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Posted to commits@mahout.apache.org by sr...@apache.org on 2009/11/29 12:20:11 UTC

svn commit: r885213 [3/6] - in /lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout: jet/math/ jet/random/ jet/random/engine/ jet/random/sampling/ jet/stat/ jet/stat/quantile/ matrix/ matrix/bitvector/ matrix/buffer/ matrix/list/ matrix/list/ada...

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractFloatList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractFloatList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractFloatList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractFloatList.java Sun Nov 29 11:19:58 2009
@@ -8,11 +8,15 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
+import org.apache.mahout.matrix.Sorting;
 import org.apache.mahout.matrix.function.FloatComparator;
 import org.apache.mahout.matrix.function.FloatProcedure;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 /**
@@ -417,7 +421,7 @@
     checkRangeFromTo(from, to, mySize);
 
     float[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1);
+    Sorting.mergeSort(myElements, from, to + 1);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -448,7 +452,7 @@
     checkRangeFromTo(from, to, mySize);
 
     float[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1, c);
+    Sorting.mergeSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -522,7 +526,7 @@
     checkRangeFromTo(from, to, mySize);
 
     float[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.quickSort(myElements, from, to + 1, c);
+    Sorting.quickSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -620,32 +624,41 @@
    * @param otherTo   the last element of the other list (inclusive)
    *
    *                  <p><b>Examples:</b><pre>
-   *                                                    a=[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    b=[50, 60, 70, 80, 90]
-   *                                                    a.R(...)=a.replaceFromToWithFromTo(...)
-   *
-   *                                                    a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90, 6, 7]
-   *                                                    a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
-   *                                                    a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
-   *                                                    a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
-   *                                                    a.R(1,6,b,1,2)-->[0, 60, 70, 7]
-   *                                                    a.R(0,6,b,1,2)-->[60, 70, 7]
-   *                                                    a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *                                                    a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *
-   *                                                    Extreme cases:
-   *                                                    a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
-   *                                                    a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
-   *                                                    a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
-   *                                                    a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
-   *                                                    a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4]
-   *                                                    </pre>
+   *                                                                     a=[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     b=[50, 60, 70, 80, 90]
+   *                                                                     a.R(...)=a.replaceFromToWithFromTo(...)
+   *
+   *                                                                     a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90,
+   *                  6, 7]
+   *                                                                     a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
+   *                                                                     a.R(1,6,b,1,2)-->[0, 60, 70, 7]
+   *                                                                     a.R(0,6,b,1,2)-->[60, 70, 7]
+   *                                                                     a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *                                                                     a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *
+   *                                                                     Extreme cases:
+   *                                                                     a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
+   *                                                                     a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
+   *                                                                     a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
+   *                                                                     a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
+   *                                                                     a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4,
+   *                  5, 6, 7]
+   *                                                                     a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2,
+   *                  3, 4, 5, 6, 7]
+   *                                                                     a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3,
+   *                  4, 5, 6, 7]
+   *                                                                     a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1,
+   *                  2, 3, 4]
+   *                                                                     </pre>
    */
   public void replaceFromToWithFromTo(int from, int to, AbstractFloatList other, int otherFrom, int otherTo) {
     if (otherFrom > otherTo) {
@@ -795,8 +808,7 @@
   public void shuffleFromTo(int from, int to) {
     checkRangeFromTo(from, to, size());
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);
 

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractIntList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractIntList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractIntList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractIntList.java Sun Nov 29 11:19:58 2009
@@ -8,11 +8,15 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
+import org.apache.mahout.matrix.Sorting;
 import org.apache.mahout.matrix.function.IntComparator;
 import org.apache.mahout.matrix.function.IntProcedure;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 /**
@@ -428,7 +432,7 @@
     checkRangeFromTo(from, to, mySize);
 
     int[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1);
+    Sorting.mergeSort(myElements, from, to + 1);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -459,7 +463,7 @@
     checkRangeFromTo(from, to, mySize);
 
     int[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1, c);
+    Sorting.mergeSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -534,7 +538,7 @@
     checkRangeFromTo(from, to, mySize);
 
     int[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.quickSort(myElements, from, to + 1, c);
+    Sorting.quickSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -632,32 +636,41 @@
    * @param otherTo   the last element of the other list (inclusive)
    *
    *                  <p><b>Examples:</b><pre>
-   *                                                    a=[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    b=[50, 60, 70, 80, 90]
-   *                                                    a.R(...)=a.replaceFromToWithFromTo(...)
-   *
-   *                                                    a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90, 6, 7]
-   *                                                    a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
-   *                                                    a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
-   *                                                    a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
-   *                                                    a.R(1,6,b,1,2)-->[0, 60, 70, 7]
-   *                                                    a.R(0,6,b,1,2)-->[60, 70, 7]
-   *                                                    a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *                                                    a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *
-   *                                                    Extreme cases:
-   *                                                    a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
-   *                                                    a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
-   *                                                    a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
-   *                                                    a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
-   *                                                    a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4]
-   *                                                    </pre>
+   *                                                                     a=[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     b=[50, 60, 70, 80, 90]
+   *                                                                     a.R(...)=a.replaceFromToWithFromTo(...)
+   *
+   *                                                                     a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90,
+   *                  6, 7]
+   *                                                                     a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
+   *                                                                     a.R(1,6,b,1,2)-->[0, 60, 70, 7]
+   *                                                                     a.R(0,6,b,1,2)-->[60, 70, 7]
+   *                                                                     a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *                                                                     a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *
+   *                                                                     Extreme cases:
+   *                                                                     a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
+   *                                                                     a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
+   *                                                                     a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
+   *                                                                     a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
+   *                                                                     a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4,
+   *                  5, 6, 7]
+   *                                                                     a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2,
+   *                  3, 4, 5, 6, 7]
+   *                                                                     a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3,
+   *                  4, 5, 6, 7]
+   *                                                                     a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1,
+   *                  2, 3, 4]
+   *                                                                     </pre>
    */
   public void replaceFromToWithFromTo(int from, int to, AbstractIntList other, int otherFrom, int otherTo) {
     if (otherFrom > otherTo) {
@@ -807,8 +820,7 @@
   public void shuffleFromTo(int from, int to) {
     checkRangeFromTo(from, to, size());
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);
 

