Create new Matrix hirearchy.

src/main/java/org/numenta/nupic/model/ProximalDendrite.java

@@ -118,7 +118,7 @@ public void setConnectedSynapsesForTest(Connections c, int[] connectedIndexes) {
      * @return
      */
     public int[] getConnectedSynapsesDense(Connections c) {
-        return c.getPotentialPools().getObject(index).getDenseConnections(c);
+        return c.getPotentialPools().get(index).getDenseConnections(c);
     }
 
     /**
@@ -127,6 +127,6 @@ public int[] getConnectedSynapsesDense(Connections c) {
      * @return
      */
     public int[] getConnectedSynapsesSparse(Connections c) {
-        return c.getPotentialPools().getObject(index).getSparseConnections();
+        return c.getPotentialPools().get(index).getSparseConnections();
     }
 }

src/main/java/org/numenta/nupic/util/BitSetMatrix.java

@@ -0,0 +1,58 @@
+/* ---------------------------------------------------------------------
+ * Numenta Platform for Intelligent Computing (NuPIC)
+ * Copyright (C) 2014, Numenta, Inc.  Unless you have an agreement
+ * with Numenta, Inc., for a separate license for this software code, the
+ * following terms and conditions apply:
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 3 as
+ * published by the Free Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ * See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see http://www.gnu.org/licenses.
+ *
+ * http://numenta.org/licenses/
+ * ---------------------------------------------------------------------
+ */
+
+package org.numenta.nupic.util;
+
+import java.util.BitSet;
+
+/**
+ * {@link FlatMatrix} implementation that store booleans in a {@link BitSet}.
+ * 
+ * @author Jose Luis Martin
+ */
+public class BitSetMatrix extends FlatMatrixSupport<Boolean> {
+
+    private BitSet data;
+
+    /**
+     * @param dimensions
+     */
+    public BitSetMatrix(int[] dimensions) {
+        this(dimensions, false);
+    }
+
+    public BitSetMatrix(int[] dimensions, boolean useColumnMajorOrdering) {
+        super(dimensions, useColumnMajorOrdering);
+        this.data = new BitSet(getSize());
+    }
+
+    @Override
+    public Boolean get(int index) {
+        return this.data.get(index);
+    }
+
+    @Override
+    public BitSetMatrix set(int index, Boolean value) {
+        this.data.set(index, value);
+        return this;
+    }
+}

src/main/java/org/numenta/nupic/util/FlatArrayMatrix.java

@@ -0,0 +1,66 @@
+/* ---------------------------------------------------------------------
+ * Numenta Platform for Intelligent Computing (NuPIC)
+ * Copyright (C) 2014, Numenta, Inc.  Unless you have an agreement
+ * with Numenta, Inc., for a separate license for this software code, the
+ * following terms and conditions apply:
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 3 as
+ * published by the Free Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ * See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see http://www.gnu.org/licenses.
+ *
+ * http://numenta.org/licenses/
+ * ---------------------------------------------------------------------
+ */
+
+package org.numenta.nupic.util;
+
+import java.lang.reflect.Array;
+import java.util.Arrays;
+
+/**
+ * {@link FlatMatrix} implementation that store objects in a flat object array.
+ * 
+ * @author Jose Luis Martin
+ */
+public class FlatArrayMatrix<T> extends FlatMatrixSupport<T> {
+
+    private T[] data;
+
+    public FlatArrayMatrix(int[] dimensions) {
+        this(dimensions, false);
+    }
+
+    @SuppressWarnings("unchecked")
+    public FlatArrayMatrix(int[] dimensions, boolean useColumnMajorOrdering) {
+        super(dimensions, useColumnMajorOrdering);
+        this.data = (T[]) new Object[getSize()];
+    }
+
+    @Override
+    public T get(int index) {
+        return this.data[index];
+    }
+
+    @Override
+    public FlatArrayMatrix<T> set(int index, T value) {
+        this.data[index] = value;
+        return this;
+    }
+
+    /**
+     * Fill array with value
+     * @param value
+     */
+    public void fill(T value) {
+        Arrays.fill(this.data, value);
+    }
+
+}

src/main/java/org/numenta/nupic/util/FlatMatrix.java

@@ -0,0 +1,55 @@
+/* ---------------------------------------------------------------------
+ * Numenta Platform for Intelligent Computing (NuPIC)
+ * Copyright (C) 2014, Numenta, Inc.  Unless you have an agreement
+ * with Numenta, Inc., for a separate license for this software code, the
+ * following terms and conditions apply:
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 3 as
+ * published by the Free Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ * See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see http://www.gnu.org/licenses.
+ *
+ * http://numenta.org/licenses/
+ * ---------------------------------------------------------------------
+ */
+
+package org.numenta.nupic.util;
+
+/**
+ * Provides contract for flat matrix implementations.
+ * 
+ * @author Jose Luis Martin
+ */
+public interface FlatMatrix<T> extends Matrix<T> {
+
+    T get(int index);
+
+    FlatMatrix<T> set(int index, T value);
+
+    int computeIndex(int[] coordinates);
+
+    /**
+     * Returns the maximum accessible flat index.
+     * @return  the maximum accessible flat index.
+     */
+    int getMaxIndex();
+
+    public int computeIndex(int[] coordinates, boolean doCheck);
+
+    /**
+     * Returns an integer array representing the coordinates of the specified index
+     * in terms of the configuration of this {@code SparseMatrix}.
+     * @param index the flat index to be returned as coordinates
+     * @return  coordinates
+     */
+    int[] computeCoordinates(int index);
+
+    int[] getDimensionMultiples();
+}