster();
+        hCluster.setUp();
+
+        m1 = new DenseMatrix(hCluster.getConf());
+
+        for (int i = 0; i < 2; i++)
+          for (int j = 0; j < 4; j++)
+            m1.set(i, j, values[i][j]);
+
+        v1 = m1.getRow(0);
+        v2 = m1.getRow(1);
+      }
+
+      protected void tearDown() {
+        LOG.info("tearDown()");
+      }
+    };
+    return setup;
+  }
+
+  /**
+   * Test |a| dot |b|
+   */
+  public void testDot() {
+    double cos = v1.dot(v2);
+    assertEquals(cos, cosine);
+  }
+
+  public void testSubVector() {
+    int start = 2;
+    Vector subVector = v1.subVector(start, v1.size() - 1);
+    Iterator<Writable> it = subVector.iterator();
+
+    int i = start;
+    while (it.hasNext()) {
+      assertEquals(v1.get(i), ((DoubleEntry) it.next()).getValue());
+      i++;
+    }
+  }
+
+  /**
+   * Test norm one
+   */
+  public void testNom1() {
+    double result = ((DenseVector) v1).getNorm1();
+    assertEquals(norm1, result);
+  }
+
+  /**
+   * Test norm two
+   */
+  public void testNom2() {
+    double result = ((DenseVector) v1).getNorm2();
+    assertEquals(norm2, result);
+  }
+
+  /**
+   * Test scaling
+   */
+  public void scalingTest() {
+    v2.scale(0.5);
+
+    for (int i = 0; i < v2.size(); i++) {
+      assertEquals(values[1][i] * 0.5, v2.get(i));
+    }
+  }
+
+  /**
+   * Test get/set methods
+   * @throws IOException 
+   */
+  public void testGetSet() throws IOException {
+    assertEquals(v1.get(0), values[0][0]);
+    assertEquals(m1.getColumn(0).size(), 2);
+  }
+
+  /**
+   * Test add()
+   */
+  public void testAdd() {
+    v1.add(v2);
+    int i = 0;
+    Iterator<Writable> it = v1.iterator();
+    while (it.hasNext()) {
+      DoubleEntry c = (DoubleEntry) it.next();
+      assertEquals(c.getValue(), values[0][i] + values[1][i]);
+      i++;
+    }
+
+    v1.add(0.5, v2);
+    int j = 0;
+    Iterator<Writable> itt = v1.iterator();
+    while (itt.hasNext()) {
+      DoubleEntry c = (DoubleEntry) itt.next();
+      assertEquals(c.getValue(), (values[0][j] + values[1][j]) + (0.5 * values[1][j]));
+      j++;
+    }
+    
+    double old = v1.get(0);
+    v1.add(0, norm1);
+    assertEquals(v1.get(0), old + norm1);
+  }
+  
+  /**
+   * Clear test
+   */
+  public void testClear() {
+    ((DenseVector) v1).clear();
+    assertEquals(v1.size(), 0);
+  }
+}

Modified: incubator/hama/trunk/src/test/org/apache/hama/examples/TestFileMatrixBlockMult.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/examples/TestFileMatrixBlockMult.java?rev=744798&r1=744797&r2=744798&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/examples/TestFileMatrixBlockMult.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/examples/TestFileMatrixBlockMult.java Mon Feb 16 04:35:23 2009
@@ -51,7 +51,6 @@
 import org.apache.hama.algebra.BlockMultiplyReduce;
 import org.apache.hama.io.BlockID;
 import org.apache.hama.io.BlockWritable;
-import org.apache.hama.io.VectorWritable;
 import org.apache.hama.mapred.CollectBlocksMap;
 import org.apache.hama.mapred.CollectBlocksMapReduceBase;
 import org.apache.hama.util.JobManager;
@@ -175,33 +174,31 @@
 
     @Override
     public void map(IntWritable key, MapWritable value,
-        OutputCollector<BlockID, VectorWritable> output, Reporter reporter)
+        OutputCollector<BlockID, MapWritable> output, Reporter reporter)
         throws IOException {
-      int startColumn;
-      int endColumn;
-      int blkRow = key.get() / mBlockRowSize;
+      int startColumn, endColumn, blkRow = key.get() / mBlockRowSize, i = 0;
       this.value = value;
-
-      int i = 0;
+      
       do {
         startColumn = i * mBlockColSize;
         endColumn = startColumn + mBlockColSize - 1;
         if (endColumn >= mColumns) // the last sub vector
           endColumn = mColumns - 1;
-        output.collect(new BlockID(blkRow, i), new VectorWritable(key.get(),
-            subVector(startColumn, endColumn)));
+        output.collect(new BlockID(blkRow, i), subVector(key.get(), startColumn, endColumn));
 
         i++;
       } while (endColumn < (mColumns - 1));
     }
 
-    private DenseVector subVector(int i0, int i1) {
+    private MapWritable subVector(int row, int i0, int i1) {
       DenseVector res = new DenseVector();
+      res.setRow(row);
+      
       for (int i = i0; i <= i1; i++) {
         res.set(i, ((DoubleWritable) this.value.get(new IntWritable(i))).get());
       }
 