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractLongList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractLongList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractLongList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractLongList.java Sun Nov 29 11:19:58 2009
@@ -8,11 +8,15 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
+import org.apache.mahout.matrix.Sorting;
 import org.apache.mahout.matrix.function.LongComparator;
 import org.apache.mahout.matrix.function.LongProcedure;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 /**
@@ -417,7 +421,7 @@
     checkRangeFromTo(from, to, mySize);
 
     long[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1);
+    Sorting.mergeSort(myElements, from, to + 1);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -448,7 +452,7 @@
     checkRangeFromTo(from, to, mySize);
 
     long[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1, c);
+    Sorting.mergeSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -522,7 +526,7 @@
     checkRangeFromTo(from, to, mySize);
 
     long[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.quickSort(myElements, from, to + 1, c);
+    Sorting.quickSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -620,32 +624,41 @@
    * @param otherTo   the last element of the other list (inclusive)
    *
    *                  <p><b>Examples:</b><pre>
-   *                                                    a=[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    b=[50, 60, 70, 80, 90]
-   *                                                    a.R(...)=a.replaceFromToWithFromTo(...)
-   *
-   *                                                    a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90, 6, 7]
-   *                                                    a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
-   *                                                    a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
-   *                                                    a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
-   *                                                    a.R(1,6,b,1,2)-->[0, 60, 70, 7]
-   *                                                    a.R(0,6,b,1,2)-->[60, 70, 7]
-   *                                                    a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *                                                    a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *
-   *                                                    Extreme cases:
-   *                                                    a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
-   *                                                    a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
-   *                                                    a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
-   *                                                    a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
-   *                                                    a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4]
-   *                                                    </pre>
+   *                                                                     a=[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     b=[50, 60, 70, 80, 90]
+   *                                                                     a.R(...)=a.replaceFromToWithFromTo(...)
+   *
+   *                                                                     a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90,
+   *                  6, 7]
+   *                                                                     a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
+   *                                                                     a.R(1,6,b,1,2)-->[0, 60, 70, 7]
+   *                                                                     a.R(0,6,b,1,2)-->[60, 70, 7]
+   *                                                                     a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *                                                                     a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *
+   *                                                                     Extreme cases:
+   *                                                                     a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
+   *                                                                     a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
+   *                                                                     a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
+   *                                                                     a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
+   *                                                                     a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4,
+   *                  5, 6, 7]
+   *                                                                     a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2,
+   *                  3, 4, 5, 6, 7]
+   *                                                                     a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3,
+   *                  4, 5, 6, 7]
+   *                                                                     a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1,
+   *                  2, 3, 4]
+   *                                                                     </pre>
    */
   public void replaceFromToWithFromTo(int from, int to, AbstractLongList other, int otherFrom, int otherTo) {
     if (otherFrom > otherTo) {
@@ -795,8 +808,7 @@
   public void shuffleFromTo(int from, int to) {
     checkRangeFromTo(from, to, size());
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);
 

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractShortList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractShortList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractShortList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/AbstractShortList.java Sun Nov 29 11:19:58 2009
@@ -8,11 +8,15 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
+import org.apache.mahout.matrix.Sorting;
 import org.apache.mahout.matrix.function.ShortComparator;
 import org.apache.mahout.matrix.function.ShortProcedure;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 /**
@@ -417,7 +421,7 @@
     checkRangeFromTo(from, to, mySize);
 
     short[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1);
+    Sorting.mergeSort(myElements, from, to + 1);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -448,7 +452,7 @@
     checkRangeFromTo(from, to, mySize);
 
     short[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.mergeSort(myElements, from, to + 1, c);
+    Sorting.mergeSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -522,7 +526,7 @@
     checkRangeFromTo(from, to, mySize);
 
     short[] myElements = elements();
-    org.apache.mahout.matrix.Sorting.quickSort(myElements, from, to + 1, c);
+    Sorting.quickSort(myElements, from, to + 1, c);
     elements(myElements);
     setSizeRaw(mySize);
   }
@@ -620,32 +624,41 @@
    * @param otherTo   the last element of the other list (inclusive)
    *
    *                  <p><b>Examples:</b><pre>
-   *                                                    a=[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    b=[50, 60, 70, 80, 90]
-   *                                                    a.R(...)=a.replaceFromToWithFromTo(...)
-   *
-   *                                                    a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90, 6, 7]
-   *                                                    a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
-   *                                                    a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
-   *                                                    a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
-   *                                                    a.R(1,6,b,1,2)-->[0, 60, 70, 7]
-   *                                                    a.R(0,6,b,1,2)-->[60, 70, 7]
-   *                                                    a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *                                                    a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *
-   *                                                    Extreme cases:
-   *                                                    a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
-   *                                                    a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
-   *                                                    a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
-   *                                                    a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
-   *                                                    a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4]
-   *                                                    </pre>
+   *                                                                     a=[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     b=[50, 60, 70, 80, 90]
+   *                                                                     a.R(...)=a.replaceFromToWithFromTo(...)
+   *
+   *                                                                     a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90,
+   *                  6, 7]
+   *                                                                     a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
+   *                                                                     a.R(1,6,b,1,2)-->[0, 60, 70, 7]
+   *                                                                     a.R(0,6,b,1,2)-->[60, 70, 7]
+   *                                                                     a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *                                                                     a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *
+   *                                                                     Extreme cases:
+   *                                                                     a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
+   *                                                                     a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
+   *                                                                     a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
+   *                                                                     a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
+   *                                                                     a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4,
+   *                  5, 6, 7]
+   *                                                                     a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2,
+   *                  3, 4, 5, 6, 7]
+   *                                                                     a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3,
+   *                  4, 5, 6, 7]
+   *                                                                     a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1,
+   *                  2, 3, 4]
+   *                                                                     </pre>
    */
   public void replaceFromToWithFromTo(int from, int to, AbstractShortList other, int otherFrom, int otherTo) {
     if (otherFrom > otherTo) {
@@ -795,8 +808,7 @@
   public void shuffleFromTo(int from, int to) {
     checkRangeFromTo(from, to, size());
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);
 

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/BooleanArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/BooleanArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/BooleanArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/BooleanArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.BooleanProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>boolean</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected boolean[] elements;
+  private boolean[] elements;
 
   /** Constructs an empty list. */
   public BooleanArrayList() {
@@ -579,8 +583,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     boolean[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ByteArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ByteArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ByteArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ByteArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.ByteProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>byte</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected byte[] elements;
+  private byte[] elements;
 
   /** Constructs an empty list. */
   public ByteArrayList() {
@@ -619,8 +623,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     byte[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/CharArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/CharArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/CharArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/CharArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.CharProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>char</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected char[] elements;
+  private char[] elements;
 
   /** Constructs an empty list. */
   public CharArrayList() {
@@ -580,8 +584,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     char[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DistinctNumberList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DistinctNumberList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DistinctNumberList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DistinctNumberList.java Sun Nov 29 11:19:58 2009
@@ -55,10 +55,10 @@
 
 /** @deprecated until unit tests are in place.  Until this time, this class/interface is unsupported. */
 @Deprecated
-public class DistinctNumberList extends org.apache.mahout.matrix.list.AbstractLongList {
+public class DistinctNumberList extends AbstractLongList {
 
-  protected long[] distinctValues;
-  protected MinMaxNumberList elements;
+  private long[] distinctValues;
+  private MinMaxNumberList elements;
 
   /**
    * Constructs an empty list with the specified initial capacity and the specified distinct values allowed to be hold

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DoubleArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DoubleArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DoubleArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/DoubleArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.DoubleProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>double</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected double[] elements;
+  private double[] elements;
 
   /** Constructs an empty list. */
   public DoubleArrayList() {
@@ -542,8 +546,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     double[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/FloatArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/FloatArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/FloatArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/FloatArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.FloatProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>float</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected float[] elements;
+  private float[] elements;
 
   /** Constructs an empty list. */
   public FloatArrayList() {
@@ -538,8 +542,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     float[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/IntArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/IntArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/IntArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/IntArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.IntProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>int</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected int[] elements;
+  private int[] elements;
 
   /** Constructs an empty list. */
   public IntArrayList() {
@@ -584,8 +588,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     int[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/LongArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/LongArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/LongArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/LongArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.LongProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>long</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected long[] elements;
+  private long[] elements;
 
   /** Constructs an empty list. */
   public LongArrayList() {
@@ -580,8 +584,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     long[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/MinMaxNumberList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/MinMaxNumberList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/MinMaxNumberList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/MinMaxNumberList.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,7 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.math.Arithmetic;
 import org.apache.mahout.matrix.bitvector.BitVector;
 import org.apache.mahout.matrix.bitvector.QuickBitVector;
 /**
@@ -136,7 +137,7 @@
   public static int bitsPerElement(long minimum, long maximum) {
     int bits;
     if (1 + maximum - minimum > 0) {
-      bits = (int) Math.round(Math.ceil(org.apache.mahout.jet.math.Arithmetic.log(2, 1 + maximum - minimum)));
+      bits = (int) Math.round(Math.ceil(Arithmetic.log(2, 1 + maximum - minimum)));
     } else {
       // overflow or underflow in calculating "1+maximum-minimum"
       // happens if signed long representation is too short for doing unsigned calculations
@@ -263,9 +264,7 @@
     this.size = 0;
   }
 
-  /**
-   * This method was created in VisualAge.
-   */
+  /** This method was created in VisualAge. */
   protected void setUpBitsPerEntry(long minimum, long maximum) {
     this.bitsPerElement = bitsPerElement(minimum, maximum);
     if (this.bitsPerElement != 64) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ObjectArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ObjectArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ObjectArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ObjectArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,12 +8,16 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
+import org.apache.mahout.matrix.Sorting;
 import org.apache.mahout.matrix.function.ObjectProcedure;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Comparator;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 /**
@@ -685,7 +689,7 @@
       return;
     }
     checkRangeFromTo(from, to, size);
-    org.apache.mahout.matrix.Sorting.quickSort(elements, from, to + 1);
+    Sorting.quickSort(elements, from, to + 1);
   }
 
   /**
@@ -713,7 +717,7 @@
       return;
     }
     checkRangeFromTo(from, to, size);
-    org.apache.mahout.matrix.Sorting.quickSort(elements, from, to + 1, c);
+    Sorting.quickSort(elements, from, to + 1, c);
   }
 