-      return res;
+      return res.getEntries();
     }
   }
 }

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=744798&r1=744797&r2=744798&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 Feb 16 04:35:23 2009
@@ -1,79 +1,79 @@
-/**
- * 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.io.IntWritable;
-import org.apache.hadoop.mapred.JobClient;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hama.DenseMatrix;
-import org.apache.hama.HCluster;
-import org.apache.hama.Matrix;
-import org.apache.hama.algebra.RowCyclicAdditionMap;
-import org.apache.hama.algebra.RowCyclicAdditionReduce;
-import org.apache.hama.io.VectorWritable;
-import org.apache.log4j.Logger;
-
-/**
- * Test Matrix Map/Reduce job
- */
-public class TestMatrixMapReduce extends HCluster {
-  static final Logger LOG = Logger.getLogger(TestMatrixMapReduce.class);
-  
-  /** constructor */
-  public TestMatrixMapReduce() {
-    super();
-  }
-
-  public void testMatrixMapReduce() throws IOException {
-    Matrix matrixA = new DenseMatrix(conf);
-    matrixA.set(0, 0, 1);
-    matrixA.set(0, 1, 0);
-    matrixA.setDimension(1, 2);
-
-    Matrix matrixB = new DenseMatrix(conf);
-    matrixB.set(0, 0, 1);
-    matrixB.set(0, 1, 1);
-    matrixB.setDimension(1, 2);
-    
-    miniMRJob(matrixA.getPath(), matrixB.getPath());
-  }
-
-  private void miniMRJob(String string, String string2) throws IOException {
-    Matrix c = new DenseMatrix(conf);
-    String output = c.getPath();
-    
-    JobConf jobConf = new JobConf(conf, TestMatrixMapReduce.class);
-    jobConf.setJobName("test MR job");
-
-    RowCyclicAdditionMap.initJob(string, string2, RowCyclicAdditionMap.class, IntWritable.class,
-        VectorWritable.class, jobConf);
-    RowCyclicAdditionReduce.initJob(output, RowCyclicAdditionReduce.class, jobConf);
-
-    jobConf.setNumMapTasks(2);
-    jobConf.setNumReduceTasks(2);
-
-    JobClient.runJob(jobConf);
-
-    assertEquals(c.get(0, 0), 2.0);
-    assertEquals(c.get(0, 1), 1.0);
-  }
-}
+/**
+ * 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.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.mapred.JobClient;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hama.DenseMatrix;
+import org.apache.hama.HCluster;
+import org.apache.hama.Matrix;
+import org.apache.hama.algebra.RowCyclicAdditionMap;
+import org.apache.hama.algebra.RowCyclicAdditionReduce;
+import org.apache.log4j.Logger;
+
+/**
+ * Test Matrix Map/Reduce job
+ */
+public class TestMatrixMapReduce extends HCluster {
+  static final Logger LOG = Logger.getLogger(TestMatrixMapReduce.class);
+  
+  /** constructor */
+  public TestMatrixMapReduce() {
+    super();
+  }
+
+  public void testMatrixMapReduce() throws IOException {
+    Matrix matrixA = new DenseMatrix(conf);
+    matrixA.set(0, 0, 1);
+    matrixA.set(0, 1, 0);
+    matrixA.setDimension(1, 2);
+
+    Matrix matrixB = new DenseMatrix(conf);
+    matrixB.set(0, 0, 1);
+    matrixB.set(0, 1, 1);
+    matrixB.setDimension(1, 2);
+    
+    miniMRJob(matrixA.getPath(), matrixB.getPath());
+  }
+
+  private void miniMRJob(String string, String string2) throws IOException {
+    Matrix c = new DenseMatrix(conf);
+    String output = c.getPath();
+    
+    JobConf jobConf = new JobConf(conf, TestMatrixMapReduce.class);
+    jobConf.setJobName("test MR job");
+
+    RowCyclicAdditionMap.initJob(string, string2, RowCyclicAdditionMap.class, IntWritable.class,
+        MapWritable.class, jobConf);
+    RowCyclicAdditionReduce.initJob(output, RowCyclicAdditionReduce.class, jobConf);
+
+    jobConf.setNumMapTasks(2);
+    jobConf.setNumReduceTasks(2);
+
+    JobClient.runJob(jobConf);
+
+    assertEquals(c.get(0, 0), 2.0);
+    assertEquals(c.get(0, 1), 1.0);
+  }
+}



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