   /**
@@ -798,32 +802,41 @@
    * @param otherTo   the last element of the other list (inclusive)
    *
    *                  <p><b>Examples:</b><pre>
-   *                                                    a=[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    b=[50, 60, 70, 80, 90]
-   *                                                    a.R(...)=a.replaceFromToWithFromTo(...)
-   *
-   *                                                    a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90, 6, 7]
-   *                                                    a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
-   *                                                    a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
-   *                                                    a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
-   *                                                    a.R(1,6,b,1,2)-->[0, 60, 70, 7]
-   *                                                    a.R(0,6,b,1,2)-->[60, 70, 7]
-   *                                                    a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70, 80, 90, 5, 6, 7]
-   *                                                    a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *                                                    a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6, 7]
-   *
-   *                                                    Extreme cases:
-   *                                                    a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
-   *                                                    a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
-   *                                                    a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
-   *                                                    a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
-   *                                                    a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4, 5, 6, 7]
-   *                                                    a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3, 4]
-   *                                                    </pre>
+   *                                                                     a=[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     b=[50, 60, 70, 80, 90]
+   *                                                                     a.R(...)=a.replaceFromToWithFromTo(...)
+   *
+   *                                                                     a.R(3,5,b,0,4)-->[0, 1, 2, 50, 60, 70, 80, 90,
+   *                  6, 7]
+   *                                                                     a.R(1,6,b,0,4)-->[0, 50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(0,6,b,0,4)-->[50, 60, 70, 80, 90, 7]
+   *                                                                     a.R(3,5,b,1,2)-->[0, 1, 2, 60, 70, 6, 7]
+   *                                                                     a.R(1,6,b,1,2)-->[0, 60, 70, 7]
+   *                                                                     a.R(0,6,b,1,2)-->[60, 70, 7]
+   *                                                                     a.R(5,3,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,0,b,0,4)-->[0, 1, 2, 3, 4, 50, 60, 70,
+   *                  80, 90, 5, 6, 7]
+   *                                                                     a.R(5,3,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *                                                                     a.R(5,0,b,1,2)-->[0, 1, 2, 3, 4, 60, 70, 5, 6,
+   *                  7]
+   *
+   *                                                                     Extreme cases:
+   *                                                                     a.R(5,3,b,0,0)-->[0, 1, 2, 3, 4, 50, 5, 6, 7]
+   *                                                                     a.R(5,3,b,4,4)-->[0, 1, 2, 3, 4, 90, 5, 6, 7]
+   *                                                                     a.R(3,5,a,0,1)-->[0, 1, 2, 0, 1, 6, 7]
+   *                                                                     a.R(3,5,a,3,5)-->[0, 1, 2, 3, 4, 5, 6, 7]
+   *                                                                     a.R(3,5,a,4,4)-->[0, 1, 2, 4, 6, 7]
+   *                                                                     a.R(5,3,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3, 4,
+   *                  5, 6, 7]
+   *                                                                     a.R(0,-1,b,0,4)-->[50, 60, 70, 80, 90, 0, 1, 2,
+   *                  3, 4, 5, 6, 7]
+   *                                                                     a.R(0,-1,a,0,4)-->[0, 1, 2, 3, 4, 0, 1, 2, 3,
+   *                  4, 5, 6, 7]
+   *                                                                     a.R(8,0,a,0,4)-->[0, 1, 2, 3, 4, 5, 6, 7, 0, 1,
+   *                  2, 3, 4]
+   *                                                                     </pre>
    */
   public void replaceFromToWithFromTo(int from, int to, ObjectArrayList other, int otherFrom, int otherTo) {
     if (otherFrom > otherTo) {
@@ -969,8 +982,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     Object[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ShortArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ShortArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ShortArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/ShortArrayList.java Sun Nov 29 11:19:58 2009
@@ -8,7 +8,11 @@
 */
 package org.apache.mahout.matrix.list;
 
+import org.apache.mahout.jet.random.Uniform;
+import org.apache.mahout.jet.random.engine.DRand;
 import org.apache.mahout.matrix.function.ShortProcedure;
+
+import java.util.Date;
 /**
  Resizable list holding <code>short</code> elements; implemented with arrays.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -22,7 +26,7 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected short[] elements;
+  private short[] elements;
 
   /** Constructs an empty list. */
   public ShortArrayList() {
@@ -580,8 +584,7 @@
     }
     checkRangeFromTo(from, to, size);
 
-    org.apache.mahout.jet.random.Uniform gen =
-        new org.apache.mahout.jet.random.Uniform(new org.apache.mahout.jet.random.engine.DRand(new java.util.Date()));
+    Uniform gen = new Uniform(new DRand(new Date()));
     short[] theElements = elements;
     for (int i = from; i < to; i++) {
       int random = gen.nextIntFromTo(i, to);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/SimpleLongArrayList.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/SimpleLongArrayList.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/SimpleLongArrayList.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/SimpleLongArrayList.java Sun Nov 29 11:19:58 2009
@@ -21,10 +21,10 @@
    * The array buffer into which the elements of the list are stored. The capacity of the list is the length of this
    * array buffer.
    */
-  protected long[] elements;
+  private long[] elements;
 
   /** The size of the list. */
-  protected int size;
+  private int size;
 
   /** Constructs an empty list. */
   public SimpleLongArrayList() {
@@ -50,7 +50,7 @@
    * @param initialCapacity the number of elements the receiver can hold without auto-expanding itself by allocating new
    *                        internal memory.
    */
-  public SimpleLongArrayList(int initialCapacity) {
+  private SimpleLongArrayList(int initialCapacity) {
     super();
     if (initialCapacity < 0) {
       throw new IllegalArgumentException("Illegal Capacity: " + initialCapacity);

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/DoubleListAdapter.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/DoubleListAdapter.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/DoubleListAdapter.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/DoubleListAdapter.java Sun Nov 29 11:19:58 2009
@@ -24,7 +24,7 @@
 @Deprecated
 public class DoubleListAdapter extends AbstractList<Double> {
 
-  protected final AbstractDoubleList content;
+  private final AbstractDoubleList content;
 
   /** Constructs a list backed by the specified content list. */
   public DoubleListAdapter(AbstractDoubleList content) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/FloatListAdapter.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/FloatListAdapter.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/FloatListAdapter.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/FloatListAdapter.java Sun Nov 29 11:19:58 2009
@@ -24,7 +24,7 @@
 @Deprecated
 public class FloatListAdapter extends AbstractList<Float> {
 
-  protected final AbstractFloatList content;
+  private final AbstractFloatList content;
 
   /** Constructs a list backed by the specified content list. */
   public FloatListAdapter(AbstractFloatList content) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/IntListAdapter.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/IntListAdapter.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/IntListAdapter.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/IntListAdapter.java Sun Nov 29 11:19:58 2009
@@ -24,7 +24,7 @@
 @Deprecated
 public class IntListAdapter extends AbstractList<Integer> {
 
-  protected final AbstractIntList content;
+  private final AbstractIntList content;
 
   /** Constructs a list backed by the specified content list. */
   public IntListAdapter(AbstractIntList content) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/LongListAdapter.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/LongListAdapter.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/LongListAdapter.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/LongListAdapter.java Sun Nov 29 11:19:58 2009
@@ -24,7 +24,7 @@
 @Deprecated
 public class LongListAdapter extends AbstractList<Long> {
 
-  protected final AbstractLongList content;
+  private final AbstractLongList content;
 
   /** Constructs a list backed by the specified content list. */
   public LongListAdapter(AbstractLongList content) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/ObjectListAdapter.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/ObjectListAdapter.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/ObjectListAdapter.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/adapter/ObjectListAdapter.java Sun Nov 29 11:19:58 2009
@@ -20,7 +20,7 @@
 @Deprecated
 public class ObjectListAdapter extends AbstractList<Object> {
 
-  protected final ObjectArrayList content;
+  private final ObjectArrayList content;
 
   /** Constructs a list backed by the specified content list. */
   public ObjectListAdapter(ObjectArrayList content) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/package.html
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/package.html?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/package.html (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/list/package.html Sun Nov 29 11:19:58 2009
@@ -80,7 +80,7 @@
 <p>The classes for lists of a given value type are derived from a common abstract
   base class tagged <tt>Abstract&lt;ElementType&gt;</tt><tt>List</tt>. For example,
   all lists operating on <tt>double</tt> elements are derived from {@link
-  org.apache.mahout.matrix.list.AbstractDoubleList},
+  AbstractDoubleList},
   which in turn is derived from an abstract base class tying together all lists
   regardless of value type, {@link org.apache.mahout.matrix.list.AbstractList}, which finally
   is rooted in grandmother {@link org.apache.mahout.matrix.list.AbstractCollection}. The abstract

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractDoubleIntMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractDoubleIntMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractDoubleIntMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractDoubleIntMap.java Sun Nov 29 11:19:58 2009
@@ -8,8 +8,11 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.matrix.GenericSorting;
+import org.apache.mahout.matrix.Swapper;
 import org.apache.mahout.matrix.function.DoubleIntProcedure;
 import org.apache.mahout.matrix.function.DoubleProcedure;
+import org.apache.mahout.matrix.function.IntComparator;
 import org.apache.mahout.matrix.list.DoubleArrayList;
 import org.apache.mahout.matrix.list.IntArrayList;
 /**
@@ -302,40 +305,12 @@
    * @param valueList the list to be filled with values, can have any size.
    */
   public void pairsSortedByKey(DoubleArrayList keyList, IntArrayList valueList) {
-    /*
-    keys(keyList);
-    values(valueList);
-
-    final double[] k = keyList.elements();
-    final int[] v = valueList.elements();
-    org.apache.mahout.matrix.Swapper swapper = new org.apache.mahout.matrix.Swapper() {
-      public void swap(int a, int b) {
-        int t1;  double t2;
-        t1 = v[a]; v[a] = v[b]; v[b] = t1;
-        t2 = k[a]; k[a] = k[b];  k[b] = t2;
-      }
-    };
-
-    org.apache.mahout.matrix.function.IntComparator comp = new org.apache.mahout.matrix.function.IntComparator() {
-      public int compare(int a, int b) {
-        return k[a]<k[b] ? -1 : k[a]==k[b] ? 0 : 1;
-      }
-    };
-    org.apache.mahout.matrix.MultiSorting.sort(0,keyList.size(),comp,swapper);
-    */
-
-
-    // this variant may be quicker
-    //org.apache.mahout.matrix.map.OpenDoubleIntHashMap.hashCollisions = 0;
-    //log.info("collisions="+org.apache.mahout.matrix.map.OpenDoubleIntHashMap.hashCollisions);
     keys(keyList);
     keyList.sort();
     valueList.setSize(keyList.size());
     for (int i = keyList.size(); --i >= 0;) {
       valueList.setQuick(i, get(keyList.getQuick(i)));
     }
-    //log.info("collisions="+org.apache.mahout.matrix.map.OpenDoubleIntHashMap.hashCollisions);
-
   }
 
   /**
@@ -354,7 +329,7 @@
 
     final double[] k = keyList.elements();
     final int[] v = valueList.elements();
-    org.apache.mahout.matrix.Swapper swapper = new org.apache.mahout.matrix.Swapper() {
+    Swapper swapper = new Swapper() {
       @Override
       public void swap(int a, int b) {
         int t1 = v[a];
@@ -366,7 +341,7 @@
       }
     };
 
-    org.apache.mahout.matrix.function.IntComparator comp = new org.apache.mahout.matrix.function.IntComparator() {
+    IntComparator comp = new IntComparator() {
       @Override
       public int compare(int a, int b) {
         return v[a] < v[b] ? -1 : v[a] > v[b] ? 1 : (k[a] < k[b] ? -1 : (k[a] == k[b] ? 0 : 1));
@@ -374,7 +349,7 @@
     };
 
     //org.apache.mahout.matrix.map.OpenDoubleIntHashMap.hashCollisions = 0;
-    org.apache.mahout.matrix.GenericSorting.quickSort(0, keyList.size(), comp, swapper);
+    GenericSorting.quickSort(0, keyList.size(), comp, swapper);
     //log.info("collisions="+org.apache.mahout.matrix.map.OpenDoubleIntHashMap.hashCollisions);
   }
 

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntDoubleMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntDoubleMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntDoubleMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntDoubleMap.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,9 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.matrix.GenericSorting;
+import org.apache.mahout.matrix.Swapper;
+import org.apache.mahout.matrix.function.IntComparator;
 import org.apache.mahout.matrix.function.IntDoubleProcedure;
 import org.apache.mahout.matrix.function.IntProcedure;
 import org.apache.mahout.matrix.list.DoubleArrayList;
@@ -42,7 +45,7 @@
    */
   public void assign(final org.apache.mahout.matrix.function.DoubleFunction function) {
     copy().forEachPair(
-        new org.apache.mahout.matrix.function.IntDoubleProcedure() {
+        new IntDoubleProcedure() {
           @Override
           public boolean apply(int key, double value) {
             put(key, function.apply(value));
@@ -360,7 +363,7 @@
 
     final int[] k = keyList.elements();
     final double[] v = valueList.elements();
-    org.apache.mahout.matrix.Swapper swapper = new org.apache.mahout.matrix.Swapper() {
+    Swapper swapper = new Swapper() {
       @Override
       public void swap(int a, int b) {
         double t1 = v[a];
@@ -372,14 +375,14 @@
       }
     };
 
-    org.apache.mahout.matrix.function.IntComparator comp = new org.apache.mahout.matrix.function.IntComparator() {
+    IntComparator comp = new IntComparator() {
       @Override
       public int compare(int a, int b) {
         return v[a] < v[b] ? -1 : v[a] > v[b] ? 1 : (k[a] < k[b] ? -1 : (k[a] == k[b] ? 0 : 1));
       }
     };
 
-    org.apache.mahout.matrix.GenericSorting.quickSort(0, keyList.size(), comp, swapper);
+    GenericSorting.quickSort(0, keyList.size(), comp, swapper);
   }
 
   /**

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntIntMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntIntMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntIntMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntIntMap.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,9 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.matrix.GenericSorting;
+import org.apache.mahout.matrix.Swapper;
+import org.apache.mahout.matrix.function.IntComparator;
 import org.apache.mahout.matrix.function.IntIntProcedure;
 import org.apache.mahout.matrix.function.IntProcedure;
 import org.apache.mahout.matrix.list.IntArrayList;
@@ -323,7 +326,7 @@
 
     final int[] k = keyList.elements();
     final int[] v = valueList.elements();
-    org.apache.mahout.matrix.Swapper swapper = new org.apache.mahout.matrix.Swapper() {
+    Swapper swapper = new Swapper() {
       @Override
       public void swap(int a, int b) {
         int t1 = v[a];
@@ -335,14 +338,14 @@
       }
     };
 
-    org.apache.mahout.matrix.function.IntComparator comp = new org.apache.mahout.matrix.function.IntComparator() {
+    IntComparator comp = new IntComparator() {
       @Override
       public int compare(int a, int b) {
         return v[a] < v[b] ? -1 : v[a] > v[b] ? 1 : (k[a] < k[b] ? -1 : (k[a] == k[b] ? 0 : 1));
       }
     };
 
-    org.apache.mahout.matrix.GenericSorting.quickSort(0, keyList.size(), comp, swapper);
+    GenericSorting.quickSort(0, keyList.size(), comp, swapper);
   }
 
   /**

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntObjectMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntObjectMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntObjectMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractIntObjectMap.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,9 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.matrix.GenericSorting;
+import org.apache.mahout.matrix.Swapper;
+import org.apache.mahout.matrix.function.IntComparator;
 import org.apache.mahout.matrix.function.IntObjectProcedure;
 import org.apache.mahout.matrix.function.IntProcedure;
 import org.apache.mahout.matrix.list.IntArrayList;
@@ -325,7 +328,7 @@
 
     final int[] k = keyList.elements();
     final Object[] v = valueList.elements();
-    org.apache.mahout.matrix.Swapper swapper = new org.apache.mahout.matrix.Swapper() {
+    Swapper swapper = new Swapper() {
       @Override
       public void swap(int a, int b) {
         Object t1 = v[a];
@@ -337,7 +340,7 @@
       }
     };
 
-    org.apache.mahout.matrix.function.IntComparator comp = new org.apache.mahout.matrix.function.IntComparator() {
+    IntComparator comp = new IntComparator() {
       @Override
       public int compare(int a, int b) {
         int ab = ((Comparable<Object>) v[a]).compareTo(v[b]);
@@ -346,7 +349,7 @@
       }
     };
 
-    org.apache.mahout.matrix.GenericSorting.quickSort(0, keyList.size(), comp, swapper);
+    GenericSorting.quickSort(0, keyList.size(), comp, swapper);
   }
 
   /**

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractLongObjectMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractLongObjectMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractLongObjectMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractLongObjectMap.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,9 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.matrix.GenericSorting;
+import org.apache.mahout.matrix.Swapper;
+import org.apache.mahout.matrix.function.IntComparator;
 import org.apache.mahout.matrix.function.LongObjectProcedure;
 import org.apache.mahout.matrix.function.LongProcedure;
 import org.apache.mahout.matrix.list.LongArrayList;
@@ -325,7 +328,7 @@
 
     final long[] k = keyList.elements();
     final Object[] v = valueList.elements();
-    org.apache.mahout.matrix.Swapper swapper = new org.apache.mahout.matrix.Swapper() {
+    Swapper swapper = new Swapper() {
       @Override
       public void swap(int a, int b) {
         Object t1 = v[a];
@@ -337,7 +340,7 @@
       }
     };
 
-    org.apache.mahout.matrix.function.IntComparator comp = new org.apache.mahout.matrix.function.IntComparator() {
+    IntComparator comp = new IntComparator() {
       @Override
       public int compare(int a, int b) {
         int ab = ((Comparable<Object>) v[a]).compareTo(v[b]);
@@ -346,7 +349,7 @@
       }
     };
 
-    org.apache.mahout.matrix.GenericSorting.quickSort(0, keyList.size(), comp, swapper);
+    GenericSorting.quickSort(0, keyList.size(), comp, swapper);
   }
 
   /**

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/AbstractMap.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,8 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.matrix.PersistentObject;
+
 /**
  Abstract base class for hash maps holding objects or primitive data types such as <code>int</code>, <code>float</code>, etc. as keys and/or values.
  First see the <a href="package-summary.html">package summary</a> and javadoc <a href="package-tree.html">tree view</a> to get the broad picture.
@@ -21,7 +23,7 @@
 
 /** @deprecated until unit tests are in place.  Until this time, this class/interface is unsupported. */
 @Deprecated
-public abstract class AbstractMap extends org.apache.mahout.matrix.PersistentObject {
+public abstract class AbstractMap extends PersistentObject {
   //public static boolean debug = false; // debug only
 
   /** The number of distinct associations in the map; its "size()". */

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenDoubleIntHashMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenDoubleIntHashMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenDoubleIntHashMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenDoubleIntHashMap.java Sun Nov 29 11:19:58 2009
@@ -29,21 +29,21 @@
 public class OpenDoubleIntHashMap extends AbstractDoubleIntMap {
 
   /** The hash table keys. */
-  protected double[] table;
+  private double[] table;
 
   /** The hash table values. */
-  protected int[] values;
+  private int[] values;
 
   /** The state of each hash table entry (FREE, FULL, REMOVED). */
-  protected byte[] state;
+  private byte[] state;
 
   /** The number of table entries in state==FREE. */
-  protected int freeEntries;
+  private int freeEntries;
 
 
-  protected static final byte FREE = 0;
-  protected static final byte FULL = 1;
-  protected static final byte REMOVED = 2;
+  private static final byte FREE = 0;
+  private static final byte FULL = 1;
+  private static final byte REMOVED = 2;
 
   /** Constructs an empty map with default capacity and default load factors. */
   public OpenDoubleIntHashMap() {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntDoubleHashMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntDoubleHashMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntDoubleHashMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntDoubleHashMap.java Sun Nov 29 11:19:58 2009
@@ -8,6 +8,8 @@
 */
 package org.apache.mahout.matrix.map;
 
+import org.apache.mahout.jet.math.Mult;
+import org.apache.mahout.matrix.function.DoubleFunction;
 import org.apache.mahout.matrix.function.IntDoubleProcedure;
 import org.apache.mahout.matrix.function.IntProcedure;
 import org.apache.mahout.matrix.list.ByteArrayList;
@@ -29,21 +31,21 @@
 public class OpenIntDoubleHashMap extends AbstractIntDoubleMap {
   //public static int hashCollisions = 0;
   /** The hash table keys. */
-  protected int[] table;
+  private int[] table;
 
   /** The hash table values. */
-  protected double[] values;
+  private double[] values;
 
   /** The state of each hash table entry (FREE, FULL, REMOVED). */
-  protected byte[] state;
+  private byte[] state;
 
   /** The number of table entries in state==FREE. */
-  protected int freeEntries;
+  private int freeEntries;
 
 
-  protected static final byte FREE = 0;
-  protected static final byte FULL = 1;
-  protected static final byte REMOVED = 2;
+  private static final byte FREE = 0;
+  private static final byte FULL = 1;
+  private static final byte REMOVED = 2;
 
   /** Constructs an empty map with default capacity and default load factors. */
   public OpenIntDoubleHashMap() {
@@ -80,10 +82,10 @@
    * @param function a function object taking as argument the current association's value.
    */
   @Override
-  public void assign(org.apache.mahout.matrix.function.DoubleFunction function) {
+  public void assign(DoubleFunction function) {
     // specialization for speed
-    if (function instanceof org.apache.mahout.jet.math.Mult) { // x[i] = mult*x[i]
-      double multiplicator = ((org.apache.mahout.jet.math.Mult) function).getMultiplicator();
+    if (function instanceof Mult) { // x[i] = mult*x[i]
+      double multiplicator = ((Mult) function).getMultiplicator();
       if (multiplicator == 1) {
         return;
       }

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntIntHashMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntIntHashMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntIntHashMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntIntHashMap.java Sun Nov 29 11:19:58 2009
@@ -42,7 +42,7 @@
 
   protected static final byte FREE = 0;
   protected static final byte FULL = 1;
-  protected static final byte REMOVED = 2;
+  private static final byte REMOVED = 2;
 
   /** Constructs an empty map with default capacity and default load factors. */
   public OpenIntIntHashMap() {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntObjectHashMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntObjectHashMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntObjectHashMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenIntObjectHashMap.java Sun Nov 29 11:19:58 2009
@@ -29,21 +29,21 @@
 public class OpenIntObjectHashMap extends AbstractIntObjectMap {
 
   /** The hash table keys. */
-  protected int[] table;
+  private int[] table;
 
   /** The hash table values. */
-  protected Object[] values;
+  private Object[] values;
 
   /** The state of each hash table entry (FREE, FULL, REMOVED). */
-  protected byte[] state;
+  private byte[] state;
 
   /** The number of table entries in state==FREE. */
-  protected int freeEntries;
+  private int freeEntries;
 
 
-  protected static final byte FREE = 0;
-  protected static final byte FULL = 1;
-  protected static final byte REMOVED = 2;
+  private static final byte FREE = 0;
+  private static final byte FULL = 1;
+  private static final byte REMOVED = 2;
 
   /** Constructs an empty map with default capacity and default load factors. */
   public OpenIntObjectHashMap() {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenLongObjectHashMap.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenLongObjectHashMap.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenLongObjectHashMap.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/OpenLongObjectHashMap.java Sun Nov 29 11:19:58 2009
@@ -29,21 +29,21 @@
 public class OpenLongObjectHashMap extends AbstractLongObjectMap {
 
   /** The hash table keys. */
-  protected long[] table;
+  private long[] table;
 
   /** The hash table values. */
-  protected Object[] values;
+  private Object[] values;
 
   /** The state of each hash table entry (FREE, FULL, REMOVED). */
-  protected byte[] state;
+  private byte[] state;
 
   /** The number of table entries in state==FREE. */
-  protected int freeEntries;
+  private int freeEntries;
 
 
-  protected static final byte FREE = 0;
-  protected static final byte FULL = 1;
-  protected static final byte REMOVED = 2;
+  private static final byte FREE = 0;
+  private static final byte FULL = 1;
+  private static final byte REMOVED = 2;
 
   /** Constructs an empty map with default capacity and default load factors. */
   public OpenLongObjectHashMap() {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/PrimeFinder.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/PrimeFinder.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/PrimeFinder.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/map/PrimeFinder.java Sun Nov 29 11:19:58 2009
@@ -132,7 +132,7 @@
    */
   public static int nextPrime(int desiredCapacity) {
     int i = java.util.Arrays.binarySearch(primeCapacities, desiredCapacity);
-    //int i = new org.apache.mahout.matrix.list.IntArrayList(primeCapacities).binarySearch(desiredCapacity); // for debug only TODO
+    //int i = new IntArrayList(primeCapacities).binarySearch(desiredCapacity); // for debug only TODO
     if (i < 0) {
       // desired capacity not found, choose next prime greater than desired capacity
       i = -i - 1; // remember the semantics of binarySearch...
@@ -141,7 +141,7 @@
   }
 
   /** Tests correctness. */
-  protected static void statistics(int from, int to) {
+  private static void statistics(int from, int to) {
     // check that primes contain no accidental errors
     for (int i = 0; i < primeCapacities.length - 1; i++) {
       if (primeCapacities[i] >= primeCapacities[i + 1]) {

Modified: lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/matrix/DoubleFactory1D.java
URL: http://svn.apache.org/viewvc/lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/matrix/DoubleFactory1D.java?rev=885213&r1=885212&r2=885213&view=diff
==============================================================================
--- lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/matrix/DoubleFactory1D.java (original)
+++ lucene/mahout/trunk/matrix/src/main/java/org/apache/mahout/matrix/matrix/DoubleFactory1D.java Sun Nov 29 11:19:58 2009
@@ -9,6 +9,11 @@
 package org.apache.mahout.matrix.matrix;
 
 import org.apache.mahout.jet.math.Functions;
+import org.apache.mahout.jet.random.engine.MersenneTwister;
+import org.apache.mahout.jet.random.sampling.RandomSamplingAssistant;
+import org.apache.mahout.matrix.PersistentObject;
+import org.apache.mahout.matrix.list.AbstractDoubleList;
+import org.apache.mahout.matrix.list.DoubleArrayList;
 import org.apache.mahout.matrix.matrix.impl.DenseDoubleMatrix1D;
 import org.apache.mahout.matrix.matrix.impl.SparseDoubleMatrix1D;
 /**
@@ -36,13 +41,13 @@
 
 /** @deprecated until unit tests are in place.  Until this time, this class/interface is unsupported. */
 @Deprecated
-public class DoubleFactory1D extends org.apache.mahout.matrix.PersistentObject {
+public class DoubleFactory1D extends PersistentObject {
 
   /** A factory producing dense matrices. */
   public static final DoubleFactory1D dense = new DoubleFactory1D();
 
   /** A factory producing sparse matrices. */
-  public static final DoubleFactory1D sparse = new DoubleFactory1D();
+  private static final DoubleFactory1D sparse = new DoubleFactory1D();
 
   /** Makes this class non instantiable, but still let's others inherit from it. */
   protected DoubleFactory1D() {
@@ -130,7 +135,7 @@
    * @param values The values to be filled into the new matrix.
    * @return a new matrix.
    */
-  public DoubleMatrix1D make(org.apache.mahout.matrix.list.AbstractDoubleList values) {
+  public DoubleMatrix1D make(AbstractDoubleList values) {
     int size = values.size();
     DoubleMatrix1D vector = make(size);
     for (int i = size; --i >= 0;) {
@@ -141,7 +146,7 @@
 
   /** Constructs a matrix with uniformly distributed values in <tt>(0,1)</tt> (exclusive). */
   public DoubleMatrix1D random(int size) {
-    return make(size).assign(org.apache.mahout.jet.math.Functions.random());
+    return make(size).assign(Functions.random());
   }
 
   /**
@@ -189,9 +194,9 @@
       return matrix;
     }
 
-    org.apache.mahout.jet.random.sampling.RandomSamplingAssistant sampler =
-        new org.apache.mahout.jet.random.sampling.RandomSamplingAssistant(n, size,
-            new org.apache.mahout.jet.random.engine.MersenneTwister());
+    RandomSamplingAssistant sampler =
+        new RandomSamplingAssistant(n, size,
+            new MersenneTwister());
     for (int i = size; --i >= 0;) {
       if (sampler.sampleNextElement()) {
         matrix.set(i, value);
@@ -210,7 +215,7 @@
    */
   public org.apache.mahout.matrix.list.DoubleArrayList toList(DoubleMatrix1D values) {
     int size = values.size();
-    org.apache.mahout.matrix.list.DoubleArrayList list = new org.apache.mahout.matrix.list.DoubleArrayList(size);
+    DoubleArrayList list = new DoubleArrayList(size);
     list.setSize(size);
     for (int i = size; --i >= 0;) {
       list.set(i, values.get(i));